4. Additional File 4: the GO enrichment analysis of the derived interlogs that get involved in drug resistance of SOS-response and DNA replication. [1]{Rv2737c,TAP1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [TAP1 only] GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0015197+F molecular_function [name] peptide transporter activity [def] "Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells." [GOC GO:0015440+F molecular_function [name] peptide-transporting ATPase activity [def] "Catalysis of the reaction GO:0015833+P biological_process [name] peptide transport [def] "The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0019885+P biological_process [name] antigen processing and presentation of endogenous peptide antigen via MHC class I [def] "The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules." [GOC GO:0030176+C cellular_component [name] integral to endoplasmic reticulum membrane [def] "Penetrating at least one phospholipid bilayer of an endoplasmic reticulum membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0042287+F molecular_function [name] MHC protein binding [def] "Interacting selectively and non-covalently with major histocompatibility complex molecules_ a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation." [GOC GO:0042626+F molecular_function [name] ATPase activity, coupled to transmembrane movement of substances [def] "Catalysis of the reaction GO:0042825+C cellular_component [name] TAP complex [def] "A heterodimer composed of the subunits TAP1 and TAP2 (transporter associated with antigen presentation). Functions in the transport of antigenic peptides from the cytosol to the lumen of the endoplasmic reticulum." [GOC GO:0046979+F molecular_function [name] TAP2 binding [def] "Interacting selectively and non-covalently with the TAP2 subunit of TAP (transporter associated with antigen processing) protein." [PMID GO:0055085+P biological_process [name] transmembrane transport [def] "The process in which a solute is transported from one side of a membrane to the other." [GOC [2]{Rv2737c,ALDH9A1} [common GO terms] GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH9A1 only] GO:0001822+P biological_process [name] kidney development [def] "The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine." [GOC GO:0001889+P biological_process [name] liver development [def] "The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes." [GOC GO:0004028+F molecular_function [name] 3-chloroallyl aldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0004029+F molecular_function [name] aldehyde dehydrogenase (NAD) activity [def] "Catalysis of the reaction GO:0006081+P biological_process [name] cellular aldehyde metabolic process [def] "The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0019145+F molecular_function [name] aminobutyraldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0033737+F molecular_function [name] 1-pyrroline dehydrogenase activity [def] "Catalysis of the reaction GO:0042136+P biological_process [name] neurotransmitter biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell." [CHEBI GO:0042445+P biological_process [name] hormone metabolic process [def] "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." [CHEBI GO:0042803+F molecular_function [name] protein homodimerization activity [def] "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC GO:0043176+F molecular_function [name] amine binding [def] "Interacting selectively and non-covalently with any organic compound that is weakly basic in character and contains an amino or a substituted amino group." [GOC GO:0045329+P biological_process [name] carnitine biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane." [GOC GO:0047105+F molecular_function [name] 4-trimethylammoniobutyraldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0051287+F molecular_function [name] NAD binding [def] "Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions_ binding may be to either the oxidized form, NAD+, or the reduced form, NADH." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [3]{Rv2737c,ALDH8A1} [common GO terms] GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH8A1 only] GO:0001758+F molecular_function [name] retinal dehydrogenase activity [def] "Catalysis of the reaction GO:0004029+F molecular_function [name] aldehyde dehydrogenase (NAD) activity [def] "Catalysis of the reaction GO:0005622+C cellular_component [name] intracellular [def] "The living contents of a cell_ the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0042573+P biological_process [name] retinoic acid metabolic process [def] "The chemical reactions and pathways involving retinoic acid, one of the three components that makes up vitamin A." [GOC GO:0042574+P biological_process [name] retinal metabolic process [def] "The chemical reactions and pathways involving retinal, a compound that plays an important role in the visual process in most vertebrates. In the retina, retinal combines with opsins to form visual pigments. Retinal is one of the forms of vitamin A." [CHEBI GO:0042904+P biological_process [name] 9-cis-retinoic acid biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of 9-cis-retinoic acid, a metabolically active vitamin A derivative." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [4]{Rv0629c,DLD} [common GO terms] [Rv0629c only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000724+P biological_process [name] double-strand break repair via homologous recombination [def] "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0004003+F molecular_function [name] ATP-dependent DNA helicase activity [def] "Catalysis of the reaction GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006302+P biological_process [name] double-strand break repair [def] "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008854+F molecular_function [name] exodeoxyribonuclease V activity [def] "Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides." [EC GO:0009338+C cellular_component [name] exodeoxyribonuclease V complex [def] "An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA." [EC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0032508+P biological_process [name] DNA duplex unwinding [def] "The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [DLD only] GO:0004148+F molecular_function [name] dihydrolipoyl dehydrogenase activity [def] "Catalysis of the reaction GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0005929+C cellular_component [name] cilium [def] "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC GO:0006086+P biological_process [name] acetyl-CoA biosynthetic process from pyruvate [def] "The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate." [GOC GO:0006090+P biological_process [name] pyruvate metabolic process [def] "The chemical reactions and pathways involving pyruvate, 2-oxopropanoate." [GOC GO:0006099+P biological_process [name] tricarboxylic acid cycle [def] "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." [ISBN GO:0006103+P biological_process [name] 2-oxoglutarate metabolic process [def] "The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism." [ISBN GO:0006120+P biological_process [name] mitochondrial electron transport, NADH to ubiquinone [def] "The transfer of electrons from NADH to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex I." [ISBN GO:0006508+P biological_process [name] proteolysis [def] "The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds." [GOC GO:0006554+P biological_process [name] lysine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of lysine, 2,6-diaminohexanoic acid." [GOC GO:0007369+P biological_process [name] gastrulation [def] "A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm." [GOC GO:0007568+P biological_process [name] aging [def] "The inherent decline over time, from the optimal fertility and viability of early maturity, that may precede death and may be preceded by other indications, such as sterility." [GOC GO:0009083+P biological_process [name] branched chain family amino acid catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine." [GOC GO:0009106+P biological_process [name] lipoate metabolic process [def] "The chemical reactions and pathways involving lipoate, 1,2-dithiolane-3-pentanoate, the anion derived from lipoic acid." [GOC GO:0010510+P biological_process [name] regulation of acetyl-CoA biosynthetic process from pyruvate [def] "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016668+F molecular_function [name] oxidoreductase activity, acting on a sulfur group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0042391+P biological_process [name] regulation of membrane potential [def] "Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC GO:0043159+C cellular_component [name] acrosomal matrix [def] "A structural framework, or 'dense core' at the interior of an acrosome. May regulate the distribution of hydrolases within the acrosome and their release during the acrosome reaction." [GOC GO:0043209+C cellular_component [name] myelin sheath [def] "An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells GO:0043544+F molecular_function [name] lipoamide binding [def] "Interacting selectively and non-covalently with lipoamide, the functional form of lipoic acid in which the carboxyl group is attached to protein by an amide linkage to a lysine amino group." [GOC GO:0045252+C cellular_component [name] oxoglutarate dehydrogenase complex [def] "A complex of multiple copies of three enzymatic components GO:0045254+C cellular_component [name] pyruvate dehydrogenase complex [def] "Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA_ comprises subunits possessing three catalytic activities GO:0045454+P biological_process [name] cell redox homeostasis [def] "Any process that maintains the redox environment of a cell or compartment within a cell." [GOC GO:0046487+P biological_process [name] glyoxylate metabolic process [def] "The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH." [ISBN GO:0048240+P biological_process [name] sperm capacitation [def] "A process required for sperm to reach fertilization competence. Sperm undergo an incompletely understood series of morphological and molecular maturational processes, termed capacitation, involving, among other processes, protein tyrosine phosphorylation and increased intracellular calcium." [GOC GO:0050660+F molecular_function [name] flavin adenine dinucleotide binding [def] "Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2." [CHEBI GO:0051068+P biological_process [name] dihydrolipoamide metabolic process [def] "The chemical reactions and pathways involving dihydrolipoamide, the reduced form of lipoamide, produced as an intermediate in the reactions in which lipoamide acts as a cofactor." [ISBN GO:0051287+F molecular_function [name] NAD binding [def] "Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions_ binding may be to either the oxidized form, NAD+, or the reduced form, NADH." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0061732+P GO:0034604+F molecular_function [name] pyruvate dehydrogenase (NAD+) activity [def] "Catalysis of the reaction [5]{Rv1629,ACAT2} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ACAT2 only] GO:0003985+F molecular_function [name] acetyl-CoA C-acetyltransferase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN GO:0006629+P biological_process [name] lipid metabolic process [def] "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids_ neutral fats, other fatty-acid esters, and soaps_ long-chain (fatty) alcohols and waxes_ sphingoids and other long-chain bases_ glycolipids, phospholipids and sphingolipids_ and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016746+F molecular_function [name] transferase activity, transferring acyl groups [def] "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor)." [GOC GO:0016747+F molecular_function [name] transferase activity, transferring acyl groups other than amino-acyl groups [def] "Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor)." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [6]{Rv2737c,ECHS1} [common GO terms] GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ECHS1 only] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0004300+F molecular_function [name] enoyl-CoA hydratase activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006629+P biological_process [name] lipid metabolic process [def] "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids_ neutral fats, other fatty-acid esters, and soaps_ long-chain (fatty) alcohols and waxes_ sphingoids and other long-chain bases_ glycolipids, phospholipids and sphingolipids_ and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC GO:0006631+P biological_process [name] fatty acid metabolic process [def] "The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN GO:0006635+P biological_process [name] fatty acid beta-oxidation [def] "A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A_ the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016829+F molecular_function [name] lyase activity [def] "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [7]{Rv1629,SMARCA1} [common GO terms] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC [Rv1629 only] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [SMARCA1 only] GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0006338+P biological_process [name] chromatin remodeling [def] "Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation." [GOC GO:0016589+C cellular_component [name] NURF complex [def] "A four subunit ISWI-containing protein complex that facilitates nucleosome mobility and transcriptional activation in an ATP-dependent manner. In contrast to other chromatin remodeling complexes, the ATPase activity of NURF requires nucleosomes rather than free DNA or histones." [GOC GO:0016818+F molecular_function [name] hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [def] "Catalysis of the hydrolysis of any acid anhydride which contains phosphorus." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0031491+F molecular_function [name] nucleosome binding [def] "Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC GO:0043044+P biological_process [name] ATP-dependent chromatin remodeling [def] "Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors." [GOC [8]{Rv2737c,ATP4A} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP4A only] GO:0005391+F molecular_function [name] sodium [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005615+C cellular_component [name] extracellular space [def] "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0005887+C cellular_component [name] integral to plasma membrane [def] "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006813+P biological_process [name] potassium ion transport [def] "The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006814+P biological_process [name] sodium ion transport [def] "The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006883+P biological_process [name] cellular sodium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of sodium ions at the level of a cell." [GOC GO:0008900+F molecular_function [name] hydrogen [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0010107+P biological_process [name] potassium ion import [def] "The directed movement of potassium ions into a cell or organelle." [GOC GO:0010248+P biological_process [name] establishment or maintenance of transmembrane electrochemical gradient [def] "The directed movement of ions to establish or maintain an electrochemical gradient across a membrane by means of some agent such as a transporter or pore." [GOC GO:0015991+P biological_process [name] ATP hydrolysis coupled proton transport [def] "The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis." [GOC GO:0015992+P biological_process [name] proton transport [def] "The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0030007+P biological_process [name] cellular potassium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of potassium ions at the level of a cell." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0036376+P GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC [9]{Rv2737c,ATP1A4} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP1A4 only] GO:0005391+F molecular_function [name] sodium [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0005887+C cellular_component [name] integral to plasma membrane [def] "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0005890+C cellular_component [name] sodium [def] "Sodium GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006813+P biological_process [name] potassium ion transport [def] "The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006814+P biological_process [name] sodium ion transport [def] "The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006883+P biological_process [name] cellular sodium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of sodium ions at the level of a cell." [GOC GO:0007283+P biological_process [name] spermatogenesis [def] "The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis." [GOC GO:0009566+P biological_process [name] fertilization [def] "The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." [GOC GO:0010107+P biological_process [name] potassium ion import [def] "The directed movement of potassium ions into a cell or organelle." [GOC GO:0010248+P biological_process [name] establishment or maintenance of transmembrane electrochemical gradient [def] "The directed movement of ions to establish or maintain an electrochemical gradient across a membrane by means of some agent such as a transporter or pore." [GOC GO:0015991+P biological_process [name] ATP hydrolysis coupled proton transport [def] "The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0030007+P biological_process [name] cellular potassium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of potassium ions at the level of a cell." [GOC GO:0030317+P biological_process [name] sperm motility [def] "Any process involved in the controlled movement of a sperm cell." [GOC GO:0030641+P biological_process [name] regulation of cellular pH [def] "Any process involved in the maintenance of an internal equilibrium of hydrogen ions (protons) within a cell or between a cell and its external environment." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0036376+P GO:0042391+P biological_process [name] regulation of membrane potential [def] "Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:1903779+P [10]{Rv2737c,ABCB8} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ABCB8 only] GO:0005215+F molecular_function [name] transporter activity [def] "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005740+C cellular_component [name] mitochondrial envelope [def] "The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm_ includes the intermembrane space." [GOC GO:0005743+C cellular_component [name] mitochondrial inner membrane [def] "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0042626+F molecular_function [name] ATPase activity, coupled to transmembrane movement of substances [def] "Catalysis of the reaction GO:0043190+C cellular_component [name] ATP-binding cassette (ABC) transporter complex [def] "A complex for the transport of metabolites into and out of the cell, typically comprised of four domains_ two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter." [GOC GO:0055085+P biological_process [name] transmembrane transport [def] "The process in which a solute is transported from one side of a membrane to the other." [GOC [11]{Rv1547,POLN} [common GO terms] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [Rv1547 only] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC [POLN only] GO:0000724+P biological_process [name] double-strand break repair via homologous recombination [def] "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0019985+P biological_process [name] translesion synthesis [def] "The replication of damaged DNA by synthesis across a lesion in the template strand_ a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide." [GOC GO:0030332+F molecular_function [name] cyclin binding [def] "Interacting selectively and non-covalently with cyclins, proteins whose levels in a cell varies markedly during the cell cycle, rising steadily until mitosis, then falling abruptly to zero. As cyclins reach a threshold level, they are thought to drive cells into G2 phase and thus to mitosis." [GOC GO:0036297+P GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN [12]{Rv2737c,CBS} [common GO terms] GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [CBS only] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0004122+F molecular_function [name] cystathionine beta-synthase activity [def] "Catalysis of the reaction GO:0004124+F molecular_function [name] cysteine synthase activity [def] "Catalysis of the reaction GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0006535+P biological_process [name] cysteine biosynthetic process from serine [def] "The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine." [GOC GO:0006563+P biological_process [name] L-serine metabolic process [def] "The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid." [CHEBI GO:0006565+P biological_process [name] L-serine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid." [CHEBI GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0008652+P biological_process [name] cellular amino acid biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents." [ISBN GO:0016829+F molecular_function [name] lyase activity [def] "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC GO:0019343+P biological_process [name] cysteine biosynthetic process via cystathionine [def] "The chemical reactions and pathways resulting in the formation of cysteine, via the intermediate cystathionine." [GOC GO:0019344+P biological_process [name] cysteine biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid." [GOC GO:0019346+P biological_process [name] transsulfuration [def] "The interconversion of homocysteine and cysteine via cystathionine. In contrast with enteric bacteria and mammals, Saccharomyces cerevisiae has two transsulfuration pathways employing two separate sets of enzymes." [MetaCyc GO:0019448+P biological_process [name] L-cysteine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid." [CHEBI GO:0019825+F molecular_function [name] oxygen binding [def] "Interacting selectively and non-covalently with oxygen (O2)." [GOC GO:0019899+F molecular_function [name] enzyme binding [def] "Interacting selectively and non-covalently with any enzyme." [GOC GO:0020037+F molecular_function [name] heme binding [def] "Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring." [CHEBI GO:0030170+F molecular_function [name] pyridoxal phosphate binding [def] "Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6." [GOC GO:0031625+F molecular_function [name] ubiquitin protein ligase binding [def] "Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins." [GOC GO:0042262+P biological_process [name] DNA protection [def] "Any process in which DNA is protected from damage by, for example, oxidative stress." [GOC GO:0042802+F molecular_function [name] identical protein binding [def] "Interacting selectively and non-covalently with an identical protein or proteins." [GOC GO:0042803+F molecular_function [name] protein homodimerization activity [def] "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC GO:0043418+P biological_process [name] homocysteine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0050421+F molecular_function [name] nitrite reductase (NO-forming) activity [def] "Catalysis of the reaction GO:0050667+P biological_process [name] homocysteine metabolic process [def] "The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine." [ISBN GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0070025+F molecular_function [name] carbon monoxide binding [def] "Interacting selectively and non-covalently with carbon monoxide (CO)." [GOC GO:0070026+F molecular_function [name] nitric oxide binding [def] "Interacting selectively and non-covalently with nitric oxide (NO)." [GOC GO:0070814+P biological_process [name] hydrogen sulfide biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S." [CHEBI GO:0072341+F molecular_function [name] modified amino acid binding [def] "Interacting selectively and non-covalently with a modified amino acid." [CHEBI GO:1904047+F [13]{Rv2737c,ALDH3A1} [common GO terms] [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH3A1 only] GO:0004030+F molecular_function [name] aldehyde dehydrogenase [NAD(P)+] activity [def] "Catalysis of the reaction GO:0006081+P biological_process [name] cellular aldehyde metabolic process [def] "The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC [14]{Rv1629,ACAA2} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ACAA2 only] GO:0003988+F molecular_function [name] acetyl-CoA C-acyltransferase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005743+C cellular_component [name] mitochondrial inner membrane [def] "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC GO:0006629+P biological_process [name] lipid metabolic process [def] "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids_ neutral fats, other fatty-acid esters, and soaps_ long-chain (fatty) alcohols and waxes_ sphingoids and other long-chain bases_ glycolipids, phospholipids and sphingolipids_ and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC GO:0006631+P biological_process [name] fatty acid metabolic process [def] "The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN GO:0006695+P biological_process [name] cholesterol biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016746+F molecular_function [name] transferase activity, transferring acyl groups [def] "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor)." [GOC GO:0016747+F molecular_function [name] transferase activity, transferring acyl groups other than amino-acyl groups [def] "Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor)." [GOC GO:0044822+F GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC GO:0071456+P biological_process [name] cellular response to hypoxia [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level." [GOC GO:1901029+P GO:1902109+P [15]{Rv0629c,POLN} [common GO terms] GO:0000724+P biological_process [name] double-strand break repair via homologous recombination [def] "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [Rv0629c only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0004003+F molecular_function [name] ATP-dependent DNA helicase activity [def] "Catalysis of the reaction GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006302+P biological_process [name] double-strand break repair [def] "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0008854+F molecular_function [name] exodeoxyribonuclease V activity [def] "Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides." [EC GO:0009338+C cellular_component [name] exodeoxyribonuclease V complex [def] "An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA." [EC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0032508+P biological_process [name] DNA duplex unwinding [def] "The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands." [GOC [POLN only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0019985+P biological_process [name] translesion synthesis [def] "The replication of damaged DNA by synthesis across a lesion in the template strand_ a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide." [GOC GO:0030332+F molecular_function [name] cyclin binding [def] "Interacting selectively and non-covalently with cyclins, proteins whose levels in a cell varies markedly during the cell cycle, rising steadily until mitosis, then falling abruptly to zero. As cyclins reach a threshold level, they are thought to drive cells into G2 phase and thus to mitosis." [GOC GO:0036297+P GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN [16]{Rv2737c,ATP2A1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP2A1 only] GO:0005388+F molecular_function [name] calcium-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005509+F molecular_function [name] calcium ion binding [def] "Interacting selectively and non-covalently with calcium ions (Ca2+)." [GOC GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005783+C cellular_component [name] endoplasmic reticulum [def] "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN GO:0005789+C cellular_component [name] endoplasmic reticulum membrane [def] "The lipid bilayer surrounding the endoplasmic reticulum." [GOC GO:0005793+C cellular_component [name] endoplasmic reticulum-Golgi intermediate compartment [def] "A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition_ involved in ER-to-Golgi transport." [GOC GO:0005887+C cellular_component [name] integral to plasma membrane [def] "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006816+P biological_process [name] calcium ion transport [def] "The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006942+P biological_process [name] regulation of striated muscle contraction [def] "Any process that modulates the frequency, rate or extent of striated muscle contraction." [GOC GO:0008637+P biological_process [name] apoptotic mitochondrial changes [def] "The morphological and physiological alterations undergone by mitochondria during apoptosis." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0016529+C cellular_component [name] sarcoplasmic reticulum [def] "A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell_ continuous over large portions of the cell and with the nuclear envelope_ that part of the endoplasmic reticulum specialized for calcium release, uptake and storage." [GOC GO:0031095+C cellular_component [name] platelet dense tubular network membrane [def] "The lipid bilayer surrounding the platelet dense tubular network." [GOC GO:0031448+P biological_process [name] positive regulation of fast-twitch skeletal muscle fiber contraction [def] "Any process that activates or increases the frequency, rate or extent of fast-twitch skeletal muscle contraction." [GOC GO:0031673+C cellular_component [name] H zone [def] "A relatively pale zone traversing the center of the A band of a sarcomere, visible in relaxed muscle fibers_ consists of the central portion of thick (myosin) filaments that are not overlapped by thin (actin) filaments." [GOC GO:0031674+C cellular_component [name] I band [def] "A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments_ contains actin, troponin, and tropomyosin_ each sarcomere includes half of an I band at each end." [ISBN GO:0032470+P biological_process [name] elevation of endoplasmic reticulum calcium ion concentration [def] "Any process that increases the concentration of calcium ions in the endoplasmic reticulum." [GOC GO:0032471+P biological_process [name] reduction of endoplasmic reticulum calcium ion concentration [def] "Any process that decreases the concentration of calcium ions in the endoplasmic reticulum." [GOC GO:0033017+C cellular_component [name] sarcoplasmic reticulum membrane [def] "The lipid bilayer surrounding the sarcoplasmic reticulum." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0034704+C cellular_component [name] calcium channel complex [def] "An ion channel complex through which calcium ions pass." [GOC GO:0034976+P biological_process [name] response to endoplasmic reticulum stress [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating endoplasmic reticulum (ER) stress. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen." [GOC GO:0042803+F molecular_function [name] protein homodimerization activity [def] "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC GO:0045988+P biological_process [name] negative regulation of striated muscle contraction [def] "Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0048471+C cellular_component [name] perinuclear region of cytoplasm [def] "Cytoplasm situated near, or occurring around, the nucleus." [GOC GO:0051561+P biological_process [name] elevation of mitochondrial calcium ion concentration [def] "Any process that increases the concentration of calcium ions in mitochondria." [GOC GO:0051659+P biological_process [name] maintenance of mitochondrion location [def] "Any process in which a mitochondrion is maintained in a specific location within a cell and prevented from moving elsewhere." [GOC GO:0070059+P biological_process [name] apoptosis in response to endoplasmic reticulum stress [def] "Apoptosis that occurs in response to a stimulus indicating endoplasmic reticulum (ER) stress. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen." [GOC GO:0070509+P biological_process [name] calcium ion import [def] "The directed movement of calcium ions into a cell or organelle." [GOC GO:0070588+P biological_process [name] calcium ion transmembrane transport [def] "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0090076+P biological_process [name] relaxation of skeletal muscle [def] "A process in which the extent of skeletal muscle tissue contraction is reduced. Muscle relaxation involves the removal of calcium from the cytoplasm to the sarcoplasmic reticulum lumen through the action of Ca2+ ATPases." [GOC GO:1903779+P [17]{Rv1629,CAD} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [CAD only] GO:0004070+F molecular_function [name] aspartate carbamoyltransferase activity [def] "Catalysis of the reaction GO:0004088+F molecular_function [name] carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity [def] "Catalysis of the reaction GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006207+P biological_process [name] 'de novo' pyrimidine base biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of pyrimidine bases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors." [GOC GO:0006520+P biological_process [name] cellular amino acid metabolic process [def] "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells." [CHEBI GO:0006541+P biological_process [name] glutamine metabolic process [def] "The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid." [GOC GO:0006807+P biological_process [name] nitrogen compound metabolic process [def] "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium." [CHEBI GO:0016597+F molecular_function [name] amino acid binding [def] "Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents." [GOC GO:0016743+F molecular_function [name] carboxyl- or carbamoyltransferase activity [def] "Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor)." [GOC GO:0016810+F molecular_function [name] hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [def] "Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds." [GOC GO:0016812+F molecular_function [name] hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides [def] "Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC [18]{Rv2737c,GFPT1} [common GO terms] GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [GFPT1 only] GO:0004360+F molecular_function [name] glutamine-fructose-6-phosphate transaminase (isomerizing) activity [def] "Catalysis of the reaction GO:0005975+P biological_process [name] carbohydrate metabolic process [def] "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC GO:0006002+P biological_process [name] fructose 6-phosphate metabolic process [def] "The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism." [ISBN GO:0006042+P biological_process [name] glucosamine biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin." [GOC GO:0006047+P biological_process [name] UDP-N-acetylglucosamine metabolic process [def] "The chemical reactions and pathways involving UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate." [GOC GO:0006048+P biological_process [name] UDP-N-acetylglucosamine biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate." [GOC GO:0006112+P biological_process [name] energy reserve metabolic process [def] "The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen." [GOC GO:0006541+P biological_process [name] glutamine metabolic process [def] "The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid." [GOC GO:0008483+F molecular_function [name] transaminase activity [def] "Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid." [ISBN GO:0009744+P biological_process [name] response to sucrose stimulus [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a sucrose stimulus." [GOC GO:0016597+F molecular_function [name] amino acid binding [def] "Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0030246+F molecular_function [name] carbohydrate binding [def] "Interacting selectively and non-covalently with any carbohydrate, any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC GO:0032868+P biological_process [name] response to insulin stimulus [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." [GOC GO:0032869+P biological_process [name] cellular response to insulin stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." [GOC GO:0032922+P biological_process [name] circadian regulation of gene expression [def] "Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours." [GOC GO:0036498+P GO:0045719+P biological_process [name] negative regulation of glycogen biosynthetic process [def] "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen." [GOC GO:0048511+P biological_process [name] rhythmic process [def] "Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism." [GOC GO:0051289+P biological_process [name] protein homotetramerization [def] "The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC GO:1901137+P [19]{Rv2737c,ALDH3A2} [common GO terms] GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH3A2 only] GO:0000302+P biological_process [name] response to reactive oxygen species [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals." [GOC GO:0001561+P biological_process [name] fatty acid alpha-oxidation [def] "A metabolic pathway by which 3-methyl branched fatty acids are degraded. These compounds are not degraded by the normal peroxisomal beta-oxidation pathway, because the 3-methyl blocks the dehydrogenation of the hydroxyl group by hydroxyacyl-CoA dehydrogenase. The 3-methyl branched fatty acid is converted in several steps to pristenic acid, which can then feed into the beta-oxidative pathway." [http GO:0004028+F molecular_function [name] 3-chloroallyl aldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0004029+F molecular_function [name] aldehyde dehydrogenase (NAD) activity [def] "Catalysis of the reaction GO:0004030+F molecular_function [name] aldehyde dehydrogenase [NAD(P)+] activity [def] "Catalysis of the reaction GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005743+C cellular_component [name] mitochondrial inner membrane [def] "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC GO:0005777+C cellular_component [name] peroxisome [def] "A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules_ contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [ISBN GO:0005778+C cellular_component [name] peroxisomal membrane [def] "The lipid bilayer surrounding a peroxisome." [GOC GO:0005783+C cellular_component [name] endoplasmic reticulum [def] "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN GO:0005789+C cellular_component [name] endoplasmic reticulum membrane [def] "The lipid bilayer surrounding the endoplasmic reticulum." [GOC GO:0006081+P biological_process [name] cellular aldehyde metabolic process [def] "The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells." [GOC GO:0006714+P biological_process [name] sesquiterpenoid metabolic process [def] "The chemical reactions and pathways involving sesquiterpenoid compounds, terpenoids with three isoprene units." [ISBN GO:0007417+P biological_process [name] central nervous system development [def] "The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain, spinal cord and spinal nerves. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord." [GOC GO:0007422+P biological_process [name] peripheral nervous system development [def] "The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0008544+P biological_process [name] epidermis development [def] "The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of a plant or animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0030148+P biological_process [name] sphingolipid biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid)." [GOC GO:0033306+P biological_process [name] phytol metabolic process [def] "The chemical reactions and pathways involving phytol, (2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-ol." [CHEBI GO:0042406+C cellular_component [name] extrinsic to endoplasmic reticulum membrane [def] "Loosely bound to one surface of the endoplasmic reticulum membrane, but not integrated into the hydrophobic region." [GOC GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC GO:0046292+P biological_process [name] formaldehyde metabolic process [def] "The chemical reactions and pathways involving formaldehyde (methanal, H2C=O), a colorless liquid or gas with a pungent odor, commonly used as a fixative or an antibacterial agent." [CHEBI GO:0046577+F molecular_function [name] long-chain-alcohol oxidase activity [def] "Catalysis of the reaction GO:0050061+F molecular_function [name] long-chain-aldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0052814+F molecular_function [name] medium-chain-aldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [20]{Rv2737c,ABCB5} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ABCB5 only] GO:0002481+P biological_process [name] antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent [def] "The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family." [GOC GO:0002485+P biological_process [name] antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent [def] "The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP-dependent ER pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and becomes associated with the MHC class I molecule in the ER following TAP-dependent transport from the cytosol. Class I here refers to classical class I molecules." [GOC GO:0002489+P biological_process [name] antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent [def] "The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family." [GOC GO:0002591+P biological_process [name] positive regulation of antigen processing and presentation of peptide antigen via MHC class I [def] "Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I." [GOC GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0005887+C cellular_component [name] integral to plasma membrane [def] "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006855+P biological_process [name] drug transmembrane transport [def] "The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0008559+F molecular_function [name] xenobiotic-transporting ATPase activity [def] "Catalysis of the reaction GO:0015562+F molecular_function [name] efflux transmembrane transporter activity [def] "Catalysis of the transfer of a specific substance or related group of substances from the inside of the cell to the outside of the cell across a membrane." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0030154+P biological_process [name] cell differentiation [def] "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN GO:0042391+P biological_process [name] regulation of membrane potential [def] "Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC GO:0042626+F molecular_function [name] ATPase activity, coupled to transmembrane movement of substances [def] "Catalysis of the reaction GO:0042908+P biological_process [name] xenobiotic transport [def] "The directed movement of a xenobiotic, a compound foreign to living organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0048058+P biological_process [name] compound eye corneal lens development [def] "The process whose specific outcome is the progression of the corneal lens in the compound eye over time, from its formation to the mature structure. The corneal lens is a chitinous extracellular secretion of the four underlying cone cells and the pigment cells." [GOC GO:0055085+P biological_process [name] transmembrane transport [def] "The process in which a solute is transported from one side of a membrane to the other." [GOC [21]{Rv2737c,POLN} [common GO terms] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC [POLN only] GO:0000724+P biological_process [name] double-strand break repair via homologous recombination [def] "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0019985+P biological_process [name] translesion synthesis [def] "The replication of damaged DNA by synthesis across a lesion in the template strand_ a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide." [GOC GO:0030332+F molecular_function [name] cyclin binding [def] "Interacting selectively and non-covalently with cyclins, proteins whose levels in a cell varies markedly during the cell cycle, rising steadily until mitosis, then falling abruptly to zero. As cyclins reach a threshold level, they are thought to drive cells into G2 phase and thus to mitosis." [GOC GO:0036297+P GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN [22]{Rv2737c,ATP1A1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP1A1 only] GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC [23]{Rv2737c,MCCC1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [MCCC1 only] GO:0002169+C cellular_component [name] 3-methylcrotonyl-CoA carboxylase complex, mitochondrial [def] "A heterodimeric complex having 3-methylcrotonyl-CoA carboxylase activity. The alpha subunit has a covalently bound biotin essential for the ATP-dependent carboxylation. The beta subunit possess carboxyltransferase activity which presumably is essential for binding to 3-methylcrotonyl-CoA." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0004075+F molecular_function [name] biotin carboxylase activity [def] "Catalysis of the reaction GO:0004485+F molecular_function [name] methylcrotonoyl-CoA carboxylase activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005743+C cellular_component [name] mitochondrial inner membrane [def] "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006552+P biological_process [name] leucine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of leucine, 2-amino-4-methylpentanoic acid." [GOC GO:0006768+P biological_process [name] biotin metabolic process [def] "The chemical reactions and pathways involving biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid_ the (+) enantiomer is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions." [ISBN GO:0009083+P biological_process [name] branched chain family amino acid catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine." [GOC GO:0009374+F molecular_function [name] biotin binding [def] "Interacting selectively and non-covalently with biotin (cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid), the (+) enantiomer of which is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions." [GOC GO:0016874+F molecular_function [name] ligase activity [def] "Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0051291+P biological_process [name] protein heterooligomerization [def] "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." [GOC [24]{Rv1629,DHTKD1} [common GO terms] [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [DHTKD1 only] GO:0002244+P biological_process [name] hemopoietic progenitor cell differentiation [def] "The process in which precursor cell type acquires the specialized features of a hemopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells." [GOC GO:0004591+F molecular_function [name] oxoglutarate dehydrogenase (succinyl-transferring) activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006091+P biological_process [name] generation of precursor metabolites and energy [def] "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." [GOC GO:0006096+P biological_process [name] glycolysis [def] "The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Glycolysis begins with phosphorylation of a monosaccharide (generally glucose) on the sixth carbon by a hexokinase, and ends with the production of pyruvate. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle." [GOC GO:0006099+P biological_process [name] tricarboxylic acid cycle [def] "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." [ISBN GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016624+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide." [GOC GO:0030976+F molecular_function [name] thiamine pyrophosphate binding [def] "Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases." [CHEBI GO:0045252+C cellular_component [name] oxoglutarate dehydrogenase complex [def] "A complex of multiple copies of three enzymatic components GO:0046487+P biological_process [name] glyoxylate metabolic process [def] "The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH." [ISBN GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [25]{Rv2737c,ABCB4} [common GO terms] GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ABCB4 only] GO:0006855+P biological_process [name] drug transmembrane transport [def] "The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0008559+F molecular_function [name] xenobiotic-transporting ATPase activity [def] "Catalysis of the reaction GO:0042908+P biological_process [name] xenobiotic transport [def] "The directed movement of a xenobiotic, a compound foreign to living organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC [26]{Rv2737c,ATP2B4} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP2B4 only] GO:0003407+P biological_process [name] neural retina development [def] "The progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells." [GOC GO:0005388+F molecular_function [name] calcium-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005516+F molecular_function [name] calmodulin binding [def] "Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states." [GOC GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0005887+C cellular_component [name] integral to plasma membrane [def] "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0005901+C cellular_component [name] caveola [def] "A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include any of the minute pits or incuppings of the cell membrane formed during pinocytosis. Such caveolae may be pinched off to form free vesicles within the cytoplasm." [GOC GO:0006357+P biological_process [name] regulation of transcription from RNA polymerase II promoter [def] "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006816+P biological_process [name] calcium ion transport [def] "The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006874+P biological_process [name] cellular calcium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell." [GOC GO:0007283+P biological_process [name] spermatogenesis [def] "The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis." [GOC GO:0010751+P biological_process [name] negative regulation of nitric oxide mediated signal transduction [def] "Any process that decreases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is a series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0016323+C cellular_component [name] basolateral plasma membrane [def] "The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis." [GOC GO:0021766+P biological_process [name] hippocampus development [def] "The progression of the hippocampus over time from its initial formation until its mature state." [GO_REF GO:0030018+C cellular_component [name] Z disc [def] "Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached." [GOC GO:0030165+F molecular_function [name] PDZ domain binding [def] "Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins." [GOC GO:0030315+C cellular_component [name] T-tubule [def] "Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane." [GOC GO:0030317+P biological_process [name] sperm motility [def] "Any process involved in the controlled movement of a sperm cell." [GOC GO:0030346+F molecular_function [name] protein phosphatase 2B binding [def] "Interacting selectively and non-covalently with the enzyme protein phosphatase 2B." [GOC GO:0033138+P biological_process [name] positive regulation of peptidyl-serine phosphorylation [def] "Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0036126+C GO:0036487+F GO:0042383+C cellular_component [name] sarcolemma [def] "The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers." [ISBN GO:0042995+C cellular_component [name] cell projection [def] "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC GO:0043005+C cellular_component [name] neuron projection [def] "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC GO:0043234+C cellular_component [name] protein complex [def] "Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules." [GOC GO:0045019+P biological_process [name] negative regulation of nitric oxide biosynthetic process [def] "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0050998+F molecular_function [name] nitric-oxide synthase binding [def] "Interacting selectively and non-covalently with the enzyme nitric-oxide synthase." [GOC GO:0051001+P biological_process [name] negative regulation of nitric-oxide synthase activity [def] "Any process that stops or reduces the activity of the enzyme nitric-oxide synthase." [GOC GO:0051599+P biological_process [name] response to hydrostatic pressure [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrostatic pressure stimulus. Hydrostatic pressure is the force acting on an object in a system where the fluid is at rest (as opposed to moving). The weight of the fluid above the object creates pressure on it." [Wikipedia GO:0070588+P biological_process [name] calcium ion transmembrane transport [def] "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0070885+P biological_process [name] negative regulation of calcineurin-NFAT signaling pathway [def] "Any process that stops, prevents, or reduces the frequency, rate or extent of signaling via the calcineurin-NFAT signaling pathway." [GOC GO:0071872+P biological_process [name] cellular response to epinephrine stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epinephrine stimulus. Epinephrine is a catecholamine that has the formula C9H13NO3_ it is secreted by the adrenal medulla to act as a hormone, and released by certain neurons to act as a neurotransmitter active in the central nervous system." [CHEBI GO:0097110+F molecular_function [name] scaffold protein binding [def] "Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes." [GOC GO:0097228+C GO:0097553+P GO:0098703+P GO:0098736+P GO:1900082+P GO:1901205+P GO:1901660+P GO:1902083+P GO:1902305+P GO:1902806+P GO:1903243+P GO:1903249+P GO:1903779+P GO:2000481+P biological_process [name] positive regulation of cAMP-dependent protein kinase activity [def] "Any process that activates or increases the frequency, rate or extent of cAMP-dependent protein kinase activity." [GOC GO:0017080+F molecular_function [name] sodium channel regulator activity [def] "Modulates the activity of a sodium channel." [GOC [27]{Rv2737c,SMARCA5} [common GO terms] GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [SMARCA5 only] GO:0016589+C cellular_component [name] NURF complex [def] "A four subunit ISWI-containing protein complex that facilitates nucleosome mobility and transcriptional activation in an ATP-dependent manner. In contrast to other chromatin remodeling complexes, the ATPase activity of NURF requires nucleosomes rather than free DNA or histones." [GOC GO:0043044+P biological_process [name] ATP-dependent chromatin remodeling [def] "Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors." [GOC [28]{Rv2737c,ABCB10} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ABCB10 only] GO:0005215+F molecular_function [name] transporter activity [def] "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005743+C cellular_component [name] mitochondrial inner membrane [def] "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0032592+C cellular_component [name] integral to mitochondrial membrane [def] "Located such that some or all of the gene product itself penetrates at least one phospholipid bilayer of a mitochondrial membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0042626+F molecular_function [name] ATPase activity, coupled to transmembrane movement of substances [def] "Catalysis of the reaction GO:0042803+F molecular_function [name] protein homodimerization activity [def] "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC GO:0055085+P biological_process [name] transmembrane transport [def] "The process in which a solute is transported from one side of a membrane to the other." [GOC [29]{Rv2737c,PCCB} [common GO terms] [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [PCCB only] GO:0016874+F molecular_function [name] ligase activity [def] "Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC [30]{Rv0629c,ERCC6} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv0629c only] GO:0000724+P biological_process [name] double-strand break repair via homologous recombination [def] "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC GO:0004003+F molecular_function [name] ATP-dependent DNA helicase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006302+P biological_process [name] double-strand break repair [def] "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0008854+F molecular_function [name] exodeoxyribonuclease V activity [def] "Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides." [EC GO:0009338+C cellular_component [name] exodeoxyribonuclease V complex [def] "An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA." [EC GO:0032508+P biological_process [name] DNA duplex unwinding [def] "The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ERCC6 only] GO:0000303+P biological_process [name] response to superoxide [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion." [GOC GO:0003682+F molecular_function [name] chromatin binding [def] "Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN GO:0006283+P biological_process [name] transcription-coupled nucleotide-excision repair [def] "The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway." [PMID GO:0006284+P biological_process [name] base-excision repair [def] "In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase." [ISBN GO:0006290+P biological_process [name] pyrimidine dimer repair [def] "The repair of UV-induced T-T, C-T and C-C dimers." [ISBN GO:0006351+P biological_process [name] transcription, DNA-dependent [def] "The cellular synthesis of RNA on a template of DNA." [GOC GO:0006355+P biological_process [name] regulation of transcription, DNA-dependent [def] "Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription." [GOC GO:0006362+P biological_process [name] transcription elongation from RNA polymerase I promoter [def] "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I." [GOC GO:0006366+P biological_process [name] transcription from RNA polymerase II promoter [def] "The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs)." [GOC GO:0006979+P biological_process [name] response to oxidative stress [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC GO:0007256+P biological_process [name] activation of JNKK activity [def] "The initiation of the activity of the inactive enzyme JUN kinase kinase (JNKK) activity in response to phosphorylation by a member of the JUN kinase kinase kinase (JNKKK) family, or another upstream kinase. JNKKs are involved in a signaling pathway that is primarily activated by cytokines and exposure to environmental stress." [GOC GO:0007257+P biological_process [name] activation of JUN kinase activity [def] "The initiation of the activity of the inactive enzyme JUN kinase by phosphorylation by a JUN kinase kinase (JNKK)." [GOC GO:0008022+F molecular_function [name] protein C-terminus binding [def] "Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0008023+C cellular_component [name] transcription elongation factor complex [def] "Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0008630+P biological_process [name] DNA damage response, signal transduction resulting in induction of apoptosis [def] "A cascade of processes initiated by the detection of DNA damage and resulting in the induction of apoptosis (programmed cell death)." [GOC GO:0009411+P biological_process [name] response to UV [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers." [GOC GO:0009636+P biological_process [name] response to toxin [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxin stimulus." [GOC GO:0010165+P biological_process [name] response to X-ray [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz)." [GOC GO:0010224+P biological_process [name] response to UV-B [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a UV-B radiation stimulus. UV-B radiation (UV-B light) spans the wavelengths 290 to 320 nm." [GOC GO:0010332+P biological_process [name] response to gamma radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum." [GOC GO:0030296+F molecular_function [name] protein tyrosine kinase activator activity [def] "Increases the activity of a protein tyrosine kinase, an enzyme which phosphorylates a tyrosyl phenolic group on a protein." [GOC GO:0032403+F molecular_function [name] protein complex binding [def] "Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0032784+P biological_process [name] regulation of transcription elongation, DNA-dependent [def] "Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase." [GOC GO:0032786+P biological_process [name] positive regulation of transcription elongation, DNA-dependent [def] "Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase." [GOC GO:0035264+P biological_process [name] multicellular organism growth [def] "The increase in size or mass of an entire multicellular organism, as opposed to cell growth." [GOC GO:0045494+P biological_process [name] photoreceptor cell maintenance [def] "Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light." [CL GO:0045815+P biological_process [name] positive regulation of gene expression, epigenetic [def] "Any epigenetic process that activates or increases the rate of gene expression." [GOC GO:0047485+F molecular_function [name] protein N-terminus binding [def] "Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0061098+P biological_process [name] positive regulation of protein tyrosine kinase activity [def] "Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity." [GOC GO:0003678+F molecular_function [name] DNA helicase activity [def] "Catalysis of the reaction [31]{Rv2737c,ABCB11} [common GO terms] GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ABCB11 only] GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0015721+P biological_process [name] bile acid and bile salt transport [def] "The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0042626+F molecular_function [name] ATPase activity, coupled to transmembrane movement of substances [def] "Catalysis of the reaction GO:0055085+P biological_process [name] transmembrane transport [def] "The process in which a solute is transported from one side of a membrane to the other." [GOC [32]{Rv1629,OGDH} [common GO terms] [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [OGDH only] GO:0004591+F molecular_function [name] oxoglutarate dehydrogenase (succinyl-transferring) activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006091+P biological_process [name] generation of precursor metabolites and energy [def] "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." [GOC GO:0006096+P biological_process [name] glycolysis [def] "The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Glycolysis begins with phosphorylation of a monosaccharide (generally glucose) on the sixth carbon by a hexokinase, and ends with the production of pyruvate. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle." [GOC GO:0006099+P biological_process [name] tricarboxylic acid cycle [def] "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." [ISBN GO:0006103+P biological_process [name] 2-oxoglutarate metabolic process [def] "The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism." [ISBN GO:0006104+P biological_process [name] succinyl-CoA metabolic process [def] "The chemical reactions and pathways involving succinyl-CoA, a compound composed of the monovalent acyl group 3-carboxypropanoyl, derived from succinic acid by loss of one OH group, linked to coenzyme A." [GOC GO:0006554+P biological_process [name] lysine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of lysine, 2,6-diaminohexanoic acid." [GOC GO:0006734+P biological_process [name] NADH metabolic process [def] "The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016624+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide." [GOC GO:0021695+P biological_process [name] cerebellar cortex development [def] "The process whose specific outcome is the progression of the cerebellar cortex over time, from its formation to the mature structure. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function." [GO_REF GO:0021756+P biological_process [name] striatum development [def] "The progression of the striatum over time from its initial formation until its mature state. The striatum is a region of the forebrain consisting of the caudate nucleus, putamen and fundus striati." [GO_REF GO:0021766+P biological_process [name] hippocampus development [def] "The progression of the hippocampus over time from its initial formation until its mature state." [GO_REF GO:0021794+P biological_process [name] thalamus development [def] "The process in which the thalamus changes over time, from its initial formation to its mature state." [GO_REF GO:0021860+P biological_process [name] pyramidal neuron development [def] "The progression of a pyramidal neuron from its initial formation to its mature state." [GO_REF GO:0022028+P biological_process [name] tangential migration from the subventricular zone to the olfactory bulb [def] "The migration of cells in the telencephalon from the subventricular zone to the olfactory bulb in which cells move orthogonally to the direction of radial migration and do not use radial glial cell processes as substrates for migration." [GO_REF GO:0030976+F molecular_function [name] thiamine pyrophosphate binding [def] "Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases." [CHEBI GO:0031072+F molecular_function [name] heat shock protein binding [def] "Interacting selectvely with a heat shock protein, any protein synthesized or activated in response to heat shock." [GOC GO:0031966+C cellular_component [name] mitochondrial membrane [def] "Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope." [GOC GO:0034602+F molecular_function [name] oxoglutarate dehydrogenase (NAD+) activity [def] "Catalysis of the reaction GO:0045252+C cellular_component [name] oxoglutarate dehydrogenase complex [def] "A complex of multiple copies of three enzymatic components GO:0046487+P biological_process [name] glyoxylate metabolic process [def] "The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH." [ISBN GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0051087+F molecular_function [name] chaperone binding [def] "Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport." [http GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0061034+P biological_process [name] olfactory bulb mitral cell layer development [def] "The progression of the olfactory bulb mitral cell layer over time from its initial formation until its mature state. The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [33]{Rv2737c,PCCA} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [PCCA only] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0004075+F molecular_function [name] biotin carboxylase activity [def] "Catalysis of the reaction GO:0004658+F molecular_function [name] propionyl-CoA carboxylase activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006768+P biological_process [name] biotin metabolic process [def] "The chemical reactions and pathways involving biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid_ the (+) enantiomer is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions." [ISBN GO:0009374+F molecular_function [name] biotin binding [def] "Interacting selectively and non-covalently with biotin (cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid), the (+) enantiomer of which is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions." [GOC GO:0016874+F molecular_function [name] ligase activity [def] "Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC GO:0019626+P biological_process [name] short-chain fatty acid catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of fatty acids with a chain length of less than 8 carbons." [ISBN GO:0019899+F molecular_function [name] enzyme binding [def] "Interacting selectively and non-covalently with any enzyme." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC [34]{Rv2737c,GFPT2} [common GO terms] GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [GFPT2 only] GO:0004360+F molecular_function [name] glutamine-fructose-6-phosphate transaminase (isomerizing) activity [def] "Catalysis of the reaction GO:0005975+P biological_process [name] carbohydrate metabolic process [def] "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC GO:0006002+P biological_process [name] fructose 6-phosphate metabolic process [def] "The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism." [ISBN GO:0006047+P biological_process [name] UDP-N-acetylglucosamine metabolic process [def] "The chemical reactions and pathways involving UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate." [GOC GO:0006048+P biological_process [name] UDP-N-acetylglucosamine biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate." [GOC GO:0006112+P biological_process [name] energy reserve metabolic process [def] "The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen." [GOC GO:0006541+P biological_process [name] glutamine metabolic process [def] "The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid." [GOC GO:0008483+F molecular_function [name] transaminase activity [def] "Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid." [ISBN GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0030246+F molecular_function [name] carbohydrate binding [def] "Interacting selectively and non-covalently with any carbohydrate, any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC GO:1901137+P [35]{Rv2737c,ABCB6} [common GO terms] GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ABCB6 only] [36]{Rv2737c,ATP1A2} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP1A2 only] GO:0001504+P biological_process [name] neurotransmitter uptake [def] "The directed movement of neurotransmitters into neurons or glial cells. This process leads to inactivation and recycling of neurotransmitters. It does not occur during cholinergic synaptic transmission. Instead, acetylcholine is enzymatically degraded in the synaptic cleft." [ISBN GO:0002026+P biological_process [name] regulation of the force of heart contraction [def] "Any process that modulates the extent of heart contraction, changing the force with which blood is propelled." [GOC GO:0002087+P biological_process [name] regulation of respiratory gaseous exchange by neurological system process [def] "A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates." [GOC GO:0005391+F molecular_function [name] sodium [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005768+C cellular_component [name] endosome [def] "A membrane-bounded organelle to which materials ingested by endocytosis are delivered." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0005890+C cellular_component [name] sodium [def] "Sodium GO:0005901+C cellular_component [name] caveola [def] "A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include any of the minute pits or incuppings of the cell membrane formed during pinocytosis. Such caveolae may be pinched off to form free vesicles within the cytoplasm." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006813+P biological_process [name] potassium ion transport [def] "The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006814+P biological_process [name] sodium ion transport [def] "The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006883+P biological_process [name] cellular sodium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of sodium ions at the level of a cell." [GOC GO:0006937+P biological_process [name] regulation of muscle contraction [def] "Any process that modulates the frequency, rate or extent of muscle contraction." [GOC GO:0006940+P biological_process [name] regulation of smooth muscle contraction [def] "Any process that modulates the frequency, rate or extent of smooth muscle contraction." [GOC GO:0006942+P biological_process [name] regulation of striated muscle contraction [def] "Any process that modulates the frequency, rate or extent of striated muscle contraction." [GOC GO:0008217+P biological_process [name] regulation of blood pressure [def] "Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure." [GOC GO:0008344+P biological_process [name] adult locomotory behavior [def] "Locomotory behavior in a fully developed and mature organism." [GOC GO:0008542+P biological_process [name] visual learning [def] "Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue." [GOC GO:0010107+P biological_process [name] potassium ion import [def] "The directed movement of potassium ions into a cell or organelle." [GOC GO:0010248+P biological_process [name] establishment or maintenance of transmembrane electrochemical gradient [def] "The directed movement of ions to establish or maintain an electrochemical gradient across a membrane by means of some agent such as a transporter or pore." [GOC GO:0010881+P biological_process [name] regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion [def] "Any process that modulates the frequency, rate or extent of cardiac muscle contraction via the regulation of the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol. The sarcoplasmic reticulum is the endoplasmic reticulum of striated muscle, specialised for the sequestration of calcium ions that are released upon receipt of a signal relayed by the T tubules from the neuromuscular junction." [GOC GO:0014704+C cellular_component [name] intercalated disc [def] "A complex cell-cell junction at which myofibrils terminate in cardiomyocytes_ mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells." [GOC GO:0015991+P biological_process [name] ATP hydrolysis coupled proton transport [def] "The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0019229+P biological_process [name] regulation of vasoconstriction [def] "Any process that modulates the frequency, rate or extent of reductions in the diameter of blood vessels." [GOC GO:0019829+F molecular_function [name] cation-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0030007+P biological_process [name] cellular potassium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of potassium ions at the level of a cell." [GOC GO:0030315+C cellular_component [name] T-tubule [def] "Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0035094+P biological_process [name] response to nicotine [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nicotine stimulus." [CHEBI GO:0036376+P GO:0040011+P biological_process [name] locomotion [def] "Self-propelled movement of a cell or organism from one location to another." [GOC GO:0042383+C cellular_component [name] sarcolemma [def] "The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers." [ISBN GO:0043005+C cellular_component [name] neuron projection [def] "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC GO:0043197+C cellular_component [name] dendritic spine [def] "Protrusion from a dendrite. Spines are specialised subcellular compartments involved in the synaptic transmission. They are linked to the dendritic shaft by a restriction. Because of their bulb shape, they function as a biochemical and an electrical compartment. Spine remodeling is though to be involved in synaptic plasticity." [GOC GO:0043209+C cellular_component [name] myelin sheath [def] "An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC GO:0045202+C cellular_component [name] synapse [def] "The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell_ the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane_ facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." [ISBN GO:0045822+P biological_process [name] negative regulation of heart contraction [def] "Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction." [GOC GO:0045988+P biological_process [name] negative regulation of striated muscle contraction [def] "Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction." [GOC GO:0046034+P biological_process [name] ATP metabolic process [def] "The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0051087+F molecular_function [name] chaperone binding [def] "Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport." [http GO:0051481+P biological_process [name] reduction of cytosolic calcium ion concentration [def] "Any process that decreases the concentration of calcium ions in the cytodol." [GOC GO:0051946+P biological_process [name] regulation of glutamate uptake involved in transmission of nerve impulse [def] "Any process that modulates the frequency, rate or extent of the directed movement of L-glutamate into a neuron or glial cell." [GOC GO:0051966+P biological_process [name] regulation of synaptic transmission, glutamatergic [def] "Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate." [GOC GO:0055119+P biological_process [name] relaxation of cardiac muscle [def] "The process in which the extent of cardiac muscle contraction is reduced." [GOC GO:0060048+P biological_process [name] cardiac muscle contraction [def] "Muscle contraction of cardiac muscle tissue." [GOC GO:0071260+P biological_process [name] cellular response to mechanical stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus." [GOC GO:0071383+P biological_process [name] cellular response to steroid hormone stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus." [GOC GO:0086004+P GO:0086009+P GO:0086012+P GO:0086064+P GO:1903170+P GO:1903280+P GO:1903416+P GO:1903561+C GO:1903779+P GO:1990239+F GO:1990573+P GO:0008144+F molecular_function [name] drug binding [def] "Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism_ in particular, any such substance used in the diagnosis, prevention, or treatment of disease." [GOC GO:0030955+F molecular_function [name] potassium ion binding [def] "Interacting selectively and non-covalently with potassium (K+) ions." [GOC GO:0031402+F molecular_function [name] sodium ion binding [def] "Interacting selectively and non-covalently with sodium ions (Na+)." [GOC [37]{Rv2737c,CPS1} [common GO terms] [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [CPS1 only] GO:0004088+F molecular_function [name] carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity [def] "Catalysis of the reaction GO:0006207+P biological_process [name] 'de novo' pyrimidine base biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of pyrimidine bases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors." [GOC GO:0006541+P biological_process [name] glutamine metabolic process [def] "The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid." [GOC GO:0006807+P biological_process [name] nitrogen compound metabolic process [def] "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium." [CHEBI [38]{Rv1547,DHTKD1} [common GO terms] [Rv1547 only] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [DHTKD1 only] GO:0002244+P biological_process [name] hemopoietic progenitor cell differentiation [def] "The process in which precursor cell type acquires the specialized features of a hemopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells." [GOC GO:0004591+F molecular_function [name] oxoglutarate dehydrogenase (succinyl-transferring) activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006091+P biological_process [name] generation of precursor metabolites and energy [def] "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." [GOC GO:0006096+P biological_process [name] glycolysis [def] "The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Glycolysis begins with phosphorylation of a monosaccharide (generally glucose) on the sixth carbon by a hexokinase, and ends with the production of pyruvate. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle." [GOC GO:0006099+P biological_process [name] tricarboxylic acid cycle [def] "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." [ISBN GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016624+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide." [GOC GO:0030976+F molecular_function [name] thiamine pyrophosphate binding [def] "Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases." [CHEBI GO:0045252+C cellular_component [name] oxoglutarate dehydrogenase complex [def] "A complex of multiple copies of three enzymatic components GO:0046487+P biological_process [name] glyoxylate metabolic process [def] "The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH." [ISBN GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [39]{Rv2737c,GAPDHS} [common GO terms] GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [GAPDHS only] GO:0004365+F molecular_function [name] glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity [def] "Catalysis of the reaction GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0006006+P biological_process [name] glucose metabolic process [def] "The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose_ it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides." [ISBN GO:0006094+P biological_process [name] gluconeogenesis [def] "The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol." [MetaCyc GO:0006096+P biological_process [name] glycolysis [def] "The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Glycolysis begins with phosphorylation of a monosaccharide (generally glucose) on the sixth carbon by a hexokinase, and ends with the production of pyruvate. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle." [GOC GO:0007286+P biological_process [name] spermatid development [def] "The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0030317+P biological_process [name] sperm motility [def] "Any process involved in the controlled movement of a sperm cell." [GOC GO:0031514+C cellular_component [name] motile cilium [def] "A cilium which has a variable arrangement of axonemal microtubules, contains molecular motors, and beats with a characteristic whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface. Motile cilia are typically found in multiple copies on epithelial cells that line the lumenal ducts of various tissues. Motile cilia may also function as sensory organelles." [GOC GO:0045821+P biological_process [name] positive regulation of glycolysis [def] "Any process that activates or increases the frequency, rate or extent of glycolysis." [GOC GO:0050661+F molecular_function [name] NADP binding [def] "Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions_ binding may be to either the oxidized form, NADP+, or the reduced form, NADPH." [GOC GO:0051287+F molecular_function [name] NAD binding [def] "Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions_ binding may be to either the oxidized form, NAD+, or the reduced form, NADH." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0061621+P [40]{Rv2737c,ATP2B3} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP2B3 only] GO:0005388+F molecular_function [name] calcium-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005516+F molecular_function [name] calmodulin binding [def] "Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states." [GOC GO:0005794+C cellular_component [name] Golgi apparatus [def] "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum_ such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0005887+C cellular_component [name] integral to plasma membrane [def] "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006816+P biological_process [name] calcium ion transport [def] "The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006874+P biological_process [name] cellular calcium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0030165+F molecular_function [name] PDZ domain binding [def] "Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0070588+P biological_process [name] calcium ion transmembrane transport [def] "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:1903561+C GO:1903779+P [41]{Rv1629,ACAT1} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ACAT1 only] GO:0001889+P biological_process [name] liver development [def] "The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes." [GOC GO:0003985+F molecular_function [name] acetyl-CoA C-acetyltransferase activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005743+C cellular_component [name] mitochondrial inner membrane [def] "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0007420+P biological_process [name] brain development [def] "The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.)." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0009083+P biological_process [name] branched chain family amino acid catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine." [GOC GO:0009725+P biological_process [name] response to hormone stimulus [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus." [GOC GO:0014070+P biological_process [name] response to organic cyclic compound [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus." [CHEBI GO:0016746+F molecular_function [name] transferase activity, transferring acyl groups [def] "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor)." [GOC GO:0016747+F molecular_function [name] transferase activity, transferring acyl groups other than amino-acyl groups [def] "Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor)." [GOC GO:0019899+F molecular_function [name] enzyme binding [def] "Interacting selectively and non-covalently with any enzyme." [GOC GO:0042594+P biological_process [name] response to starvation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment." [GOC GO:0042803+F molecular_function [name] protein homodimerization activity [def] "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0046951+P biological_process [name] ketone body biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of ketone bodies, any one of the three substances GO:0046952+P biological_process [name] ketone body catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of ketone bodies, any one of the three substances GO:0050662+F molecular_function [name] coenzyme binding [def] "Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed." [ISBN GO:0051260+P biological_process [name] protein homooligomerization [def] "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." [GOC GO:0060612+P biological_process [name] adipose tissue development [def] "The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC GO:0072229+P biological_process [name] metanephric proximal convoluted tubule development [def] "The process whose specific outcome is the progression of the metanephric proximal convoluted tubule over time, from its formation to the mature structure. The metanephric proximal convoluted tubule is the most proximal portion of the metanephric proximal tubule and extends from the metanephric glomerular capsule to the metanephric proximal straight tubule." [GOC [42]{Rv2737c,ATP2B2} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP2B2 only] GO:0005388+F molecular_function [name] calcium-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0070588+P biological_process [name] calcium ion transmembrane transport [def] "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC [43]{Rv2737c,ATP1A3} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP1A3 only] GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC [44]{Rv2737c,GAPDH} [common GO terms] [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [GAPDH only] GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC [45]{Rv2737c,ALDH2} [common GO terms] [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH2 only] GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC [46]{Rv1629,SOD2} [common GO terms] [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [SOD2 only] GO:0001315+P biological_process [name] age-dependent response to reactive oxygen species [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC GO:0004784+F molecular_function [name] superoxide dismutase activity [def] "Catalysis of the reaction GO:0006357+P biological_process [name] regulation of transcription from RNA polymerase II promoter [def] "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC GO:0006801+P biological_process [name] superoxide metabolic process [def] "The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species." [CHEBI GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0019430+P biological_process [name] removal of superoxide radicals [def] "Any process involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2)." [CHEBI GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC [47]{Rv0629c,ACO1} [common GO terms] GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv0629c only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000724+P biological_process [name] double-strand break repair via homologous recombination [def] "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0004003+F molecular_function [name] ATP-dependent DNA helicase activity [def] "Catalysis of the reaction GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006302+P biological_process [name] double-strand break repair [def] "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008854+F molecular_function [name] exodeoxyribonuclease V activity [def] "Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides." [EC GO:0009338+C cellular_component [name] exodeoxyribonuclease V complex [def] "An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA." [EC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0032508+P biological_process [name] DNA duplex unwinding [def] "The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ACO1 only] GO:0003723+F molecular_function [name] RNA binding [def] "Interacting selectively and non-covalently with an RNA molecule or a portion thereof." [GOC GO:0003994+F molecular_function [name] aconitate hydratase activity [def] "Catalysis of the reactions GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005783+C cellular_component [name] endoplasmic reticulum [def] "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN GO:0005794+C cellular_component [name] Golgi apparatus [def] "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum_ such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function GO:0006099+P biological_process [name] tricarboxylic acid cycle [def] "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." [ISBN GO:0006101+P biological_process [name] citrate metabolic process [def] "The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle." [ISBN GO:0006417+P biological_process [name] regulation of translation [def] "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA." [GOC GO:0006879+P biological_process [name] cellular iron ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0009791+P biological_process [name] post-embryonic development [def] "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." [GOC GO:0010040+P biological_process [name] response to iron(II) ion [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron(II) ion stimulus." [GOC GO:0010468+P biological_process [name] regulation of gene expression [def] "Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC GO:0016829+F molecular_function [name] lyase activity [def] "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC GO:0030350+F molecular_function [name] iron-responsive element binding [def] "Interacting selectively and non-covalently with the iron-responsive element, a regulatory sequence found in the 5'- and 3'-untranslated regions of mRNAs encoding many iron-binding proteins." [PMID GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0050892+P biological_process [name] intestinal absorption [def] "Any process in which nutrients are taken up from the contents of the intestine." [GOC GO:0051536+F molecular_function [name] iron-sulfur cluster binding [def] "Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms." [GOC GO:0051539+F molecular_function [name] 4 iron, 4 sulfur cluster binding [def] "Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster_ this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [48]{Rv1629,IMPDH2} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [IMPDH2 only] GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC [49]{Rv0629c,BTAF1} [common GO terms] GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN [Rv0629c only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000724+P biological_process [name] double-strand break repair via homologous recombination [def] "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0004003+F molecular_function [name] ATP-dependent DNA helicase activity [def] "Catalysis of the reaction GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006302+P biological_process [name] double-strand break repair [def] "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008854+F molecular_function [name] exodeoxyribonuclease V activity [def] "Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides." [EC GO:0009338+C cellular_component [name] exodeoxyribonuclease V complex [def] "An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA." [EC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0032508+P biological_process [name] DNA duplex unwinding [def] "The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [BTAF1 only] [50]{Rv0629c,SMARCA5} [common GO terms] GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN [Rv0629c only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000724+P biological_process [name] double-strand break repair via homologous recombination [def] "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0004003+F molecular_function [name] ATP-dependent DNA helicase activity [def] "Catalysis of the reaction GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006302+P biological_process [name] double-strand break repair [def] "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008854+F molecular_function [name] exodeoxyribonuclease V activity [def] "Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides." [EC GO:0009338+C cellular_component [name] exodeoxyribonuclease V complex [def] "An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA." [EC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0032508+P biological_process [name] DNA duplex unwinding [def] "The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [SMARCA5 only] GO:0016589+C cellular_component [name] NURF complex [def] "A four subunit ISWI-containing protein complex that facilitates nucleosome mobility and transcriptional activation in an ATP-dependent manner. In contrast to other chromatin remodeling complexes, the ATPase activity of NURF requires nucleosomes rather than free DNA or histones." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0043044+P biological_process [name] ATP-dependent chromatin remodeling [def] "Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors." [GOC [51]{Rv1629,NVL} [common GO terms] [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [NVL only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005697+C cellular_component [name] telomerase holoenzyme complex [def] "Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits." [PMID GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0042254+P biological_process [name] ribosome biogenesis [def] "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits_ includes transport to the sites of protein synthesis." [GOC GO:0044822+F GO:0051973+P biological_process [name] positive regulation of telomerase activity [def] "Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction GO:1990275+F [52]{Rv1629,PEX1} [common GO terms] GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [PEX1 only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005777+C cellular_component [name] peroxisome [def] "A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules_ contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [ISBN GO:0005778+C cellular_component [name] peroxisomal membrane [def] "The lipid bilayer surrounding a peroxisome." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006625+P biological_process [name] protein targeting to peroxisome [def] "The process of directing proteins towards the peroxisome, usually using signals contained within the protein." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0007031+P biological_process [name] peroxisome organization [def] "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules." [GOC GO:0008022+F molecular_function [name] protein C-terminus binding [def] "Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0015031+P biological_process [name] protein transport [def] "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016558+P biological_process [name] protein import into peroxisome matrix [def] "The import of proteins into the peroxisomal matrix. A peroxisome targeting signal (PTS) binds to a soluble receptor protein in the cytosol, and the resulting complex then binds to a receptor protein in the peroxisome membrane and is imported." [ISBN GO:0032403+F molecular_function [name] protein complex binding [def] "Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0042623+F molecular_function [name] ATPase activity, coupled [def] "Catalysis of the reaction GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC GO:0060152+P biological_process [name] microtubule-based peroxisome localization [def] "The microtubule-based process in which a peroxisome is transported to, and/or maintained in, a specific location. A peroxisome is a small membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [53]{Rv1629,ACAA1} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ACAA1 only] GO:0000038+P biological_process [name] very long chain fatty acid metabolic process [def] "The chemical reactions and pathways involving fatty acids with a chain length of C18 or greater." [GOC GO:0003988+F molecular_function [name] acetyl-CoA C-acyltransferase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005777+C cellular_component [name] peroxisome [def] "A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules_ contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [ISBN GO:0005782+C cellular_component [name] peroxisomal matrix [def] "The volume contained within the membranes of a peroxisome_ in many cells the matrix contains a crystalloid core largely composed of urate oxidase." [GOC GO:0006629+P biological_process [name] lipid metabolic process [def] "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids_ neutral fats, other fatty-acid esters, and soaps_ long-chain (fatty) alcohols and waxes_ sphingoids and other long-chain bases_ glycolipids, phospholipids and sphingolipids_ and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC GO:0006631+P biological_process [name] fatty acid metabolic process [def] "The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN GO:0006635+P biological_process [name] fatty acid beta-oxidation [def] "A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A_ the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0008206+P biological_process [name] bile acid metabolic process [def] "The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." [GOC GO:0008775+F molecular_function [name] acetate CoA-transferase activity [def] "Catalysis of the reaction GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016401+F molecular_function [name] palmitoyl-CoA oxidase activity [def] "Catalysis of the reaction GO:0016746+F molecular_function [name] transferase activity, transferring acyl groups [def] "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor)." [GOC GO:0016747+F molecular_function [name] transferase activity, transferring acyl groups other than amino-acyl groups [def] "Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor)." [GOC GO:0033540+P biological_process [name] fatty acid beta-oxidation using acyl-CoA oxidase [def] "A fatty acid beta-oxidation pathway in which the initial step, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA oxidase_ the electrons removed by oxidation pass directly to oxygen and produce hydrogen peroxide, which is cleaved by peroxisomal catalases. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC GO:0036109+P GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC [54]{Rv1629,IMPDH1} [common GO terms] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN [Rv1629 only] GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [IMPDH1 only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0003723+F molecular_function [name] RNA binding [def] "Interacting selectively and non-covalently with an RNA molecule or a portion thereof." [GOC GO:0003938+F molecular_function [name] IMP dehydrogenase activity [def] "Catalysis of the reaction GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006164+P biological_process [name] purine nucleotide biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC GO:0006177+P biological_process [name] GMP biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate." [ISBN GO:0009168+P biological_process [name] purine ribonucleoside monophosphate biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC GO:0009409+P biological_process [name] response to cold [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0030054+C cellular_component [name] cell junction [def] "A plasma membrane part that forms a specialized region of connection between two cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix." [GOC GO:0046651+P biological_process [name] lymphocyte proliferation [def] "The expansion of a lymphocyte population by cell division." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0060041+P biological_process [name] retina development in camera-type eye [def] "The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC [55]{Rv2737c,OLA1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [OLA1 only] GO:0005525+F molecular_function [name] GTP binding [def] "Interacting selectively and non-covalently with GTP, guanosine triphosphate." [GOC GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN GO:0005813+C cellular_component [name] centrosome [def] "A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle." [GOC GO:0005913+C cellular_component [name] cell-cell adherens junction [def] "An adherens junction which connects two cells to each other." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0043022+F molecular_function [name] ribosome binding [def] "Interacting selectively and non-covalently with any part of a ribosome." [GOC GO:0043023+F molecular_function [name] ribosomal large subunit binding [def] "Interacting selectively and non-covalently with any part of the larger ribosomal subunit." [GOC GO:0046034+P biological_process [name] ATP metabolic process [def] "The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC GO:0098609+P GO:0098641+F [56]{Rv2737c,HADHA} [common GO terms] GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [HADHA only] GO:0000062+F molecular_function [name] fatty-acyl-CoA binding [def] "Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003857+F molecular_function [name] 3-hydroxyacyl-CoA dehydrogenase activity [def] "Catalysis of the reaction GO:0003985+F molecular_function [name] acetyl-CoA C-acetyltransferase activity [def] "Catalysis of the reaction GO:0003988+F molecular_function [name] acetyl-CoA C-acyltransferase activity [def] "Catalysis of the reaction GO:0004300+F molecular_function [name] enoyl-CoA hydratase activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005743+C cellular_component [name] mitochondrial inner membrane [def] "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC GO:0006629+P biological_process [name] lipid metabolic process [def] "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids_ neutral fats, other fatty-acid esters, and soaps_ long-chain (fatty) alcohols and waxes_ sphingoids and other long-chain bases_ glycolipids, phospholipids and sphingolipids_ and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC GO:0006631+P biological_process [name] fatty acid metabolic process [def] "The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN GO:0006635+P biological_process [name] fatty acid beta-oxidation [def] "A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A_ the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016507+C cellular_component [name] fatty acid beta-oxidation multienzyme complex [def] "A complex that includes the long-chain 3-hydroxyacyl-CoA dehydrogenase and long-chain enoyl-CoA hydratase activities in two subunits (alpha and beta), catalyzing two steps of the fatty acid beta-oxidation cycle within the mitochondrial matrix." [GOC GO:0016508+F molecular_function [name] long-chain-enoyl-CoA hydratase activity [def] "Catalysis of the reaction GO:0016509+F molecular_function [name] long-chain-3-hydroxyacyl-CoA dehydrogenase activity [def] "Catalysis of the reaction GO:0016829+F molecular_function [name] lyase activity [def] "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC GO:0031012+C cellular_component [name] extracellular matrix [def] "A structure lying external to one or more cells, which provides structural support for cells or tissues_ may be completely external to the cell (as in animals) or be part of the cell (as in plants)." [GOC GO:0032403+F molecular_function [name] protein complex binding [def] "Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0032868+P biological_process [name] response to insulin stimulus [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." [GOC GO:0035965+P biological_process [name] cardiolipin acyl-chain remodeling [def] "Remodeling the acyl chains of premature (de novo synthesized) cardiolipin (1,3-bis(3-phosphatidyl)glycerol), through sequential deacylation and re-acylation reactions, to generate mature cardiolipin containing high-levels of unsaturated fatty acids." [GOC GO:0042493+P biological_process [name] response to drug [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease." [GOC GO:0042645+C cellular_component [name] mitochondrial nucleoid [def] "The region of a mitochondrion to which the DNA is confined." [GOC GO:0051287+F molecular_function [name] NAD binding [def] "Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions_ binding may be to either the oxidized form, NAD+, or the reduced form, NADH." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC [57]{Rv1547,CCBL2} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN [Rv1547 only] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [CCBL2 only] GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0006103+P biological_process [name] 2-oxoglutarate metabolic process [def] "The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism." [ISBN GO:0006520+P biological_process [name] cellular amino acid metabolic process [def] "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells." [CHEBI GO:0008483+F molecular_function [name] transaminase activity [def] "Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid." [ISBN GO:0009058+P biological_process [name] biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of substances_ typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC GO:0016212+F molecular_function [name] kynurenine-oxoglutarate transaminase activity [def] "Catalysis of the reaction GO:0016829+F molecular_function [name] lyase activity [def] "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC GO:0030170+F molecular_function [name] pyridoxal phosphate binding [def] "Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6." [GOC GO:0042803+F molecular_function [name] protein homodimerization activity [def] "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC GO:0044822+F GO:0047315+F molecular_function [name] kynurenine-glyoxylate transaminase activity [def] "Catalysis of the reaction GO:0047804+F molecular_function [name] cysteine-S-conjugate beta-lyase activity [def] "Catalysis of the reaction GO:0070189+P biological_process [name] kynurenine metabolic process [def] "The chemical reactions and pathways involving kynurenine, the amino acid 3-(2-aminobenzoyl)-alanine." [CHEBI GO:0097052+P biological_process [name] L-kynurenine metabolic process [def] "The chemical reactions and pathways involving L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine)." [CHEBI [58]{Rv1629,SMARCA5} [common GO terms] [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [SMARCA5 only] GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016589+C cellular_component [name] NURF complex [def] "A four subunit ISWI-containing protein complex that facilitates nucleosome mobility and transcriptional activation in an ATP-dependent manner. In contrast to other chromatin remodeling complexes, the ATPase activity of NURF requires nucleosomes rather than free DNA or histones." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0043044+P biological_process [name] ATP-dependent chromatin remodeling [def] "Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors." [GOC [59]{Rv2737c,ALDH4A1} [common GO terms] [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH4A1 only] GO:0003842+F molecular_function [name] 1-pyrroline-5-carboxylate dehydrogenase activity [def] "Catalysis of the reaction GO:0004029+F molecular_function [name] aldehyde dehydrogenase (NAD) activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006537+P biological_process [name] glutamate biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid." [GOC GO:0006560+P biological_process [name] proline metabolic process [def] "The chemical reactions and pathways involving proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins." [GOC GO:0006561+P biological_process [name] proline biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins." [ISBN GO:0006562+P biological_process [name] proline catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0009055+F molecular_function [name] electron carrier activity [def] "Any molecular entity that serves as an electron acceptor and electron donor in an electron transport system." [ISBN GO:0010133+P biological_process [name] proline catabolic process to glutamate [def] "The chemical reactions and pathways resulting in the breakdown of proline into other compounds, including glutamate." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0019470+P biological_process [name] 4-hydroxyproline catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of 4-hydroxyproline, C5H9NO3, a derivative of the amino acid proline." [GOC GO:0042802+F molecular_function [name] identical protein binding [def] "Interacting selectively and non-covalently with an identical protein or proteins." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC [60]{Rv2737c,PC} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [PC only] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0004075+F molecular_function [name] biotin carboxylase activity [def] "Catalysis of the reaction GO:0004736+F molecular_function [name] pyruvate carboxylase activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006090+P biological_process [name] pyruvate metabolic process [def] "The chemical reactions and pathways involving pyruvate, 2-oxopropanoate." [GOC GO:0006094+P biological_process [name] gluconeogenesis [def] "The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol." [MetaCyc GO:0006107+P biological_process [name] oxaloacetate metabolic process [def] "The chemical reactions and pathways involving oxaloacetate, the anion of oxobutanedioic acid, an important intermediate in metabolism, especially as a component of the TCA cycle." [ISBN GO:0006629+P biological_process [name] lipid metabolic process [def] "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids_ neutral fats, other fatty-acid esters, and soaps_ long-chain (fatty) alcohols and waxes_ sphingoids and other long-chain bases_ glycolipids, phospholipids and sphingolipids_ and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC GO:0006768+P biological_process [name] biotin metabolic process [def] "The chemical reactions and pathways involving biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid_ the (+) enantiomer is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions." [ISBN GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0009374+F molecular_function [name] biotin binding [def] "Interacting selectively and non-covalently with biotin (cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid), the (+) enantiomer of which is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions." [GOC GO:0010629+P biological_process [name] negative regulation of gene expression [def] "Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC GO:0016874+F molecular_function [name] ligase activity [def] "Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC GO:0019074+P biological_process [name] viral RNA genome packaging [def] "The packaging of viral RNA into a nucleocapsid." [ISBN GO:0031406+F molecular_function [name] carboxylic acid binding [def] "Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC GO:0044791+P GO:0044794+P GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC [61]{Rv2737c,CAD} [common GO terms] GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [CAD only] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0004070+F molecular_function [name] aspartate carbamoyltransferase activity [def] "Catalysis of the reaction GO:0004088+F molecular_function [name] carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity [def] "Catalysis of the reaction GO:0006207+P biological_process [name] 'de novo' pyrimidine base biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of pyrimidine bases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors." [GOC GO:0006520+P biological_process [name] cellular amino acid metabolic process [def] "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells." [CHEBI GO:0006541+P biological_process [name] glutamine metabolic process [def] "The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid." [GOC GO:0006807+P biological_process [name] nitrogen compound metabolic process [def] "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium." [CHEBI GO:0016597+F molecular_function [name] amino acid binding [def] "Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents." [GOC GO:0016743+F molecular_function [name] carboxyl- or carbamoyltransferase activity [def] "Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor)." [GOC GO:0016810+F molecular_function [name] hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [def] "Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds." [GOC GO:0016812+F molecular_function [name] hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides [def] "Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC [62]{Rv2737c,BTAF1} [common GO terms] GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [BTAF1 only] [63]{Rv1629,RRM1} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [RRM1 only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000278+P biological_process [name] mitotic cell cycle [def] "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC GO:0004748+F molecular_function [name] ribonucleoside-diphosphate reductase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005635+C cellular_component [name] nuclear envelope [def] "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm_ includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0005971+C cellular_component [name] ribonucleoside-diphosphate reductase complex [def] "An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate and thioredoxin disulfide from ribonucleoside diphosphate and thioredoxin." [BRENDA GO:0006206+P biological_process [name] pyrimidine base metabolic process [def] "The chemical reactions and pathways involving pyrimidine bases, 1,3-diazine, organic nitrogenous bases." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0008584+P biological_process [name] male gonad development [def] "The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure." [GOC GO:0009263+P biological_process [name] deoxyribonucleotide biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0015949+P biological_process [name] nucleobase-containing small molecule interconversion [def] "The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0017076+F molecular_function [name] purine nucleotide binding [def] "Interacting selectively and non-covalently with purine nucleotides, any compound consisting of a purine nucleoside esterified with (ortho)phosphate." [GOC GO:0021846+P biological_process [name] cell proliferation in forebrain [def] "The creation of greater cell numbers in the forebrain due to cell division of progenitor cells." [GO_REF GO:0042995+C cellular_component [name] cell projection [def] "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC GO:0043025+C cellular_component [name] neuronal cell body [def] "The portion of a neuron that includes the nucleus, but excludes all cell projections such as axons and dendrites." [GOC GO:0051259+P biological_process [name] protein oligomerization [def] "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers_ protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." [GOC GO:0051290+P biological_process [name] protein heterotetramerization [def] "The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0060041+P biological_process [name] retina development in camera-type eye [def] "The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [64]{Rv2737c,ALDH1L1} [common GO terms] GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH1L1 only] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0004029+F molecular_function [name] aldehyde dehydrogenase (NAD) activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0006730+P biological_process [name] one-carbon metabolic process [def] "The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0009058+P biological_process [name] biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of substances_ typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC GO:0009258+P biological_process [name] 10-formyltetrahydrofolate catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of 10-formyltetrahydrofolate, the formylated derivative of tetrahydrofolate." [GOC GO:0016155+F molecular_function [name] formyltetrahydrofolate dehydrogenase activity [def] "Catalysis of the reaction GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0016742+F molecular_function [name] hydroxymethyl-, formyl- and related transferase activity [def] "Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor)." [EC GO:0019145+F molecular_function [name] aminobutyraldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0046655+P biological_process [name] folic acid metabolic process [def] "The chemical reactions and pathways involving folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines." [ISBN GO:0047105+F molecular_function [name] 4-trimethylammoniobutyraldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [65]{Rv2737c,MCCC2} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [MCCC2 only] GO:0002169+C cellular_component [name] 3-methylcrotonyl-CoA carboxylase complex, mitochondrial [def] "A heterodimeric complex having 3-methylcrotonyl-CoA carboxylase activity. The alpha subunit has a covalently bound biotin essential for the ATP-dependent carboxylation. The beta subunit possess carboxyltransferase activity which presumably is essential for binding to 3-methylcrotonyl-CoA." [GOC GO:0004485+F molecular_function [name] methylcrotonoyl-CoA carboxylase activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006552+P biological_process [name] leucine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of leucine, 2-amino-4-methylpentanoic acid." [GOC GO:0006768+P biological_process [name] biotin metabolic process [def] "The chemical reactions and pathways involving biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid_ the (+) enantiomer is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions." [ISBN GO:0009083+P biological_process [name] branched chain family amino acid catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine." [GOC GO:0015936+P biological_process [name] coenzyme A metabolic process [def] "The chemical reactions and pathways involving coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester." [ISBN GO:0016874+F molecular_function [name] ligase activity [def] "Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC GO:0051291+P biological_process [name] protein heterooligomerization [def] "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." [GOC [66]{Rv1629,ERCC3} [common GO terms] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ERCC3 only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000439+C cellular_component [name] core TFIIH complex [def] "The 5 subunit core of TFIIH that has tightly associated subunits and is found in both the general transcription factor holo-TFIIH and in the nucleotide-excision repair factor 3 complex. In S. cerevisiae, it is composed of Rad3, Tfb1, Tfb2, Ssl1, Tfb4. In humans, it is composed of XPD, p62, p55, p44, p34." [GOC GO:0000717+P biological_process [name] nucleotide-excision repair, DNA duplex unwinding [def] "The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage." [GOC GO:0001666+P biological_process [name] response to hypoxia [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level." [GOC GO:0003684+F molecular_function [name] damaged DNA binding [def] "Interacting selectively and non-covalently with damaged DNA." [GOC GO:0004003+F molecular_function [name] ATP-dependent DNA helicase activity [def] "Catalysis of the reaction GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005525+F molecular_function [name] GTP binding [def] "Interacting selectively and non-covalently with GTP, guanosine triphosphate." [GOC GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005675+C cellular_component [name] holo TFIIH complex [def] "A complex that contains kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. In S. cerevisiae, it is composed of the 5-subunit core (Rad3p, Tfb1p, Tfb2p, Ssl1p and Tfb4p), Ssl2p, and TFIIK (Kin28p, Ccl1p, and Tfb3p). All of the subunits have equivalents in humans GO:0006265+P biological_process [name] DNA topological change [def] "The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number." [ISBN GO:0006283+P biological_process [name] transcription-coupled nucleotide-excision repair [def] "The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway." [PMID GO:0006289+P biological_process [name] nucleotide-excision repair [def] "A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts)." [PMID GO:0006293+P biological_process [name] nucleotide-excision repair, preincision complex stabilization [def] "The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage." [GOC GO:0006294+P biological_process [name] nucleotide-excision repair, preincision complex assembly [def] "The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage." [GOC GO:0006295+P biological_process [name] nucleotide-excision repair, DNA incision, 3'-to lesion [def] "The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage." [GOC GO:0006296+P biological_process [name] nucleotide-excision repair, DNA incision, 5'-to lesion [def] "The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage." [GOC GO:0006351+P biological_process [name] transcription, DNA-dependent [def] "The cellular synthesis of RNA on a template of DNA." [GOC GO:0006355+P biological_process [name] regulation of transcription, DNA-dependent [def] "Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription." [GOC GO:0006361+P biological_process [name] transcription initiation from RNA polymerase I promoter [def] "Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC GO:0006362+P biological_process [name] transcription elongation from RNA polymerase I promoter [def] "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I." [GOC GO:0006363+P biological_process [name] termination of RNA polymerase I transcription [def] "The process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit." [GOC GO:0006366+P biological_process [name] transcription from RNA polymerase II promoter [def] "The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs)." [GOC GO:0006367+P biological_process [name] transcription initiation from RNA polymerase II promoter [def] "Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC GO:0006368+P biological_process [name] transcription elongation from RNA polymerase II promoter [def] "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II." [GOC GO:0006370+P biological_process [name] mRNA capping [def] "Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript." [GOC GO:0006468+P biological_process [name] protein phosphorylation [def] "The process of introducing a phosphate group on to a protein." [GOC GO:0006915+P biological_process [name] apoptotic process [def] "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathways) which typically lead to rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. The process ends when the cell has died. The process is divided into a signaling pathway phase and into an execution phase, which is triggered by the former." [GOC GO:0006979+P biological_process [name] response to oxidative stress [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC GO:0008022+F molecular_function [name] protein C-terminus binding [def] "Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0008104+P biological_process [name] protein localization [def] "Any process in which a protein is transported to, or maintained in, a specific location." [GOC GO:0008134+F molecular_function [name] transcription factor binding [def] "Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription." [ISBN GO:0008353+F molecular_function [name] RNA polymerase II carboxy-terminal domain kinase activity [def] "Catalysis of the reaction GO:0009411+P biological_process [name] response to UV [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0016032+P biological_process [name] viral reproduction [def] "The process in which a virus reproduces. Usually, this is by infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0032564+F molecular_function [name] dATP binding [def] "Interacting selectively and non-covalently with dATP, deoxyadenosine triphosphate." [GOC GO:0033683+P biological_process [name] nucleotide-excision repair, DNA incision [def] "A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound." [GOC GO:0035315+P biological_process [name] hair cell differentiation [def] "The process in which a relatively unspecialized cell acquires specialized features of a hair cell." [GOC GO:0042277+F molecular_function [name] peptide binding [def] "Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds." [GOC GO:0043065+P biological_process [name] positive regulation of apoptotic process [def] "Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process." [GOC GO:0043138+F molecular_function [name] 3'-5' DNA helicase activity [def] "Catalysis of the unwinding of the DNA helix in the direction 3' to 5'." [GOC GO:0045944+P biological_process [name] positive regulation of transcription from RNA polymerase II promoter [def] "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC GO:0047485+F molecular_function [name] protein N-terminus binding [def] "Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0048568+P biological_process [name] embryonic organ development [def] "Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC GO:0070911+P biological_process [name] global genome nucleotide-excision repair [def] "The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome." [PMID GO:1901990+P GO:0004672+F molecular_function [name] protein kinase activity [def] "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction [67]{Rv1547,MTR} [common GO terms] GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN [Rv1547 only] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [MTR only] GO:0000096+P biological_process [name] sulfur amino acid metabolic process [def] "The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005622+C cellular_component [name] intracellular [def] "The living contents of a cell_ the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0007399+P biological_process [name] nervous system development [def] "The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state." [GOC GO:0008168+F molecular_function [name] methyltransferase activity [def] "Catalysis of the transfer of a methyl group to an acceptor molecule." [ISBN GO:0008270+F molecular_function [name] zinc ion binding [def] "Interacting selectively and non-covalently with zinc (Zn) ions." [GOC GO:0008652+P biological_process [name] cellular amino acid biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents." [ISBN GO:0008705+F molecular_function [name] methionine synthase activity [def] "Catalysis of the reaction GO:0008898+F molecular_function [name] homocysteine S-methyltransferase activity [def] "Catalysis of the reaction GO:0009086+P biological_process [name] methionine biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins." [GOC GO:0009235+P biological_process [name] cobalamin metabolic process [def] "The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom." [GOC GO:0031103+P biological_process [name] axon regeneration [def] "The regrowth of axons following their loss or damage." [GOC GO:0031419+F molecular_function [name] cobalamin binding [def] "Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom." [GOC GO:0032259+P biological_process [name] methylation [def] "The process in which a methyl group is covalently attached to a molecule." [GOC GO:0042558+P biological_process [name] pteridine-containing compound metabolic process [def] "The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid." [GOC GO:0044237+P biological_process [name] cellular metabolic process [def] "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0048678+P biological_process [name] response to axon injury [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an axon injury stimulus." [GOC GO:0071732+P biological_process [name] cellular response to nitric oxide [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus." [GOC [68]{Rv2737c,ATP12A} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP12A only] GO:0005391+F molecular_function [name] sodium [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0005889+C cellular_component [name] hydrogen [def] "A protein complex that possesses hydrogen GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006813+P biological_process [name] potassium ion transport [def] "The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006814+P biological_process [name] sodium ion transport [def] "The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006883+P biological_process [name] cellular sodium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of sodium ions at the level of a cell." [GOC GO:0006885+P biological_process [name] regulation of pH [def] "Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell." [GOC GO:0008900+F molecular_function [name] hydrogen [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0010038+P biological_process [name] response to metal ion [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus." [GOC GO:0010107+P biological_process [name] potassium ion import [def] "The directed movement of potassium ions into a cell or organelle." [GOC GO:0010248+P biological_process [name] establishment or maintenance of transmembrane electrochemical gradient [def] "The directed movement of ions to establish or maintain an electrochemical gradient across a membrane by means of some agent such as a transporter or pore." [GOC GO:0014070+P biological_process [name] response to organic cyclic compound [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus." [CHEBI GO:0015991+P biological_process [name] ATP hydrolysis coupled proton transport [def] "The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis." [GOC GO:0015992+P biological_process [name] proton transport [def] "The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0016323+C cellular_component [name] basolateral plasma membrane [def] "The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis." [GOC GO:0016324+C cellular_component [name] apical plasma membrane [def] "The region of the plasma membrane located at the apical end of the cell." [GOC GO:0019829+F molecular_function [name] cation-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0030001+P biological_process [name] metal ion transport [def] "The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0030007+P biological_process [name] cellular potassium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of potassium ions at the level of a cell." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0036376+P GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0055075+P biological_process [name] potassium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of potassium ions within an organism or cell." [GOC [69]{Rv2737c,ALDH1A2} [common GO terms] GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH1A2 only] GO:0001568+P biological_process [name] blood vessel development [def] "The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood." [GOC GO:0001758+F molecular_function [name] retinal dehydrogenase activity [def] "Catalysis of the reaction GO:0001822+P biological_process [name] kidney development [def] "The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine." [GOC GO:0001889+P biological_process [name] liver development [def] "The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes." [GOC GO:0001936+P biological_process [name] regulation of endothelial cell proliferation [def] "Any process that modulates the frequency, rate, or extent of endothelial cell proliferation." [GOC GO:0002138+P biological_process [name] retinoic acid biosynthetic process [def] "The chemical reactions and pathways resulting in the biosynthesis of retinoic acid, one of the three components that makes up vitamin A." [GOC GO:0003007+P biological_process [name] heart morphogenesis [def] "The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." [GOC GO:0004028+F molecular_function [name] 3-chloroallyl aldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0004029+F molecular_function [name] aldehyde dehydrogenase (NAD) activity [def] "Catalysis of the reaction GO:0006776+P biological_process [name] vitamin A metabolic process [def] "The chemical reactions and pathways involving any of the vitamin A compounds, retinol, retinal (retinaldehyde) and retinoic acid, all of which are derivatives of beta-carotene." [GOC GO:0007494+P biological_process [name] midgut development [def] "The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0008284+P biological_process [name] positive regulation of cell proliferation [def] "Any process that activates or increases the rate or extent of cell proliferation." [GOC GO:0008285+P biological_process [name] negative regulation of cell proliferation [def] "Any process that stops, prevents or reduces the rate or extent of cell proliferation." [GOC GO:0009855+P biological_process [name] determination of bilateral symmetry [def] "The establishment of an organism's body plan or part of an organism with respect to a single longitudinal plane. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry." [GOC GO:0009952+P biological_process [name] anterior/posterior pattern specification [def] "The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." [GOC GO:0009954+P biological_process [name] proximal/distal pattern formation [def] "The regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end)." [GOC GO:0010628+P biological_process [name] positive regulation of gene expression [def] "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC GO:0014032+P biological_process [name] neural crest cell development [def] "The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." [GOC GO:0016331+P biological_process [name] morphogenesis of embryonic epithelium [def] "The process in which the anatomical structures of embryonic epithelia are generated and organized." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0016918+F molecular_function [name] retinal binding [def] "Interacting selectively and non-covalently with retinal, one of the forms of vitamin A. Retinal plays an important role in the visual process in most vertebrates, combining with opsins to form visual pigments in the retina." [CHEBI GO:0021915+P biological_process [name] neural tube development [def] "The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium." [GO_REF GO:0021983+P biological_process [name] pituitary gland development [def] "The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands." [GO_REF GO:0030182+P biological_process [name] neuron differentiation [def] "The process in which a relatively unspecialized cell acquires specialized features of a neuron." [GOC GO:0030324+P biological_process [name] lung development [def] "The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax." [GOC GO:0030326+P biological_process [name] embryonic limb morphogenesis [def] "The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping." [GOC GO:0030900+P biological_process [name] forebrain development [def] "The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions)." [http GO:0030902+P biological_process [name] hindbrain development [def] "The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium)." [http GO:0031016+P biological_process [name] pancreas development [def] "The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes." [GOC GO:0031076+P biological_process [name] embryonic camera-type eye development [def] "The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure." [GOC GO:0032355+P biological_process [name] response to estradiol stimulus [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen." [GOC GO:0033189+P biological_process [name] response to vitamin A [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin A stimulus." [GOC GO:0034097+P biological_process [name] response to cytokine stimulus [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus." [GOC GO:0035115+P biological_process [name] embryonic forelimb morphogenesis [def] "The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal." [ISBN GO:0035799+P biological_process [name] ureter maturation [def] "A developmental process, independent of morphogenetic (shape) change, that is required for the ureter to attain its fully functional state. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut." [GOC GO:0042572+P biological_process [name] retinol metabolic process [def] "The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A." [GOC GO:0042573+P biological_process [name] retinoic acid metabolic process [def] "The chemical reactions and pathways involving retinoic acid, one of the three components that makes up vitamin A." [GOC GO:0042574+P biological_process [name] retinal metabolic process [def] "The chemical reactions and pathways involving retinal, a compound that plays an important role in the visual process in most vertebrates. In the retina, retinal combines with opsins to form visual pigments. Retinal is one of the forms of vitamin A." [CHEBI GO:0042904+P biological_process [name] 9-cis-retinoic acid biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of 9-cis-retinoic acid, a metabolically active vitamin A derivative." [GOC GO:0043010+P biological_process [name] camera-type eye development [def] "The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field." [GOC GO:0043065+P biological_process [name] positive regulation of apoptotic process [def] "Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process." [GOC GO:0048384+P biological_process [name] retinoic acid receptor signaling pathway [def] "The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands." [GOC GO:0048471+C cellular_component [name] perinuclear region of cytoplasm [def] "Cytoplasm situated near, or occurring around, the nucleus." [GOC GO:0048566+P biological_process [name] embryonic digestive tract development [def] "The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus." [GOC GO:0048738+P biological_process [name] cardiac muscle tissue development [def] "The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0060324+P biological_process [name] face development [def] "The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head." [GOC GO:0071300+P biological_process [name] cellular response to retinoic acid [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus." [GOC [70]{Rv2737c,PEX1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [PEX1 only] GO:0005777+C cellular_component [name] peroxisome [def] "A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules_ contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [ISBN GO:0005778+C cellular_component [name] peroxisomal membrane [def] "The lipid bilayer surrounding a peroxisome." [GOC GO:0006625+P biological_process [name] protein targeting to peroxisome [def] "The process of directing proteins towards the peroxisome, usually using signals contained within the protein." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0007031+P biological_process [name] peroxisome organization [def] "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules." [GOC GO:0008022+F molecular_function [name] protein C-terminus binding [def] "Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0015031+P biological_process [name] protein transport [def] "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016558+P biological_process [name] protein import into peroxisome matrix [def] "The import of proteins into the peroxisomal matrix. A peroxisome targeting signal (PTS) binds to a soluble receptor protein in the cytosol, and the resulting complex then binds to a receptor protein in the peroxisome membrane and is imported." [ISBN GO:0032403+F molecular_function [name] protein complex binding [def] "Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0042623+F molecular_function [name] ATPase activity, coupled [def] "Catalysis of the reaction GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC GO:0060152+P biological_process [name] microtubule-based peroxisome localization [def] "The microtubule-based process in which a peroxisome is transported to, and/or maintained in, a specific location. A peroxisome is a small membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [71]{Rv1629,BTAF1} [common GO terms] [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [BTAF1 only] GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN [72]{Rv2737c,WRNIP1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [WRNIP1 only] GO:0000731+P biological_process [name] DNA synthesis involved in DNA repair [def] "Synthesis of DNA that proceeds from the broken 3' single-strand DNA end uses the homologous intact duplex as the template." [PMID GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0030174+P biological_process [name] regulation of DNA-dependent DNA replication initiation [def] "Any process that modulates the frequency, rate or extent of initiation of DNA-dependent DNA replication_ the process in which DNA becomes competent to replicate. In eukaryotes, replication competence is established in early G1 and lost during the ensuing S phase." [GOC GO:0042802+F molecular_function [name] identical protein binding [def] "Interacting selectively and non-covalently with an identical protein or proteins." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0048471+C cellular_component [name] perinuclear region of cytoplasm [def] "Cytoplasm situated near, or occurring around, the nucleus." [GOC GO:0000784+C cellular_component [name] nuclear chromosome, telomeric region [def] "The terminal region of a linear chromosome in the nucleus that includes the telomeric DNA repeats and associated proteins." [GOC [73]{Rv2737c,HIBCH} [common GO terms] GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [HIBCH only] GO:0003860+F molecular_function [name] 3-hydroxyisobutyryl-CoA hydrolase activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006574+P biological_process [name] valine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of valine, 2-amino-3-methylbutanoic acid." [GOC GO:0006635+P biological_process [name] fatty acid beta-oxidation [def] "A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A_ the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC GO:0009083+P biological_process [name] branched chain family amino acid catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [74]{Rv2737c,ATP2A2} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP2A2 only] GO:0002026+P biological_process [name] regulation of the force of heart contraction [def] "Any process that modulates the extent of heart contraction, changing the force with which blood is propelled." [GOC GO:0005388+F molecular_function [name] calcium-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005509+F molecular_function [name] calcium ion binding [def] "Interacting selectively and non-covalently with calcium ions (Ca2+)." [GOC GO:0005783+C cellular_component [name] endoplasmic reticulum [def] "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN GO:0005789+C cellular_component [name] endoplasmic reticulum membrane [def] "The lipid bilayer surrounding the endoplasmic reticulum." [GOC GO:0005887+C cellular_component [name] integral to plasma membrane [def] "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006816+P biological_process [name] calcium ion transport [def] "The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006874+P biological_process [name] cellular calcium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell." [GOC GO:0006984+P biological_process [name] ER-nucleus signaling pathway [def] "Any series of molecular signals that conveys information from the endoplasmic reticulum to the nucleus, usually resulting in a change in transcriptional regulation." [GOC GO:0006996+P biological_process [name] organelle organization [def] "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC GO:0007155+P biological_process [name] cell adhesion [def] "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." [GOC GO:0008022+F molecular_function [name] protein C-terminus binding [def] "Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0008544+P biological_process [name] epidermis development [def] "The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of a plant or animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." [GOC GO:0010460+P biological_process [name] positive regulation of heart rate [def] "Any process that activates or increases the frequency or rate of heart contraction." [GOC GO:0010882+P biological_process [name] regulation of cardiac muscle contraction by calcium ion signaling [def] "Any process that modulates the frequency, rate or extent of cardiac muscle contraction by changing the calcium ion signals that trigger contraction." [GOC GO:0012506+C cellular_component [name] vesicle membrane [def] "The lipid bilayer surrounding any membrane-bounded vesicle in the cell." [GOC GO:0014801+C cellular_component [name] longitudinal sarcoplasmic reticulum [def] "The portion of the free sarcoplasmic reticulum consisting of longitudinal tubules that connect terminal cisternae." [GOC GO:0014883+P biological_process [name] transition between fast and slow fiber [def] "The process of conversion of fast-contracting muscle fibers to a slower character. This may involve slowing of contractile rate, slow myosin gene induction, increase in oxidative metabolic properties, altered electrophysiology and altered innervation. This process also regulates skeletal muscle adapatation." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0016529+C cellular_component [name] sarcoplasmic reticulum [def] "A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell_ continuous over large portions of the cell and with the nuclear envelope_ that part of the endoplasmic reticulum specialized for calcium release, uptake and storage." [GOC GO:0019899+F molecular_function [name] enzyme binding [def] "Interacting selectively and non-covalently with any enzyme." [GOC GO:0031095+C cellular_component [name] platelet dense tubular network membrane [def] "The lipid bilayer surrounding the platelet dense tubular network." [GOC GO:0031234+C cellular_component [name] extrinsic to internal side of plasma membrane [def] "Loosely bound to the surface of the plasma membrane that faces the cytoplasm, but not integrated into the hydrophobic region." [GOC GO:0031775+F molecular_function [name] lutropin-choriogonadotropic hormone receptor binding [def] "Interacting selectively and non-covalently with a lutropin-choriogonadotropic hormone receptor." [GOC GO:0032469+P biological_process [name] endoplasmic reticulum calcium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of calcium ions within the endoplasmic reticulum of a cell or between the endoplasmic reticulum and its surroundings." [GOC GO:0032470+P biological_process [name] elevation of endoplasmic reticulum calcium ion concentration [def] "Any process that increases the concentration of calcium ions in the endoplasmic reticulum." [GOC GO:0033017+C cellular_component [name] sarcoplasmic reticulum membrane [def] "The lipid bilayer surrounding the sarcoplasmic reticulum." [GOC GO:0033292+P biological_process [name] T-tubule organization [def] "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of the T-tubule. A T-tubule is an invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0034599+P biological_process [name] cellular response to oxidative stress [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC GO:0034976+P biological_process [name] response to endoplasmic reticulum stress [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating endoplasmic reticulum (ER) stress. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen." [GOC GO:0043234+C cellular_component [name] protein complex [def] "Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules." [GOC GO:0043434+P biological_process [name] response to peptide hormone stimulus [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals." [PMID GO:0044548+F GO:0045822+P biological_process [name] negative regulation of heart contraction [def] "Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0048471+C cellular_component [name] perinuclear region of cytoplasm [def] "Cytoplasm situated near, or occurring around, the nucleus." [GOC GO:0055119+P biological_process [name] relaxation of cardiac muscle [def] "The process in which the extent of cardiac muscle contraction is reduced." [GOC GO:0070296+P biological_process [name] sarcoplasmic reticulum calcium ion transport [def] "The directed movement of calcium ions (Ca2+) into, out of or within the sarcoplasmic reticulum." [GOC GO:0070588+P biological_process [name] calcium ion transmembrane transport [def] "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0086036+P GO:0086039+F GO:0090534+C GO:0097470+C GO:0098909+P GO:1903233+P GO:1903515+P GO:1903779+P GO:1990036+P GO:0014704+C cellular_component [name] intercalated disc [def] "A complex cell-cell junction at which myofibrils terminate in cardiomyocytes_ mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells." [GOC [75]{Rv2737c,ABCB9} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ABCB9 only] GO:0002481+P biological_process [name] antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent [def] "The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family." [GOC GO:0002485+P biological_process [name] antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent [def] "The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP-dependent ER pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and becomes associated with the MHC class I molecule in the ER following TAP-dependent transport from the cytosol. Class I here refers to classical class I molecules." [GOC GO:0002489+P biological_process [name] antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent [def] "The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family." [GOC GO:0002591+P biological_process [name] positive regulation of antigen processing and presentation of peptide antigen via MHC class I [def] "Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I." [GOC GO:0005764+C cellular_component [name] lysosome [def] "A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [GOC GO:0005765+C cellular_component [name] lysosomal membrane [def] "The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0015031+P biological_process [name] protein transport [def] "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0015421+F molecular_function [name] oligopeptide-transporting ATPase activity [def] "Catalysis of the reaction GO:0015440+F molecular_function [name] peptide-transporting ATPase activity [def] "Catalysis of the reaction GO:0015833+P biological_process [name] peptide transport [def] "The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0022891+F molecular_function [name] substrate-specific transmembrane transporter activity [def] "Enables the transfer of a specific substance or group of related substances from one side of a membrane to the other." [GOC GO:0030176+C cellular_component [name] integral to endoplasmic reticulum membrane [def] "Penetrating at least one phospholipid bilayer of an endoplasmic reticulum membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0035672+P biological_process [name] oligopeptide transmembrane transport [def] "The directed movement of an oligopeptide across a membrane by means of some agent such as a transporter or pore. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages." [GOC GO:0042626+F molecular_function [name] ATPase activity, coupled to transmembrane movement of substances [def] "Catalysis of the reaction GO:0042803+F molecular_function [name] protein homodimerization activity [def] "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC GO:0055085+P biological_process [name] transmembrane transport [def] "The process in which a solute is transported from one side of a membrane to the other." [GOC GO:0002474+P biological_process [name] antigen processing and presentation of peptide antigen via MHC class I [def] "The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules." [GOC GO:0005769+C cellular_component [name] early endosome [def] "A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis_ vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways." [GOC GO:0005783+C cellular_component [name] endoplasmic reticulum [def] "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN [76]{Rv1547,OGDH} [common GO terms] [Rv1547 only] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [OGDH only] GO:0004591+F molecular_function [name] oxoglutarate dehydrogenase (succinyl-transferring) activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006091+P biological_process [name] generation of precursor metabolites and energy [def] "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." [GOC GO:0006096+P biological_process [name] glycolysis [def] "The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Glycolysis begins with phosphorylation of a monosaccharide (generally glucose) on the sixth carbon by a hexokinase, and ends with the production of pyruvate. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle." [GOC GO:0006099+P biological_process [name] tricarboxylic acid cycle [def] "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." [ISBN GO:0006103+P biological_process [name] 2-oxoglutarate metabolic process [def] "The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism." [ISBN GO:0006104+P biological_process [name] succinyl-CoA metabolic process [def] "The chemical reactions and pathways involving succinyl-CoA, a compound composed of the monovalent acyl group 3-carboxypropanoyl, derived from succinic acid by loss of one OH group, linked to coenzyme A." [GOC GO:0006554+P biological_process [name] lysine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of lysine, 2,6-diaminohexanoic acid." [GOC GO:0006734+P biological_process [name] NADH metabolic process [def] "The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016624+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide." [GOC GO:0021695+P biological_process [name] cerebellar cortex development [def] "The process whose specific outcome is the progression of the cerebellar cortex over time, from its formation to the mature structure. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function." [GO_REF GO:0021756+P biological_process [name] striatum development [def] "The progression of the striatum over time from its initial formation until its mature state. The striatum is a region of the forebrain consisting of the caudate nucleus, putamen and fundus striati." [GO_REF GO:0021766+P biological_process [name] hippocampus development [def] "The progression of the hippocampus over time from its initial formation until its mature state." [GO_REF GO:0021794+P biological_process [name] thalamus development [def] "The process in which the thalamus changes over time, from its initial formation to its mature state." [GO_REF GO:0021860+P biological_process [name] pyramidal neuron development [def] "The progression of a pyramidal neuron from its initial formation to its mature state." [GO_REF GO:0022028+P biological_process [name] tangential migration from the subventricular zone to the olfactory bulb [def] "The migration of cells in the telencephalon from the subventricular zone to the olfactory bulb in which cells move orthogonally to the direction of radial migration and do not use radial glial cell processes as substrates for migration." [GO_REF GO:0030976+F molecular_function [name] thiamine pyrophosphate binding [def] "Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases." [CHEBI GO:0031072+F molecular_function [name] heat shock protein binding [def] "Interacting selectvely with a heat shock protein, any protein synthesized or activated in response to heat shock." [GOC GO:0031966+C cellular_component [name] mitochondrial membrane [def] "Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope." [GOC GO:0034602+F molecular_function [name] oxoglutarate dehydrogenase (NAD+) activity [def] "Catalysis of the reaction GO:0045252+C cellular_component [name] oxoglutarate dehydrogenase complex [def] "A complex of multiple copies of three enzymatic components GO:0046487+P biological_process [name] glyoxylate metabolic process [def] "The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH." [ISBN GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0051087+F molecular_function [name] chaperone binding [def] "Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport." [http GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0061034+P biological_process [name] olfactory bulb mitral cell layer development [def] "The progression of the olfactory bulb mitral cell layer over time from its initial formation until its mature state. The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [77]{Rv1629,CBS} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [CBS only] GO:0004122+F molecular_function [name] cystathionine beta-synthase activity [def] "Catalysis of the reaction GO:0004124+F molecular_function [name] cysteine synthase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006535+P biological_process [name] cysteine biosynthetic process from serine [def] "The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine." [GOC GO:0006563+P biological_process [name] L-serine metabolic process [def] "The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid." [CHEBI GO:0006565+P biological_process [name] L-serine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid." [CHEBI GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0008652+P biological_process [name] cellular amino acid biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents." [ISBN GO:0016829+F molecular_function [name] lyase activity [def] "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC GO:0019343+P biological_process [name] cysteine biosynthetic process via cystathionine [def] "The chemical reactions and pathways resulting in the formation of cysteine, via the intermediate cystathionine." [GOC GO:0019344+P biological_process [name] cysteine biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid." [GOC GO:0019346+P biological_process [name] transsulfuration [def] "The interconversion of homocysteine and cysteine via cystathionine. In contrast with enteric bacteria and mammals, Saccharomyces cerevisiae has two transsulfuration pathways employing two separate sets of enzymes." [MetaCyc GO:0019448+P biological_process [name] L-cysteine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid." [CHEBI GO:0019825+F molecular_function [name] oxygen binding [def] "Interacting selectively and non-covalently with oxygen (O2)." [GOC GO:0019899+F molecular_function [name] enzyme binding [def] "Interacting selectively and non-covalently with any enzyme." [GOC GO:0020037+F molecular_function [name] heme binding [def] "Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring." [CHEBI GO:0030170+F molecular_function [name] pyridoxal phosphate binding [def] "Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6." [GOC GO:0031625+F molecular_function [name] ubiquitin protein ligase binding [def] "Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins." [GOC GO:0042262+P biological_process [name] DNA protection [def] "Any process in which DNA is protected from damage by, for example, oxidative stress." [GOC GO:0042802+F molecular_function [name] identical protein binding [def] "Interacting selectively and non-covalently with an identical protein or proteins." [GOC GO:0042803+F molecular_function [name] protein homodimerization activity [def] "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC GO:0043418+P biological_process [name] homocysteine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0050421+F molecular_function [name] nitrite reductase (NO-forming) activity [def] "Catalysis of the reaction GO:0050667+P biological_process [name] homocysteine metabolic process [def] "The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine." [ISBN GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0070025+F molecular_function [name] carbon monoxide binding [def] "Interacting selectively and non-covalently with carbon monoxide (CO)." [GOC GO:0070026+F molecular_function [name] nitric oxide binding [def] "Interacting selectively and non-covalently with nitric oxide (NO)." [GOC GO:0070814+P biological_process [name] hydrogen sulfide biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S." [CHEBI GO:0072341+F molecular_function [name] modified amino acid binding [def] "Interacting selectively and non-covalently with a modified amino acid." [CHEBI GO:1904047+F [78]{Rv2737c,ALDH1A1} [common GO terms] [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH1A1 only] GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC [79]{Rv1629,CPS1} [common GO terms] [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [CPS1 only] GO:0004088+F molecular_function [name] carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity [def] "Catalysis of the reaction GO:0006207+P biological_process [name] 'de novo' pyrimidine base biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of pyrimidine bases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors." [GOC GO:0006541+P biological_process [name] glutamine metabolic process [def] "The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid." [GOC GO:0006807+P biological_process [name] nitrogen compound metabolic process [def] "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium." [CHEBI [80]{Rv2737c,ERCC6} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ERCC6 only] GO:0000303+P biological_process [name] response to superoxide [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion." [GOC GO:0003682+F molecular_function [name] chromatin binding [def] "Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN GO:0006283+P biological_process [name] transcription-coupled nucleotide-excision repair [def] "The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway." [PMID GO:0006284+P biological_process [name] base-excision repair [def] "In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase." [ISBN GO:0006290+P biological_process [name] pyrimidine dimer repair [def] "The repair of UV-induced T-T, C-T and C-C dimers." [ISBN GO:0006351+P biological_process [name] transcription, DNA-dependent [def] "The cellular synthesis of RNA on a template of DNA." [GOC GO:0006355+P biological_process [name] regulation of transcription, DNA-dependent [def] "Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription." [GOC GO:0006362+P biological_process [name] transcription elongation from RNA polymerase I promoter [def] "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I." [GOC GO:0006366+P biological_process [name] transcription from RNA polymerase II promoter [def] "The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs)." [GOC GO:0006979+P biological_process [name] response to oxidative stress [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC GO:0007256+P biological_process [name] activation of JNKK activity [def] "The initiation of the activity of the inactive enzyme JUN kinase kinase (JNKK) activity in response to phosphorylation by a member of the JUN kinase kinase kinase (JNKKK) family, or another upstream kinase. JNKKs are involved in a signaling pathway that is primarily activated by cytokines and exposure to environmental stress." [GOC GO:0007257+P biological_process [name] activation of JUN kinase activity [def] "The initiation of the activity of the inactive enzyme JUN kinase by phosphorylation by a JUN kinase kinase (JNKK)." [GOC GO:0008022+F molecular_function [name] protein C-terminus binding [def] "Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0008023+C cellular_component [name] transcription elongation factor complex [def] "Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation." [GOC GO:0008630+P biological_process [name] DNA damage response, signal transduction resulting in induction of apoptosis [def] "A cascade of processes initiated by the detection of DNA damage and resulting in the induction of apoptosis (programmed cell death)." [GOC GO:0009411+P biological_process [name] response to UV [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers." [GOC GO:0009636+P biological_process [name] response to toxin [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxin stimulus." [GOC GO:0010165+P biological_process [name] response to X-ray [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz)." [GOC GO:0010224+P biological_process [name] response to UV-B [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a UV-B radiation stimulus. UV-B radiation (UV-B light) spans the wavelengths 290 to 320 nm." [GOC GO:0010332+P biological_process [name] response to gamma radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum." [GOC GO:0030296+F molecular_function [name] protein tyrosine kinase activator activity [def] "Increases the activity of a protein tyrosine kinase, an enzyme which phosphorylates a tyrosyl phenolic group on a protein." [GOC GO:0032403+F molecular_function [name] protein complex binding [def] "Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0032784+P biological_process [name] regulation of transcription elongation, DNA-dependent [def] "Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase." [GOC GO:0032786+P biological_process [name] positive regulation of transcription elongation, DNA-dependent [def] "Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase." [GOC GO:0035264+P biological_process [name] multicellular organism growth [def] "The increase in size or mass of an entire multicellular organism, as opposed to cell growth." [GOC GO:0045494+P biological_process [name] photoreceptor cell maintenance [def] "Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light." [CL GO:0045815+P biological_process [name] positive regulation of gene expression, epigenetic [def] "Any epigenetic process that activates or increases the rate of gene expression." [GOC GO:0047485+F molecular_function [name] protein N-terminus binding [def] "Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0061098+P biological_process [name] positive regulation of protein tyrosine kinase activity [def] "Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity." [GOC GO:0003678+F molecular_function [name] DNA helicase activity [def] "Catalysis of the reaction [81]{Rv1629,OGDHL} [common GO terms] [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [OGDHL only] GO:0004591+F molecular_function [name] oxoglutarate dehydrogenase (succinyl-transferring) activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006096+P biological_process [name] glycolysis [def] "The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Glycolysis begins with phosphorylation of a monosaccharide (generally glucose) on the sixth carbon by a hexokinase, and ends with the production of pyruvate. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle." [GOC GO:0006099+P biological_process [name] tricarboxylic acid cycle [def] "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." [ISBN GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016624+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide." [GOC GO:0030976+F molecular_function [name] thiamine pyrophosphate binding [def] "Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases." [CHEBI GO:0045252+C cellular_component [name] oxoglutarate dehydrogenase complex [def] "A complex of multiple copies of three enzymatic components GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [82]{Rv2737c,NVL} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [NVL only] GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005697+C cellular_component [name] telomerase holoenzyme complex [def] "Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits." [PMID GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0042254+P biological_process [name] ribosome biogenesis [def] "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits_ includes transport to the sites of protein synthesis." [GOC GO:0044822+F GO:0051973+P biological_process [name] positive regulation of telomerase activity [def] "Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction GO:1990275+F [83]{Rv1547,OGDHL} [common GO terms] [Rv1547 only] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [OGDHL only] GO:0004591+F molecular_function [name] oxoglutarate dehydrogenase (succinyl-transferring) activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006096+P biological_process [name] glycolysis [def] "The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Glycolysis begins with phosphorylation of a monosaccharide (generally glucose) on the sixth carbon by a hexokinase, and ends with the production of pyruvate. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle." [GOC GO:0006099+P biological_process [name] tricarboxylic acid cycle [def] "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." [ISBN GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016624+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide." [GOC GO:0030976+F molecular_function [name] thiamine pyrophosphate binding [def] "Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases." [CHEBI GO:0045252+C cellular_component [name] oxoglutarate dehydrogenase complex [def] "A complex of multiple copies of three enzymatic components GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [84]{Rv1629,MOCS3} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [MOCS3 only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0002098+P biological_process [name] tRNA wobble uridine modification [def] "The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified." [GOC GO:0002143+P biological_process [name] tRNA wobble position uridine thiolation [def] "The process in which a uridine residue at position 34 in the anticodon of a tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from cysteine to position C2 by several steps." [PMID GO:0004792+F molecular_function [name] thiosulfate sulfurtransferase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006777+P biological_process [name] Mo-molybdopterin cofactor biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands." [http GO:0008033+P biological_process [name] tRNA processing [def] "The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0008641+F molecular_function [name] small protein activating enzyme activity [def] "Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond." [GOC GO:0016783+F molecular_function [name] sulfurtransferase activity [def] "Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor)." [GOC GO:0018117+P biological_process [name] protein adenylylation [def] "The addition of an adenylyl group (adenosine 5'-monophosphate_ AMP) to a protein amino acid." [GOC GO:0018192+P biological_process [name] enzyme active site formation via L-cysteine persulfide [def] "The modification of peptidyl-cysteine to form peptidyl-L-cysteine persulfide. A persulfurated cysteine promotes active site reactivity in Azotobacter vinelandii Rhodanese." [PMID GO:0032324+P biological_process [name] molybdopterin cofactor biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands." [GOC GO:0032447+P biological_process [name] protein urmylation [def] "Covalent attachment of the ubiquitin-like protein URM1 to another protein." [GOC GO:0034227+P biological_process [name] tRNA thio-modification [def] "The addition a sulfur atom to a nucleotide in a tRNA molecule." [GOC GO:0042292+F molecular_function [name] URM1 activating enzyme activity [def] "Catalysis of the activation of the small ubiquitin-related modifier URM1, through the formation of an ATP-dependent high-energy thiolester bond." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0061604+F GO:0061605+F GO:0070733+F molecular_function [name] protein adenylyltransferase activity [def] "Catalysis of the reaction [85]{Rv2737c,ABCB1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ABCB1 only] GO:0000086+P biological_process [name] G2/M transition of mitotic cell cycle [def] "Progression from G2 phase to M phase of the mitotic cell cycle." [GOC GO:0002481+P biological_process [name] antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent [def] "The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family." [GOC GO:0002485+P biological_process [name] antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent [def] "The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP-dependent ER pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and becomes associated with the MHC class I molecule in the ER following TAP-dependent transport from the cytosol. Class I here refers to classical class I molecules." [GOC GO:0002489+P biological_process [name] antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent [def] "The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family." [GOC GO:0002591+P biological_process [name] positive regulation of antigen processing and presentation of peptide antigen via MHC class I [def] "Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I." [GOC GO:0005215+F molecular_function [name] transporter activity [def] "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006855+P biological_process [name] drug transmembrane transport [def] "The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0008559+F molecular_function [name] xenobiotic-transporting ATPase activity [def] "Catalysis of the reaction GO:0009986+C cellular_component [name] cell surface [def] "The external part of the cell wall and/or plasma membrane." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0042493+P biological_process [name] response to drug [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease." [GOC GO:0042626+F molecular_function [name] ATPase activity, coupled to transmembrane movement of substances [def] "Catalysis of the reaction GO:0042908+P biological_process [name] xenobiotic transport [def] "The directed movement of a xenobiotic, a compound foreign to living organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0055085+P biological_process [name] transmembrane transport [def] "The process in which a solute is transported from one side of a membrane to the other." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC GO:0072089+P biological_process [name] stem cell proliferation [def] "The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [GOC [86]{Rv1629,SCP2} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [SCP2 only] GO:0000062+F molecular_function [name] fatty-acyl-CoA binding [def] "Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group." [GOC GO:0005102+F molecular_function [name] receptor binding [def] "Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005777+C cellular_component [name] peroxisome [def] "A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules_ contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [ISBN GO:0005782+C cellular_component [name] peroxisomal matrix [def] "The volume contained within the membranes of a peroxisome_ in many cells the matrix contains a crystalloid core largely composed of urate oxidase." [GOC GO:0006694+P biological_process [name] steroid biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus_ includes de novo formation and steroid interconversion by modification." [GOC GO:0006699+P biological_process [name] bile acid biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile." [GOC GO:0006701+P biological_process [name] progesterone biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006869+P biological_process [name] lipid transport [def] "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN GO:0007031+P biological_process [name] peroxisome organization [def] "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0008289+F molecular_function [name] lipid binding [def] "Interacting selectively and non-covalently with a lipid." [GOC GO:0008526+F molecular_function [name] phosphatidylinositol transporter activity [def] "Enables the directed movement of phosphatidylinositol into, out of or within a cell, or between cells. Phosphatidylinositol refers to any glycophospholipids with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol." [GOC GO:0015248+F molecular_function [name] sterol transporter activity [def] "Enables the directed movement of sterols into, out of or within a cell, or between cells. Sterol are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC GO:0015485+F molecular_function [name] cholesterol binding [def] "Interacting selectively and non-covalently with cholesterol (cholest-5-en-3-beta-ol)_ the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones." [GOC GO:0015914+P biological_process [name] phospholipid transport [def] "The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Phospholipids are any lipids containing phosphoric acid as a mono- or diester." [GOC GO:0015918+P biological_process [name] sterol transport [def] "The directed movement of sterols into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016746+F molecular_function [name] transferase activity, transferring acyl groups [def] "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor)." [GOC GO:0016747+F molecular_function [name] transferase activity, transferring acyl groups other than amino-acyl groups [def] "Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor)." [GOC GO:0032385+P biological_process [name] positive regulation of intracellular cholesterol transport [def] "Any process that activates or increases the frequency, rate or extent of the directed movement of cholesterol within cells." [GOC GO:0032959+P biological_process [name] inositol trisphosphate biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of inositol trisphosphate, 1,2,3,4,5,6-cyclohexanehexol, with three phosphate groups attached." [CHEBI GO:0033540+P biological_process [name] fatty acid beta-oxidation using acyl-CoA oxidase [def] "A fatty acid beta-oxidation pathway in which the initial step, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA oxidase_ the electrons removed by oxidation pass directly to oxygen and produce hydrogen peroxide, which is cleaved by peroxisomal catalases. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC GO:0033814+F molecular_function [name] propanoyl-CoA C-acyltransferase activity [def] "Catalysis of the reaction GO:0036042+F molecular_function [name] long-chain fatty acyl-CoA [def] "Interacting selectively and non-covalently with a long-chain fatty acyl-CoA. A long-chain fatty acyl-CoA is any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths ranging from C12-18." [CHEBI GO:0036109+P GO:0043231+C cellular_component [name] intracellular membrane-bounded organelle [def] "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC GO:0043234+C cellular_component [name] protein complex [def] "Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules." [GOC GO:0045940+P biological_process [name] positive regulation of steroid metabolic process [def] "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids." [GOC GO:0050632+F molecular_function [name] propionyl-CoA C2-trimethyltridecanoyltransferase activity [def] "Catalysis of the reaction GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC GO:0070538+F molecular_function [name] oleic acid binding [def] "Interacting selectively and non-covalently with oleic acid, the 18-carbon monounsaturated fatty acid (9Z)-octadec-9-enoic acid." [CHEBI GO:0072659+P biological_process [name] protein localization in plasma membrane [def] "A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane." [GOC GO:1901373+P [87]{Rv2737c,ATP2B1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP2B1 only] GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC [88]{Rv0629c,RRM1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv0629c only] GO:0000724+P biological_process [name] double-strand break repair via homologous recombination [def] "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0004003+F molecular_function [name] ATP-dependent DNA helicase activity [def] "Catalysis of the reaction GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006302+P biological_process [name] double-strand break repair [def] "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008854+F molecular_function [name] exodeoxyribonuclease V activity [def] "Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides." [EC GO:0009338+C cellular_component [name] exodeoxyribonuclease V complex [def] "An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA." [EC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0032508+P biological_process [name] DNA duplex unwinding [def] "The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [RRM1 only] GO:0000278+P biological_process [name] mitotic cell cycle [def] "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0004748+F molecular_function [name] ribonucleoside-diphosphate reductase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005635+C cellular_component [name] nuclear envelope [def] "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm_ includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005971+C cellular_component [name] ribonucleoside-diphosphate reductase complex [def] "An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate and thioredoxin disulfide from ribonucleoside diphosphate and thioredoxin." [BRENDA GO:0006206+P biological_process [name] pyrimidine base metabolic process [def] "The chemical reactions and pathways involving pyrimidine bases, 1,3-diazine, organic nitrogenous bases." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0008584+P biological_process [name] male gonad development [def] "The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure." [GOC GO:0009263+P biological_process [name] deoxyribonucleotide biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0015949+P biological_process [name] nucleobase-containing small molecule interconversion [def] "The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0017076+F molecular_function [name] purine nucleotide binding [def] "Interacting selectively and non-covalently with purine nucleotides, any compound consisting of a purine nucleoside esterified with (ortho)phosphate." [GOC GO:0021846+P biological_process [name] cell proliferation in forebrain [def] "The creation of greater cell numbers in the forebrain due to cell division of progenitor cells." [GO_REF GO:0042995+C cellular_component [name] cell projection [def] "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC GO:0043025+C cellular_component [name] neuronal cell body [def] "The portion of a neuron that includes the nucleus, but excludes all cell projections such as axons and dendrites." [GOC GO:0051259+P biological_process [name] protein oligomerization [def] "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers_ protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." [GOC GO:0051290+P biological_process [name] protein heterotetramerization [def] "The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0060041+P biological_process [name] retina development in camera-type eye [def] "The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [89]{Rv1629,ERCC6} [common GO terms] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ERCC6 only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000303+P biological_process [name] response to superoxide [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion." [GOC GO:0003682+F molecular_function [name] chromatin binding [def] "Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005730+C cellular_component [name] nucleolus [def] "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors_ these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN GO:0006283+P biological_process [name] transcription-coupled nucleotide-excision repair [def] "The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway." [PMID GO:0006284+P biological_process [name] base-excision repair [def] "In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase." [ISBN GO:0006290+P biological_process [name] pyrimidine dimer repair [def] "The repair of UV-induced T-T, C-T and C-C dimers." [ISBN GO:0006351+P biological_process [name] transcription, DNA-dependent [def] "The cellular synthesis of RNA on a template of DNA." [GOC GO:0006355+P biological_process [name] regulation of transcription, DNA-dependent [def] "Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription." [GOC GO:0006362+P biological_process [name] transcription elongation from RNA polymerase I promoter [def] "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I." [GOC GO:0006366+P biological_process [name] transcription from RNA polymerase II promoter [def] "The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs)." [GOC GO:0006979+P biological_process [name] response to oxidative stress [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC GO:0007256+P biological_process [name] activation of JNKK activity [def] "The initiation of the activity of the inactive enzyme JUN kinase kinase (JNKK) activity in response to phosphorylation by a member of the JUN kinase kinase kinase (JNKKK) family, or another upstream kinase. JNKKs are involved in a signaling pathway that is primarily activated by cytokines and exposure to environmental stress." [GOC GO:0007257+P biological_process [name] activation of JUN kinase activity [def] "The initiation of the activity of the inactive enzyme JUN kinase by phosphorylation by a JUN kinase kinase (JNKK)." [GOC GO:0008022+F molecular_function [name] protein C-terminus binding [def] "Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0008023+C cellular_component [name] transcription elongation factor complex [def] "Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0008630+P biological_process [name] DNA damage response, signal transduction resulting in induction of apoptosis [def] "A cascade of processes initiated by the detection of DNA damage and resulting in the induction of apoptosis (programmed cell death)." [GOC GO:0009411+P biological_process [name] response to UV [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers." [GOC GO:0009636+P biological_process [name] response to toxin [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxin stimulus." [GOC GO:0010165+P biological_process [name] response to X-ray [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz)." [GOC GO:0010224+P biological_process [name] response to UV-B [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a UV-B radiation stimulus. UV-B radiation (UV-B light) spans the wavelengths 290 to 320 nm." [GOC GO:0010332+P biological_process [name] response to gamma radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum." [GOC GO:0030296+F molecular_function [name] protein tyrosine kinase activator activity [def] "Increases the activity of a protein tyrosine kinase, an enzyme which phosphorylates a tyrosyl phenolic group on a protein." [GOC GO:0032403+F molecular_function [name] protein complex binding [def] "Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0032784+P biological_process [name] regulation of transcription elongation, DNA-dependent [def] "Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase." [GOC GO:0032786+P biological_process [name] positive regulation of transcription elongation, DNA-dependent [def] "Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase." [GOC GO:0035264+P biological_process [name] multicellular organism growth [def] "The increase in size or mass of an entire multicellular organism, as opposed to cell growth." [GOC GO:0045494+P biological_process [name] photoreceptor cell maintenance [def] "Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light." [CL GO:0045815+P biological_process [name] positive regulation of gene expression, epigenetic [def] "Any epigenetic process that activates or increases the rate of gene expression." [GOC GO:0047485+F molecular_function [name] protein N-terminus binding [def] "Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN GO:0061098+P biological_process [name] positive regulation of protein tyrosine kinase activity [def] "Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity." [GOC GO:0003678+F molecular_function [name] DNA helicase activity [def] "Catalysis of the reaction [90]{Rv2737c,ALDH6A1} [common GO terms] [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH6A1 only] GO:0000062+F molecular_function [name] fatty-acyl-CoA binding [def] "Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group." [GOC GO:0004029+F molecular_function [name] aldehyde dehydrogenase (NAD) activity [def] "Catalysis of the reaction GO:0004491+F molecular_function [name] methylmalonate-semialdehyde dehydrogenase (acylating) activity [def] "Catalysis of the reaction GO:0005654+C cellular_component [name] nucleoplasm [def] "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006210+P biological_process [name] thymine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base." [GOC GO:0006573+P biological_process [name] valine metabolic process [def] "The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid." [GOC GO:0006574+P biological_process [name] valine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of valine, 2-amino-3-methylbutanoic acid." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0009083+P biological_process [name] branched chain family amino acid catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0016790+F molecular_function [name] thiolester hydrolase activity [def] "Catalysis of the reaction GO:0018478+F molecular_function [name] malonate-semialdehyde dehydrogenase (acetylating) activity [def] "Catalysis of the reaction GO:0019484+P biological_process [name] beta-alanine catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of beta-alanine (3-aminopropanoic acid), an achiral amino acid and an isomer of alanine. It occurs free (e.g. in brain) and in combination (e.g. in pantothenate) but it is not a constituent of proteins." [GOC GO:0019859+P biological_process [name] thymine metabolic process [def] "The chemical reactions and pathways involving thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base." [GOC GO:0044822+F GO:0050873+P biological_process [name] brown fat cell differentiation [def] "The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria." [PMID GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [91]{Rv2737c,ALDH1A3} [common GO terms] GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH1A3 only] GO:0001758+F molecular_function [name] retinal dehydrogenase activity [def] "Catalysis of the reaction GO:0002072+P biological_process [name] optic cup morphogenesis involved in camera-type eye development [def] "The invagination of the optic vesicle to form two-walled indentations, the optic cups, that will go on to form the retina. This process begins with the optic vesicle becoming a two-walled structure and its subsequent shape changes. It does not include the fate commitment of cells to become the pigmented retina and the neural retina. An example of this process is found in Mus musculus." [GOC GO:0002138+P biological_process [name] retinoic acid biosynthetic process [def] "The chemical reactions and pathways resulting in the biosynthesis of retinoic acid, one of the three components that makes up vitamin A." [GOC GO:0004029+F molecular_function [name] aldehyde dehydrogenase (NAD) activity [def] "Catalysis of the reaction GO:0004030+F molecular_function [name] aldehyde dehydrogenase [NAD(P)+] activity [def] "Catalysis of the reaction GO:0007626+P biological_process [name] locomotory behavior [def] "The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0021768+P biological_process [name] nucleus accumbens development [def] "The progression of the nucleus accumbens over time from its initial formation until its mature state. The nucleus accumbens is a collection of pleomorphic cells in the caudal part of the anterior horn of the lateral ventricle, in the region of the olfactory tubercle, lying between the head of the caudate nucleus and the anterior perforated substance. It is part of the ventral striatum, a composite structure considered part of the basal ganglia." [GO_REF GO:0031076+P biological_process [name] embryonic camera-type eye development [def] "The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure." [GOC GO:0042472+P biological_process [name] inner ear morphogenesis [def] "The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively." [GOC GO:0042572+P biological_process [name] retinol metabolic process [def] "The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A." [GOC GO:0042573+P biological_process [name] retinoic acid metabolic process [def] "The chemical reactions and pathways involving retinoic acid, one of the three components that makes up vitamin A." [GOC GO:0042574+P biological_process [name] retinal metabolic process [def] "The chemical reactions and pathways involving retinal, a compound that plays an important role in the visual process in most vertebrates. In the retina, retinal combines with opsins to form visual pigments. Retinal is one of the forms of vitamin A." [CHEBI GO:0042803+F molecular_function [name] protein homodimerization activity [def] "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC GO:0043065+P biological_process [name] positive regulation of apoptotic process [def] "Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process." [GOC GO:0048048+P biological_process [name] embryonic eye morphogenesis [def] "The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized." [GOC GO:0050885+P biological_process [name] neuromuscular process controlling balance [def] "Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0060013+P biological_process [name] righting reflex [def] "A reflex process in which an animal immediately tries to turn over after being placed in a supine position." [GOC GO:0060166+P biological_process [name] olfactory pit development [def] "The biological process whose specific outcome is the progression of the olfactory pit from an initial condition to its mature state. This process begins with the formation of the olfactory pit, which is an indentation of the olfactory placode, and ends when the pits hollows out to form the nasopharynx." [GOC GO:0060324+P biological_process [name] face development [def] "The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC GO:0070324+F molecular_function [name] thyroid hormone binding [def] "Interacting selectively and non-covalently with thyroxine (T4) or triiodothyronine (T3), tyrosine-based hormones produced by the thyroid gland." [GOC GO:0070403+F molecular_function [name] NAD+ binding [def] "Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions." [GOC [92]{Rv2737c,SMARCA1} [common GO terms] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [SMARCA1 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0006338+P biological_process [name] chromatin remodeling [def] "Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation." [GOC GO:0016589+C cellular_component [name] NURF complex [def] "A four subunit ISWI-containing protein complex that facilitates nucleosome mobility and transcriptional activation in an ATP-dependent manner. In contrast to other chromatin remodeling complexes, the ATPase activity of NURF requires nucleosomes rather than free DNA or histones." [GOC GO:0016818+F molecular_function [name] hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [def] "Catalysis of the hydrolysis of any acid anhydride which contains phosphorus." [GOC GO:0031491+F molecular_function [name] nucleosome binding [def] "Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC GO:0043044+P biological_process [name] ATP-dependent chromatin remodeling [def] "Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors." [GOC [93]{Rv2737c,ATP2C2} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP2C2 only] GO:0000139+C cellular_component [name] Golgi membrane [def] "The lipid bilayer surrounding any of the compartments of the Golgi apparatus." [GOC GO:0005388+F molecular_function [name] calcium-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005887+C cellular_component [name] integral to plasma membrane [def] "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006816+P biological_process [name] calcium ion transport [def] "The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006874+P biological_process [name] cellular calcium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell." [GOC GO:0015410+F molecular_function [name] manganese-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0070588+P biological_process [name] calcium ion transmembrane transport [def] "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0071421+P biological_process [name] manganese ion transmembrane transport [def] "A process in which a manganese ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC [94]{Rv2737c,ALDH1L2} [common GO terms] GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH1L2 only] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0004029+F molecular_function [name] aldehyde dehydrogenase (NAD) activity [def] "Catalysis of the reaction GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005759+C cellular_component [name] mitochondrial matrix [def] "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC GO:0006730+P biological_process [name] one-carbon metabolic process [def] "The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0009058+P biological_process [name] biosynthetic process [def] "The chemical reactions and pathways resulting in the formation of substances_ typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC GO:0009258+P biological_process [name] 10-formyltetrahydrofolate catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of 10-formyltetrahydrofolate, the formylated derivative of tetrahydrofolate." [GOC GO:0016155+F molecular_function [name] formyltetrahydrofolate dehydrogenase activity [def] "Catalysis of the reaction GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0016742+F molecular_function [name] hydroxymethyl-, formyl- and related transferase activity [def] "Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor)." [EC GO:0019145+F molecular_function [name] aminobutyraldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0046655+P biological_process [name] folic acid metabolic process [def] "The chemical reactions and pathways involving folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines." [ISBN GO:0047105+F molecular_function [name] 4-trimethylammoniobutyraldehyde dehydrogenase activity [def] "Catalysis of the reaction GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [95]{Rv2737c,ATP2C1} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP2C1 only] GO:0000139+C cellular_component [name] Golgi membrane [def] "The lipid bilayer surrounding any of the compartments of the Golgi apparatus." [GOC GO:0004871+F molecular_function [name] signal transducer activity [def] "Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC GO:0005388+F molecular_function [name] calcium-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005509+F molecular_function [name] calcium ion binding [def] "Interacting selectively and non-covalently with calcium ions (Ca2+)." [GOC GO:0005794+C cellular_component [name] Golgi apparatus [def] "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum_ such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function GO:0005802+C cellular_component [name] trans-Golgi network [def] "The network of interconnected tubular and cisternal structures located at the side of the Golgi apparatus distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination." [GOC GO:0005887+C cellular_component [name] integral to plasma membrane [def] "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006816+P biological_process [name] calcium ion transport [def] "The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006828+P biological_process [name] manganese ion transport [def] "The directed movement of manganese (Mn) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006874+P biological_process [name] cellular calcium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell." [GOC GO:0007165+P biological_process [name] signal transduction [def] "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC GO:0008544+P biological_process [name] epidermis development [def] "The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of a plant or animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." [GOC GO:0015410+F molecular_function [name] manganese-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0016339+P biological_process [name] calcium-dependent cell-cell adhesion [def] "The attachment of one cell to another cell via adhesion molecules that require the presence of calcium for the interaction." [GOC GO:0030026+P biological_process [name] cellular manganese ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of manganese ions at the level of a cell." [GOC GO:0031532+P biological_process [name] actin cytoskeleton reorganization [def] "A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins." [GOC GO:0032468+P biological_process [name] Golgi calcium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of calcium ions within the Golgi apparatus of a cell or between the Golgi and its surroundings." [GOC GO:0032472+P biological_process [name] Golgi calcium ion transport [def] "The directed movement of calcium ions (Ca2+) into, out of or within the Golgi apparatus." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0043123+P biological_process [name] positive regulation of I-kappaB kinase/NF-kappaB cascade [def] "Any process that activates or increases the frequency, rate or extent of an I-kappaB kinase/NF-kappaB induced cascade." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0070588+P biological_process [name] calcium ion transmembrane transport [def] "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0071421+P biological_process [name] manganese ion transmembrane transport [def] "A process in which a manganese ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC [96]{Rv1547,G6PD} [common GO terms] [Rv1547 only] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [G6PD only] GO:0004345+F molecular_function [name] glucose-6-phosphate dehydrogenase activity [def] "Catalysis of the reaction GO:0005975+P biological_process [name] carbohydrate metabolic process [def] "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC GO:0006006+P biological_process [name] glucose metabolic process [def] "The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose_ it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides." [ISBN GO:0006098+P biological_process [name] pentose-phosphate shunt [def] "The process in which glucose is oxidized, coupled to NADPH synthesis. Glucose 6-P is oxidized with the formation of carbon dioxide (CO2), ribulose 5-phosphate and reduced NADP_ ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses." [ISBN GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0050661+F molecular_function [name] NADP binding [def] "Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions_ binding may be to either the oxidized form, NADP+, or the reduced form, NADPH." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC [97]{Rv2737c,ATP2A3} [common GO terms] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ATP2A3 only] GO:0005388+F molecular_function [name] calcium-transporting ATPase activity [def] "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0005783+C cellular_component [name] endoplasmic reticulum [def] "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN GO:0005789+C cellular_component [name] endoplasmic reticulum membrane [def] "The lipid bilayer surrounding the endoplasmic reticulum." [GOC GO:0005887+C cellular_component [name] integral to plasma membrane [def] "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC GO:0006810+P biological_process [name] transport [def] "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC GO:0006811+P biological_process [name] ion transport [def] "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006816+P biological_process [name] calcium ion transport [def] "The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC GO:0006874+P biological_process [name] cellular calcium ion homeostasis [def] "Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016021+C cellular_component [name] integral to membrane [def] "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC GO:0016529+C cellular_component [name] sarcoplasmic reticulum [def] "A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell_ continuous over large portions of the cell and with the nuclear envelope_ that part of the endoplasmic reticulum specialized for calcium release, uptake and storage." [GOC GO:0031095+C cellular_component [name] platelet dense tubular network membrane [def] "The lipid bilayer surrounding the platelet dense tubular network." [GOC GO:0031965+C cellular_component [name] nuclear membrane [def] "Either of the lipid bilayers that surround the nucleus and form the nuclear envelope_ excludes the intermembrane space." [GOC GO:0033017+C cellular_component [name] sarcoplasmic reticulum membrane [def] "The lipid bilayer surrounding the sarcoplasmic reticulum." [GOC GO:0034220+P biological_process [name] ion transmembrane transport [def] "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:0046872+F molecular_function [name] metal ion binding [def] "Interacting selectively and non-covalently with any metal ion." [GOC GO:0070588+P biological_process [name] calcium ion transmembrane transport [def] "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC GO:1903779+P [98]{Rv1629,HADHB} [common GO terms] GO:0003824+F molecular_function [name] catalytic activity [def] "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN GO:0016740+F molecular_function [name] transferase activity [def] "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN [Rv1629 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003887+F molecular_function [name] DNA-directed DNA polymerase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006139+P biological_process [name] nucleobase-containing compound metabolic process [def] "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC GO:0006260+P biological_process [name] DNA replication [def] "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC GO:0006261+P biological_process [name] DNA-dependent DNA replication [def] "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008408+F molecular_function [name] 3'-5' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GOC GO:0008409+F molecular_function [name] 5'-3' exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GOC GO:0016779+F molecular_function [name] nucleotidyltransferase activity [def] "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0040007+P biological_process [name] growth [def] "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC GO:0071897+P biological_process [name] DNA biosynthetic process [def] "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [HADHB only] GO:0003857+F molecular_function [name] 3-hydroxyacyl-CoA dehydrogenase activity [def] "Catalysis of the reaction GO:0003988+F molecular_function [name] acetyl-CoA C-acyltransferase activity [def] "Catalysis of the reaction GO:0004300+F molecular_function [name] enoyl-CoA hydratase activity [def] "Catalysis of the reaction GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0005740+C cellular_component [name] mitochondrial envelope [def] "The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm_ includes the intermembrane space." [GOC GO:0005741+C cellular_component [name] mitochondrial outer membrane [def] "The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope." [GOC GO:0005743+C cellular_component [name] mitochondrial inner membrane [def] "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC GO:0005783+C cellular_component [name] endoplasmic reticulum [def] "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN GO:0006629+P biological_process [name] lipid metabolic process [def] "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids_ neutral fats, other fatty-acid esters, and soaps_ long-chain (fatty) alcohols and waxes_ sphingoids and other long-chain bases_ glycolipids, phospholipids and sphingolipids_ and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC GO:0006631+P biological_process [name] fatty acid metabolic process [def] "The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN GO:0006635+P biological_process [name] fatty acid beta-oxidation [def] "A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A_ the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0016020+C cellular_component [name] membrane [def] "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles_ may be a single or double lipid bilayer_ also includes associated proteins." [GOC GO:0016509+F molecular_function [name] long-chain-3-hydroxyacyl-CoA dehydrogenase activity [def] "Catalysis of the reaction GO:0016746+F molecular_function [name] transferase activity, transferring acyl groups [def] "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor)." [GOC GO:0016747+F molecular_function [name] transferase activity, transferring acyl groups other than amino-acyl groups [def] "Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor)." [GOC GO:0035965+P biological_process [name] cardiolipin acyl-chain remodeling [def] "Remodeling the acyl chains of premature (de novo synthesized) cardiolipin (1,3-bis(3-phosphatidyl)glycerol), through sequential deacylation and re-acylation reactions, to generate mature cardiolipin containing high-levels of unsaturated fatty acids." [GOC GO:0042645+C cellular_component [name] mitochondrial nucleoid [def] "The region of a mitochondrion to which the DNA is confined." [GOC GO:0044822+F GO:0070062+C cellular_component [name] extracellular vesicular exosome [def] "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC [99]{Rv0629c,SMARCA1} [common GO terms] GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN [Rv0629c only] GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000724+P biological_process [name] double-strand break repair via homologous recombination [def] "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC GO:0004003+F molecular_function [name] ATP-dependent DNA helicase activity [def] "Catalysis of the reaction GO:0004386+F molecular_function [name] helicase activity [def] "Catalysis of the reaction GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004527+F molecular_function [name] exonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC GO:0005618+C cellular_component [name] cell wall [def] "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin_ in fungi it is composed largely of polysaccharides_ in bacteria it is composed of peptidoglycan." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0005886+C cellular_component [name] plasma membrane [def] "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006302+P biological_process [name] double-strand break repair [def] "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008854+F molecular_function [name] exodeoxyribonuclease V activity [def] "Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides." [EC GO:0009338+C cellular_component [name] exodeoxyribonuclease V complex [def] "An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA." [EC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0032508+P biological_process [name] DNA duplex unwinding [def] "The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [SMARCA1 only] GO:0003676+F molecular_function [name] nucleic acid binding [def] "Interacting selectively and non-covalently with any nucleic acid." [GOC GO:0005634+C cellular_component [name] nucleus [def] "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC GO:0006338+P biological_process [name] chromatin remodeling [def] "Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation." [GOC GO:0016589+C cellular_component [name] NURF complex [def] "A four subunit ISWI-containing protein complex that facilitates nucleosome mobility and transcriptional activation in an ATP-dependent manner. In contrast to other chromatin remodeling complexes, the ATPase activity of NURF requires nucleosomes rather than free DNA or histones." [GOC GO:0016818+F molecular_function [name] hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [def] "Catalysis of the hydrolysis of any acid anhydride which contains phosphorus." [GOC GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0031491+F molecular_function [name] nucleosome binding [def] "Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC GO:0043044+P biological_process [name] ATP-dependent chromatin remodeling [def] "Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors." [GOC [100]{Rv2737c,ALDH5A1} [common GO terms] [Rv2737c only] GO:0000150+F molecular_function [name] recombinase activity [def] "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC GO:0000166+F molecular_function [name] nucleotide binding [def] "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC GO:0000287+F molecular_function [name] magnesium ion binding [def] "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC GO:0000400+F molecular_function [name] four-way junction DNA binding [def] "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC GO:0000725+P biological_process [name] recombinational repair [def] "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC GO:0000730+P biological_process [name] DNA recombinase assembly [def] "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID GO:0003677+F molecular_function [name] DNA binding [def] "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC GO:0003690+F molecular_function [name] double-stranded DNA binding [def] "Interacting selectively and non-covalently with double-stranded DNA." [GOC GO:0003697+F molecular_function [name] single-stranded DNA binding [def] "Interacting selectively and non-covalently with single-stranded DNA." [GOC GO:0004518+F molecular_function [name] nuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN GO:0004519+F molecular_function [name] endonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC GO:0004520+F molecular_function [name] endodeoxyribonuclease activity [def] "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC GO:0005515+F molecular_function [name] protein binding [def] "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC GO:0005524+F molecular_function [name] ATP binding [def] "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN GO:0005737+C cellular_component [name] cytoplasm [def] "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN GO:0005829+C cellular_component [name] cytosol [def] "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC GO:0006259+P biological_process [name] DNA metabolic process [def] "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN GO:0006281+P biological_process [name] DNA repair [def] "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID GO:0006310+P biological_process [name] DNA recombination [def] "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN GO:0006312+P biological_process [name] mitotic recombination [def] "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC GO:0006314+P biological_process [name] intron homing [def] "Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron." [PMID GO:0006974+P biological_process [name] response to DNA damage stimulus [def] "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC GO:0008094+F molecular_function [name] DNA-dependent ATPase activity [def] "Catalysis of the reaction GO:0009432+P biological_process [name] SOS response [def] "An error-prone process for repairing damaged microbial DNA." [GOC GO:0009650+P biological_process [name] UV protection [def] "Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." [GOC GO:0010212+P biological_process [name] response to ionizing radiation [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays." [PMID GO:0016539+P biological_process [name] intein-mediated protein splicing [def] "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation_ the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC GO:0016787+F molecular_function [name] hydrolase activity [def] "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN GO:0016887+F molecular_function [name] ATPase activity [def] "Catalysis of the reaction GO:0030145+F molecular_function [name] manganese ion binding [def] "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC GO:0042148+P biological_process [name] strand invasion [def] "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC GO:0046677+P biological_process [name] response to antibiotic [def] "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC GO:0090305+P biological_process [name] nucleic acid phosphodiester bond hydrolysis [def] "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC [ALDH5A1 only] GO:0005739+C cellular_component [name] mitochondrion [def] "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN GO:0008152+P biological_process [name] metabolic process [def] "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC GO:0009013+F molecular_function [name] succinate-semialdehyde dehydrogenase [NAD(P)+] activity [def] "Catalysis of the reaction GO:0009450+P biological_process [name] gamma-aminobutyric acid catabolic process [def] "The chemical reactions and pathways resulting in the breakdown of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." [GOC GO:0016491+F molecular_function [name] oxidoreductase activity [def] "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC GO:0016620+F molecular_function [name] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [def] "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC GO:0055114+P biological_process [name] oxidation-reduction process [def] "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC