{"text_format":"2","workbook":"xlsx","n_sheets":6,"sheets":["Header","Supplementary table S1","Supplementary table S4","Supplementary table S8","Supplementary table S9","Supplementary table S12"],"not_rendered":{"charts":0,"images":0,"macros":0,"external_links":0,"defined_names":0,"comments":0,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":5,"cells_raw":0,"read":"whole","date_system":"1900"}

{"sheet":"Header","index":0,"n_rows":1,"n_cols":1,"rows_kept":1,"cut":false,"hidden":false,"merged":[]}
["Supporting Information Tables S1, S4, S8, S9 and S12"]

{"sheet":"Supplementary table S1","index":1,"n_rows":24,"n_cols":11,"rows_kept":24,"cut":false,"hidden":false,"merged":[[1,0,2,0],[1,1,2,1],[1,2,1,3],[1,7,2,7],[1,8,2,8],[1,9,2,9],[1,10,2,10]]}
["Table S1. qPCR validation of selected genes differentially expressed at T2."]
["Gene ID","Gene Function","Log2 average relative expression",{"$nulls":4},"qPCR Validation","Forward primer","Reverse primers","Amplicon length (bp)"]
[null,null,"qPCR MT+","qPCR MT-","RNA-seq","RNA-seq for MT-","RNA-seq for MT+"]
["PSNMU-V1.4_AUG-EV-PASAV3_0001670.1","No annotation",3.472,2.615,7.03141997824325,null,null,"Yes","CGAGTTTCTCACATTTGCTGG","CTCTTTTGGATGTGGACCG",169]
["PSNMU-V1.4_AUG-EV-PASAV3_0113130.1","COBW domain",1.916,0.266999999999999,4.83192381655059,null,null,"Yes in MT+","AAGACGACCCTCCTGAACC","CGTTCTCCGACAAAATGTTC",115]
["PSNMU-V1.4_AUG-EV-PASAV3_0104930.1","oxidoreductase TM_0325",3.018,2.516,4.33697985229106,null,null,"Yes","CCTCCGAGGTTTTTGCTGC","ATGCTTGGGAAGAGGTGTC",117]
["PSNMU-V1.4_AUG-EV-PASAV3_0102760.1","Protein aardvark",5.629,5.413,6.08584147457331,null,null,"Yes","ACGACATCCACAGCAATCTC","TTCCTTGAGCCGTTCCAGAC",149]
["PSNMU-V1.4_AUG-EV-PASAV3_0012110.1","No annotation",0.0309999999999987,0.712000000000003,7.25886155715729,null,null,"No","CACCAACTACCACCATGAAG","CCTTCTCTGGTTTCTGGTTG",140]
["PSNMU-V1.4_AUG-EV-PASAV3_0035170.1","Heme-thiolate peroxidase",0.0269999999999974,-2.427,6.96733951501137,null,null,"No","TCATCAATCGCAACGGAACC","TTCGTCCTCGTAAGTCTGG",140]
["PSNMU-V1.4_AUG-EV-PASAV3_0001190.1","No annotation",3.434,2.552,2.28998914235228,null,null,"Yes","AAAGCCACCCAGCACATC","TGAGGTTGTTGGTCGTCTTG",121]
["PSNMU-V1.4_AUG-EV-PASAV3_0081540.1","G2/mitotic-specific cyclin",-4.407,-0.985999999999997,-1.65672885074391,null,null,"Yes","AACAATCCCAGCCACAGTGC","AGAGAAAAGACCACGACCTC",127]
["PSNMU-V1.4_AUG-EV-PASAV3_0095090.1","Cyclin-B2-2",-2.086,-0.377999999999996,-2.1425721733744,null,null,"Yes","ACAACAGGTCTTGAGAGCAC","CGTGGTCTTTCGATTCCTTC",163]
["PSNMU-V1.4_AUG-EV-PASAV3_0023490.1","Radical S-adenosyl methionine domain-containing protein 2",0.898,0.384,6.65465837309707,null,null,"No","CGAACCATACTCTATCCGCA","ACTACCGTAACAACCGTTCG",156]
["PSNMU-V1.4_AUG-EV-PASAV3_0063520.1","Uncharacterised",0.147000000000002,1.325,4.12776044257249,6.9059689850648,null,"Yes in MT-","CACACTTCGTCCTTCCGTTCTC","CGCCGAGTTTGCTCTTGG",171]
["PSNMU-V1.4_AUG-EV-PASAV3_0103000.1","Cathepsin D",0.134,6.678,3.36917746614758,6.95574318367133,null,"Yes in MT-","CCATTGTCGACTCGGGAACC","GTAGGTTTTCCCGCCGATCC",170]
["PSNMU-V1.4_AUG-EV-PASAV3_0020420.1","No annotation",-1.847,9.78,3.07779677513402,6.79873242962317,null,"Yes in MT-","AGCAAAGCCGACGATGCC","AATTCGTGCGATTCTCCGTTG",170]
["PSNMU-V1.4_AUG-EV-PASAV3_0041130.1","Heat shock factor protein 3",-3.023,3.867,2.13226659873693,3.41133344469506,null,"Yes in MT-","CCCCTACAAGCTCTTTGATTTG","GAAATTGTGGTGCCCAAAG",160]
["asmbl_11458|m.14428","No annotation",4.965,5.509,6.4,null,null,"Yes","GACCCAGTTGTTTCGCAGAG","GACTGCCACCATTGCCATTC",113]
["PsnmuV1.4_aug-pasa-abinitio_v2_0037900.1","No annotation",9.638,10.395,8.4,null,null,"Yes","AGACGCAACAAGGCATCGC","GTGTTTCCCGTTTCAGGGTC",173]
["MT- specific"]
["PSNMU-V1.4_AUG-EV-PASAV3_0011090.1","No annotation",-0.666,10.777,null,8.42340496127108,null,"Yes","GCTTGCGTCATCCGTTTTG","GAGACAAACGCCTTGGCAAG",170]
["PSNMU-V1.4_AUG-EV-PASAV3_0093450.1","No annotation",-0.366,1.557,null,6.25811910524172,null,"Yes","GGTACTTGGAGTTTTGGGCG","GATTCTCTCTTGATGACCGCC",121]
["MT+ specific"]
["PSNMU-V1.4_AUG-EV-PASAV3_0024820.1","No annotation",8.585,-1.618,null,null,3.60217594658568,"Yes","GTATGGCGCTCACCACTTC","CGTCTTCGACTGCGTCTTC",156]

{"sheet":"Supplementary table S4","index":2,"n_rows":9,"n_cols":6,"rows_kept":9,"cut":false,"hidden":false,"merged":[[0,0,0,5],[1,2,1,5]]}
["Table S4. Statistics of LTR insertion time"]
[null,null,"% of LTRs with insertion time below given threshold"]
["Organism","No. of LTRs","0.5 Mya","1 Mya","1.5 Mya","2 Mya"]
["P. multistriata",166,45,62,73,81]
["P. multiseries",4414,45,72,83,88]
["F. cylindrus",270,80,91,95,97]
["P. tricornutum",108,65,80,86,93]
["T. pseudonana",41,61,73,80,88]
["O. sativa",3576,29,47,63,75]

{"sheet":"Supplementary table S8","index":3,"n_rows":125,"n_cols":14,"rows_kept":125,"cut":false,"hidden":false,"merged":[]}
["Table S8. Annotation for diatom genes of red algal origin"]
["idf","Row.names","tree","bootstrapJTT","av.bootstrapJTT","classJTT","bootstrapWAG","av.bootstrapWAG","classWAG","TransLength","HSPNameSP","DescriptionSP","CDName","CDDesc"]
["PSNMU-V1.4_AUG-EV-PASAV3_0000610.1",563511,"test6499.tree",0.874,0.755170731707317,"high",0.862,0.79290243902439,"high",2148,"F4HVA6","Transcription initiation factor TFIID subunit 6b","cd08050]---[COG5095]---[PTZ00157]---[pfam00935]---[COG1631]---[pfam07571]---[PRK05767","cd08050  TAF6  TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA  TFIIB  TFIID  TFIIE  TFIIF  and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new  unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites  core-promoter recognition or a role in essential catalytic activity. These TAFs  with the help of specific activators  are required only for expression of a subset of genes and are not universally involved for transcription as are GTFs. In yeast and human cells  TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs  the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones  TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF6 is a shared subunit of histone acetyltransferase complex SAGA and TFIID complexes. TAF6 domain interacts with TAF9 and makes a novel histone-like heterodimer that is structurally related to histones H4 and H3. TAF6 may also interact with the downstream core promoter element (DPE).]---[COG5095  TAF6  Transcription initiation factor TFIID  subunit TAF6 (also component of histone acetyltransferase SAGA)  Transcription .]---[PTZ00157  PTZ00157  60S ribosomal protein L36a  Provisional.]---[pfam00935  Ribosomal_L44  Ribosomal protein L44. ]---[COG1631  RPL42A  Ribosomal protein L44E  Translation  ribosomal structure and biogenesis .]---[pfam07571  DUF1546  Protein of unknown function (DUF1546). Associated with pfam02969 in Transcription initiation factor TFIID subunit 6 (TAF6).]---[PRK05767  rpl44e  50S ribosomal protein L44e  Validated."]
["PSNMU-V1.4_AUG-EV-PASAV3_0001820.1",563374,"test10648.tree",0.314,0.879,"medium",0.067,0.850653846153846,"medium",4732,"P70388","DNA repair protein RAD50","TIGR00606]---[TIGR00606]---[TIGR00606]---[COG0419]---[COG0419]---[COG0419]---[COG0419]---[COG0419]---[COG1196]---[COG1196]---[COG1196]---[COG1196]---[COG1196]---[COG1196]---[COG1196]---[COG1196]---[cd03240]---[cd03240]---[TIGR02169]---[TIGR02169]---[TIGR02169]---[TIGR02169]---[TIGR02169]---[TIGR02169]---[TIGR02169]---[TIGR02169]---[pfam02463]---[TIGR04523]---[TIGR04523]---[TIGR04523]---[PRK03918]---[PRK03918]---[PRK03918]---[PRK03918]---[PRK01156]---[PRK01156]---[PRK01156]---[PRK01156]---[TIGR02168]---[TIGR02168]---[TIGR02168]---[TIGR02168]---[TIGR02168]---[TIGR02168]---[pfam13476]---[pfam13166]---[PRK02224]---[PRK02224]---[PRK02224]---[PRK02224]---[PRK02224]---[PRK02224]---[PRK02224]---[pfam01576]---[pfam01576]---[pfam01576]---[pfam01576]---[TIGR03185]---[pfam10174]---[pfam10174]---[COG1340]---[pfam05483]---[pfam12128]---[TIGR01612","TIGR00606  RAD50_homologue_ceRAD50  rad50. All proteins in this family for which functions are known are involvedin recombination  recombinational repair  and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999  Ph.D. Thesis  Stanford University).]---[COG0419  SbcC  ATPase involved in DNA repair  DNA replication  recombination  and repair .]---[COG1196  Smc  Chromosome segregation ATPases  Cell division and chromosome partitioning .]---[cd03240  ABC_Rad50  ATP-binding cassette domain of Rad50. The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters  but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs  the Q loop  a histidine residue in the switch region  a D-loop  and a conserved LSGG sequence. This conserved sequence  LSGG  is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.]---[TIGR02169  chromosome_segregation_protein_related_ptotein  chromosome segregation protein SMC  primarily archaeal type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria  archaea  and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes  but six paralogs (excluded from this family) are found in eukarotes  where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex  Synechocystis  etc)  the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved  but the central hinge region is skewed in composition and highly divergent.  Cellular processes  Cell division  DNA metabolism  Chromosome-associated proteins .]---[pfam02463  SMC_N  RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini  and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers  the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes  which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolizm and recombination.]---[TIGR04523  conserved_hypothetical_protein  helix-rich Mycoplasma protein. Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length  including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D E N Q  and K. Genes encoding these proteins are often found in tandem. The function is unknown.]---[PRK03918  PRK03918  chromosome segregation protein  Provisional.]---[PRK01156  PRK01156  chromosome segregation protein  Provisional.]---[TIGR02168  Chromosome_partition_protein_Smc  chromosome segregation protein SMC  common bacterial type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria  archaea  and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes  where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.  Cellular processes  Cell division  DNA metabolism  Chromosome-associated proteins .]---[pfam13476  AAA_23  AAA domain. ]---[pfam13166  AAA_13  AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.]---[PRK02224  PRK02224  chromosome segregation protein  Provisional.]---[pfam01576  Myosin_tail_1  Myosin tail. The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.]---[TIGR03185  DNA_S_dndD  DNA sulfur modification protein DndD.  This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria  much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes  Actinomycetes  Proteobacteria  and Cyanobacteria.  DNA metabolism  Restriction/modification .]---[pfam10174  Cast  RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.]---[COG1340  COG1340  Uncharacterized archaeal coiled-coil protein  Function unknown .]---[pfam05483  SCP-1  Synaptonemal complex protein 1 (SCP-1). Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.]---[pfam12128  DUF3584  Protein of unknown function (DUF3584). This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication.]---[TIGR01612  235kDa-fam  reticulocyte binding/rhoptry protein.  This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein  235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum  P. vivax and P. yoelii."]
["PSNMU-V1.4_AUG-EV-PASAV3_0002140.1",563406,"test6293.tree",0.831,0.769904761904762,"high",0.867,0.757738095238095,"high",3832,"Q69S81","Phosphopantothenate--cysteine ligase 1","pfam04127]---[PRK05579","pfam04127  DFP  DNA / pantothenate metabolizm flavoprotein. The DNA/pantothenate metabolizm flavoprotein (EC 4.1.1.36) affects synthesis of DNA  and pantothenate metabolizm.]---[PRK05579  PRK05579  bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase  Validated."]
["PSNMU-V1.4_AUG-EV-PASAV3_0003810.1",563683,"test7961.tree",0.849,0.633264705882353,"high",0.884,0.661852941176471,"high",869,"Q9UTE9","Mitochondrial import inner membrane translocase subunit tim10","pfam02953","pfam02953  zf-Tim10_DDP  Tim10/DDP family zinc finger. Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein TIMM8A. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import. Members of this family seem to be localized to the mitochondrial intermembrane space."]
["PSNMU-V1.4_AUG-EV-PASAV3_0005600.1",563857,"test9165.tree",0.548,0.7607,"high",0.639,0.750166666666667,"high",2640,"Q566T0","Polycomb protein eed","cd00200]---[cd00200]---[cd00200]---[cd00200]---[COG2319]---[COG2319","cd00200  WD40  WD40 domain  found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction  pre-mRNA processing and cytoskeleton assembly  typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long  hence the name WD40  between GH and WD lies a conserved core  serves as a stable propeller-like platform to which proteins can bind either stably or reversibly  forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet  instances with few detectable copies are hypothesized to form larger structures by dimerization  each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade  the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure  residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands  7 copies of the repeat are present in this alignment.]---[COG2319  COG2319  FOG  WD40 repeat  General function prediction only ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0006850.1",563941,"test9424.tree",0.864,0.783965517241379,"high",0.629,0.745551724137931,"high",677,"Q4P9K6","Protein SYM1","pfam04117","pfam04117  Mpv17_PMP22  Mpv17 / PMP22 family. The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesized on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse  the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolizm and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs  typically muscle or liver  or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities  hypoglycemia  and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy  peripheral neuropathy  corneal anesthesia and scarring  acral mutilation  cerebral leukoencephalopathy  failure to thrive  and recurrent metabolic acidosis with intercurrent infections. Infantile  childhood  and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients  suggesting a primary defect in mtDNA maintenance."]
["PSNMU-V1.4_AUG-EV-PASAV3_0007100.1",563966,"test38066.tree",1,0.673714285714286,"high",1,0.618428571428571,"high",1156,"Q9LU39","Glutamyl-tRNA reductase-binding protein  chloroplastic","pfam13883]---[COG0748","pfam13883  Pyrid_oxidase_2  Pyridoxamine 5'-phosphate oxidase. ]---[COG0748  HugZ  Putative heme iron utilization protein  Inorganic ion transport and metabolism ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0008010.1",564092,"test33901.tree",1,0.70775,"high",1,0.68575,"high",1027,"P27525","Chlorophyll a-b binding protein CP24 10B  chloroplastic","pfam00504]---[pfam00504]---[pfam00504]---[PLN00100]---[PLN00089]---[PLN00170]---[PLN00120]---[PLN00098]---[PLN00101]---[PLN00099]---[PLN00147]---[PLN00048]---[PLN00097","pfam00504  Chloroa_b-bind  Chlorophyll A-B binding protein. ]---[PLN00100  PLN00100  light-harvesting complex chlorophyll-a/b protein of photosystem I (Lhca)  Provisional.]---[PLN00089  PLN00089  fucoxanthin-chlorophyll a/c binding protein  Provisional.]---[PLN00170  PLN00170  photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24)  Provisional.]---[PLN00120  PLN00120  fucoxanthin-chlorophyll a-c binding protein  Provisional.]---[PLN00098  PLN00098  light-harvesting complex I chlorophyll a/b-binding protein (Lhac)  Provisional.]---[PLN00101  PLN00101  Photosystem I light-harvesting complex type 4 protein  Provisional.]---[PLN00099  PLN00099  light-harvesting complex IChlorophyll A-B binding protein Lhca1  Provisional.]---[PLN00147  PLN00147  light-harvesting complex I chlorophyll-a/b binding protein Lhca5  Provisional.]---[PLN00048  PLN00048  photosystem I light harvesting chlorophyll a/b binding protein 3  Provisional.]---[PLN00097  PLN00097  photosystem I light harvesting complex Lhca2/4  chlorophyll a/b binding  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0008520.1",564142,"test3750.tree",0.898,0.776348484848485,"high",0.807,0.741454545454545,"high",1384,"-","-","cd03390]---[cd03384]---[cd01610]---[pfam01569]---[smart00014]---[COG0671]---[cd03389","cd03390  PAP2_containing_1_like  PAP2  subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both diacylglycerol pyrophosphate phosphatase activity as well as phosphatidate (PA) phosphatase activity  they may have a more generic housekeeping role in lipid metabolism.]---[cd03384  PAP2_wunen  PAP2  wunen subfamily. Most likely a family of membrane associated phosphatidic acid phosphatases. Wunen is a drosophila protein expressed in the central nervous system  which provides repellent activity towards primordial germ cells (PGCs)  controls the survival of PGCs and is essential in the migration process of these cells towards the somatic gonadal precursors.]---[cd01610  PAP2_like  PAP2_like proteins  a super-family of histidine phosphatases and vanadium haloperoxidases  includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP)  Glucose-6-phosphatase  Phosphatidylglycerophosphatase B and bacterial acid phosphatase  vanadium chloroperoxidases  vanadium bromoperoxidases  and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins.]---[pfam01569  PAP2  PAP2 superfamily. This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2)  Glucose-6-phosphatase EC 3.1.3.9  Phosphatidylglycerophosphatase B EC 3.1.3.27 and bacterial acid phosphatase EC 3.1.3.2. The family also includes a variety of haloperoxidases that function by oxidizing halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.]---[smart00014  acidPPc  Acid phosphatase homologues. ]---[COG0671  PgpB  Membrane-associated phospholipid phosphatase  Lipid metabolism .]---[cd03389  PAP2_lipid_A_1_phosphatase  PAP2_like proteins  Lipid A 1-phosphatase subfamily. Lipid A 1-phosphatase  or LpxE from Francisella novicida selectively dephosphorylates lipid A at the 1-position. Lipid A is the membrane-anchor component of lipopolysaccharides (LPS)  the major constituents of the outer membrane in many gram-negative bacteria."]
["PSNMU-V1.4_AUG-EV-PASAV3_0009480.1",564233,"test38092.tree",1,0.630285714285714,"high",1,0.643142857142857,"high",1250,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0010230.1",564305,"test112764.tree",1,1,"high",1,1,"high",2051,"Q55720","Ycf49-like protein","pfam10693]---[pfam12159","pfam10693  DUF2499  Protein of unknown function (DUF2499). Members of this family are found in plants  lower eukaryotes  and bacteria and the chloroplast where it is annotated as Ycf49 or Ycf49-like. The function is not known though several members are annotated as putative membrane proteins.]---[pfam12159  DUF3593  Protein of unknown function (DUF3593). This family of proteins is functionally uncharacterized.This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 98 and 228 amino acids in length. There is a conserved LHG sequence motif."]
["PSNMU-V1.4_AUG-EV-PASAV3_0012120.1",564488,"test11066.tree",0.843,0.77788,"high",0.836,0.69452,"high",1253,"Q8R2M2","Deoxynucleotidyltransferase terminal-interacting protein 2","pfam08698","pfam08698  Fcf2  Fcf2 pre-rRNA processing. This is a family of eukaryotic nucleolar proteins that are involved in pre-rRNA processing."]
["PSNMU-V1.4_AUG-EV-PASAV3_0013940.1",564664,"test5674.tree",0.814,0.691913043478261,"high",0.091,0.723586956521739,"medium",690,"-","-","cd00073]---[pfam00538]---[smart00526","cd00073  H15  linker histone 1 and histone 5 domains  the basic subunit of chromatin is the nucleosome  consisting of an octamer of core histones  two full turns of DNA  a linker histone (H1 or H5) and a variable length of linker DNA  H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers  stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments  through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala  Lys  Pro)  thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber.]---[pfam00538  Linker_histone  linker histone H1 and H5 family. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.]---[smart00526  H15  Domain in histone families 1 and 5. "]
["PSNMU-V1.4_AUG-EV-PASAV3_0015100.1",564776,"test8854.tree",0.986,0.805032258064516,"high",1,0.790451612903226,"high",1363,"-","-","pfam06485","pfam06485  DUF1092  Protein of unknown function (DUF1092). This family consists of several hypothetical proteins of unknown function all from photosynthetic organisms including plants and cyanobacteria."]
["PSNMU-V1.4_AUG-EV-PASAV3_0015590.1",564823,"test49806.tree",1,0.7838,"high",1,0.7814,"high",1603,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0015740.1",564838,"test43152.tree",1,0.794833333333333,"high",1,0.704166666666667,"high",3619,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0016510.1",564912,"test70002.tree",1,0.611,"high",1,0.607,"high",2260,"-","-","pfam07082]---[pfam07082","pfam07082  DUF1350  Protein of unknown function (DUF1350). This family consists of several hypothetical proteins from both cyanobacteria and plants. Members of this family are typically around 250 residues in length. The function of this family is unknown but the species distribution indicates that the family may be involved in photosynthesis."]
["PSNMU-V1.4_AUG-EV-PASAV3_0016610.1",564922,"test43172.tree",1,0.787666666666667,"high",1,0.786333333333333,"high",914,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0018200.1",565055,"test7450.tree",0.707,0.807805555555556,"high",0.543,0.772305555555556,"high",2134,"Q9ZWG1","Mitochondrial uncoupling protein 2","pfam10914]---[pfam00153]---[pfam00153]---[pfam00153]---[PTZ00169]---[PTZ00169","pfam10914  DUF2781  Protein of unknown function (DUF2781). This is a eukaryotic family of uncharacterized proteins. Some of the proteins in this family are annotated as membrane proteins.]---[pfam00153  Mito_carr  Mitochondrial carrier protein. ]---[PTZ00169  PTZ00169  ADP/ATP transporter on adenylate translocase  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0018240.1",565059,"test6843.tree",0.745,0.839538461538462,"high",0.671,0.874589743589744,"high",5130,"Q60520","Paired amphipathic helix protein Sin3a","COG5602]---[COG5602]---[COG5602]---[pfam08295]---[smart00761]---[pfam02671]---[pfam02671","COG5602  SIN3  Histone deacetylase complex  SIN3 component  Chromatin structure and dynamics .]---[pfam08295  Sin3_corepress  Sin3 family co-repressor. This domain is found on transcriptional regulators. It forms interactions with histone deacetylases.]---[smart00761  HDAC_interact  Histone deacetylase (HDAC) interacting.  This domain is found on transcriptional regulators. It forms interactions with histone deacetylases.]---[pfam02671  PAH  Paired amphipathic helix repeat. This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif  which mediate protein-protein interactions."]
["PSNMU-V1.4_AUG-EV-PASAV3_0018380.1",565073,"test86459.tree",1,0.5,"high",1,0.5,"high",1991,"Q9SVE7","MATE efflux family protein 3  chloroplastic","cd13136]---[cd13136]---[TIGR00797]---[COG0534]---[COG0534]---[COG0534]---[cd13137]---[cd13138]---[cd12082]---[cd12082]---[cd12082]---[cd13133]---[cd13133]---[cd13142]---[cd13131]---[cd13143]---[cd13134]---[cd13147]---[cd13139]---[cd13135]---[cd13149]---[pfam01554]---[cd13146]---[cd13140]---[cd13148","cd13136  MATE_DinF_like  DinF and similar proteins  a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins. Escherichia coli DinF is a membrane protein that has been found to protect cells against oxidative stress and bile salts. The expression of DinF is regulated as part of the SOS system. It may act by detoxifying oxidizing molecules that have the potential to damage DNA. Some member of this family have been reported to enhance the virulence of plant pathogenic bacteria by enhancing their ability to grow in the presence of toxic compounds. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR).]---[TIGR00797  Multidrug_resistance_protein_HmrM  putative efflux protein  MATE family. The Multi Antimicrobial Extrusion (MATE) Family (TC 2.A.66) The MATE family consists of probable efflux proteins including a functionally characterized multi drug efflux system from Vibrio parahaemolyticus  a putative ethionine resistance protein of Saccharomyces cerevisiae  and the functionally uncharacterized DNA damage-inducible protein F (DinF) of E. coli. These proteins have 12 probable TMS.  Transport and binding proteins  Other .]---[COG0534  NorM  Na -driven multidrug efflux pump  Defense mechanisms .]---[cd13137  MATE_NorM_like  Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd13138  MATE_yoeA_like  Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd12082  MATE_like  Multidrug and toxic compound extrusion family and similar proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants  where the proteins are linked to disease resistance. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd13133  MATE_like_7  Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd13142  MATE_like_12  Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd13131  MATE_NorM_like  Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. This subfamily includes Vibrio cholerae NorM and functions most likely as a multidrug efflux pump  removing xenobiotics from the interior of the cell. The pump utilizes a cation gradient across the membrane to facilitate the export process. NorM appears to bind monovalent cations in an outward-facing conformation and may subsequently cycle through an inward-facing and outward-facing conformation to capture and release its substrate.]---[cd13143  MATE_MepA_like  Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. This subfamily includes Streptococcus aureus MepA and Vibrio vulnificus VmrA and functions most likely as a multidrug efflux pump.]---[cd13134  MATE_like_8  Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd13147  MATE_MJ0709_like  Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins  similar to Methanocaldococcus jannaschii MJ0709. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd13139  MATE_like_14  Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd13135  MATE_like_9  Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd13149  MATE_like_2  Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[pfam01554  MatE  MatE. The MatE domain.]---[cd13146  MATE_like_6  Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd13140  MATE_like_1  Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants  where the proteins are linked to disease resistance. A number of family members are involved in the synthesis of peptidoglycan components in bacteria.]---[cd13148  MATE_like_3  Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria."]
["PSNMU-V1.4_AUG-EV-PASAV3_0019820.1",565230,"test8840.tree",0.887,0.790258064516129,"high",0.907,0.794806451612903,"high",1232,"O48781","SPX domain-containing protein 2","pfam03105]---[cd14447]---[cd14481]---[cd14476]---[cd14484","pfam03105  SPX  SPX domain. We have named this region the SPX domain after (SYG1  Pho81 and XPR1). This 180 residue length domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1  the N-terminus directly binds to the G- protein beta subunit and inhibits transduction of the mating pheromone signal. This finding suggests that all the members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2 NUC-2 contains several ankyrin repeats pfam00023. Several members of this family are annotated as XPR1 proteins  the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with murine leukaemia viruses (MLV). The similarity between SYG1  phosphate regulators and XPR1 sequences has been previously noted  as has the additional similarity to several predicted proteins  of unknown function  from Drosophila melanogaster  Arabidopsis thaliana  Caenorhabditis elegans  Schizosaccharomyces pombe  and Saccharomyces cerevisiae. In addition  given the similarities between XPR1 and SYG1 and phosphate regulatory proteins  it has been proposed that XPR1 might be involved in G-protein associated signal transduction and may itself function as a phosphate sensor.]---[cd14447  SPX  Domain found in Syg1  Pho81  XPR1  and related proteins. This region has been named the SPX domain after (Syg1  Pho81 and XPR1). This domain is found at the amino terminus of a variety of proteins. In the yeast protein Syg1  the N-terminus directly binds to the G-protein beta subunit and inhibits transduction of the mating pheromone signal. Similarly  the N-terminus of the human XPR1 protein binds directly to the beta subunit of the G-protein heterotrimer leading to increased production of cAMP. These findings suggest that members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2. NUC-2 contains several ankyrin repeats. Several members of this family are annotated as XPR1 proteins  the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with xenotropic and polytropic murine leukaemia viruses (MLV). Infection by these retroviruses can inhibit XPR1-mediated cAMP signaling and result in cell toxicity and death. The similarity between Syg1  phosphate regulators and XPR1 sequences has been previously noted  as has the additional similarity to several predicted proteins  of unknown function  from Drosophila melanogaster  Arabidopsis thaliana  Caenorhabditis elegans  Schizosaccharomyces pombe  S. cerevisiae  and many other diverse organisms.]---[cd14481  SPX_AtSPX1_like  SPX domain of the plant protein SPX1 and similar proteins. This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. This family of plant proteins contains a single SPX domain. Arabidopsis thaliana SPX1 and SPX3 have been reported to play roles in the adaptation to low-phosphate conditions  SPX3 may be involved in the regulation of SPX1 activity. Oryza sativa SPX1 suppresses the regulation of expression of OsPT2  a low-affinity phosphate transporter  by the MYB-like OsPHR2.]---[cd14476  SPX_PHO1_like  SPX domain of the plant protein PHOSPHATE1 (PHO1). This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The PHO1 gene family conserved in plants is involved in a variety of processes  most notably the transport of inorganic phosphate from the root to the shoot of the plant and mediating the response to low levels of inorganic phosphate. More recently it has become evident that PHO1 gene families have diverged in various plants and may play roles in stress response as well as the stomatal response to abscisic acid.]---[cd14484  SPX_GDE1_like  SPX domain of Gde1 and similar proteins.  This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. The yeast protein Gde1/Ypl110c is similar to both  NUC-2 and Pho81  in sharing their multi-domain architecture  which includes the SPX N-terminal domain followed by several ankyrin repeats and a C-terminal glycerophosphodiester phosphodiesterase domain (GDPD). Gde1 hydrolyzes intracellular glycerophosphocholine into glycerolphosphate and choline  and plays a role in the utilization of glycerophosphocholine as a source for phosphate."]
["PSNMU-V1.4_AUG-EV-PASAV3_0020040.1",565250,"test12107.tree",0.779,0.839478260869565,"high",0.8,0.836,"high",1483,"Q9VXT2","DnaJ homolog subfamily C member 25 homolog","pfam00226]---[cd06257]---[TIGR02349]---[smart00271]---[PRK10266]---[COG0484]---[COG2214]---[PRK14291]---[PRK14293]---[PRK14295]---[PRK14278]---[PRK14283]---[PRK14298]---[PRK14290]---[PRK14280]---[PRK14279]---[PRK14276]---[PRK14299]---[PRK14277]---[PRK14282","pfam00226  DnaJ  DnaJ domain. DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens  although not in Prosite are confirmed as DnaJ containing domains from literature.]---[cd06257  DnaJ  DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation  folding  unfolding  translocation  and degradation. They act primarily by stimulating the ATPase activity of Hsp70s  an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain  which mediates the interaction with Hsp70. They may contain other domains as well  and the architectures provide a means of classification.]---[TIGR02349  Chaperone_protein_DnaJ  chaperone protein DnaJ. This model represents bacterial forms of DnaJ  part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes  typically not near DnaK and GrpE-like genes  most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.]---[smart00271  DnaJ  DnaJ molecular chaperone homology domain. ]---[PRK10266  PRK10266  curved DNA-binding protein CbpA  Provisional.]---[COG0484  DnaJ  DnaJ-class molecular chaperone with C-terminal Zn finger domain  Posttranslational modification  protein turnover  chaperones .]---[COG2214  CbpA  DnaJ-class molecular chaperone  Posttranslational modification  protein turnover  chaperones .]---[PRK14291  PRK14291  chaperone protein DnaJ  Provisional.]---[PRK14293  PRK14293  chaperone protein DnaJ  Provisional.]---[PRK14295  PRK14295  chaperone protein DnaJ  Provisional.]---[PRK14278  PRK14278  chaperone protein DnaJ  Provisional.]---[PRK14283  PRK14283  chaperone protein DnaJ  Provisional.]---[PRK14298  PRK14298  chaperone protein DnaJ  Provisional.]---[PRK14290  PRK14290  chaperone protein DnaJ  Provisional.]---[PRK14280  PRK14280  chaperone protein DnaJ  Provisional.]---[PRK14279  PRK14279  chaperone protein DnaJ  Provisional.]---[PRK14276  PRK14276  chaperone protein DnaJ  Provisional.]---[PRK14299  PRK14299  chaperone protein DnaJ  Provisional.]---[PRK14277  PRK14277  chaperone protein DnaJ  Provisional.]---[PRK14282  PRK14282  chaperone protein DnaJ  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0020480.1",565294,"test43315.tree",1,0.6735,"high",1,0.7375,"high",1353,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0020860.1",565332,"test153492.tree",1,1,"high",1,1,"high",836,"B7FRU7","Lipoyl synthase 1  mitochondrial","PLN02428]---[PLN02428]---[PTZ00413]---[PTZ00413]---[COG0320]---[COG0320]---[PRK05481]---[PRK05481]---[TIGR00510]---[TIGR00510]---[PRK12928]---[PRK12928]---[pfam04055]---[smart00729]---[cd01335","PLN02428  PLN02428  lipoic acid synthase.]---[PTZ00413  PTZ00413  lipoate synthase  Provisional.]---[COG0320  LipA  Lipoate synthase  Coenzyme metabolism .]---[PRK05481  PRK05481  lipoyl synthase  Provisional.]---[TIGR00510  Lipoyl_synthase  lipoate synthase. This enzyme is an iron-sulfur protein. It is localized to mitochondria in yeast and Arabidopsis. It generates lipoic acid  a thiol antioxidant that is linked to a specific Lys as prosthetic group for the pyruvate and alpha-ketoglutarate dehydrogenase complexes and the glycine-cleavage system. The family shows strong sequence conservation.  Biosynthesis of cofactors  prosthetic groups  and carriers  Lipoate .]---[PRK12928  PRK12928  lipoyl synthase  Provisional.]---[pfam04055  Radical_SAM  Radical SAM superfamily. Radical SAM proteins catalyse diverse reactions  including unusual methylations  isomerization  sulphur insertion  ring formation  anaerobic oxidation and protein radical formation.]---[smart00729  Elp3  Elongator protein 3  MiaB family  Radical SAM.  This superfamily contains MoaA  NifB  PqqE  coproporphyrinogen III oxidase  biotin synthase and MiaB families  and includes a representative in the eukaryotic elongator subunit  Elp-3. Some members of the family are methyltransferases.]---[cd01335  Radical_SAM  Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif  which coordinates the conserved iron-sulfur cluster. Mechanistically  they share the transfer of a single electron from the iron-sulfur cluster to SAM  which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical  which  in turn  abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme  SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism  DNA repair  the biosynthesis of vitamins and coenzymes  and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB)  lipoyl synthase (LipA)  pyruvate formate-lyase (PFL)  coproporphyrinogen oxidase (HemN)  lysine 2 3-aminomutase (LAM)  anaerobic ribonucleotide reductase (ARR)  and MoaA  an enzyme of the biosynthesis of molybdopterin."]
["PSNMU-V1.4_AUG-EV-PASAV3_0021870.1",565515,"test4872.tree",0.874,0.749288461538461,"high",0.911,0.779,"high",1371,"Q54TS4","Protein YIPF1 homolog","pfam04893","pfam04893  Yip1  Yip1 domain. The Yip1 integral membrane domain contains four transmembrane alpha helices. The domain is characterized by the motifs DLYGP and GY. The Yip1 protein is a golgi protein involved in vesicular transport that interacts with GTPases."]
["PSNMU-V1.4_AUG-EV-PASAV3_0023430.1",565577,"test3687.tree",0.821,0.691746268656716,"high",0.548,0.684641791044776,"high",2535,"Q9LFT9","Ras-related protein RABH1e","cd01861]---[smart00175]---[cd00154]---[pfam00071]---[cd01860]---[PTZ00099]---[cd04123]---[cd01868]---[cd01863]---[cd01867]---[cd01864]---[cd01869]---[cd04113]---[pfam02263]---[cd00876]---[cd01866]---[cd01865]---[cd04111]---[cd01862]---[cd04122",{"$cut":{"chars":22099,"head":"cd01861  Rab6  Rab GTPase family 6 (Rab6). Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack  and is also required for a slow  COPI-independent  retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p  the homolog of the mammalian Rab6 GTPase  is not essential for cell viability. Ypt6p acts in endosome-to-Golgi  in intra-Golgi retrograde transport  and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs)  which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus  with sequence motifs CC  CXC  or CCX. Lipid binding is essential for membrane attachment  a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD  the lipid modification site is not available for annotation.]---[smart00175  RAB  Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.]---[cd00154  Rab  Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases). Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome  and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small  monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes  where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form  Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors  Rab GTPases regulate vesicle formation  actin- and tubulin-dependent vesicle movement  and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs)  which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members  several have been found to possess 60 or more Rabs  for many of these Rab isoforms  homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus  with sequence motifs CC  CXC  or CCX. Lipid binding is essential for membrane attachment  a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues  the lipid modification site is not available for annotation in many of the CDs in the hierarchy  but is included where possible.]---[pfam00071  Ras  Ras family. Includes sub-families Ras  Rab  Rac  Ral  Ran  Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU  arf and myosin_head. See pfam00009 pfam00025  pfam00063. As regards Rab GTPases  these are important regulators of vesicle formation  motility and fusion. They share a fold in common with all Ras GTPases  this is a six-stranded beta-sheet surrounded by five alpha-helices.]---[cd01860  Rab5_related  Rab-related GTPase family includes Rab5 and Rab22  regulates early endosome fusion. The Rab5-related subfamily includes Rab5 and Rab22 of mammals  Ypt51/Ypt52/Ypt53 of yeast  and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals  Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early en"}}]
["PSNMU-V1.4_AUG-EV-PASAV3_0024150.1",565648,"test58600.tree",1,0.71775,"high",1,0.71425,"high",3797,"Q9FNS4","PsbB mRNA maturation factor Mbb1  chloroplastic","TIGR02917]---[TIGR02917]---[TIGR02917]---[TIGR02917]---[sd00006]---[sd00006]---[sd00006]---[sd00006]---[sd00006]---[COG0457]---[TIGR02521]---[pfam13414]---[COG3063]---[TIGR00990]---[PRK11788","TIGR02917  TPR_domain_protein  putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system  analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction  possibly for the regulation of PEP-CTERM protein expression  since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.]---[sd00006  TPR  Tetratricopeptide repeat. The Tetratricopeptide repeat (TPR) typically contains 34 amino acids and is found in a variety of organisms including bacteria  cyanobacteria  yeast  fungi  plants  and humans. It is present in a variety of proteins including those involved in chaperone  cell-cycle  transcription  and protein transport complexes. The number of TPR motifs varies among proteins. Those containing 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accommodate an alpha-helix of a target protein. It has been proposed that TPR proteins preferentially interact with WD-40 repeat proteins  but in many instances several TPR-proteins seem to aggregate to multi-protein complexes.]---[COG0457  NrfG  FOG  TPR repeat  General function prediction only .]---[TIGR02521  Uncharacterized_protein_HI_0366  type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF and PilW. This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.]---[pfam13414  TPR_11  TPR repeat. ]---[COG3063  PilF  Tfp pilus assembly protein PilF  Cell motility and secretion / Intracellular trafficking and secretion .]---[TIGR00990  Mitochondrial_import_receptor_subunit_TOM70  mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).   Transport and binding proteins  Amino acids  peptides and amines .]---[PRK11788  PRK11788  tetratricopeptide repeat protein  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0025120.1",565743,"test49623.tree",1,0.7308,"high",1,0.6444,"high",1117,"B8ELF8","50S ribosomal protein L22","pfam00237]---[cd00336]---[COG0091]---[PRK00565]---[TIGR01044","pfam00237  Ribosomal_L22  Ribosomal protein L22p/L17e. This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes.]---[cd00336  Ribosomal_L22  Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit.  It is the only ribosomal protein that interacts with all six domains of 23S rRNA  and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel  the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.]---[COG0091  RplV  Ribosomal protein L22  Translation  ribosomal structure and biogenesis .]---[PRK00565  rplV  50S ribosomal protein L22  Reviewed.]---[TIGR01044  50S_ribosomal_protein_L22  ribosomal protein L22  bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.  Protein synthesis  Ribosomal proteins  synthesis and modification ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0027330.1",565960,"test43247.tree",0.891,0.804166666666667,"high",0.944,0.8085,"high",2335,"P61869","Mono- and diacylglycerol lipase","cd00519]---[pfam01764]---[cd00741]---[PLN02847","cd00519  Lipase_3  Lipase (class 3). Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides  glycerol  and free fatty acids at a water/lipid interface. A typical feature of lipases is  interfacial activation   the process of becoming active at the lipid/water interface  although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu  but unlike most serine proteases  the active site is buried inside the structure. A  lid  or  flap  covers the active site  making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation  allowing the lipid substrate access to the active site. .]---[pfam01764  Lipase_3  Lipase (class 3). ]---[cd00741  Lipase  Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides  glycerol  and free fatty acids at a water/lipid interface.  A typical feature of lipases is  interfacial activation   the process of becoming active at the lipid/water interface  although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu  but unlike most serine proteases  the active site is buried inside the structure. A  lid  or  flap  covers the active site  making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation  allowing the lipid substrate access to the active site.]---[PLN02847  PLN02847  triacylglycerol lipase."]
["PSNMU-V1.4_AUG-EV-PASAV3_0027530.1",565980,"test5795.tree",0.992,0.753866666666667,"high",0.986,0.770244444444444,"high",1662,"Q94AG6","S-adenosylmethionine carrier 1  chloroplastic/mitochondrial","pfam00153]---[pfam00153]---[pfam00153]---[PTZ00168]---[PTZ00169","pfam00153  Mito_carr  Mitochondrial carrier protein. ]---[PTZ00168  PTZ00168  mitochondrial carrier protein  Provisional.]---[PTZ00169  PTZ00169  ADP/ATP transporter on adenylate translocase  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0027740.1",566001,"test5796.tree",0.823,0.736244444444444,"high",0.8,0.711377777777778,"high",1786,"Q9JJ80","Ribosome production factor 2 homolog","COG5106]---[pfam04427]---[smart00879","COG5106  RPF2  Uncharacterized conserved protein  Function unknown .]---[pfam04427  Brix  Brix domain. ]---[smart00879  Brix  The Brix domain is found in a number of eukaryotic proteins. Members include SSF proteins from yeast and humans  Arabidopsis thaliana Peter Pan-like protein and several hypothetical proteins."]
["PSNMU-V1.4_AUG-EV-PASAV3_0027780.1",566005,"test70888.tree",1,0.666666666666667,"high",1,0.666666666666667,"high",3269,"-","-","cd00020","cd00020  ARM  Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo  these repeats were also found in the mammalian armadillo homolog beta-catenin  the junctional plaque protein plakoglobin  the adenomatous polyposis coli (APC) tumor suppressor protein  and a number of other proteins. ARM has been implicated in mediating protein-protein interactions  but no common features among the target proteins recognized by the ARM repeats have been identified  related to the HEAT domain  three consecutive copies of the repeat are represented by this alignment model."]
["PSNMU-V1.4_AUG-EV-PASAV3_0028250.1",566052,"test9138.tree",0.215,0.805566666666667,"medium",0.999,0.776233333333333,"high",1336,"Q5ZKP7","Solute carrier family 25 member 36","pfam00153]---[pfam00153]---[pfam00153]---[PTZ00169]---[PTZ00169]---[PTZ00168","pfam00153  Mito_carr  Mitochondrial carrier protein. ]---[PTZ00169  PTZ00169  ADP/ATP transporter on adenylate translocase  Provisional.]---[PTZ00168  PTZ00168  mitochondrial carrier protein  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0028590.1",566085,"test37971.tree",1,0.694,"high",1,0.788571428571428,"high",1871,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0031660.1",566383,"test23311.tree",0.869,0.7895,"high",0.843,0.795666666666667,"high",1154,"Q6FU96","2 5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase","COG1985]---[TIGR00227]---[pfam01872]---[TIGR00326]---[PRK05625]---[TIGR01508","COG1985  RibD  Pyrimidine reductase  riboflavin biosynthesis  Coenzyme metabolism .]---[TIGR00227  ribD_Cterm  riboflavin-specific deaminase C-terminal domain. Eubacterial riboflavin-specific deaminases have a zinc-binding domain recognized by the dCMP_cyt_deam model toward the N-terminus and this domain toward the C-terminus. Yeast HTP reductase  a riboflavin-biosynthetic enzyme  and several archaeal proteins believed related to riboflavin biosynthesis consist only of this domain and lack the dCMP_cyt_deam domain.]---[pfam01872  RibD_C  RibD C-terminal domain. The function of this domain is not known  but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG  in combination with pfam00383  as well as in isolation in some archaebacterial proteins. This family appears to be related to pfam00186.]---[TIGR00326  eubact_ribD  riboflavin biosynthesis protein RibD.  This model describes the ribD protein as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region captured in the model dCMP_cyt_deam and shared by proteins such as cytosine deaminase  mammalian apolipoprotein B mRNA editing protein  blasticidin-S deaminase  and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase  a protein required for riboflavin biosynthesis. A number of archaeal proteins believed related to riboflavin biosynthesis contain only this C-terminal domain and are not found as full-length matches to this model.  Biosynthesis of cofactors  prosthetic groups  and carriers  Riboflavin  FMN  and FAD .]---[PRK05625  PRK05625  5-amino-6-(5-phosphoribosylamino)uracil reductase  Validated.]---[TIGR01508  rib_reduct_arch  2 5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1'-reductase  archaeal. This model represents a specific reductase of riboflavin biosynthesis in the Archaea  diaminohydroxyphosphoribosylaminopyrimidine reductase. It should not be confused with bacterial 5-amino-6-(5-phosphoribosylamino)uracil reductase. The intermediate 2 5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine in riboflavin biosynthesis is reduced first  and then deaminated  in both Archaea and Fungi  opposite the order in Bacteria. The subsequent deaminase is not presently known and is not closely homologous to the deaminase domain (3.5.4.26) fused to the reductase domain (1.1.1.193) similar to this protein but found in most bacteria."]
["PSNMU-V1.4_AUG-EV-PASAV3_0031900.1",566406,"test30420.tree",1,0.851111111111111,"high",1,0.819666666666667,"high",3405,"Q86GL4","Superoxide-generating NADPH oxidase heavy chain subunit B","cd06186]---[PLN02844]---[PLN02631]---[COG4097]---[cd00322]---[cd06198]---[pfam08022]---[PLN02292]---[cd06187]---[cd06189]---[COG0543]---[COG1018]---[PRK00054]---[cd06212]---[cd06192","cd06186  NOX_Duox_like_FAD_NADP  NADPH oxidase (NOX) catalyzes the generation of reactive oxygen species (ROS) such as superoxide and hydrogen peroxide. ROS were originally identified as bactericidal agents in phagocytes  but are now also implicated in cell signaling and metabolism. NOX has a 6-alpha helix heme-binding transmembrane domain fused to a flavoprotein with the nucleotide binding domain located in the cytoplasm. Duox enzymes link a peroxidase domain to the NOX domain via a single transmembrane and EF-hand Ca2  binding sites. The flavoprotein module has a ferredoxin like FAD/NADPH binding domain. In classical phagocytic NOX2  electron transfer occurs from NADPH to FAD to the heme of cytb to oxygen leading to superoxide formation.]---[PLN02844  PLN02844  oxidoreductase/ferric-chelate reductase.]---[PLN02631  PLN02631  ferric-chelate reductase.]---[COG4097  COG4097  Predicted ferric reductase  Inorganic ion transport and metabolism .]---[cd00322  FNR_like  Ferredoxin reductase (FNR)  an FAD and NAD(P) binding protein  was intially identified as a chloroplast reductase activity  catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP  as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP  to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation  dinitrogen fixation  steroid hydroxylation  fatty acid metabolism  oxygenase activity  and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized  semiquinone (one- electron reduced)  or fully reduced hydroquinone forms  FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H).]---[cd06198  FNR_like_3  NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain  which varies in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP  reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP  to NADPH.]---[pfam08022  FAD_binding_8  FAD-binding domain. ]---[PLN02292  PLN02292  ferric-chelate reductase.]---[cd06187  O2ase_reductase_like  The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an  2FE-2S  ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate  while mono-oxygenases (aka mixed oxygenases) add one atom to the substrate and one atom to water. In dioxygenases  Class I enzymes are 2 component  containing a reductase with Rieske type   2Fe-2S  redox centers and an oxygenase. Class II are 3 component  having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2  2Fe-2S  centers  one fused to the flavin domain and the other separate.]---[cd06189  flavin_oxioreductase  NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases  but with only 15  sequence identity  flavin reductases reduce FAD  FMN  or riboflavin via NAD(P)H. Flavin is used as a substrate  rather than a tightly bound prosthetic group as in flavoenzymes  weaker binding is due to the absence of a binding site for the AMP moeity of FAD.]---[COG0543  UbiB  2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases  Coenzyme metabolism / Energy production and conversion .]---[COG1018  Hmp  Flavodoxin reductases (ferredoxin-NADPH reductases) family 1  Energy production and conversion .]---[PRK00054  PRK00054  dihydroorotate dehydrogenase electron transfer subunit  Reviewed.]---[cd06212  monooxygenase_like  The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is incorportated into the aromatic compond  while the other is used to form a molecule of water. In contrast dioxygenases add both atoms of oxygen to the substrate.]---[cd06192  DHOD_e_trans_like  FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD . In L. lactis  DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity  as well as NAD binding. NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP  reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP  to NADPH."]
["PSNMU-V1.4_AUG-EV-PASAV3_0033410.1",566554,"test33902.tree",1,0.647375,"high",1,0.6185,"high",1137,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0034570.1",566666,"test3750.tree",0.898,0.776348484848485,"high",0.807,0.741454545454545,"high",1333,"Q3UMZ3","Phosphatidate phosphatase PPAPDC1B","cd03390]---[cd03384]---[cd01610]---[pfam01569]---[PLN02250","cd03390  PAP2_containing_1_like  PAP2  subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both diacylglycerol pyrophosphate phosphatase activity as well as phosphatidate (PA) phosphatase activity  they may have a more generic housekeeping role in lipid metabolism.]---[cd03384  PAP2_wunen  PAP2  wunen subfamily. Most likely a family of membrane associated phosphatidic acid phosphatases. Wunen is a drosophila protein expressed in the central nervous system  which provides repellent activity towards primordial germ cells (PGCs)  controls the survival of PGCs and is essential in the migration process of these cells towards the somatic gonadal precursors.]---[cd01610  PAP2_like  PAP2_like proteins  a super-family of histidine phosphatases and vanadium haloperoxidases  includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP)  Glucose-6-phosphatase  Phosphatidylglycerophosphatase B and bacterial acid phosphatase  vanadium chloroperoxidases  vanadium bromoperoxidases  and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins.]---[pfam01569  PAP2  PAP2 superfamily. This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2)  Glucose-6-phosphatase EC 3.1.3.9  Phosphatidylglycerophosphatase B EC 3.1.3.27 and bacterial acid phosphatase EC 3.1.3.2. The family also includes a variety of haloperoxidases that function by oxidizing halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.]---[PLN02250  PLN02250  lipid phosphate phosphatase."]
["PSNMU-V1.4_AUG-EV-PASAV3_0035070.1",566713,"test5960.tree",0.341,0.709340909090909,"medium",0.673,0.728272727272727,"high",1907,"Q9SH88","Ribosome biogenesis regulatory protein homolog","pfam04939]---[COG5225","pfam04939  RRS1  Ribosome biogenesis regulatory protein (RRS1).  This family consists of several eukaryotic ribosome biogenesis regulatory (RRS1) proteins. RRS1 is a nuclear protein that is essential for the maturation of 25 S rRNA and the 60 S ribosomal subunit assembly in Saccharomyces cerevisiae.]---[COG5225  RRS1  Uncharacterized protein involved in ribosome biogenesis  Translation  ribosomal structure and biogenesis ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0035500.1",566744,"test4766.tree",0.377,0.820301886792453,"medium",0.583,0.823433962264151,"high",3212,"Q6Z382","Coatomer subunit gamma-2","COG5240]---[pfam01602]---[pfam08752]---[COG5096","COG5240  SEC21  Vesicle coat complex COPI  gamma subunit  Intracellular trafficking and secretion .]---[pfam01602  Adaptin_N  Adaptin N terminal region. This family consists of the N terminal region of various alpha  beta and gamma subunits of the AP-1  AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family  and it has been proposed that this constant region interacts with another uniform component of the coated vesicles.]---[pfam08752  COP-gamma_platf  Coatomer gamma subunit appendage platform subdomain. COPI-coated vesicles function in retrograde transport from the Golgi to the ER  and in intra-Golgi transport. This is the platform subdomain of the coatomer gamma subunit appendage domain. It carries a protein-protein interaction site at UniProt P53620  residue W776  which in yeast binds to the ARFGAP Glo3p  and in mammalian gamma-COP binds to a Glo3p orthologue  ARFGAP2.]---[COG5096  COG5096  Vesicle coat complex  various subunits  Intracellular trafficking and secretion ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0038230.1",567191,"test7985.tree",0.832,0.679029411764706,"high",0.78,0.687970588235294,"high",1668,"A8XLW0","Golgi SNAP receptor complex member 1","pfam12352]---[cd15864","pfam12352  V-SNARE_C  Snare region anchored in the vesicle membrane C-terminus. Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion  whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the vesicle pfam05008.]---[cd15864  SNARE_GS28  SNARE motif of GS28. GS28 (also known as golgi SNAP receptor complex member 1 or GOSR1) forms complexes with syntaxin-5 (Qa)  Ykt6 (R-SNARE) and either Bet1 (Qc) or GS15 (Qc). These complexes regulate the early secretory pathway of eukaryotic cells at the level of the transport from the ER-Golgi intermediate compartment (ERGIC) to the cis-Golgi and transport from the trans-Golgi network to the cis-Golgi  respectively. GS28 is a member of the Qb subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins which contain coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins  and a transmembrane domain. The SNARE complex mediates membrane fusion  important for trafficking of newly synthesized proteins  recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups  Qa-  Qb-  Qc- and R-SNAREs  depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-  as well as Qb- and Qc-SNAREs  are localized to target organelle membranes  while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup  that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles."]
["PSNMU-V1.4_AUG-EV-PASAV3_0038400.1",567122,"test18798.tree",0.812,0.843666666666667,"high",0.805,0.840133333333333,"high",1036,"-","-","cd03424]---[pfam00293","cd03424  ADPRase_NUDT5  ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily  it requires a divalent cation  such as Mg2   for its activity. It also contains a highly conserved 23-residue Nudix motif (GX5EX7REUXEEXGU  where U   I  L or V) which functions as a metal binding site/catalytic site. In addition to the Nudix motif  there are additional conserved amino acid residues  distal from the signature sequence  that correlate with substrate specificity. In humans  there are four distinct ADPRase activities  three putative cytosolic enzymes (ADPRase-I  -II  and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirement for metal ions. NUDT5 forms a homodimer.]---[pfam00293  NUDIX  NUDIX domain. "]
["PSNMU-V1.4_AUG-EV-PASAV3_0038570.1",567137,"test7730.tree",0.795,0.781542857142857,"high",0.848,0.737571428571429,"high",3125,"Q4IJT0","Dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1 3-glucosyltransferase","pfam03155]---[cd15568]---[cd15568]---[cd15568]---[cd15532]---[cd15532]---[cd15532]---[cd15567]---[cd15567]---[cd15567]---[cd15539]---[cd15539]---[cd15539]---[pfam00628]---[pfam00628]---[pfam00628]---[cd15522]---[cd15522]---[cd15522]---[cd15656]---[cd15656]---[smart00249]---[smart00249]---[cd15523]---[cd15523]---[cd15545]---[cd15545]---[cd15529]---[cd15529]---[cd15544]---[cd15489]---[cd15489]---[cd15519]---[cd15519]---[cd15533]---[cd15533]---[cd15541]---[cd15541]---[cd15536]---[cd15536]---[cd15492]---[cd15658",{"$cut":{"chars":22352,"head":"pfam03155  Alg6_Alg8  ALG6  ALG8 glycosyltransferase family.  N-linked (asparagine-linked) glycosylation of proteins is mediated by a highly conserved pathway in eukaryotes  in which a lipid (dolichol phosphate)-linked oligosaccharide is assembled at the endoplasmic reticulum membrane prior to the transfer of the oligosaccharide moiety to the target asparagine residues. This oligosaccharide is composed of Glc(3)Man(9)GlcNAc(2). The addition of the three glucose residues is the final series of steps in the synthesis of the oligosaccharide precursor. Alg6 transfers the first glucose residue  and Alg8 transfers the second one. In the human alg6 gene  a C- T transition  which causes Ala333 to be replaced with Val  has been identified as the cause of a congenital disorder of glycosylation  designated as type Ic OMIM 603147.]---[cd15568  PHD5_NSD  PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins. The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases  NSD1  NSD2/MMSET/WHSC1  and NSD3/WHSC1L1  that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36  and they play non-redundant roles during development. NSD1 plays a role in several pathologies  including but not limited to Sotos and Weaver syndromes  acute myeloid leukemia  breast cancer  neuroblastoma  and glioblastoma formation. NSD2 is involved in cancer cell proliferation  survival  and tumor growth  by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover  translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation  enhancer of zeste and trithorax (SET) domain  two proline-tryptophan-tryptophan-proline (PWWP) domains  five plant homeodomain (PHD) fingers  and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.]---[cd15532  PHD2_CHD_II  PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins. Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3  CHD4  and CHD5  which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling  DSB repair and/or p53-dependent pathways such as apoptosis and senescence  as well as in the maintenance of genomic stability  and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex  which is generally associated with gene repression  heterochromatin formation  and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2)  class II CHD proteins lack identifiable DNA-binding domains  but possess a C-terminal coiled-coil region. Moreover  in addition to the tandem chromodomains and a helicase domain  they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.]---[cd15567  PHD4_NSD  PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins. The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases  NSD1  NSD2/MMSET/WHSC1  and NSD3/WHSC1L1  that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36  and they play non-redundant roles during development. NSD1 plays a role in several pathologies  including but not limited to Sotos and Weaver syndromes  acute myeloid leukemia  breast cancer  neuroblastoma  and glioblastoma formation. NSD2 is involved in cancer cell proliferation  survival  and tumor growth  "}}]
["PSNMU-V1.4_AUG-EV-PASAV3_0042340.1",567388,"test21805.tree",0.961,0.868923076923077,"high",0.968,0.867923076923077,"high",2047,"Q6EIG3","Cytochrome P450 26B1","COG2124]---[pfam00067]---[PLN02987]---[PLN03141]---[PLN02302]---[PTZ00404]---[PLN02738]---[PLN02774]---[PLN02936]---[PLN02196]---[PLN03112","COG2124  CypX  Cytochrome P450  Secondary metabolites biosynthesis  transport  and catabolism .]---[pfam00067  p450  Cytochrome P450. Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes  according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander'  a four-helix bundle  helices J and K  and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron)  the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins  most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures.]---[PLN02987  PLN02987  Cytochrome P450  family 90  subfamily A.]---[PLN03141  PLN03141  3-epi-6-deoxocathasterone 23-monooxygenase  Provisional.]---[PLN02302  PLN02302  ent-kaurenoic acid oxidase.]---[PTZ00404  PTZ00404  cytochrome P450  Provisional.]---[PLN02738  PLN02738  carotene beta-ring hydroxylase.]---[PLN02774  PLN02774  brassinosteroid-6-oxidase.]---[PLN02936  PLN02936  epsilon-ring hydroxylase.]---[PLN02196  PLN02196  abscisic acid 8'-hydroxylase.]---[PLN03112  PLN03112  cytochrome P450 family protein  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0042850.1",567439,"test25348.tree",0.71,0.687090909090909,"high",0.803,0.677,"high",1307,"Q9A706","Ribosome-recycling factor","pfam01765]---[cd00520]---[COG0233]---[PRK00083]---[TIGR00496","pfam01765  RRF  Ribosome recycling factor. The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation  and is essential bacterial growth. Thus ribosomes are  recycled  and ready for another round of protein synthesis.]---[cd00520  RRF  Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex  composed of the ribosome  deacylated tRNA  and mRNA  after termination of translation. Thus ribosomes are  recycled  and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA  but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes  but is found in mitochondria or chloroplasts of some eukaryotic species.]---[COG0233  Frr  Ribosome recycling factor  Translation  ribosomal structure and biogenesis .]---[PRK00083  frr  ribosome recycling factor  Reviewed.]---[TIGR00496  Ribosome-recycling_factor  ribosome recycling factor.  This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis  it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD 53116 YHR038W is part of the frr superfamily.  Protein synthesis  Translation factors ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0042900.1",567444,"test3228.tree",0.858,0.713155844155844,"high",0.847,0.760662337662338,"high",2559,"Q9NRN9","Methyltransferase-like protein 5","COG2263]---[COG2263","COG2263  COG2263  Predicted RNA methylase  Translation  ribosomal structure and biogenesis ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0047250.1",567969,"test70584.tree",1,0.554333333333333,"high",1,0.589666666666667,"high",1293,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0048010.1",567936,"test7236.tree",0.367,0.699756756756757,"medium",0.557,0.682675675675676,"high",1642,"Q556Y9","Mitotic spindle assembly checkpoint protein MAD2A","pfam02301","pfam02301  HORMA  HORMA domain. The HORMA (for Hop1p  Rev7p and MAD2) domain has been suggested to recognize chromatin states that result from DNA adducts  double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity."]
["PSNMU-V1.4_AUG-EV-PASAV3_0048100.1",567945,"test14119.tree",0.994,0.88875,"high",0.993,0.85435,"high",1277,"Q1PF33","Mitochondrial import inner membrane translocase subunit TIM44-1","TIGR00984]---[pfam04280]---[smart00978","TIGR00984  3a0801s03tim44  mitochondrial import inner membrane  translocase subunit. The mitochondrial protein translocase (MPT) family  which brings nuclearly encoded preproteins into mitochondria  is very complex with 19 currently identified protein constituents.These proteins include several chaperone proteins  four proteins of the outer membrane translocase (Tom) import receptor  five proteins of the Tom channel complex  five proteins of the inner membrane translocase (Tim) and three  motor  proteins. This family is specific for the Tim proteins.  Transport and binding proteins  Amino acids  peptides and amines .]---[pfam04280  Tim44  Tim44-like domain. Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region. This family includes the C-terminal region of Tim44 that has been shown to form a stable proteolytic fragment in yeast. This region is also found in a set of smaller bacterial proteins. The molecular function of the bacterial members of this family is unknown but transport seems likely. The crystal structure of the C terminal of Tim44 has revealed a large hydrophobic pocket which might play an important role in interacting with the acyl chains of lipid molecules in the mitochondrial membrane.]---[smart00978  Tim44  Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region."]
["PSNMU-V1.4_AUG-EV-PASAV3_0048200.1",567955,"test7712.tree",0.828,0.657171428571429,"high",0.789,0.697971428571428,"high",428,"O65154","RNA polymerase II transcriptional coactivator KIWI","pfam02229","pfam02229  PC4  Transcriptional Coactivator p15 (PC4). p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain."]
["PSNMU-V1.4_AUG-EV-PASAV3_0048350.1",567992,"test2730.tree",0.651,0.798489130434783,"high",0.638,0.813152173913044,"high",2183,"Q9LR30","Glutamate--glyoxylate aminotransferase 1","PTZ00377]---[PLN02231]---[PLN02368]---[COG0436]---[PRK09265]---[cd00609]---[PRK08363]---[PRK13355]---[PRK07568]---[PRK06855]---[TIGR01265]---[pfam00155]---[PRK06108]---[PRK05764]---[PRK05764]---[PLN02450]---[PLN02187]---[PLN00145]---[TIGR01264]---[PLN00143]---[PLN02656","PTZ00377  PTZ00377  alanine aminotransferase  Provisional.]---[PLN02231  PLN02231  alanine transaminase.]---[PLN02368  PLN02368  alanine transaminase.]---[COG0436  COG0436  Aspartate/tyrosine/aromatic aminotransferase  Amino acid transport and metabolism .]---[PRK09265  PRK09265  aminotransferase AlaT  Validated.]---[cd00609  AAT_like  Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate  which depending on the reaction  is the substrate in four kinds of reactions (1) transamination (movement of amino groups)  (2) racemization (redistribution of enantiomers)  (3) decarboxylation (removing COOH groups)  and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha  beta and gamma classes  based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes  and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. The major groups in this CD corresponds to Aspartate aminotransferase a  b and c  Tyrosine  Alanine  Aromatic-amino-acid  Glutamine phenylpyruvate  1-Aminocyclopropane-1-carboxylate synthase  Histidinol-phosphate  gene products of malY and cobC  Valine-pyruvate aminotransferase and Rhizopine catabolism regulatory protein.]---[PRK08363  PRK08363  alanine aminotransferase  Validated.]---[PRK13355  PRK13355  bifunctional HTH-domain containing protein/aminotransferase  Provisional.]---[PRK07568  PRK07568  aspartate aminotransferase  Provisional.]---[PRK06855  PRK06855  aminotransferase  Validated.]---[TIGR01265  tyrosine_aminotransferase  tyrosine/nicotianamine family aminotransferase. This subfamily of pyridoxal phosphate-dependent enzymes includes known examples of both tyrosine aminotransferase from animals and nicotianamine aminotransferase from barley.]---[pfam00155  Aminotran_1_2  Aminotransferase class I and II. ]---[PRK06108  PRK06108  aspartate aminotransferase  Provisional.]---[PRK05764  PRK05764  aspartate aminotransferase  Provisional.]---[PLN02450  PLN02450  1-aminocyclopropane-1-carboxylate synthase.]---[PLN02187  PLN02187  rooty/superroot1.]---[PLN00145  PLN00145  tyrosine/nicotianamine aminotransferase  Provisional.]---[TIGR01264  tyrosine_aminotransferase  tyrosine aminotransferase  eukaryotic. This model describes tyrosine aminotransferase as found in animals and Trypanosoma cruzi. It is the first enzyme of a pathway of tyrosine degradation via homogentisate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase  an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway. These plant sequences are excluded from the model seed and score between the trusted an noise cutoffs.  Energy metabolism  Amino acids and amines .]---[PLN00143  PLN00143  tyrosine/nicotianamine aminotransferase  Provisional.]---[PLN02656  PLN02656  tyrosine transaminase."]
["PSNMU-V1.4_AUG-EV-PASAV3_0048640.1",568020,"test3684.tree",0.946,0.82834328358209,"high",0.366,0.830701492537314,"medium",4522,"Q8VHK9","ATP-dependent RNA helicase DHX36","COG1643]---[COG1643]---[TIGR01967]---[TIGR01967]---[PRK11131]---[PRK11131]---[TIGR01970]---[TIGR01970]---[PRK11664]---[PRK11664]---[cd00046]---[smart00487]---[PHA02653]---[pfam07717]---[pfam04408]---[smart00847]---[pfam00271]---[smart00490]---[cd00079","COG1643  HrpA  HrpA-like helicases  DNA replication  recombination  and repair .]---[TIGR01967  ATP-dependent_RNA_helicase_HrpA  RNA helicase HrpA.  This model represents HrpA  one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long  while its paralog HrpB  also uncharacterized  is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB.  Unknown function  Enzymes of unknown specificity .]---[PRK11131  PRK11131  ATP-dependent RNA helicase HrpA  Provisional.]---[TIGR01970  ATP-dependent_RNA_helicase_HrpB  ATP-dependent helicase HrpB. This model represents HrpB  one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria  but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length  while its paralog HrpA (TIGR01967)  also uncharacterized  is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.  Unknown function  Enzymes of unknown specificity .]---[PRK11664  PRK11664  ATP-dependent RNA helicase HrpB  Provisional.]---[cd00046  DEXDc  DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.]---[smart00487  DEXDc  DEAD-like helicases superfamily. ]---[PHA02653  PHA02653  RNA helicase NPH-II  Provisional.]---[pfam07717  OB_NTP_bind  Oligonucleotide/oligosaccharide-binding (OB)-fold. This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself. The structure PDB 3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases  this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.]---[pfam04408  HA2  Helicase associated domain (HA2). This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown  however it seems likely to be involved in nucleic acid binding.]---[smart00847  HA2  Helicase associated domain (HA2) Add an annotation.  This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown  however it seems likely to be involved in nucleic acid binding.]---[pfam00271  Helicase_C  Helicase conserved C-terminal domain.  The Prosite family is restricted to DEAD/H helicases  whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit  but an integral part of the helicase.]---[smart00490  HELICc  helicase superfamily c-terminal domain. ]---[cd00079  HELICc  Helicase superfamily c-terminal domain  associated with DEXDc-  DEAD-  and DEAH-box proteins  yeast initiation factor 4A  Ski2p  and Hepatitis C virus NS3 helicases  this domain is found in a wide variety of helicases and helicase related proteins  may not be an autonomously folding unit  but an integral part of the helicase  4 helicase superfamilies at present according to the organization of their signature motifs  all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity  they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA  unwinding the duplex in the process."]
["PSNMU-V1.4_AUG-EV-PASAV3_0049140.1",568068,"test34251.tree",1,0.820875,"high",1,0.833125,"high",2091,"-","-","cd03398]---[PHA03307]---[PHA03247","cd03398  PAP2_haloperoxidase  PAP2  haloperoxidase_like subfamily. Haloperoxidases catalyze the oxidation of halides such as bromide or chloride by hydrogen peroxide  which results in subsequent halogenation of organic substrates  or halide-assisted disproportionation of hydrogen peroxide forming dioxygen. They are likely to participate in the biosynthesis of halogenated natural products  such as volatile halogenated hydrocarbons  chiral halogenated terpenes  acetogenins and indoles.]---[PHA03307  PHA03307  transcriptional regulator ICP4  Provisional.]---[PHA03247  PHA03247  large tegument protein UL36  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0049950.1",568145,"test27708.tree",1,0.8373,"high",1,0.842,"high",2738,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0050220.1",568236,"test1899.tree",0.346,0.82631884057971,"medium",0.291,0.809108695652174,"medium",2169,"P0DKC4","Phosphoglycolate phosphatase 1B  chloroplastic","PLN02645]---[TIGR01452]---[COG0647]---[TIGR01460]---[TIGR01457]---[pfam13344]---[PRK10444]---[pfam13242]---[cd01427]---[cd01427]---[TIGR01459","PLN02645  PLN02645  phosphoglycolate phosphatase.]---[TIGR01452  PGP_euk  phosphoglycolate/pyridoxal phosphate phosphatase family. PGP is an essential enzyme in the glycolate salvage pathway in higher organisms (photorespiration in plants). Phosphoglycolate results from the oxidase activity of RubisCO in the Calvin cycle when concentrations of carbon dioxide are low relative to oxygen. In mammals  PGP is found in many tissues  notably in red blood cells where P-glycolate is and important activator of the hydrolysis of 2 3-bisphosphoglycerate  a major modifier of the oxygen affinity of hemoglobin. Pyridoxal phosphate (PLP  Vitamin B6) phosphatase is involved in the degradation of PLP in mammals and is widely distributed in human tissues including erythrocyes. The enzymes described here are members of the Haloacid dehalogenase superfamily of hydrolase enzymes (pfam00702). Unlike the bacterial PGP equivalog (TIGR01449)  which is a member of class (subfamily) I  these enzymes are members of class (subfamily) II. These two families have almost certainly arisen from convergent evolution (although these two ancestors may themselves have diverged from a more distant HAD superfamily progenitor). The primary seed sequence for this model comes from Chlamydomonas reinhardtii  a photosynthetic alga. The enzyme has been purified and characterized and these data are fully consistent with the assignment of function as a PGPase involved in photorespiration. The second seed  from Homo sapiens chromosome 22 has been characterized as a pyridoxal phosphatase. Biochemical characterization of partially purified PGP's from various tissues including red blood cells have been performed while one gene for PGP has been localized to chromosome 16p13.3. The sequence used here maps to chromosome 22. There is indeed a related gene on chromosome 16 (and it is expressed  since EST's are found) which shows 46  identity. The chromosome 16 gene is not in evidence in nraa but translated from the genomic sequence. The third seed  from C. elegans  is only supported by sequence similarity. This model is limited to eukaryotic species including S. pombe and S. cerevisiae  although several archaea score between the trusted and noise cutoffs. This model is closely related to a family of bacterial sequences including the E. coli NagD and B. subtilus AraL genes which are characterized by the ability to hydrolyze para-nitrophenylphosphate (pNPPases or NPPases). The chlamydomonas PGPase d.]---[COG0647  NagD  Predicted sugar phosphatases of the HAD superfamily  Carbohydrate transport and metabolism .]---[TIGR01460  Protein_nagD.  Haloacid Dehalogenase Superfamily Class (subfamily) IIA. This model represents one structural subclass of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The classes are defined based on the location and the observed or predicted fold of a so-called  capping domain   or the absence of such a domain. Class I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Class II consists of sequences in which the capping domain is found between the second and third motifs. Class III sequences have no capping domain in iether of these positions. The Class IIA capping domain is predicted by PSI-PRED to consist of a mixed alpha-beta fold with the basic pattern  Helix-Helix-Helix-Sheet-Helix-Loop-Sheet-Helix-Sheet-Helix. Presently  this subfamily encompasses a single equivalog model (TIGR01452) for the eukaryotic phosphoglycolate phosphatase  as well as four hypothetical equivalogs covering closely related sequences (TIGR01456 and TIGR01458 in eukaryotes  TIGR01457 in gram positive bacteria and TIGR01459 in gram negative bacteria). The Escherishia coli NagD gene and the Bacillus subtilus AraL gene are members of this subfamily but are not members of the any of the presently defined equivalogs within it. NagD is part of the NAG operon responsible for N-acetylglucosamine metabolism. The function of this gene is unknown. Genes from several organisms have been annotated as NagD  or NagD-like. However  without data on the presence of other members of this pathway  (such as in the case of Yersinia pestis) these assignments should not be given great weight. The AraL gene is similar  it is part of the L-arabinose operon  but the function is unknown. A gene from Halobacterium has been annotated as AraL  but no other Ara operon genes have been annotated. Many of the genes in this subfamily have been annotated as  pNPPase   4-nitrophenyl phosphatase  or  NPPase . These all refer to the same activity versus a common lab test compound used to determine phosphatase activity. There is no evidence that this activity is physiologically relevant.  Unknown function  Enzymes of unknown specificity .]---[TIGR01457  HAD-SF-IIA-hyp2  HAD-superfamily subfamily IIA hydrolase  TIGR01457. This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all gram positive (low-GC) bacteria. Sequences found in this model are annotated variously as related to NagD or 4-nitrophenyl phosphatase  and this hypothetical equivalog  of all of those within the Class IIA subfamily  is most closely related to the E. coli NagD enzyme and the PGP_euk equivalog (TIGR01452). However  there is presently no evidence that this hypothetical equivalog has the same function of either those.  Unknown function  Enzymes of unknown specificity .]---[pfam13344  Hydrolase_6  Haloacid dehalogenase-like hydrolase.  This family is part of the HAD superfamily.]---[PRK10444  PRK10444  UMP phosphatase  Provisional.]---[pfam13242  Hydrolase_like  HAD-hyrolase-like. ]---[cd01427  HAD_like  Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase  epoxide hydrolase  phosphoserine phosphatase  phosphomannomutase  phosphoglycolate phosphatase  P-type ATPase  and many others  all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain  and many also possess a small cap domain  the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.]---[TIGR01459  HAD-SF-IIA-hyp4  HAD-superfamily class IIA hydrolase  TIGR01459. This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all gram negative and primarily alpha proteobacteria. Only one sequence hase been annotated as other than  hypothetical.  That one  from Brucella  is annotated as related to NagD  but only by sequence similarity and should be treated with some skepticism. (See comments for Class IIA subfamily model)."]
["PSNMU-V1.4_AUG-EV-PASAV3_0051360.1",568281,"test7018.tree",0.629,0.79178947368421,"high",0.378,0.80428947368421,"medium",3128,"A7TSF4","tRNA m(4)X modification enzyme TRM13","pfam05206]---[pfam11722","pfam05206  TRM13  Methyltransferase TRM13. This is a family of eukaryotic proteins which are responsible for 2'-O-methylation of tRNA at position 4. TRM13 shows no sequence similarity to other known methyltransferases.]---[pfam11722  zf-TRM13_CCCH  CCCH zinc finger in TRM13 protein.  This domain is found at the N-terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain."]
["PSNMU-V1.4_AUG-EV-PASAV3_0052510.1",568395,"test5803.tree",0.708,0.850133333333333,"high",0.668,0.856311111111111,"high",3986,"F4J738","Importin beta-like SAD2 homolog","COG5656]---[COG5657]---[pfam08506","COG5656  SXM1  Importin  protein involved in nuclear import  Posttranslational modification  protein turnover  chaperones .]---[COG5657  CSE1  CAS/CSE protein involved in chromosome segregation  Cell division and chromosome partitioning .]---[pfam08506  Cse1  Cse1. This domain is present in Cse1 nuclear export receptor proteins. Cse1 mediates the nuclear export of importin alpha. This domain contains HEAT repeats."]
["PSNMU-V1.4_AUG-EV-PASAV3_0052590.1",568403,"test70715.tree",1,0.656,"high",1,0.656333333333333,"high",1358,"Q0WRJ7","Peptidyl-prolyl cis-trans isomerase FKBP20-2  chloroplastic","pfam00254]---[COG0545]---[PRK10902","pfam00254  FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase. ]---[COG0545  FkpA  FKBP-type peptidyl-prolyl cis-trans isomerases 1  Posttranslational modification  protein turnover  chaperones .]---[PRK10902  PRK10902  FKBP-type peptidyl-prolyl cis-trans isomerase  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0053480.1",568490,"test58263.tree",1,0.724,"high",1,0.719,"high",1604,"Q9LNB6","Hsp70-Hsp90 organizing protein 1","sd00006]---[sd00006]---[PLN03088]---[pfam13414]---[pfam13414]---[TIGR00990]---[pfam00226]---[TIGR02917]---[TIGR02917]---[TIGR02917]---[cd06257]---[smart00271]---[COG0457","sd00006  TPR  Tetratricopeptide repeat. The Tetratricopeptide repeat (TPR) typically contains 34 amino acids and is found in a variety of organisms including bacteria  cyanobacteria  yeast  fungi  plants  and humans. It is present in a variety of proteins including those involved in chaperone  cell-cycle  transcription  and protein transport complexes. The number of TPR motifs varies among proteins. Those containing 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accommodate an alpha-helix of a target protein. It has been proposed that TPR proteins preferentially interact with WD-40 repeat proteins  but in many instances several TPR-proteins seem to aggregate to multi-protein complexes.]---[PLN03088  PLN03088  SGT1  suppressor of G2 allele of SKP1  Provisional.]---[pfam13414  TPR_11  TPR repeat. ]---[TIGR00990  Mitochondrial_import_receptor_subunit_TOM70  mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).   Transport and binding proteins  Amino acids  peptides and amines .]---[pfam00226  DnaJ  DnaJ domain. DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens  although not in Prosite are confirmed as DnaJ containing domains from literature.]---[TIGR02917  TPR_domain_protein  putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system  analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction  possibly for the regulation of PEP-CTERM protein expression  since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.]---[cd06257  DnaJ  DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation  folding  unfolding  translocation  and degradation. They act primarily by stimulating the ATPase activity of Hsp70s  an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain  which mediates the interaction with Hsp70. They may contain other domains as well  and the architectures provide a means of classification.]---[smart00271  DnaJ  DnaJ molecular chaperone homology domain. ]---[COG0457  NrfG  FOG  TPR repeat  General function prediction only ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0053590.1",568501,"test5370.tree",0.896,0.78525,"high",0.965,0.7700625,"high",2010,"Q9W088","DNA polymerase delta small subunit","cd07387]---[pfam04042","cd07387  MPP_PolD2_C  PolD2 (DNA polymerase delta  subunit 2)  C-terminal domain. PolD2 (DNA polymerase delta  subunit 2) is an auxiliary subunit of the eukaryotic DNA polymerase delta (PolD) complex thought to play a regulatory role and to serve as a scaffold for PolD assembly by interacting simultaneously with all of the other three subunits. PolD2 is catalytically inactive and lacks the active site residues required for phosphoesterase activity in other members of this superfamily.  PolD2 is also involved in the recruitment of several proteins regulating DNA metabolism  including p21  PDIP1  PDIP38  PDIP46  and WRN. Human PolD consists of four subunits  p125 (PolD1)  p50 (PolD2)  p66(PolD3)  and p12(PolD4).  PolD is one of three major replicases in eukaryotes. PolD also plays an essential role in translesion DNA synthesis  homologous recombination  and DNA repair. Within the PolD complex  PolD2 tightly associates with PolD3. PolD2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse  but share a conserved domain with an active site consisting of two metal ions (usually manganese  iron  or zinc) coordinated with octahedral geometry by a cage of histidine  aspartate  and asparagine residues. The MPP superfamily includes  Mre11/SbcD-like exonucleases  Dbr1-like RNA lariat debranching enzymes  YfcE-like phosphodiesterases  purple acid phosphatases (PAPs)  YbbF-like UDP-2 3-diacylglucosamine hydrolases  and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.]---[pfam04042  DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B. This family contains a number of DNA polymerase subunits.  The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition  DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse  the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure."]
["PSNMU-V1.4_AUG-EV-PASAV3_0053870.1",568529,"test5242.tree",0.968,0.706818181818182,"high",0.955,0.732204545454545,"high",1408,"O94760","N(G) N(G)-dimethylarginine dimethylaminohydrolase 1","COG1834]---[pfam02274]---[PRK01388]---[TIGR01078","COG1834  COG1834  N-Dimethylarginine dimethylaminohydrolase  Amino acid transport and metabolism .]---[pfam02274  Amidinotransf  Amidinotransferase. This family contains glycine (EC 2.1.4.1) and inosamine (EC 2.1.4.2) amidinotransferases  enzymes involved in creatine and streptomycin biosynthesis respectively. This family also includes arginine deiminases  EC 3.5.3.6. These enzymes catalyse the reaction  arginine   H2O     citrulline   NH3. Also found in this family is the Streptococcus anti tumor glycoprotein.]---[PRK01388  PRK01388  arginine deiminase  Provisional.]---[TIGR01078  Arginine_deiminase  arginine deiminase. Arginine deiminase is the first enzyme of the arginine deiminase pathway of arginine degradation.  Energy metabolism  Amino acids and amines ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0054540.1",568593,"test12671.tree",0.925,0.6765,"high",0.963,0.781863636363636,"high",2788,"Q02241","Kinesin-like protein KIF23","cd01368]---[smart00129]---[pfam00225]---[cd00106]---[cd01370]---[cd01366]---[cd01374]---[cd01364]---[cd01372]---[COG5059]---[cd01367]---[cd01365]---[cd01369]---[cd01376]---[cd01373]---[cd01371]---[cd01375]---[PLN03188]---[TIGR04523]---[TIGR04523]---[TIGR04523]---[TIGR04523]---[TIGR02169]---[TIGR02169",{"$cut":{"chars":20655,"head":"cd01368  KISc_KIF23_like  Kinesin motor domain  KIF23-like subgroup.  Kinesin motor domain  KIF23-like subgroup. Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins  the motor domain is found at the N-terminus (N-type). N-type kinesins are ( ) end-directed motors  i.e. they transport cargo towards the ( ) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second  and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that  kinesin head groups work in pairs. Upon replacing ADP with ATP  a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also  the neck linker binds to the motor domain  which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer  about 80 Angstroms along the microtubule. Meanwhile  ATP hydrolysis takes place  and when the second head domain binds to the microtubule  the first domain again replaces ADP with ATP  triggering a conformational change that pulls the first domain forward.]---[smart00129  KISc  Kinesin motor  catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.]---[pfam00225  Kinesin  Kinesin motor domain. ]---[cd00106  KISc  Kinesin motor domain. Kinesin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins  the motor domain is found at the N-terminus (N-type)  in some its is found in the middle (M-type)  or C-terminal (C-type). N-type and M-type kinesins are ( ) end-directed motors  while C-type kinesins are (-) end-directed motors  i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second  and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that  kinesin head groups work in pairs. Upon replacing ADP with ATP  a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also  the neck linker binds to the motor domain  which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer  about 80 Angstroms along the microtubule. Meanwhile  ATP hydrolysis takes place  and when the second head domain binds to the microtubule  the first domain again replaces ADP with ATP  triggering a conformational change that pulls the first domain forward.]---[cd01370  KISc_KIP3_like  Kinesin motor domain  KIP3-like subgroup.  Kinesin motor domain  KIP3-like subgroup. The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins  the motor domain is found at the N-terminus (N-type). N-type kinesins are ( ) end-directed motors  i.e. they transport cargo towards the ( ) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second  and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that  kinesin head groups work in pairs. Upon replacing ADP with ATP  a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also  the neck linker binds to the motor domain  which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer  about 80 Angstroms along the microtubule. Meanwhile  ATP hydrolysis takes place  and when the second head domain binds to the microtubule  the first domain"}}]
["PSNMU-V1.4_AUG-EV-PASAV3_0055870.1",568717,"test5372.tree",0.85,0.870625,"high",0.748,0.859229166666667,"high",4406,"Q9LF41","Probable ubiquitin conjugation factor E4","pfam10408]---[COG5113]---[pfam04564]---[smart00504","pfam10408  Ufd2P_core  Ubiquitin elongating factor core. This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4  running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit  the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus  pfam04564  which has ligase activity.]---[COG5113  UFD2  Ubiquitin fusion degradation protein 2  Posttranslational modification  protein turnover  chaperones .]---[pfam04564  U-box  U-box domain. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.]---[smart00504  Ubox  Modified RING finger domain. Modified RING finger domain  without the full complement of Zn2 -binding ligands. Probable involvement in E2-dependent ubiquitination."]
["PSNMU-V1.4_AUG-EV-PASAV3_0056450.1",568775,"test9513.tree",0.522,0.847551724137931,"high",0.626,0.874724137931035,"high",2491,"Q6GPQ3","Major facilitator superfamily domain-containing protein 8","cd06174]---[pfam07690]---[pfam07690","cd06174  MFS  The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters  symporters  and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions  sugar phosphates  drugs  neurotransmitters  nucleosides  amino acids  and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate  while symporters and antiporters transport two substrates in the same or in opposite directions  respectively  across membranes. MFS proteins are typically 400 to 600 amino acids in length  and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members  GlpT (glycerol-3-phosphate transporter)  LacY (lactose permease)  and EmrD (multidrug transporter)  MFS proteins are thought to function through a single substrate binding site  alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake  and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4  which is impaired in type II diabetes  and glucose-6-phosphate transporter (G6PT)  which causes glycogen storage disease when mutated.]---[pfam07690  MFS_1  Major Facilitator Superfamily. "]
["PSNMU-V1.4_AUG-EV-PASAV3_0057090.1",568893,"test33834.tree",1,0.728,"high",1,0.70425,"high",1864,"Q9SR77","Heme-binding-like protein At3g10130  chloroplastic","pfam04832","pfam04832  SOUL  SOUL heme-binding protein. This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues."]
["PSNMU-V1.4_AUG-EV-PASAV3_0058550.1",568979,"test33862.tree",1,0.85275,"high",1,0.8505,"high",3143,"Q55680","Uncharacterized protein sll0005","COG0661]---[cd05121]---[TIGR01982]---[cd13970]---[cd13969]---[pfam03109]---[PRK04750]---[cd13972]---[cd13971","COG0661  AarF  Predicted unusual protein kinase  General function prediction only .]---[cd05121  ABC1_ADCK3-like  Activator of bc1 complex (ABC1) kinases (also called aarF domain containing kinase 3) and similar proteins. This family is composed of the atypical yeast protein kinase Abc1p  its human homolog ADCK3 (also called CABC1)  and similar proteins. Abc1p (also called Coq8p) is required for the biosynthesis of Coenzyme Q (ubiquinone or Q)  which is an essential lipid component in respiratory electron and proton transport. It is necessary for the formation of a multi-subunit Q-biosynthetic complex and may also function in the regulation of Q synthesis. Human ADCK3 is able to rescue defects in Q synthesis and the phosphorylation state of Coq proteins in yeast Abc1 (or Coq8) mutants. Mutations in ADCK3 cause progressive cerebellar ataxia and atrophy due to Q10 deficiency. Eukaryotes contain at least two more ABC1/ADCK3-like proteins  in humans  these are the putative atypical protein kinases named ADCK1 and ADCK2. In algae and higher plants  ABC1 kinases have proliferated to more than 15 subfamilies  most of which are located in plastids or mitochondria. Eight of these plant ABC1 kinase subfamilies (ABC1K1-8) are specific for photosynthetic organisms. ABC1 kinases are not related to the ATP-binding cassette (ABC) membrane transporter family.]---[TIGR01982  Probable_protein_kinase_UbiB  2-polyprenylphenol 6-hydroxylase.  This model represents the enzyme (UbiB) which catalyzes the first hydroxylation step in the ubiquinone biosynthetic pathway in bacteria. It is believed that the reaction is 2-polyprenylphenol -  6-hydroxy-2-polyprenylphenol. This model finds hits primarily in the proteobacteria. The gene is also known as AarF in certain species.  Biosynthesis of cofactors  prosthetic groups  and carriers  Menaquinone and ubiquinone .]---[cd13970  ABC1_ADCK3  Activator of bc1 complex (ABC1) kinases  also called aarF domain containing kinase 3. This subfamily is composed of the atypical yeast protein kinase Abc1p  its human homolog ADCK3 (also called CABC1)  and similar proteins. Abc1p (also called Coq8p) is required for the biosynthesis of Coenzyme Q (ubiquinone or Q)  which is an essential lipid component in respiratory electron and proton transport. It is necessary for the formation of a multi-subunit Q-biosynthetic complex and may also function in the regulation of Q synthesis. Human ADCK3 is able to rescue defects in Q synthesis and the phosphorylation state of Coq proteins in yeast Abc1 (or Coq8) mutants. Mutations in ADCK3 cause progressive cerebellar ataxia and atrophy due to Q10 deficiency. In algae and higher plants  ABC1 kinases have proliferated to more than 15 subfamilies  most of which are located in plastids or mitochondria. Subfamily 13 (ABC1K13) of plant ABC1 kinases belongs in this subfamily with yeast Abc1p and human ADCK3. ABC1 kinases are not related to the ATP-binding cassette (ABC) membrane transporter family.]---[cd13969  ADCK1-like  aarF domain containing kinase 1 and similar proteins. This subfamily is composed of uncharacterized ABC1 kinase-like proteins including the human protein called aarF domain containing kinase 1 (ADCK1). Eukaryotes contain at least three ABC1-like proteins  in humans  these are ADCK3 and the putative protein kinases named ADCK1 and ADCK2. Yeast Abc1p and its human homolog ADCK3 are atypical protein kinases required for the biosynthesis of Coenzyme Q (ubiquinone or Q)  which is an essential lipid component in respiratory electron and proton transport. In algae and higher plants  ABC1 kinases have proliferated to more than 15 subfamilies  most of which are located in plastids or mitochondria. Plant subfamilies 14 and 15 (ABC1K14-15) belong to the same group of ABC1 kinases as human ADCK1. ABC1 kinases are not related to the ATP-binding cassette (ABC) membrane transporter family.]---[pfam03109  ABC1  ABC1 family. This family includes ABC1 from yeast and AarF from Escherichia coli. These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear  however yeast ABC1 suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex and Escherichia coli AarF is required for ubiquinone production. It has been suggested that members of the ABC1 family are novel chaperonins. These proteins are unrelated to the ABC transporter proteins.]---[PRK04750  ubiB  putative ubiquinone biosynthesis protein UbiB  Reviewed.]---[cd13972  UbiB  Ubiquinone biosynthetic protein UbiB. UbiB is the prokaryotic homolog of yeast Abc1p and human ADCK3 (aarF domain containing kinase 3). It is required for the biosynthesis of Coenzyme Q (ubiquinone or Q)  which is an essential lipid component in respiratory electron and proton transport. It is required in the first monooxygenase step in Q biosynthesis. Mutant strains with disrupted ubiB genes lack Q and accumulate octaprenylphenol  a Q biosynthetic intermediate.]---[cd13971  ADCK2-like  aarF domain containing kinase 2 and similar proteins. This subfamily is composed of uncharacterized ABC1 kinase-like proteins including the human protein called aarF domain containing kinase 2 (ADCK2). Eukaryotes contain at least three ABC1-like proteins  in humans  these are ADCK3 and the putative protein kinases named ADCK1 and ADCK2. Yeast Abc1p and its human homolog ADCK3 are atypical protein kinases required for the biosynthesis of Coenzyme Q (ubiquinone or Q)  which is an essential lipid component in respiratory electron and proton transport. In algae and higher plants  ABC1 kinases have proliferated to more than 15 subfamilies  most of which are located in plastids or mitochondria. Plant subfamily 10 (ABC1K10) belong to the same group of ABC1 kinases as human ADCK2. ABC1 kinases are not related to the ATP-binding cassette (ABC) membrane transporter family."]
["PSNMU-V1.4_AUG-EV-PASAV3_0059040.1",569017,"test58484.tree",1,0.72475,"high",1,0.71925,"high",1027,"B8HQ62","Protein Thf1","pfam11264]---[PRK13266]---[TIGR03060]---[PLN03060]---[PLN00047","pfam11264  ThylakoidFormat  Thylakoid formation protein. THF1 is localized to the outer plastid membrane and the stroma. THF1 has a role in sugar signalling. THF1 is also thought to have a role in chloroplast and leaf development. THF1 has been shown to play a crucial role in vesicle-mediated thylakoid membrane biogenesis.]---[PRK13266  PRK13266  Thf1-like protein  Reviewed.]---[TIGR03060  PS_II_psb29  photosystem II biogenesis protein Psp29.  Psp29  originally designated sll1414 in Synechocystis 6803  is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown  mutant studies show an impairment in photosystem II biogenesis and/or stability  rather than in PS II core function.  Energy metabolism  Photosynthesis .]---[PLN03060  PLN03060  inositol phosphatase-like protein  Provisional.]---[PLN00047  PLN00047  photosystem II biogenesis protein Psb29  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0059580.1",569075,"test25648.tree",0.809,0.841909090909091,"high",0.842,0.849545454545455,"high",2148,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0060230.1",569137,"test5105.tree",0.922,0.90104,"high",0.913,0.86424,"high",1896,"P0A100","Amino-acid acetyltransferase","PRK05279]---[TIGR01890]---[PLN02825]---[cd04237]---[COG0548]---[COG1246]---[PRK07757]---[PRK12308]---[PRK07922","PRK05279  PRK05279  N-acetylglutamate synthase  Validated.]---[TIGR01890  Amino-acid_acetyltransferase  amino-acid N-acetyltransferase.  This model represents a clade of amino-acid N-acetyltransferases acting mainly on glutamate in the first step of the  acetylated  ornithine biosynthesis pathway. For this reason it is also called N-acetylglutamate synthase. The enzyme may also act on aspartate.  Amino acid biosynthesis  Glutamate family .]---[PLN02825  PLN02825  amino-acid N-acetyltransferase.]---[cd04237  AAK_NAGS-ABP  AAK_NAGS-ABP  N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an N-terminal NAG kinase-like (ArgB) domain (this CD) and a C-terminal NAG synthase  acetyltransferase (ArgA) domain. Both bacterial and plant sequences in this CD have a conserved N-terminal extension  a similar sequence in the NAG kinases of the cyclic arginine-biosynthesis pathway has been implicated in feedback inhibition sensing. Plant sequences also have an N-terminal chloroplast transit peptide and an insert (approx. 70 residues) in the C-terminal region of ArgB. Members of this CD belong to the Amino Acid Kinase Superfamily (AAK).]---[COG0548  ArgB  Acetylglutamate kinase  Amino acid transport and metabolism .]---[COG1246  ArgA  N-acetylglutamate synthase and related acetyltransferases  Amino acid transport and metabolism .]---[PRK07757  PRK07757  acetyltransferase  Provisional.]---[PRK12308  PRK12308  bifunctional argininosuccinate lyase/N-acetylglutamate synthase  Provisional.]---[PRK07922  PRK07922  N-acetylglutamate synthase  Validated."]
["PSNMU-V1.4_AUG-EV-PASAV3_0061590.1",569251,"test4671.tree",0.912,0.733407407407407,"high",0.929,0.759111111111111,"high",1109,"Q5JK24","Thiamine pyrophosphokinase 1","PLN02714]---[cd07995]---[TIGR01378]---[COG1564]---[pfam04263]---[pfam04265]---[smart00983","PLN02714  PLN02714  thiamin pyrophosphokinase.]---[cd07995  TPK  Thiamine pyrophosphokinase. Thiamine pyrophosphokinase (TPK  EC 2.7.6.2  also spelled thiamin pyrophosphokinase) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamine) to form the coenzyme thiamine pyrophosphate (TPP). TPP is required for central metabolic functions  and thiamine deficiency is associated with potentially fatal human diseases. The structure of thiamine pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.]---[TIGR01378  Thiamine_pyrophosphokinase  thiamine pyrophosphokinase.  This model has been revised. Originally  it described strictly eukaryotic thiamine pyrophosphokinase. However  it is now expanded to include also homologous enzymes  apparently functionally equivalent  from species that rely on thiamine pyrophosphokinase rather than thiamine-monophosphate kinase (TIGR01379) to produce the active TPP cofactor. This includes the thiamine pyrophosphokinase from Bacillus subtilis  previously designated YloS.  Biosynthesis of cofactors  prosthetic groups  and carriers  Thiamine .]---[COG1564  THI80  Thiamine pyrophosphokinase  Coenzyme metabolism .]---[pfam04263  TPK_catalytic  Thiamin pyrophosphokinase  catalytic domain. Family of thiamin pyrophosphokinase (EC 2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyses the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus  TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.]---[pfam04265  TPK_B1_binding  Thiamin pyrophosphokinase  vitamin B1 binding domain. Family of thiamin pyrophosphokinase (EC 2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyses the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus  TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.]---[smart00983  TPK_B1_binding  Thiamin pyrophosphokinase  vitamin B1 binding domain. Thiamin pyrophosphokinase (TPK) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus  TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis."]
["PSNMU-V1.4_AUG-EV-PASAV3_0061920.1",569300,"test6308.tree",0.22,0.712547619047619,"medium",0.756,0.788666666666667,"high",2599,"Q1EB31","ATP-dependent RNA helicase DBP4","COG0513]---[PRK11776]---[cd00268]---[PRK11192]---[PTZ00110]---[PRK04837]---[PRK04537]---[PRK01297]---[PRK11634]---[PRK10590]---[PLN00206]---[pfam00270]---[smart00487]---[PTZ00424]---[cd00079]---[cd00046]---[pfam00271]---[TIGR01389]---[smart00490]---[COG1201","COG0513  SrmB  Superfamily II DNA and RNA helicases  DNA replication  recombination  and repair / Transcription / Translation  ribosomal structure and biogenesis .]---[PRK11776  PRK11776  ATP-dependent RNA helicase DbpA  Provisional.]---[cd00268  DEADc  DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding  needed in a variety of cellular processes including splicing  ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.]---[PRK11192  PRK11192  ATP-dependent RNA helicase SrmB  Provisional.]---[PTZ00110  PTZ00110  helicase  Provisional.]---[PRK04837  PRK04837  ATP-dependent RNA helicase RhlB  Provisional.]---[PRK04537  PRK04537  ATP-dependent RNA helicase RhlB  Provisional.]---[PRK01297  PRK01297  ATP-dependent RNA helicase RhlB  Provisional.]---[PRK11634  PRK11634  ATP-dependent RNA helicase DeaD  Provisional.]---[PRK10590  PRK10590  ATP-dependent RNA helicase RhlE  Provisional.]---[PLN00206  PLN00206  DEAD-box ATP-dependent RNA helicase  Provisional.]---[pfam00270  DEAD  DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolizm  including nuclear transcription  pre mRNA splicing  ribosome biogenesis  nucleocytoplasmic transport  translation  RNA decay and organellar gene expression.]---[smart00487  DEXDc  DEAD-like helicases superfamily. ]---[PTZ00424  PTZ00424  helicase 45  Provisional.]---[cd00079  HELICc  Helicase superfamily c-terminal domain  associated with DEXDc-  DEAD-  and DEAH-box proteins  yeast initiation factor 4A  Ski2p  and Hepatitis C virus NS3 helicases  this domain is found in a wide variety of helicases and helicase related proteins  may not be an autonomously folding unit  but an integral part of the helicase  4 helicase superfamilies at present according to the organization of their signature motifs  all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity  they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA  unwinding the duplex in the process.]---[cd00046  DEXDc  DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.]---[pfam00271  Helicase_C  Helicase conserved C-terminal domain.  The Prosite family is restricted to DEAD/H helicases  whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit  but an integral part of the helicase.]---[TIGR01389  recQ  ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions  as well as more distantly related bacterial helicases related to RecQ.  DNA metabolism  DNA replication  recombination  and repair .]---[smart00490  HELICc  helicase superfamily c-terminal domain. ]---[COG1201  Lhr  Lhr-like helicases  General function prediction only ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0062510.1",569357,"test25635.tree",0.993,0.875818181818182,"high",0.985,0.875545454545455,"high",1414,"Q84W65","SufE-like protein 1  chloroplastic/mitochondrial","COG2166]---[pfam02657]---[PRK09296]---[TIGR03391]---[pfam01722]---[PLN02673]---[COG0271]---[PRK15019","COG2166  sufE  Cysteine desulfurase SufE subunit  Posttranslational modification  protein turnover  chaperones .]---[pfam02657  SufE  Fe-S metabolizm associated domain. This family consists of the SufE-related proteins. These have been implicated in Fe-S metabolizm and export).]---[PRK09296  PRK09296  cysteine desufuration protein SufE  Provisional.]---[TIGR03391  FeS_syn_CsdE  cysteine desulfurase  sulfur acceptor subunit CsdE. Members of this protein family are CsdE  formerly called YgdK. This protein  found as a paralog to SufE in Escherichia coli  Yersinia pestis  Photorhabdus luminescens  and related species  works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE)  in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair  although involved in FeS cluster biosynthesis  is not found next to other such genes as are its paralogs from the Suf or Isc systems.  Biosynthesis of cofactors  prosthetic groups  and carriers  Other .]---[pfam01722  BolA  BolA-like protein. This family consist of the morphoprotein BolA from Escherichia coli and its various homologues. In Escherichia coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase. BolA is also induced by stress during early stages of growth and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5.]---[PLN02673  PLN02673  quinolinate synthetase A.]---[COG0271  BolA  Stress-induced morphogen (activity unknown)  Signal transduction mechanisms .]---[PRK15019  PRK15019  CsdA-binding activator  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0064160.1",569436,"test6818.tree",0.715,0.722820512820513,"high",0.556,0.770564102564102,"high",1888,"Q9BRX9","WD repeat domain-containing protein 83","cd00200]---[cd00200]---[cd00200]---[COG2319]---[COG2319]---[COG2319]---[COG2319]---[smart00320]---[pfam00400","cd00200  WD40  WD40 domain  found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction  pre-mRNA processing and cytoskeleton assembly  typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long  hence the name WD40  between GH and WD lies a conserved core  serves as a stable propeller-like platform to which proteins can bind either stably or reversibly  forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet  instances with few detectable copies are hypothesized to form larger structures by dimerization  each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade  the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure  residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands  7 copies of the repeat are present in this alignment.]---[COG2319  COG2319  FOG  WD40 repeat  General function prediction only .]---[smart00320  WD40  WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.]---[pfam00400  WD40  WD domain  G-beta repeat. "]
["PSNMU-V1.4_AUG-EV-PASAV3_0064850.1",569504,"test34236.tree",0.647,0.7785,"high",0.918,0.825125,"high",2595,"Q869K3","3'(2') 5'-bisphosphate nucleotidase 1","cd01640]---[pfam00459]---[COG1218]---[cd01638]---[smart00587]---[pfam02958]---[pfam07914]---[pfam01636","cd01640  IPPase  IPPase  Inositol polyphosphate-1-phosphatase  a member of the Mg   dependent family of inositol monophosphatase-like domains  hydrolyzes the 1' position phosphate from inositol 1 3 4-trisphosphate and inositol 1 4-bisphosphate. Members in this group may also exhibit 3'-phosphoadenosine 5'-phosphate phosphatase activity  and they all appear to be inhibited by lithium. IPPase is one of the proposed targets of Li  therapy in manic-depressive illness.]---[pfam00459  Inositol_P  Inositol monophosphatase family. ]---[COG1218  CysQ  3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase  Inorganic ion transport and metabolism .]---[cd01638  CysQ  CysQ  a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase  is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS  which is an intermediate in cysteine biosynthesis (a principal route of sulfur assimilation).]---[smart00587  CHK  ZnF_C4 abd HLH domain containing kinases domain.  subfamily of choline kinases.]---[pfam02958  EcKinase  Ecdysteroid kinase. This family includes ecdysteroid 22-kinase  an enzyme responsible for the phosphorylation of ecdysteroids (insect growth and moulting hormones) at C-22  to form physiologically inactive ecdysteroid 22-phosphates.]---[pfam07914  DUF1679  Protein of unknown function (DUF1679). The region featured in this family is found in a number of C. elegans proteins  in one case as a repeat. In many of the family members  this region is associated with the CHK region described by SMART as being found in ZnF_C4 and HLH domain-containing kinases. In fact  one member of this family is annotated as being a member of the nuclear hormone receptor family  and contains regions typical of such proteins (Interpro IPR000536  Interpro IPR008946  and Interpro IPR001628).]---[pfam01636  APH  Phosphotransferase enzyme family. This family consists of bacterial antibiotic resistance proteins  which confer resistance to various aminoglycosides they include  aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-kinase or streptomycin 3''-phosphotransferase. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation. This family also includes homoserine kinase. This family is related to fructosamine kinase pfam03881."]
["PSNMU-V1.4_AUG-EV-PASAV3_0066380.1",569719,"test71634.tree",1,0.563333333333333,"high",1,0.572666666666667,"high",835,"Q39VA2","30S ribosomal protein S15","PRK05626]---[COG0184]---[TIGR00952]---[cd00353]---[pfam00312]---[CHL00027]---[cd00677]---[PTZ00119","PRK05626  rpsO  30S ribosomal protein S15  Reviewed.]---[COG0184  RpsO  Ribosomal protein S15P/S13E  Translation  ribosomal structure and biogenesis .]---[TIGR00952  30S_ribosomal_protein_S15  ribosomal protein S15  bacterial/organelle. This model is built to recognize specifically bacterial  chloroplast  and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13.  Protein synthesis  Ribosomal proteins  synthesis and modification .]---[cd00353  Ribosomal_S15p_S13e  Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association  thus representing a key element in the assembly of the whole ribosome. S15 also plays an important autoregulatory role by binding and preventing its own mRNA from being translated. S15 has a predominantly alpha-helical fold that is highly structured except for the N-terminal alpha helix.]---[pfam00312  Ribosomal_S15  Ribosomal protein S15. ]---[CHL00027  rps15  ribosomal protein S15.]---[cd00677  S15_NS1_EPRS_RNA-bind  S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure  which can bind to several types of RNA. It is found in the ribosomal protein S15  the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs)  where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found  they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism.]---[PTZ00119  PTZ00119  40S ribosomal protein S15  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0067200.1",569810,"test3750.tree",0.898,0.776348484848485,"high",0.807,0.741454545454545,"high",2427,"Q8NEB5","Phosphatidate phosphatase PPAPDC1B","cd03390]---[cd01610]---[cd03384]---[pfam01569]---[PLN02250]---[smart00014]---[cd03392]---[PLN02715]---[COG0671","cd03390  PAP2_containing_1_like  PAP2  subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both diacylglycerol pyrophosphate phosphatase activity as well as phosphatidate (PA) phosphatase activity  they may have a more generic housekeeping role in lipid metabolism.]---[cd01610  PAP2_like  PAP2_like proteins  a super-family of histidine phosphatases and vanadium haloperoxidases  includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP)  Glucose-6-phosphatase  Phosphatidylglycerophosphatase B and bacterial acid phosphatase  vanadium chloroperoxidases  vanadium bromoperoxidases  and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins.]---[cd03384  PAP2_wunen  PAP2  wunen subfamily. Most likely a family of membrane associated phosphatidic acid phosphatases. Wunen is a drosophila protein expressed in the central nervous system  which provides repellent activity towards primordial germ cells (PGCs)  controls the survival of PGCs and is essential in the migration process of these cells towards the somatic gonadal precursors.]---[pfam01569  PAP2  PAP2 superfamily. This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2)  Glucose-6-phosphatase EC 3.1.3.9  Phosphatidylglycerophosphatase B EC 3.1.3.27 and bacterial acid phosphatase EC 3.1.3.2. The family also includes a variety of haloperoxidases that function by oxidizing halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.]---[PLN02250  PLN02250  lipid phosphate phosphatase.]---[smart00014  acidPPc  Acid phosphatase homologues. ]---[cd03392  PAP2_like_2  PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup  which is specific to bacteria  lacks functional characterization and may act as a membrane-associated lipid phosphatase.]---[PLN02715  PLN02715  lipid phosphate phosphatase.]---[COG0671  PgpB  Membrane-associated phospholipid phosphatase  Lipid metabolism ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0067330.1",569822,"test88123.tree",1,0.437,"medium",1,0.366,"medium",3700,"Q42290","Probable mitochondrial-processing peptidase subunit beta","COG0612]---[pfam00675]---[pfam05193]---[COG1025]---[TIGR02110]---[COG1026","COG0612  PqqL  Predicted Zn-dependent peptidases  General function prediction only .]---[pfam00675  Peptidase_M16  Insulinase (Peptidase family M16). ]---[pfam05193  Peptidase_M16_C  Peptidase M16 inactive domain. Peptidase M16 consists of two structurally related domains. One is the active peptidase  whereas the other is inactive. The two domains hold the substrate like a clamp.]---[COG1025  Ptr  Secreted/periplasmic Zn-dependent peptidases  insulinase-like  Posttranslational modification  protein turnover  chaperones .]---[TIGR02110  Coenzyme_PQQ_synthesis_protein_F  coenzyme PQQ biosynthesis probable peptidase PqqF. In a subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone)  this probable peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA (TIGR02107)  a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.  Biosynthesis of cofactors  prosthetic groups  and carriers  Other .]---[COG1026  COG1026  Predicted Zn-dependent peptidases  insulinase-like  General function prediction only ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0067640.1",569853,"test6455.tree",0.881,0.787219512195122,"high",0.91,0.784121951219512,"high",2270,"Q5F3D7","U3 small nucleolar RNA-associated protein 15 homolog","pfam09384]---[cd00200]---[cd00200]---[cd00200]---[COG2319]---[COG2319]---[COG2319]---[COG2319","pfam09384  UTP15_C  UTP15 C terminal. U3 snoRNA is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA. It is a component of the ribosomal small subunit (SSU) processome. UTP15 is needed for optimal pre-ribosomal RNA transcription by RNA polymerase I  together with a subset of U3 proteins required for transcription (t-UTPs). This entry represents the C terminal of UTP15  and is found adjacent to WD40 repeats (pfam00400).]---[cd00200  WD40  WD40 domain  found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction  pre-mRNA processing and cytoskeleton assembly  typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long  hence the name WD40  between GH and WD lies a conserved core  serves as a stable propeller-like platform to which proteins can bind either stably or reversibly  forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet  instances with few detectable copies are hypothesized to form larger structures by dimerization  each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade  the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure  residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands  7 copies of the repeat are present in this alignment.]---[COG2319  COG2319  FOG  WD40 repeat  General function prediction only ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0068040.1",569881,"test17629.tree",0.871,0.8161875,"high",0.888,0.8020625,"high",2101,"Q9XI84"," Fructose-bisphosphate aldolase -lysine N-methyltransferase  chloroplastic","pfam09273","pfam09273  Rubis-subs-bind  Rubisco LSMT substrate-binding. Members of this family adopt a multihelical structure  with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate  such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex."]
["PSNMU-V1.4_AUG-EV-PASAV3_0070580.1",570131,"test111197.tree",1,1,"high",1,1,"high",3307,"Q5WI27","Xanthine phosphoribosyltransferase","PRK09219]---[TIGR01744]---[COG0503]---[PRK08558]---[TIGR01743]---[PRK09213]---[cd06223]---[PRK02304]---[PRK07322]---[pfam00156]---[TIGR01090]---[PRK06031]---[PRK00455]---[PLN02293","PRK09219  PRK09219  xanthine phosphoribosyltransferase  Validated.]---[TIGR01744  Xanthine_phosphoribosyltransferase  xanthine phosphoribosyltransferase.  This model represent a xanthine-specific phosphoribosyltransferase of Bacillus subtilis and closely related proteins from other species  mostly from other Gram-positive bacteria. The adjacent gene is a xanthine transporter  B. subtilis can import xanthine for the purine salvage pathway or for catabolism to obtain nitrogen.  Purines  pyrimidines  nucleosides  and nucleotides  Salvage of nucleosides and nucleotides .]---[COG0503  Apt  Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins  Nucleotide transport and metabolism .]---[PRK08558  PRK08558  adenine phosphoribosyltransferase  Provisional.]---[TIGR01743  Pur_operon_repressor.  pur operon repressor  Bacillus subtilis type. This model represents the puring operon repressor PurR of low-GC Gram-positive bacteria. This homodimeric repressor contains a large region homologous to phosphoribosyltransferases and is inhibited by 5-phosphoribosyl 1-pyrophosphate.  Purines  pyrimidines  nucleosides  and nucleotides  Purine ribonucleotide biosynthesis  Regulatory functions  DNA interactions .]---[PRK09213  PRK09213  pur operon repressor  Provisional.]---[cd06223  PRTases_typeI  Phosphoribosyl transferase (PRT)-type I domain. Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP). PRPP  an activated form of ribose-5-phosphate  is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways  including adenine phosphoribosyltransferase EC 2.4.2.7.  hypoxanthine-guanine-xanthine phosphoribosyltransferase  hypoxanthine phosphoribosyltransferase EC 2.4.2.8.  ribose-phosphate pyrophosphokinase EC 2.7.6.1.  amidophosphoribosyltransferase EC 2.4.2.14.  orotate phosphoribosyltransferase EC 2.4.2.10.  uracil phosphoribosyltransferase EC 2.4.2.9.  and xanthine-guanine phosphoribosyltransferase EC 2.4.2.22.]---[PRK02304  PRK02304  adenine phosphoribosyltransferase  Provisional.]---[PRK07322  PRK07322  adenine phosphoribosyltransferase  Provisional.]---[pfam00156  Pribosyltran  Phosphoribosyl transferase domain. This family includes a range of diverse phosphoribosyl transferase enzymes. This family includes  Adenine phosphoribosyl-transferase EC 2.4.2.7. Hypoxanthine-guanine-xanthine phosphoribosyl-transferase. Hypoxanthine phosphoribosyl-transferase EC 2.4.2.8. Ribose-phosphate pyrophosphokinase i EC 2.7.6.1. Amidophosphoribosyltransferase EC 2.4.2.14. Orotate phosphoribosyl-transferase EC 2.4.2.10. Uracil phosphoribosyl-transferase EC 2.4.2.9. Xanthine-guanine phosphoribosyl-transferase EC 2.4.2.22. In Arabidopsis  At the very N-terminus of this domain is the P-Loop NTPase domain.]---[TIGR01090  Adenine_phosphoribosyltransferase  adenine phosphoribosyltransferase.  A phylogenetic analysis suggested omitting the bi-directional best hit homologs from the spirochetes from the seed for this model and making only tentative predictions of adenine phosphoribosyltransferase function for this lineage. The trusted cutoff score is made high for this reason. Most proteins scoring between the trusted and noise cutoffs are likely to act as adenine phosphotransferase.  Purines  pyrimidines  nucleosides  and nucleotides  Salvage of nucleosides and nucleotides .]---[PRK06031  PRK06031  phosphoribosyltransferase  Provisional.]---[PRK00455  pyrE  orotate phosphoribosyltransferase  Validated.]---[PLN02293  PLN02293  adenine phosphoribosyltransferase."]
["PSNMU-V1.4_AUG-EV-PASAV3_0075660.1",570620,"test43411.tree",1,0.579666666666667,"high",1,0.665,"high",981,"-","-","PRK01490]---[pfam05697]---[TIGR00115]---[COG0544","PRK01490  tig  trigger factor  Provisional.]---[pfam05697  Trigger_N  Bacterial trigger factor protein (TF).  In the Escherichia coli cytosol  a fraction of the newly synthesized proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF)  and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains  an N-terminal domain which mediates association with the large ribosomal subunit  a central substrate binding and PPIase domain with homology to FKBP proteins  and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel  together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains. This family represents the N-terminal region of the protein.]---[TIGR00115  tig  trigger factor. Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. Trigger factor can bind at the same time as the signal recognition particle (SRP)  but is excluded by the SRP receptor (FtsY). The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity. This protein is found in a single copy in virtually every bacterial genome.  Protein fate  Protein folding and stabilization .]---[COG0544  Tig  FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor)  Posttranslational modification  protein turnover  chaperones ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0075860.1",570637,"test3482.tree",0.838,0.757943661971831,"high",0.855,0.733901408450704,"high",1265,"Q9HFQ2","Serine/threonine-protein phosphatase PP2A catalytic subunit","cd07415]---[PTZ00239]---[smart00156]---[cd07414]---[PTZ00480]---[cd00144]---[cd07416]---[cd07417]---[PTZ00244]---[cd07419]---[cd07420]---[cd07418]---[COG0639]---[pfam00149",{"$cut":{"chars":16752,"head":"cd07415  MPP_PP2A_PP4_PP6  PP2A  PP4  and PP6 phosphoprotein phosphatases  metallophosphatase domain. PP2A-like family of phosphoprotein phosphatases (PPP's) including PP4 and PP6.  PP2A (Protein phosphatase 2A) is a critical regulator of many cellular activities. PP2A comprises about 1  of total cellular proteins. PP2A  together with protein phosphatase 1 (PP1)  accounts for more than 90  of all serine/threonine phosphatase activities in most cells and tissues. The PP2A subunit  in addition to having a catalytic domain homologous to PP1  has a unique C-terminal tail  containing a motif that is conserved in the catalytic subunits of all PP2A-like phosphatases including PP4 and PP6  and has an important role in PP2A regulation. The PP2A-like family of phosphatases all share a similar heterotrimeric architecture  that includes  a 65kDa scaffolding subunit (A)  a 36kDa catalytic subunit (C)  and one of 18 regulatory subunits (B). The PPP (phosphoprotein phosphatase) family  to which PP2A belongs  is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes  PP1  PP2B (calcineurin)  PP4  PP5  PP6  PP7  Bsu1  RdgC  PrpE  PrpA/PrpB  and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-  -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes  and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse  but all share a conserved domain with an active site consisting of two metal ions (usually manganese  iron  or zinc) coordinated with octahedral geometry by a cage of histidine  aspartate  and asparagine residues. The MPP superfamily includes  Mre11/SbcD-like exonucleases  Dbr1-like RNA lariat debranching enzymes  YfcE-like phosphodiesterases  purple acid phosphatases (PAPs)  YbbF-like UDP-2 3-diacylglucosamine hydrolases  and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets.  This domain is thought to allow for productive metal coordination.]---[PTZ00239  PTZ00239  serine/threonine protein phosphatase 2A  Provisional.]---[smart00156  PP2Ac  Protein phosphatase 2A homologues  catalytic domain. Large family of serine/threonine phosphatases  that includes PP1  PP2A and PP2B (calcineurin) family members.]---[cd07414  MPP_PP1_PPKL  PP1  PPKL (PP1 and kelch-like) enzymes   and related proteins  metallophosphatase domain. PP1 (protein phosphatase type 1) is a serine/threonine phosphatase that regulates many cellular processes including  cell-cycle progression  protein synthesis  muscle contraction  carbohydrate metabolism  transcription and neuronal signaling  through its interaction with at least 180 known targeting proteins.  PP1 occurs in all tissues and regulates many pathways  ranging from cell-cycle progression to carbohydrate metabolism.  Also included here are the PPKL (PP1 and kelch-like) enzymes including the PPQ  PPZ1  and PPZ2 fungal phosphatases.  These PPKLs have a large N-terminal kelch repeat in addition to a C-terminal phosphoesterase domain. The PPP (phosphoprotein phosphatase) family  to which PP1 belongs  is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes  PP2A  PP2B (calcineurin)  PP4  PP5  PP6  PP7  Bsu1  RdgC  PrpE  PrpA/PrpB  and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-  -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes  and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse  but all sh"}}]
["PSNMU-V1.4_AUG-EV-PASAV3_0076860.1",570733,"test6880.tree",0.247,0.801128205128205,"medium",0.315,0.802820512820513,"medium",4159,"Q8H1U5","Anaphase-promoting complex subunit 2","pfam00888]---[COG5647]---[smart00182]---[smart01013]---[pfam08672","pfam00888  Cullin  Cullin family. ]---[COG5647  COG5647  Cullin  a subunit of E3 ubiquitin ligase  Posttranslational modification  protein turnover  chaperones .]---[smart00182  CULLIN  Cullin. ]---[smart01013  APC2  Anaphase promoting complex (APC) subunit 2.  The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2)  to the substrate protein.]---[pfam08672  APC2  Anaphase promoting complex (APC) subunit 2.  The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2)  to the substrate protein."]
["PSNMU-V1.4_AUG-EV-PASAV3_0079810.1",571019,"test7243.tree",0.98,0.850243243243243,"high",0.981,0.867513513513513,"high",4087,"Q9CW03","Structural maintenance of chromosomes protein 3","COG1196]---[COG1196]---[COG1196]---[COG1196]---[COG1196]---[TIGR02169]---[TIGR02169]---[TIGR02169]---[pfam02463]---[pfam02463]---[TIGR02168]---[TIGR02168]---[TIGR02168]---[TIGR02168]---[TIGR02168]---[TIGR02168]---[cd03272]---[cd03272]---[COG0419]---[COG0419]---[COG0419]---[COG0419]---[cd03273]---[cd03273]---[cd03239]---[cd03239]---[smart00968]---[PRK03918]---[PRK03918]---[PRK03918]---[pfam06470]---[cd03278]---[cd03278]---[PRK01156]---[cd03227]---[cd03227]---[cd03275]---[cd03275]---[pfam13476]---[PRK02224]---[PRK02224]---[PRK02224]---[PRK02224]---[cd03274]---[cd03274]---[TIGR04523]---[TIGR04523]---[COG0497","COG1196  Smc  Chromosome segregation ATPases  Cell division and chromosome partitioning .]---[TIGR02169  chromosome_segregation_protein_related_ptotein  chromosome segregation protein SMC  primarily archaeal type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria  archaea  and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes  but six paralogs (excluded from this family) are found in eukarotes  where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex  Synechocystis  etc)  the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved  but the central hinge region is skewed in composition and highly divergent.  Cellular processes  Cell division  DNA metabolism  Chromosome-associated proteins .]---[pfam02463  SMC_N  RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini  and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers  the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes  which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolizm and recombination.]---[TIGR02168  Chromosome_partition_protein_Smc  chromosome segregation protein SMC  common bacterial type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria  archaea  and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes  where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.  Cellular processes  Cell division  DNA metabolism  Chromosome-associated proteins .]---[cd03272  ABC_SMC3_euk  ATP-binding cassette domain of eukaryotic SMC3 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa)  and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T  in the single-letter amino-acid code)  which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif  and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group  whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells  the proteins are found as heterodimers of SMC1 paired with SMC3  SMC2 with SMC4  and SMC5 with SMC6 (formerly known as Rad18).]---[COG0419  SbcC  ATPase involved in DNA repair  DNA replication  recombination  and repair .]---[cd03273  ABC_SMC2_euk  ATP-binding cassette domain of eukaryotic SMC2 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa)  and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T  in the single-letter amino-acid code)  which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif  and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group  whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells  the proteins are found as heterodimers of SMC1 paired with SMC3  SMC2 with SMC4  and SMC5 with SMC6 (formerly known as Rad18).]---[cd03239  ABC_SMC_head  The SMC head domain belongs to the ATP-binding cassette superfamily. The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria  and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa  and each has five distinct domains  amino- and carboxy-terminal globular domains  which contain sequences characteristic of ATPases  two coiled-coil regions separating the terminal domains   and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions  including chromosome condensation  sister-chromatid cohesion  recombination  DNA repair  and epigenetic silencing of gene expression.]---[smart00968  SMC_hinge  SMC proteins Flexible Hinge Domain. This entry represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction.]---[PRK03918  PRK03918  chromosome segregation protein  Provisional.]---[pfam06470  SMC_hinge  SMC proteins Flexible Hinge Domain. This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction.]---[cd03278  ABC_SMC_barmotin  ATP-binding cassette domain of barmotin  a member of the SMC protein family. Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa)  and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T  in the single-letter amino-acid code)  which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif  and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group  whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells  the proteins are found as heterodimers of SMC1 paired with SMC3  SMC2 with SMC4  and SMC5 with SMC6 (formerly known as Rad18).]---[PRK01156  PRK01156  chromosome segregation protein  Provisional.]---[cd03227  ABC_Class2  ATP-binding cassette domain of non-transporter proteins. ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated  fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.]---[cd03275  ABC_SMC1_euk  ATP-binding cassette domain of eukaryotic SMC1 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa)  and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T  in the single-letter amino-acid code)  which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif  and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group  whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells  the proteins are found as heterodimers of SMC1 paired with SMC3  SMC2 with SMC4  and SMC5 with SMC6 (formerly known as Rad18).]---[pfam13476  AAA_23  AAA domain. ]---[PRK02224  PRK02224  chromosome segregation protein  Provisional.]---[cd03274  ABC_SMC4_euk  ATP-binding cassette domain of eukaryotic SMC4 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa)  and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T  in the single-letter amino-acid code)  which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif  and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group  whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells  the proteins are found as heterodimers of SMC1 paired with SMC3  SMC2 with SMC4  and SMC5 with SMC6 (formerly known as Rad18).]---[TIGR04523  conserved_hypothetical_protein  helix-rich Mycoplasma protein. Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length  including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D E N Q  and K. Genes encoding these proteins are often found in tandem. The function is unknown.]---[COG0497  RecN  ATPase involved in DNA repair  DNA replication  recombination  and repair ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0080460.1",571195,"test33820.tree",1,0.8535,"high",1,0.850875,"high",4105,"Q6D6A4","UPF0176 protein ECA1781","PRK00142]---[COG1054]---[COG4122]---[pfam01596]---[cd01518]---[PRK01415]---[PRK05320]---[smart00450]---[PLN02781]---[PLN02476]---[PLN02589]---[cd00158]---[COG0607]---[pfam00581]---[cd01444","PRK00142  PRK00142  putative rhodanese-related sulfurtransferase  Provisional.]---[COG1054  COG1054  Predicted sulfurtransferase  General function prediction only .]---[COG4122  COG4122  Predicted O-methyltransferase  General function prediction only .]---[pfam01596  Methyltransf_3  O-methyltransferase. Members of this family are O-methyltransferases. The family includes catechol o-methyltransferase  caffeoyl-CoA O-methyltransferase  and a family of bacterial O-methyltransferases that may be involved in antibiotic production.]---[cd01518  RHOD_YceA  Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA  Bacillus subtilis YbfQ  and similar uncharacterized proteins.]---[PRK01415  PRK01415  hypothetical protein  Validated.]---[PRK05320  PRK05320  rhodanese superfamily protein  Provisional.]---[smart00450  RHOD  Rhodanese Homology Domain. An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants  PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases  ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.]---[PLN02781  PLN02781  Probable caffeoyl-CoA O-methyltransferase.]---[PLN02476  PLN02476  O-methyltransferase.]---[PLN02589  PLN02589  caffeoyl-CoA O-methyltransferase.]---[cd00158  RHOD  Rhodanese Homology Domain (RHOD)  an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants  PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases  ubiquitin hydrolases from yeast and in sulfuryltransferases  where they are believed to play a regulatory role in multidomain proteins.]---[COG0607  PspE  Rhodanese-related sulfurtransferase  Inorganic ion transport and metabolism .]---[pfam00581  Rhodanese  Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins  including phosphatases and ubiquitin C-terminal hydrolases.]---[cd01444  GlpE_ST  GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases  GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine."]
["PSNMU-V1.4_AUG-EV-PASAV3_0082080.1",571236,"test23336.tree",0.331,0.704583333333333,"medium",0.467,0.761,"medium",1225,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0087770.1",571774,"test5521.tree",0.928,0.85868085106383,"high",0.99,0.843595744680851,"high",1840,"Q32LP4","Sodium-driven chloride bicarbonate exchanger","TIGR00834]---[pfam00955]---[COG0659]---[pfam00916","TIGR00834  Band_3_anion_transport_protein  anion exchange protein.  The Anion Exchanger (AE) Family (TC 2.A.31)Characterized protein members of the AE family are found only in animals.They preferentially catalyze anion exchange (antiport) reactions  typically acting as HCO3- Cl- antiporters  but also transporting a range of other inorganic and organic anions. Additionally  renal Na  HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule.  Transport and binding proteins  Anions .]---[pfam00955  HCO3_cotransp  HCO3- transporter family. This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na /HCO3-.]---[COG0659  SUL1  Sulfate permease and related transporters (MFS superfamily)  Inorganic ion transport and metabolism .]---[pfam00916  Sulfate_transp  Sulfate transporter family. Mutations in human SLC26A2 lead to several human diseases."]
["PSNMU-V1.4_AUG-EV-PASAV3_0088640.1",571853,"test12710.tree",0.036,0.697227272727273,"medium",0.038,0.753818181818182,"medium",2003,"Q9FVQ4","Plastidal glycolate/glycerate translocator 1  chloroplastic","COG1346]---[pfam04172","COG1346  LrgB  Putative effector of murein hydrolase  Cell envelope biogenesis  outer membrane .]---[pfam04172  LrgB  LrgB-like family. The two products of the lrgAB operon are potential membrane proteins  and LrgA and LrgB are both thought to control of murein hydrolase activity and penicillin tolerance."]
["PSNMU-V1.4_AUG-EV-PASAV3_0088660.1",571855,"test12710.tree",0.036,0.697227272727273,"medium",0.038,0.753818181818182,"medium",3273,"Q9FVQ4","Plastidal glycolate/glycerate translocator 1  chloroplastic","pfam04172]---[COG1346]---[TIGR00659]---[PRK10711]---[PRK04288","pfam04172  LrgB  LrgB-like family. The two products of the lrgAB operon are potential membrane proteins  and LrgA and LrgB are both thought to control of murein hydrolase activity and penicillin tolerance.]---[COG1346  LrgB  Putative effector of murein hydrolase  Cell envelope biogenesis  outer membrane .]---[TIGR00659  Uncharacterized_protein_HI_1298  TIGR00659 family protein. Members of this small but broadly distibuted (Gram-positive  Gram-negative  and Archaeal) family appear to have multiple transmembrane segments. The function is unknown. A homolog  LrgB of Staphylococcus aureus  in the same small superfamily but in an outgroup to this subfamily  is regulated by LytSR and is suggested to act as a murein hydrolase. Of the three paralogous proteins in B. subtilis  one is a full length member of this family  one lacks the C-terminal 60 residues and has an additional 128 N-terminal residues but branches within the family in a phylogenetic tree  and one is closely related to LrgB and part of the outgroup.  Hypothetical proteins  Conserved .]---[PRK10711  PRK10711  hypothetical protein  Provisional.]---[PRK04288  PRK04288  antiholin-like protein LrgB  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0088940.1",571888,"test6166.tree",0.685,0.731871794871795,"high",0.672,0.680564102564103,"high",1802,"P60027","General transcription factor IIH subunit 4","pfam03849]---[TIGR00625]---[COG5144","pfam03849  Tfb2  Transcription factor Tfb2. ]---[TIGR00625  General_transcription_factor_IIH_subunit_4  Transcription factor tfb2. All proteins in this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999  Ph.D. Thesis  Stanford University).  DNA metabolism  DNA replication  recombination  and repair .]---[COG5144  TFB2  RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH  subunit TFB2  Transcription / DNA replication  recombination  and repair ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0089580.1",572001,"test33804.tree",1,0.786,"high",1,0.792,"high",1704,"-","-","COG0170","COG0170  SEC59  Dolichol kinase  Lipid metabolism ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0089870.1",571965,"test38098.tree",1,0.651,"high",1,0.667,"high",774,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0090120.1",571990,"test4849.tree",0.996,0.814596153846154,"high",0.998,0.832673076923077,"high",1863,"Q9XI84"," Fructose-bisphosphate aldolase -lysine N-methyltransferase  chloroplastic","pfam09273]---[pfam00856","pfam09273  Rubis-subs-bind  Rubisco LSMT substrate-binding. Members of this family adopt a multihelical structure  with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate  such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex.]---[pfam00856  SET  SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains  but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C  an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure."]
["PSNMU-V1.4_AUG-EV-PASAV3_0090280.1",572016,"test49629.tree",1,0.7824,"high",1,0.7814,"high",2428,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0090420.1",572029,"test33804.tree",1,0.786,"high",1,0.792,"high",1625,"-","-","COG0170","COG0170  SEC59  Dolichol kinase  Lipid metabolism ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0090640.1",572051,"test8840.tree",0.887,0.790258064516129,"high",0.907,0.794806451612903,"high",1171,"-","-","pfam03105]---[cd14447]---[cd14481]---[cd14483]---[cd14484]---[cd14480]---[COG5036","pfam03105  SPX  SPX domain. We have named this region the SPX domain after (SYG1  Pho81 and XPR1). This 180 residue length domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1  the N-terminus directly binds to the G- protein beta subunit and inhibits transduction of the mating pheromone signal. This finding suggests that all the members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2 NUC-2 contains several ankyrin repeats pfam00023. Several members of this family are annotated as XPR1 proteins  the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with murine leukaemia viruses (MLV). The similarity between SYG1  phosphate regulators and XPR1 sequences has been previously noted  as has the additional similarity to several predicted proteins  of unknown function  from Drosophila melanogaster  Arabidopsis thaliana  Caenorhabditis elegans  Schizosaccharomyces pombe  and Saccharomyces cerevisiae. In addition  given the similarities between XPR1 and SYG1 and phosphate regulatory proteins  it has been proposed that XPR1 might be involved in G-protein associated signal transduction and may itself function as a phosphate sensor.]---[cd14447  SPX  Domain found in Syg1  Pho81  XPR1  and related proteins. This region has been named the SPX domain after (Syg1  Pho81 and XPR1). This domain is found at the amino terminus of a variety of proteins. In the yeast protein Syg1  the N-terminus directly binds to the G-protein beta subunit and inhibits transduction of the mating pheromone signal. Similarly  the N-terminus of the human XPR1 protein binds directly to the beta subunit of the G-protein heterotrimer leading to increased production of cAMP. These findings suggest that members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2. NUC-2 contains several ankyrin repeats. Several members of this family are annotated as XPR1 proteins  the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with xenotropic and polytropic murine leukaemia viruses (MLV). Infection by these retroviruses can inhibit XPR1-mediated cAMP signaling and result in cell toxicity and death. The similarity between Syg1  phosphate regulators and XPR1 sequences has been previously noted  as has the additional similarity to several predicted proteins  of unknown function  from Drosophila melanogaster  Arabidopsis thaliana  Caenorhabditis elegans  Schizosaccharomyces pombe  S. cerevisiae  and many other diverse organisms.]---[cd14481  SPX_AtSPX1_like  SPX domain of the plant protein SPX1 and similar proteins. This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. This family of plant proteins contains a single SPX domain. Arabidopsis thaliana SPX1 and SPX3 have been reported to play roles in the adaptation to low-phosphate conditions  SPX3 may be involved in the regulation of SPX1 activity. Oryza sativa SPX1 suppresses the regulation of expression of OsPT2  a low-affinity phosphate transporter  by the MYB-like OsPHR2.]---[cd14483  SPX_PHO81_NUC-2_like  SPX domain of Pho81  NUC-2  and similar proteins. This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. NUC-2 plays an important role in the phosphate-regulated signal transduction pathway in N. crassa. It shows high similarity to a cyclin-dependent kinase inhibitory protein Pho81  which is part of the phosphate regulatory cascade in S. cerevisiae. Both  NUC-2 and Pho81  have multi-domain architecture  including the SPX N-terminal domain following by several ankyrin repeats and a putative C-terminal glycerophosphodiester phosphodiesterase domain (GDPD) with unknown function.]---[cd14484  SPX_GDE1_like  SPX domain of Gde1 and similar proteins.  This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. The yeast protein Gde1/Ypl110c is similar to both  NUC-2 and Pho81  in sharing their multi-domain architecture  which includes the SPX N-terminal domain followed by several ankyrin repeats and a C-terminal glycerophosphodiester phosphodiesterase domain (GDPD). Gde1 hydrolyzes intracellular glycerophosphocholine into glycerolphosphate and choline  and plays a role in the utilization of glycerophosphocholine as a source for phosphate.]---[cd14480  SPX_VTC2_like  SPX domain of the vacuolar transport chaperone Vtc2 and similar proteins. This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. Vtc2 is part of the Saccharomyces cerevisiae membrane-integral VTC complex  together with Vtc1  Vtc3  and Vtc4. It contains an N-terminal SPX domain next to a central polyphosphate polymerase domain and a C-terminal domain of unknown function.]---[COG5036  COG5036  SPX domain-containing protein involved in vacuolar polyphosphate accumulation  Inorganic ion transport and metabolism ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0090660.1",572053,"test8840.tree",0.887,0.790258064516129,"high",0.907,0.794806451612903,"high",1391,"-","-","pfam03105]---[cd14447]---[cd14481]---[cd14483]---[cd14484]---[cd14480]---[COG5036","pfam03105  SPX  SPX domain. We have named this region the SPX domain after (SYG1  Pho81 and XPR1). This 180 residue length domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1  the N-terminus directly binds to the G- protein beta subunit and inhibits transduction of the mating pheromone signal. This finding suggests that all the members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2 NUC-2 contains several ankyrin repeats pfam00023. Several members of this family are annotated as XPR1 proteins  the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with murine leukaemia viruses (MLV). The similarity between SYG1  phosphate regulators and XPR1 sequences has been previously noted  as has the additional similarity to several predicted proteins  of unknown function  from Drosophila melanogaster  Arabidopsis thaliana  Caenorhabditis elegans  Schizosaccharomyces pombe  and Saccharomyces cerevisiae. In addition  given the similarities between XPR1 and SYG1 and phosphate regulatory proteins  it has been proposed that XPR1 might be involved in G-protein associated signal transduction and may itself function as a phosphate sensor.]---[cd14447  SPX  Domain found in Syg1  Pho81  XPR1  and related proteins. This region has been named the SPX domain after (Syg1  Pho81 and XPR1). This domain is found at the amino terminus of a variety of proteins. In the yeast protein Syg1  the N-terminus directly binds to the G-protein beta subunit and inhibits transduction of the mating pheromone signal. Similarly  the N-terminus of the human XPR1 protein binds directly to the beta subunit of the G-protein heterotrimer leading to increased production of cAMP. These findings suggest that members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2. NUC-2 contains several ankyrin repeats. Several members of this family are annotated as XPR1 proteins  the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with xenotropic and polytropic murine leukaemia viruses (MLV). Infection by these retroviruses can inhibit XPR1-mediated cAMP signaling and result in cell toxicity and death. The similarity between Syg1  phosphate regulators and XPR1 sequences has been previously noted  as has the additional similarity to several predicted proteins  of unknown function  from Drosophila melanogaster  Arabidopsis thaliana  Caenorhabditis elegans  Schizosaccharomyces pombe  S. cerevisiae  and many other diverse organisms.]---[cd14481  SPX_AtSPX1_like  SPX domain of the plant protein SPX1 and similar proteins. This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. This family of plant proteins contains a single SPX domain. Arabidopsis thaliana SPX1 and SPX3 have been reported to play roles in the adaptation to low-phosphate conditions  SPX3 may be involved in the regulation of SPX1 activity. Oryza sativa SPX1 suppresses the regulation of expression of OsPT2  a low-affinity phosphate transporter  by the MYB-like OsPHR2.]---[cd14483  SPX_PHO81_NUC-2_like  SPX domain of Pho81  NUC-2  and similar proteins. This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. NUC-2 plays an important role in the phosphate-regulated signal transduction pathway in N. crassa. It shows high similarity to a cyclin-dependent kinase inhibitory protein Pho81  which is part of the phosphate regulatory cascade in S. cerevisiae. Both  NUC-2 and Pho81  have multi-domain architecture  including the SPX N-terminal domain following by several ankyrin repeats and a putative C-terminal glycerophosphodiester phosphodiesterase domain (GDPD) with unknown function.]---[cd14484  SPX_GDE1_like  SPX domain of Gde1 and similar proteins.  This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-termini of several proteins involved in the regulation of phosphate transport  including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa  are also members of this family. The yeast protein Gde1/Ypl110c is similar to both  NUC-2 and Pho81  in sharing their multi-domain architecture  which includes the SPX N-terminal domain followed by several ankyrin repeats and a C-terminal glycerophosphodiester phosphodiesterase domain (GDPD). Gde1 hydrolyzes intracellular glycerophosphocholine into glycerolphosphate and choline  and plays a role in the utilization of glycerophosphocholine as a source for phosphate.]---[cd14480  SPX_VTC2_like  SPX domain of the vacuolar transport chaperone Vtc2 and similar proteins. This region has been named the SPX domain after (Syg1  Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. Vtc2 is part of the Saccharomyces cerevisiae membrane-integral VTC complex  together with Vtc1  Vtc3  and Vtc4. It contains an N-terminal SPX domain next to a central polyphosphate polymerase domain and a C-terminal domain of unknown function.]---[COG5036  COG5036  SPX domain-containing protein involved in vacuolar polyphosphate accumulation  Inorganic ion transport and metabolism ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0094850.1",572448,"test5521.tree",0.928,0.85868085106383,"high",0.99,0.843595744680851,"high",2775,"Q8JZR6","Electroneutral sodium bicarbonate exchanger 1","pfam00955]---[TIGR00834","pfam00955  HCO3_cotransp  HCO3- transporter family. This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na /HCO3-.]---[TIGR00834  Band_3_anion_transport_protein  anion exchange protein.  The Anion Exchanger (AE) Family (TC 2.A.31)Characterized protein members of the AE family are found only in animals.They preferentially catalyze anion exchange (antiport) reactions  typically acting as HCO3- Cl- antiporters  but also transporting a range of other inorganic and organic anions. Additionally  renal Na  HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule.  Transport and binding proteins  Anions ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0095970.1",572554,"test58647.tree",1,0.71125,"high",1,0.70125,"high",1288,"-","-","smart00724]---[pfam03798","smart00724  TLC  TRAM  LAG1 and CLN8 homology domains. Protein domain with at least 5 transmembrane alpha-helices. Lag1p and Lac1p are essential for acyl-CoA-dependent ceramide synthesis  TRAM is a subunit of the translocon and the CLN8 gene is mutated in Northern epilepsy syndrome. The family may possess multiple functions such as lipid trafficking  metabolism  or sensing. Trh homologues possess additional homeobox domains.]---[pfam03798  TRAM_LAG1_CLN8  TLC domain. "]
["PSNMU-V1.4_AUG-EV-PASAV3_0099850.1",572924,"test38012.tree",0.779,0.701428571428571,"high",0.825,0.710285714285714,"high",2379,"Q6R3M4","DNA polymerase iota","cd01703]---[cd01703]---[pfam00817]---[cd03586]---[cd03586]---[PRK01810]---[COG0389]---[cd00424]---[cd01702]---[cd01702]---[PRK02406]---[cd01701]---[PRK03348]---[PRK03858]---[PRK02794]---[PRK14133","cd01703  PolY_Pol_iota  DNA Polymerase iota. Pol iota  also called Rad30B  is a translesion synthesis (TLS) polymerase.  Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases  particularly when opposite pyrimidines  it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine  and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing  which may explain the varying efficiency for different template nucleotides.]---[pfam00817  IMS  impB/mucB/samB family. These proteins are involved in UV protection.]---[cd03586  PolY_Pol_IV_kappa  DNA Polymerase IV/Kappa. Pol IV  also known as Pol kappa  DinB  and Dpo4  is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes  this polymerase has a propensity for generating frameshift mutations.  The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of  75 residues known as the  N-clasp  region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa  with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a higher error rate than other Y-family polymerases.]---[PRK01810  PRK01810  DNA polymerase IV  Validated.]---[COG0389  DinP  Nucleotidyltransferase/DNA polymerase involved in DNA repair  DNA replication  recombination  and repair .]---[cd00424  PolY  Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS)  a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases  TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family  including Pol eta  Pol kappa/IV  Pol iota  Rev1  and Pol V  which is found exclusively in bacteria. In eukaryotes  the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA  which provides a scaffold for TLS polymerases to bind in order to access the lesion.  Because of their high error rates  TLS polymerases are potential targets for cancer treatment and prevention.]---[cd01702  PolY_Pol_eta  DNA Polymerase eta. Pol eta  also called Rad30A  is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members  Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions  the PIP box in pol eta interacting with PCNA  and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed  facilitating a lesion-dependent dissociation from the DNA.]---[PRK02406  PRK02406  DNA polymerase IV  Validated.]---[cd01701  PolY_Rev1  DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions.  Rev1 has both structural and enzymatic roles. Structurally  it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold.  Enzymatically  it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations  potentially making it a significant target for cancer treatment.]---[PRK03348  PRK03348  DNA polymerase IV  Provisional.]---[PRK03858  PRK03858  DNA polymerase IV  Validated.]---[PRK02794  PRK02794  DNA polymerase IV  Provisional.]---[PRK14133  PRK14133  DNA polymerase IV  Provisional."]
["PSNMU-V1.4_AUG-EV-PASAV3_0101320.1",573061,"test5372.tree",0.85,0.870625,"high",0.748,0.859229166666667,"high",4604,"Q9LF41","Probable ubiquitin conjugation factor E4","pfam10408]---[COG5113]---[pfam04564]---[smart00504","pfam10408  Ufd2P_core  Ubiquitin elongating factor core. This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4  running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit  the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus  pfam04564  which has ligase activity.]---[COG5113  UFD2  Ubiquitin fusion degradation protein 2  Posttranslational modification  protein turnover  chaperones .]---[pfam04564  U-box  U-box domain. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.]---[smart00504  Ubox  Modified RING finger domain. Modified RING finger domain  without the full complement of Zn2 -binding ligands. Probable involvement in E2-dependent ubiquitination."]
["PSNMU-V1.4_AUG-EV-PASAV3_0103700.1",573291,"test49793.tree",0.818,0.7464,"high",0.831,0.7508,"high",1409,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0107670.1",573652,"test30859.tree",1,0.804444444444445,"high",1,0.77,"high",3320,"-","-","COG0664]---[pfam00027]---[cd00038","COG0664  Crp  cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases  Signal transduction mechanisms .]---[pfam00027  cNMP_binding  Cyclic nucleotide-binding domain. ]---[cd00038  CAP_ED  effector domain of the CAP family of transcription factors  members include CAP (or cAMP receptor protein (CRP))  which binds cAMP  FNR (fumarate and nitrate reduction)  which uses an iron-sulfur cluster to sense oxygen) and CooA  a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain  proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues  the best studied is the prokaryotic catabolite gene activator  CAP  where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded  antiparallel beta-barrel structure  three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel  CooA is a homodimeric transcription factor that belongs to CAP family  cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain  cAPK's are composed of two different subunits  a catalytic chain and a regulatory chain  which contains both copies of the domain  cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section  also found in vertebrate cyclic nucleotide-gated ion-channels."]
["PSNMU-V1.4_AUG-EV-PASAV3_0107830.1",573668,"test33929.tree",1,0.82975,"high",1,0.834625,"high",1498,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0107960.1",573680,"test5512.tree",0.877,0.688617021276596,"high",0.917,0.675404255319149,"high",1465,"D9IFD5","Deoxyhypusine hydroxylase","pfam13646]---[pfam13646]---[pfam13646]---[COG1413","pfam13646  HEAT_2  HEAT repeats. This family includes multiple HEAT repeats.]---[COG1413  COG1413  FOG  HEAT repeat  Energy production and conversion ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0108100.1",573694,"test4149.tree",0.542,0.772383333333333,"high",0.887,0.756716666666667,"high",1892,"Q24572","Probable histone-binding protein Caf1","cd00200]---[cd00200]---[cd00200]---[cd00200]---[cd00200]---[COG2319]---[COG2319]---[COG2319]---[COG2319]---[pfam12265]---[PLN00181]---[PTZ00420]---[PTZ00420]---[PTZ00421]---[PTZ00421]---[pfam00400","cd00200  WD40  WD40 domain  found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction  pre-mRNA processing and cytoskeleton assembly  typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long  hence the name WD40  between GH and WD lies a conserved core  serves as a stable propeller-like platform to which proteins can bind either stably or reversibly  forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet  instances with few detectable copies are hypothesized to form larger structures by dimerization  each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade  the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure  residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands  7 copies of the repeat are present in this alignment.]---[COG2319  COG2319  FOG  WD40 repeat  General function prediction only .]---[pfam12265  CAF1C_H4-bd  Histone-binding protein RBBP4 or subunit C of CAF1 complex. The CAF-1 complex is a conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair  specifically it facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). This domain is an alpha helix which sits just upstream of the WD40 seven-bladed beta-propeller in the human RbAp46 protein. RbAp46 folds into the beta-propeller and binds histone H4 in a groove formed between this N-terminal helix and an extended loop inserted into blade six.]---[PLN00181  PLN00181  protein SPA1-RELATED  Provisional.]---[PTZ00420  PTZ00420  coronin  Provisional.]---[PTZ00421  PTZ00421  coronin  Provisional.]---[pfam00400  WD40  WD domain  G-beta repeat. "]
["PSNMU-V1.4_AUG-EV-PASAV3_0111340.1",574000,"test12112.tree",0.7,0.769086956521739,"high",0.938,0.72395652173913,"high",491,"Q2JM43","30S ribosomal protein S21","PRK00270]---[pfam01165]---[COG0828]---[TIGR00030","PRK00270  rpsU  30S ribosomal protein S21  Reviewed.]---[pfam01165  Ribosomal_S21  Ribosomal protein S21. ]---[COG0828  RpsU  Ribosomal protein S21  Translation  ribosomal structure and biogenesis .]---[TIGR00030  30S_ribosomal_protein_S21  ribosomal protein S21.  This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents.  Protein synthesis  Ribosomal proteins  synthesis and modification ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0111540.1",574023,"test12834.tree",0.899,0.833727272727273,"high",0.895,0.850590909090909,"high",2152,"Q9P3U2","Uncharacterized AAA domain-containing protein C328.04","COG0464]---[COG0464]---[TIGR01243]---[TIGR01243]---[COG1222]---[PRK03992]---[TIGR01242]---[PTZ00454]---[PTZ00361]---[TIGR01241]---[pfam00004]---[CHL00176]---[COG1223]---[PRK10733]---[COG0465]---[TIGR03689]---[cd00009]---[smart00382]---[CHL00195]---[COG0714]---[PRK04195]---[TIGR00382","COG0464  SpoVK  ATPases of the AAA  class  Posttranslational modification  protein turnover  chaperones .]---[TIGR01243  Cell_division_cycle_protein_48_homolog_MJ1156  AAA family ATPase  CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog  transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.]---[COG1222  RPT1  ATP-dependent 26S proteasome regulatory subunit  Posttranslational modification  protein turnover  chaperones .]---[PRK03992  PRK03992  proteasome-activating nucleotidase  Provisional.]---[TIGR01242  Proteasome-activating_nucleotidase  26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal.]---[PTZ00454  PTZ00454  26S protease regulatory subunit 6B-like protein  Provisional.]---[PTZ00361  PTZ00361  26 proteosome regulatory subunit 4-like protein  Provisional.]---[TIGR01241  ATP-dependent_zinc_metalloprotease_FtsH  ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.  Cellular processes  Cell division  Protein fate  Degradation of proteins  peptides  and glycopeptides .]---[pfam00004  AAA  ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly  operation  or disassembly of protein complexes.]---[CHL00176  ftsH  cell division protein  Validated.]---[COG1223  COG1223  Predicted ATPase (AAA  superfamily)  General function prediction only .]---[PRK10733  hflB  ATP-dependent metalloprotease  Reviewed.]---[COG0465  HflB  ATP-dependent Zn proteases  Posttranslational modification  protein turnover  chaperones .]---[TIGR03689  pup_AAA  proteasome ATPase. In the Actinobacteria  as shown for Mycobacterium tuberculosis  some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup  the Pup ligase PafA  and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.  Protein fate  Degradation of proteins  peptides  and glycopeptides .]---[cd00009  AAA  The AAA  (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand  catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC  RecA-like  VirD4-like  PilT-like  and SF1/2 helicases. Members of the AAA  ATPases function as molecular chaperons  ATPase subunits of proteases  helicases  or nucleic-acid stimulated ATPases. The AAA  proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.]---[smart00382  AAA  ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.]---[CHL00195  ycf46  Ycf46  Provisional.]---[COG0714  COG0714  MoxR-like ATPases  General function prediction only .]---[PRK04195  PRK04195  replication factor C large subunit  Provisional.]---[TIGR00382  clpX  endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases  ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.  Protein fate  Protein folding and stabilization  Protein fate  Degradation of proteins  peptides  and glycopeptides ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0113170.1",574167,"test2340.tree",0.994,0.770037037037037,"high",0.992,0.78912037037037,"high",2307,"Q54PW5","Diphthamide biosynthesis protein 1","TIGR00322]---[pfam01866]---[COG1736]---[TIGR03682]---[TIGR00272","TIGR00322  diphthamide_biosynthesis_protein_predicted  diphthamide biosynthesis enzyme Dph1/Dph2 domain. Archaea and Eukaryotes  but not Eubacteria  share the property of having a covalently modified residue  2'- 3-carboxamido-3-(trimethylammonio)propyl histidine  as a part of a cytosolic protein. The modified His  termed diphthamide  is part of translation elongation factor EF-2 and is the site for ADP-ribosylation by diphtheria toxin. This model includes both Dph1 and Dph2 from Saccharomyces cerevisiae  although only Dph2 is found in the Archaea (see TIGR03682). Dph2 has been shown to act analogously to the radical SAM (rSAM) family (pfam04055)  with 4Fe-4S-assisted cleavage of S-adenosylmethionine to create a free radical  but a different organic radical than in rSAM.]---[pfam01866  Diphthamide_syn  Putative diphthamide synthesis protein.  Human DPH1 is a candidate tumor suppressor gene. DPH2 from yeast  which confers resistance to diphtheria toxin has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide  a posttranslationally modified histidine residue present in EF2. The exact function of the members of this family is unknown.]---[COG1736  DPH2  Diphthamide synthase subunit DPH2  Translation  ribosomal structure and biogenesis .]---[TIGR03682  arCOG04112  diphthamide biosynthesis enzyme Dph2.  Members of this family are the archaeal protein Dph2  members of the universal archaeal protein family designated arCOG04112. The chemical function of this protein is analogous to the radical SAM family (pfam04055)  although the sequence is not homologous. The chemistry involves  4Fe-4S -aided formation of a 3-amino-3-carboxypropyl radical rather than the canonical 5'-deoxyadenosyl radical of the radical SAM family.]---[TIGR00272  Diphthamide_biosynthesis_protein_2  diphthamide biosynthesis protein 2. This protein has been shown in Saccharomyces cerevisiae to be one of several required for the modification of a particular histidine residue of translation elongation factor 2 to diphthamide. This modified site can then become the target for ADP-ribosylation by diphtheria toxin.  Protein fate  Protein modification and repair ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0114450.1",574278,"test3750.tree",0.898,0.776348484848485,"high",0.807,0.741454545454545,"high",1331,"Q3UMZ3","Phosphatidate phosphatase PPAPDC1B","cd03390]---[cd03384]---[cd01610]---[pfam01569]---[PLN02250","cd03390  PAP2_containing_1_like  PAP2  subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both diacylglycerol pyrophosphate phosphatase activity as well as phosphatidate (PA) phosphatase activity  they may have a more generic housekeeping role in lipid metabolism.]---[cd03384  PAP2_wunen  PAP2  wunen subfamily. Most likely a family of membrane associated phosphatidic acid phosphatases. Wunen is a drosophila protein expressed in the central nervous system  which provides repellent activity towards primordial germ cells (PGCs)  controls the survival of PGCs and is essential in the migration process of these cells towards the somatic gonadal precursors.]---[cd01610  PAP2_like  PAP2_like proteins  a super-family of histidine phosphatases and vanadium haloperoxidases  includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP)  Glucose-6-phosphatase  Phosphatidylglycerophosphatase B and bacterial acid phosphatase  vanadium chloroperoxidases  vanadium bromoperoxidases  and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins.]---[pfam01569  PAP2  PAP2 superfamily. This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2)  Glucose-6-phosphatase EC 3.1.3.9  Phosphatidylglycerophosphatase B EC 3.1.3.27 and bacterial acid phosphatase EC 3.1.3.2. The family also includes a variety of haloperoxidases that function by oxidizing halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.]---[PLN02250  PLN02250  lipid phosphate phosphatase."]
["PSNMU-V1.4_AUG-EV-PASAV3_0115490.1",574468,"test2730.tree",0.651,0.798489130434783,"high",0.638,0.813152173913044,"high",3209,"P52894","Alanine aminotransferase 2","PTZ00377]---[PLN02231]---[PLN02368]---[COG0436]---[PRK09265]---[cd00609]---[PRK08363]---[pfam00155]---[PRK13355]---[PRK06855]---[TIGR01265]---[PRK05764]---[PRK07568]---[TIGR01264]---[PTZ00433]---[PRK06108]---[PLN02607]---[PRK07682]---[COG1167]---[TIGR03540","PTZ00377  PTZ00377  alanine aminotransferase  Provisional.]---[PLN02231  PLN02231  alanine transaminase.]---[PLN02368  PLN02368  alanine transaminase.]---[COG0436  COG0436  Aspartate/tyrosine/aromatic aminotransferase  Amino acid transport and metabolism .]---[PRK09265  PRK09265  aminotransferase AlaT  Validated.]---[cd00609  AAT_like  Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate  which depending on the reaction  is the substrate in four kinds of reactions (1) transamination (movement of amino groups)  (2) racemization (redistribution of enantiomers)  (3) decarboxylation (removing COOH groups)  and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha  beta and gamma classes  based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes  and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. The major groups in this CD corresponds to Aspartate aminotransferase a  b and c  Tyrosine  Alanine  Aromatic-amino-acid  Glutamine phenylpyruvate  1-Aminocyclopropane-1-carboxylate synthase  Histidinol-phosphate  gene products of malY and cobC  Valine-pyruvate aminotransferase and Rhizopine catabolism regulatory protein.]---[PRK08363  PRK08363  alanine aminotransferase  Validated.]---[pfam00155  Aminotran_1_2  Aminotransferase class I and II. ]---[PRK13355  PRK13355  bifunctional HTH-domain containing protein/aminotransferase  Provisional.]---[PRK06855  PRK06855  aminotransferase  Validated.]---[TIGR01265  tyrosine_aminotransferase  tyrosine/nicotianamine family aminotransferase. This subfamily of pyridoxal phosphate-dependent enzymes includes known examples of both tyrosine aminotransferase from animals and nicotianamine aminotransferase from barley.]---[PRK05764  PRK05764  aspartate aminotransferase  Provisional.]---[PRK07568  PRK07568  aspartate aminotransferase  Provisional.]---[TIGR01264  tyrosine_aminotransferase  tyrosine aminotransferase  eukaryotic. This model describes tyrosine aminotransferase as found in animals and Trypanosoma cruzi. It is the first enzyme of a pathway of tyrosine degradation via homogentisate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase  an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway. These plant sequences are excluded from the model seed and score between the trusted an noise cutoffs.  Energy metabolism  Amino acids and amines .]---[PTZ00433  PTZ00433  tyrosine aminotransferase  Provisional.]---[PRK06108  PRK06108  aspartate aminotransferase  Provisional.]---[PLN02607  PLN02607  1-aminocyclopropane-1-carboxylate synthase.]---[PRK07682  PRK07682  hypothetical protein  Validated.]---[COG1167  ARO8  Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs  Transcription / Amino acid transport and metabolism .]---[TIGR03540  DapC_direct  LL-diaminopimelate aminotransferase.  This clade of the pfam00155 superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). Every member of this clade is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known aminotransferases  succinylases  desuccinylases  acetylases or deacetylases typical of the acylated versions of this pathway nor do they have the direct  NADPH-dependent enzyme (ddh). Although there is no experimental characterization of any of the sequences in this clade  a direct pathway is known in plants and Chlamydia and the clade containing the Chlamydia gene is a neighboring one in the same pfam00155 superfamily so it seems quite reasonable that these enzymes catalyze the same transformation."]
["PSNMU-V1.4_AUG-EV-PASAV3_0117090.1",574528,"test58733.tree",1,0.47575,"medium",1,0.475,"medium",1091,"-","-","pfam11833","pfam11833  DUF3353  Protein of unknown function (DUF3353). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length."]
["PSNMU-V1.4_AUG-EV-PASAV3_0117100.1",574529,"test58733.tree",1,0.47575,"medium",1,0.475,"medium",1362,"-","-","pfam11833","pfam11833  DUF3353  Protein of unknown function (DUF3353). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length."]
["PSNMU-V1.4_AUG-EV-PASAV3_0118470.1",574653,"test5060.tree",0.01,0.6299,"medium",0.674,0.71036,"high",2583,"Q20263","Probable Golgi transport protein 1","COG5120]---[pfam04178]---[cd00204]---[cd00204]---[cd00204]---[cd00204]---[cd00204]---[cd00204","COG5120  GOT1  Membrane protein involved in Golgi transport  Intracellular trafficking and secretion .]---[pfam04178  Got1  Got1/Sft2-like family. Traffic through the yeast Golgi complex depends on a member of the syntaxin family of SNARE proteins  Sed5  present in early Golgi cisternae. Got1 is thought to facilitate Sed5-dependent fusion events. This is a family of sequences derived from eukaryotic proteins. They are similar to a region of a SNARE-like protein required for traffic through the Golgi complex  SFT2 protein. This is a conserved protein with four putative transmembrane helices  thought to be involved in vesicular transport in later Golgi compartments.]---[cd00204  ANK  ankyrin repeats  ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins  for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin  repeats are stacked in a superhelical arrangement  this alignment contains 4 consecutive repeats."]
["PSNMU-V1.4_AUG-EV-PASAV3_0119210.1",574722,"test23311.tree",0.869,0.7895,"high",0.843,0.795666666666667,"high",1302,"Q6FU96","2 5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase","COG1985]---[pfam01872]---[TIGR00227]---[PRK05625]---[TIGR00326]---[TIGR01508","COG1985  RibD  Pyrimidine reductase  riboflavin biosynthesis  Coenzyme metabolism .]---[pfam01872  RibD_C  RibD C-terminal domain. The function of this domain is not known  but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG  in combination with pfam00383  as well as in isolation in some archaebacterial proteins. This family appears to be related to pfam00186.]---[TIGR00227  ribD_Cterm  riboflavin-specific deaminase C-terminal domain. Eubacterial riboflavin-specific deaminases have a zinc-binding domain recognized by the dCMP_cyt_deam model toward the N-terminus and this domain toward the C-terminus. Yeast HTP reductase  a riboflavin-biosynthetic enzyme  and several archaeal proteins believed related to riboflavin biosynthesis consist only of this domain and lack the dCMP_cyt_deam domain.]---[PRK05625  PRK05625  5-amino-6-(5-phosphoribosylamino)uracil reductase  Validated.]---[TIGR00326  eubact_ribD  riboflavin biosynthesis protein RibD.  This model describes the ribD protein as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region captured in the model dCMP_cyt_deam and shared by proteins such as cytosine deaminase  mammalian apolipoprotein B mRNA editing protein  blasticidin-S deaminase  and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase  a protein required for riboflavin biosynthesis. A number of archaeal proteins believed related to riboflavin biosynthesis contain only this C-terminal domain and are not found as full-length matches to this model.  Biosynthesis of cofactors  prosthetic groups  and carriers  Riboflavin  FMN  and FAD .]---[TIGR01508  rib_reduct_arch  2 5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1'-reductase  archaeal. This model represents a specific reductase of riboflavin biosynthesis in the Archaea  diaminohydroxyphosphoribosylaminopyrimidine reductase. It should not be confused with bacterial 5-amino-6-(5-phosphoribosylamino)uracil reductase. The intermediate 2 5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine in riboflavin biosynthesis is reduced first  and then deaminated  in both Archaea and Fungi  opposite the order in Bacteria. The subsequent deaminase is not presently known and is not closely homologous to the deaminase domain (3.5.4.26) fused to the reductase domain (1.1.1.193) similar to this protein but found in most bacteria."]
["PSNMU-V1.4_AUG-EV-PASAV3_0120310.1",574825,"test14149.tree",0.761,0.8363,"high",0.784,0.83215,"high",1699,"Q9ZAE9","2-epi-5-epi-valiolone synthase","cd08199]---[PLN02834]---[cd08169]---[cd08195]---[pfam01761]---[COG0337]---[PRK00002]---[TIGR01357]---[PRK06203]---[cd08198]---[cd08197]---[PRK14021]---[cd08196]---[TIGR04425]---[PRK13951]---[cd07766]---[pfam13685]---[COG0371","cd08199  EEVS  2-epi-5-epi-valiolone synthase (EEVS). 2-epi-5-epi-valiolone synthases catalyze the cyclization of sedoheptulose 7-phosphate to 2-epi-5-epi-valiolone in the biosynthesis of C(7)N-aminocyclitol-containing products. The cyclization product  2-epi-5-epi-valiolone ((2S 3S 4S 5R)-5-(hydroxymethyl)cyclohexanon-2 3 4 5-tetrol)  is a precursor of the valienamine moiety. The valienamine unit is responsible for their biological activities as various glycosidic hydrolases inhibitors. Two important microbial secondary metabolites  i.e.  validamycin and acarbose  are used in agricultural and biomedical applications. Validamycine A is an antifungal antibiotic which has a strong trehalase inhibitory activity and has been used to control sheath blight disease in rice caused by Rhizoctonia solani. Acarbose is an alpha-glucosidase inhibitor used for the treatment of type II insulin-independent diabetes. Salbostatin produced by Streptomyces albus also belongs to this family. It exhibits strong trehalase inhibitory activity.]---[PLN02834  PLN02834  3-dehydroquinate synthase.]---[cd08169  DHQ-like  Dehydroquinate synthase-like which includes dehydroquinate synthase  2-deoxy-scyllo-inosose synthase  and 2-epi-5-epi-valiolone synthase. Dehydroquinate synthase-like. This group contains dehydroquinate synthase  2-deoxy-scyllo-inosose synthase  and 2-epi-5-epi-valiolone synthase. They exhibit the dehydroquinate synthase structural fold. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds.  2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-Deoxystreptamine (DOS)-containing aminoglycoside antibiotics includes neomycin  kanamycin  gentamicin  and ribostamycin. 2-epi-5-epi-valiolone synthases catalyze the cyclization of sedoheptulose 7-phosphate to 2-epi-5-epi-valiolone in the biosynthesis of C(7)N-aminocyclitol-containing products. The cyclization product  2-epi-5-epi-valiolone ((2S 3S 4S 5R)-5-(hydroxymethyl)cyclohexanon-2 3 4 5-tetrol)  is a precursor of the valienamine moiety. The valienamine unit is responsible for their biological activities as various glycosidic hydrolases inhibitors. Two important microbial secondary metabolites  i.e. validamycin and acarbose  are used in agricultural and biomedical applications.]---[cd08195  DHQS  Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway  which involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds  is found in bacteria  microbial eukaryotes  and plants  but not in mammals. Therefore  enzymes of this pathway are attractive targets for the development of non-toxic antimicrobial compounds  herbicides and anti-parasitic agents. The activity of DHQS requires nicotinamide adenine dinucleotide (NAD) as cofactor. A single active site in DHQS catalyzes five sequential reactions involving alcohol oxidation  phosphate elimination  carbonyl reduction  ring opening  and intramolecular aldol condensation. The binding of substrates and ligands induces domain conformational changes. In some fungi and protozoa  this domain is fused with the other four domains in shikimate pathway and forms a penta-domain AROM protein  which catalyzes steps 2-6 in the shikimate pathway.]---[pfam01761  DHQ_synthase  3-dehydroquinate synthase. The 3-dehydroquinate synthase EC 4.6.1.3 domain is present in isolation in various bacterial 3-dehydroquinate synthases and also present as a domain in the pentafunctional AROM polypeptide. 3-dehydroquinate (DHQ) synthase catalyses the formation of dehydroquinate (DHQ) and orthophosphate from 3-deoxy-D-arabino heptulosonic 7 phosphate. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids.]---[COG0337  AroB  3-dehydroquinate synthetase  Amino acid transport and metabolism .]---[PRK00002  aroB  3-dehydroquinate synthase  Reviewed.]---[TIGR01357  3-dehydroquinate_synthase  3-dehydroquinate synthase.  This model represents 3-dehydroquinate synthase  the enzyme catalyzing the second of seven steps in the shikimate pathway of chorismate biosynthesis. Chorismate is the last common intermediate in the biosynthesis of all three aromatic amino acids.  Amino acid biosynthesis  Aromatic amino acid family .]---[PRK06203  aroB  3-dehydroquinate synthase  Reviewed.]---[cd08198  DHQS-like2  Dehydroquinate synthase (DHQS)-like. DHQS catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis. Dehydroquinate synthase-like proteins. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. The activity of DHQS requires NAD as cofactor. Proteins of this family share sequence similarity and functional motifs with that of dehydroquinate synthase  but the specific function has not been characterized.]---[cd08197  DOIS  2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-Deoxystreptamine (DOS)-containing aminoglycoside antibiotics includes neomycin  kanamycin  gentamicin  and ribostamycin. They are important antibacterial agents. DOIS is a homologue of the dehydroquinate synthase which catalyzes the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate (DHQ) in the shikimate pathway.]---[PRK14021  PRK14021  bifunctional shikimate kinase/3-dehydroquinate synthase  Provisional.]---[cd08196  DHQS-like1  Dehydroquinate synthase (DHQS)-like. DHQS catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis. Dehydroquinate synthase-like proteins. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. The activity of DHQS requires NAD as cofactor. Proteins of this family share sequence similarity and functional motifs with that of dehydroquinate synthase  but the specific function has not been characterized.]---[TIGR04425  3-dehydroquinate_synthase  putative sugar phosphate phospholyase (cyclizing). Members of this family tend to be found in O-antigen biosynthesis regions. Members frequently are misidentified as the closely related 3-dehydroquinate synthase  AroB (see family TIGR01357)  the phospholyase that converts 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate to 3-dehydroquinate during chorismate biosynthesis. Most bacteria with this enzyme have a true AroB in a chorismate biosynthesis gene cluster.  Biosynthesis of cofactors  prosthetic groups  and carriers  Lipoate .]---[PRK13951  PRK13951  bifunctional shikimate kinase/3-dehydroquinate synthase  Provisional.]---[cd07766  DHQ_Fe-ADH  Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH). Dehydroquinate synthase-like. This superfamily divides into two subgroups  the dehydroquinate synthase-like  and a large metal-containing  alcohol dehydrogenases (ADH)  known as iron-containing alcohol dehydrogenases. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. Dehydroquinate synthase-like group includes dehydroquinate synthase  2-deoxy-scyllo-inosose synthase  and 2-epi-5-epi-valiolone synthase. The alcohol dehydrogenases in this superfamily contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases  Zinc-containing long-chain alcohol dehydrogenases  insect-type  or short-chain alcohol dehydrogenases  iron-containing alcohol dehydrogenases  and others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases  but lacks sequence homology  and differs in strand arrangement. ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)  to NAD(P)H.]---[pfam13685  Fe-ADH_2  Iron-containing alcohol dehydrogenase. ]---[COG0371  GldA  Glycerol dehydrogenase and related enzymes  Energy production and conversion ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0121160.1",574877,"test3397.tree",0.403,0.803315068493151,"medium",0.626,0.786753424657534,"high",2835,"P97789","5'-3' exoribonuclease 1","COG5049]---[pfam03159","COG5049  XRN1  5'-3' exonuclease  DNA replication  recombination  and repair / Cell division and chromosome partitioning / Translation .]---[pfam03159  XRN_N  XRN 5'-3' exonuclease N-terminus. This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC 3.1.11.-. Thus  the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalyzing cytoplasmic mRNA degradation in multiple decay pathways  whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus."]
["PSNMU-V1.4_AUG-EV-PASAV3_0122040.1",574987,"test33949.tree",1,0.76375,"high",1,0.714875,"high",1017,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0122800.1",575060,"test43195.tree",1,0.774833333333333,"high",1,0.769666666666667,"high",737,"-","-","-","-"]
["PSNMU-V1.4_AUG-EV-PASAV3_0123890.1",575154,"test6113.tree",0.285,0.792046511627907,"medium",0.435,0.805162790697675,"medium",1785,"Q9GPF1","AP-3 complex subunit mu","cd09252]---[pfam00928]---[cd09260]---[cd09261]---[cd09251]---[cd09250]---[cd07954]---[cd09253]---[cd09258]---[cd09259]---[cd09256]---[cd09255]---[cd09262",{"$cut":{"chars":22721,"head":"cd09252  AP-3_Mu3_Cterm  C-terminal domain of medium Mu3 subunit in adaptor protein (AP) complex AP-3. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes  AP-1  AP-2  AP-3  and AP-4  described in various eukaryotic organisms. Each AP complex consists of four subunits  two large chains (one each of gamma/alpha/delta/epsilon and beta1-4  respectively)  a medium mu chain (mu1-4)  and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3 subunit  which includes two closely related homologs  mu3A (P47A  encoded by ap3m1) and mu1B (P47B  encoded by ap3m2). Mu3A is ubiquitously expressed  but mu3B is specifically expressed in neurons and neuroendocrine cells. AP-3 is particularly important for targeting integral membrane proteins to lysosomes and lysome-related organelles at trans-Golgi network (TGN) and/or endosomes  such as the yeast vacuole  fly pigment granules and mammalian melanosomes  platelet dense bodies and the secretory lysosomes of cytotoxic T lymphocytes. Unlike AP-1 and AP-2  which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles  the nature of the outer shell of AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi  where Y is tyrosine  X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu  Ile  Met  Phe  or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3 subunit  also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets  one for the tyrosine-binding and one for the bulky hydrophobic residue-binding.]---[pfam00928  Adap_comp_sub  Adaptor complexes medium subunit family.  This family also contains members which are coatomer subunits.]---[cd09260  AP-3_Mu3A_Cterm  C-terminal domain of medium Mu3A subunit in ubiquitously expressed adaptor protein (AP) complex AP-3. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes  AP-1  AP-2  AP-3  and AP-4  described in various eukaryotic organisms. Each AP complex consists of four subunits  two large chains (one each of gamma/alpha/delta/epsilon and beta1-4  respectively)  a medium mu chain (mu1-4)  and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3A subunit encoded by ap3m1gene. Mu3A is ubiquitously expressed in all mammalian tissues and cells. It appears to be localized to the trans-Golgi network (TGN) and/or endosomes and participates in trafficking to the vacuole/lysosome in yeast  flies  and mammals. Unlike AP-1 and AP-2  which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles  the nature of the outer shell of ubiquitous AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi  where Y is tyrosine  X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu  Ile  Met  Phe  or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3A subunit  a"}}]
["PSNMU-V1.4_AUG-EV-PASAV3_0124170.1",575181,"test14142.tree",0.938,0.7094,"high",0.947,0.7613,"high",823,"-","-","pfam01242]---[COG0720]---[TIGR00039]---[TIGR03367","pfam01242  PTPS  6-pyruvoyl tetrahydropterin synthase. 6-Pyruvoyl tetrahydrobiopterin synthase catalyses the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin  the second of three enzymatic steps in the synthesis of tetrahydrobiopterin from GTP. The functional enzyme is a hexamer of identical subunits.]---[COG0720  COG0720  6-pyruvoyl-tetrahydropterin synthase  Coenzyme metabolism .]---[TIGR00039  Putative_6-carboxy-5678-tetrahydropterin_synthase  6-pyruvoyl tetrahydropterin synthase/QueD family protein. This model has been downgraded from hypothetical_equivalog to subfamily. The animal enzymes are known to be 6-pyruvoyl tetrahydropterin synthase. The function of the bacterial branch of the sequence lineage had been thought to be the same  but many are now taken to be QueD  and enzyme of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of some tRNAs in most species. A new model is built to be the QueD equivalog model.  Protein synthesis  tRNA and rRNA base modification .]---[TIGR03367  queuosine_QueD  queuosine biosynthesis protein QueD.  Members of this protein family  closely related to eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase enzymes  are the QueD protein of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of tRNAs for Tyr  His  Asp  and Asn in many species. This modification  although widespread  appears not to be important for viability. The queuosine precursor made by this enzyme may be converted instead to archeaosine as in some Archaea.  Protein synthesis  tRNA and rRNA base modification ."]
["PSNMU-V1.4_AUG-EV-PASAV3_0124830.1",575244,"test2730.tree",0.651,0.798489130434783,"high",0.638,0.813152173913044,"high",875,"Q9LR30","Glutamate--glyoxylate aminotransferase 1","PTZ00377]---[PTZ00377]---[PLN02368]---[PLN02368]---[PLN02231]---[PLN02231]---[cd00609]---[PRK09265]---[COG0436]---[pfam00155]---[PRK13355]---[PRK08363]---[TIGR01265]---[PRK07683]---[TIGR01264]---[PLN02607]---[PRK06855]---[PRK05764]---[PRK07682]---[PRK07309]---[PRK07568]---[PRK06107]---[PLN02187","PTZ00377  PTZ00377  alanine aminotransferase  Provisional.]---[PLN02368  PLN02368  alanine transaminase.]---[PLN02231  PLN02231  alanine transaminase.]---[cd00609  AAT_like  Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate  which depending on the reaction  is the substrate in four kinds of reactions (1) transamination (movement of amino groups)  (2) racemization (redistribution of enantiomers)  (3) decarboxylation (removing COOH groups)  and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha  beta and gamma classes  based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes  and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. The major groups in this CD corresponds to Aspartate aminotransferase a  b and c  Tyrosine  Alanine  Aromatic-amino-acid  Glutamine phenylpyruvate  1-Aminocyclopropane-1-carboxylate synthase  Histidinol-phosphate  gene products of malY and cobC  Valine-pyruvate aminotransferase and Rhizopine catabolism regulatory protein.]---[PRK09265  PRK09265  aminotransferase AlaT  Validated.]---[COG0436  COG0436  Aspartate/tyrosine/aromatic aminotransferase  Amino acid transport and metabolism .]---[pfam00155  Aminotran_1_2  Aminotransferase class I and II. ]---[PRK13355  PRK13355  bifunctional HTH-domain containing protein/aminotransferase  Provisional.]---[PRK08363  PRK08363  alanine aminotransferase  Validated.]---[TIGR01265  tyrosine_aminotransferase  tyrosine/nicotianamine family aminotransferase. This subfamily of pyridoxal phosphate-dependent enzymes includes known examples of both tyrosine aminotransferase from animals and nicotianamine aminotransferase from barley.]---[PRK07683  PRK07683  aminotransferase A  Validated.]---[TIGR01264  tyrosine_aminotransferase  tyrosine aminotransferase  eukaryotic. This model describes tyrosine aminotransferase as found in animals and Trypanosoma cruzi. It is the first enzyme of a pathway of tyrosine degradation via homogentisate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase  an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway. These plant sequences are excluded from the model seed and score between the trusted an noise cutoffs.  Energy metabolism  Amino acids and amines .]---[PLN02607  PLN02607  1-aminocyclopropane-1-carboxylate synthase.]---[PRK06855  PRK06855  aminotransferase  Validated.]---[PRK05764  PRK05764  aspartate aminotransferase  Provisional.]---[PRK07682  PRK07682  hypothetical protein  Validated.]---[PRK07309  PRK07309  aromatic amino acid aminotransferase  Validated.]---[PRK07568  PRK07568  aspartate aminotransferase  Provisional.]---[PRK06107  PRK06107  aspartate aminotransferase  Provisional.]---[PLN02187  PLN02187  rooty/superroot1."]

{"sheet":"Supplementary table S9","index":4,"n_rows":18,"n_cols":9,"rows_kept":18,"cut":false,"hidden":false,"merged":[[0,0,0,8]]}
["Table S9. Summary statistics of RNA-seq reads mapping results for Pseudo-nitzschia multistriata samples. Strains B938 and B857 were used in experiment 1, strains B956 and B939 were used in experiment 2."]
["Sample name","Sample ID","MT","Treatment","Time point","Library Code","Input reads","Unique mapped reads","% mapped reads"]
["VF2.4","B938"," +","Control","2 hours",33,25608372,18173601,{"$f":"(H3/G3)*100","v":70.9674203420663}]
["VF2.4","B938"," +","Sexualised","2 hours",35,23193297,18779125,{"$f":"(H4/G4)*100","v":80.9678977508028}]
["VF2.5","B857"," -","Control","2 hours",37,24216508,21623700,{"$f":"(H5/G5)*100","v":89.2932209714134}]
["VF2.5","B857"," -","Sexualised","2 hours",39,20757476,18243176,{"$f":"(H6/G6)*100","v":87.8872556567089}]
["VF2.3","B856"," +","Control","2 hours",66,18442509,16832241,{"$f":"(H7/G7)*100","v":91.2687151189678}]
["VF2.3","B856"," +","Sexualised","2 hours",67,16840957,15352298,{"$f":"(H8/G8)*100","v":91.1604845259091}]
["GM 50b","B939"," -","Control","2 hours",69,20661659,17863361,{"$f":"(H9/G9)*100","v":86.4565667258375}]
["GM50b","B939"," -","Sexualised","2 hours",71,21557084,18325039,{"$f":"(H10/G10)*100","v":85.0070399131905}]
["VF2.4","B938"," +","Control","6 hours",41,28133282,22195156,78.89]
["VF2.4","B938"," +","Sexualised","6 hours",44,28930754,23121135,79.92]
["VF2.5","B857"," -","Control","6 hours",45,33589434,29311998,87.27]
["VF2.5","B857"," -","Sexualised","6 hours",48,25209373,21847799,86.67]
["VF2.3","B856"," +","Control","6 hours",74,19055343,17105134,89.77]
["VF2.3","B856"," +","Sexualised","6 hours",76,20592431,18507677,89.88]
["GM 50b","B939"," -","Control","6 hours",77,27503548,23494275,85.44]
["GM50b","B939"," -","Sexualised","6 hours",79,17427724,14927418,85.65]

{"sheet":"Supplementary table S12","index":5,"n_rows":11,"n_cols":4,"rows_kept":11,"cut":false,"hidden":false,"merged":[]}
["Table S12. Statistics of genes differentially expressed during two stages of sexual reproduction"]
[]
["T1 (2 hours)","Sex_vs_Control","MT+","MT-"]
["Total no. of upregulated genes",31,32,188]
["Total no. of downregulated genes",19,110,44]
["Total no of differentially expressed genes",{"$f":"+SUM(B4:B5)","v":50},{"$f":"+SUM(C4:C5)","v":142},{"$f":"+SUM(D4:D5)","v":232}]
[]
["T2 (6 hours)","Sex_vs_Control","MT+","MT-"]
["Total no. of upregulated genes",381,36,182]
["Total no. of downregulated genes",456,5,269]
["Total no of differentially expressed genes",{"$f":"+SUM(B9:B10)","v":837},{"$f":"+SUM(C9:C10)","v":41},{"$f":"+SUM(D9:D10)","v":451}]