TABLE 7.
Protein-coding genes in the hypothetical minimal actinobacterial cells
| ORF designationa | Prominent features |
|---|---|
| BL0053 | Mrp; COG family, ATPases involved in chromosome partitioning; PFAM_ID, DUF59; PFAM_ID, fer4_NifH |
| BL0065 | Involved in peptide bond synthesis; alters affinity of the ribosome for aminoacyl-tRNA |
| BL0067 | Composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate |
| BL0068 | CarB |
| BL0070 | Gmp kinase; COG family, guanylate kinase; PFAM_ID, Guanylate_kin |
| BL0097 | Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-d-xylulose-5-phosphate (DXP) to 2-C-methyl-d-erythritol 4-phosphate |
| BL0100 | Involved in DNA repair and recF pathway recombination |
| BL0118 | GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA interact with and regulate FtsZ function |
| BL0193 | COG family, Mg-dependent DNase; PFAM_ID, TatD_DNase |
| BL0291 | Pantetheine-phosphate adenylyltransferase; PpaT; dephospho-CoA pyrophosphorylase; CoaD; COG family, phosphopantetheine adenylyltransferase; PFAM_ID, Cytidylyltransf |
| BL0295 | RNase III; RncS; COG family, double-stranded-RNA-specific RNase; PFAM_ID, Ribonuclease_3; PFAM_ID, dsrm |
| BL0305 | RpsP; COG family, ribosomal protein S16; PFAM_ID, Ribosomal_S16 |
| BL0327 | M1g-methyltransferase; tRNA [GM37] methyltransferase; TrmD; COG family, tRNA-(guanine-N1)-methyltransferase; PFAM_ID, tRNA_m1G_MT |
| BL0328 | COG family, N6-adenine-specific methylase |
| BL0358 | AtpG; COG family, F0F1-type ATP synthase gamma subunit; PFAM_ID, ATP-synt |
| BL0395 | Catalyzes formation of valyl-tRNA(Val) from valine and tRNA(Val) |
| BL0402 | Allows formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases |
| BL0413 | RplI; COG family, ribosomal protein L9; PFAM_ID, Ribosomal_L9 |
| BL0431 | DnaB; COG family, replicative DNA helicase; PFAM_ID, DnaB |
| BL0499 | COG family, recombinational DNA repair protein; PFAM_ID, RecR; PFAM_ID, Toprim |
| BL0500 | Plays a role in assembling DnaB onto the primer template and interacts with the core polymerase |
| BL0519 | Hsp-70 cofactor; GrpE; COG family, molecular chaperone GrpE (heat shock protein); PFAM_ID, GrpE |
| BL0549 | Catalyzes formation of N6-(1,2,-dicarboxyethyl)-AMP from l-aspartate, IMP, and GTP in AMP biosynthesis |
| BL0637 | COG family, recombinational DNA repair ATPase |
| BL0640 | DnaA; COG family, ATPase involved in DNA replication initiation; PFAM_ID, AAA; PFAM_ID, bac_DNAA |
| BL0648 | ParB; COG family, predicted transcriptional regulators; PFAM_ID, ParBc |
| BL0703 | UvrC; COG family, nuclease subunit of the excinuclease complex; PFAM_ID, Exci_endo_N; PFAM_ID, UVR; PFAM_ID, HHH |
| BL0706 | COG family, uncharacterized Bcr; PFAM_ID, DUF199 |
| BL0707 | Catalyzes formation of 3-phospho-d-glyceroyl phosphate from 3-phospho-d-glycerate |
| BL0726 | COG family, uncharacterized Acr; PFAM_ID, DUF28 |
| BL0727 | Cleaves the cruciform structure in supercoiled DNA by nicking strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms |
| BL0728 | COG family, Holliday junction resolvasome DNA-binding subunit; PFAM_ID, RuvA; PFAM_ID, RuvA_II |
| BL0729 | COG family, Holliday junction resolvasome helicase subunit; PFAM_ID, AAA |
| BL0735 | Involved in de novo purine biosynthesis |
| BL0848 | Binds to the ribosome on the universally conserved alpha-sarcin loop |
| BL0849 | RpsT; COG family, ribosomal protein S20; PFAM_ID, Ribosomal_S20p |
| BL0859 | Bex; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds cell membrane through apparent C-terminal domain |
| BL0861 | COG family, predicted metal-dependent hydrolase; PFAM_ID, UPF0054 |
| BL0870 | COG family, iron-regulated ABC transporter ATPase subunit SufC; PFAM_ID, ABC_tran |
| BL0878 | Catalyzes formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis |
| BL0881 | COG family, predicted endonuclease involved in recombination (possible Holliday junction resolvase in mycoplasmas and B. subtilis) |
| BL0926 | COG family, predicted GTPase |
| BL0943 | Binds and unfolds substrates as part of the ClpXP protease |
| BL0947 | Tig; RopA; peptidyl-prolyl cis/trans-isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer |
| BL0960 | Contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway |
| BL0964 | N-Acetylglucosamine-1-phosphate uridyltransferase; Tms protein; GlmU; COG family, N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains); PFAM_ID, NTP_transferase |
| BL0990 | UvrABC repair system catalyzes recognition and processing of DNA lesions; beta-hairpin of the UvrB subunit is inserted between the strands, where it probes for the presence of a lesion |
| BL0992 | Binds mRNA to the ribosomes and plays a role in delivering transfer mRNA to stalled ribosomes |
| BL1032 | Transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD), which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria |
| BL1043 | Recombination protein N; COG family, ATPases involved in DNA repair |
| BL1051 | Tyrosine-tRNA ligase; TyrRS; TyrS; COG family, tyrosyl-tRNA synthetase; PFAM_ID, tRNA-synt_1b; PFAM_ID, S4 |
| BL1066 | Phenylalanine-tRNA ligase beta chain; PheRS; PheT; COG family, emap domain |
| BL1067 | Catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesiusm |
| BL1099 | One of the primary rRNA-binding proteins; binds directly to 16S rRNA, where it nucleates assembly of the head domain of the 30S subunit; is located at the subunit interface close to the decoding center |
| BL1100 | Important for translational accuracy; interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit |
| BL1108 | PurL |
| BL1121 | Glutamine phosphoribosylpyrophosphate amidotransferase; PurF; COG family, glutamine phosphoribosylpyrophosphate amidotransferase; PFAM_ID, GATase_2; PFAM_ID, Pribosyltran |
| BL1122 | Catalyzes formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1- (5-phosphoribosyl)acetamidine and ATP in purine biosynthesis |
| BL1123 | GarS; glycinamide ribonucleotide synthetase; phosphoribosylglycinamide synthetase; PurD; COG family, phosphoribosylamine-glycine ligase; PFAM_ID, GARS_N; PFAM_ID, GARS_B; PFAM_ID, GARS; PFAM_ID, GARS_C |
| BL1130 | Air carboxylase; AirC; PurE; COG family, phosphoribosylcarboxyaminoimidazole (ncair) mutase; PFAM_ID, AIRC |
| BL1180 | Binds to ssrA RNA and is required for its successful binding to ribosomes |
| BL1182 | FtsX; COG family, cell division protein; PFAM_ID, DUF214 |
| BL1187 | MrsA; COG family, phosphomannomutase; PFAM_ID, PGM_PMM_I; PFAM_ID, PGM_PMM_II; PFAM_ID, PGM_PMM_III; PFAM_ID, PGM_PMM |
| BL1192 | COG family, predicted hydrolase of the metallo-beta-lactamase superfamily; PFAM_ID, lactamase_B; PFAM_ID, UPF0036 |
| BL1204 | DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates |
| BL1275 | HK; ThrB; COG family, homoserine kinase; PFAM_ID, GHMP_kinases |
| BL1282 | RplU; COG family, ribosomal protein L21; PFAM_ID, Ribosomal_L21p |
| BL1283 | Function of this ribosomal subunit is unknown |
| BL1284 | Obg; COG family, predicted GTPase; PFAM_ID, GTP1_OBG |
| BL1288 | NusG; COG family, transcription antiterminator; PFAM_ID, NusG |
| BL1312 | COG family, predicted transcriptional regulator; consists of a Zn-ribbon and ATP-cone domains; PFAM_ID, DUF193 |
| BL1316 | COG family, predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis; PFAM_ID, Methyltransf_5 |
| BL1320 | Catalyzes binding of UDP-N-acetylmuramoyl(pentapeptide) to bactoprenol to produce lipid I in peptidoglycan synthesis |
| BL1321 | UDP-N-acetylmuramoyl-l-alanyl-d-glutamate synthetase; d-glutamic acid-adding enzyme; MurD; COG family, UDP-N-acetylmuramoylalanine-d-glutamate ligase; PFAM_ID, Mur_ligase; PFAM_ID, Mur_ligase_C |
| BL1323 | UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane associated; last step of peptidoglycan synthesis |
| BL1324 | UDP-N-acetylmuramoyl-l-alanine synthetase; MurC; COG family, UDP-N-acetylmuramate-alanine ligase; PFAM_ID, Mur_ligase; PFAM_ID, Mur_ligase; PFAM_ID, Mur_ligase_C |
| BL1366 | InfC; COG family, translation initiation factor If3; PFAM_ID, IF3 |
| BL1366a | RpmI; COG family, ribosomal protein L35; PFAM_ID, Ribosomal_L35p |
| BL1367 | Protein binds directly to 23S rRNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit |
| BL1415 | Catalyzes hydrolysis of ATP in the presence of single-stranded DNA, ATP-dependent uptake of single-stranded DNA by duplex DNA, and ATP-dependent hybridization of homologous single-stranded DNAs |
| BL1438 | dUTPase; dUTP pyrophosphatase; DutP; COG family, dUTPase; PFAM_ID, dUTPase |
| BL1450 | Leucine-tRNA ligase; LeuRS; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA |
| BL1503 | Essential for binding of S1 to the small ribosomal subunit |
| BL1504 | EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP, resulting in regeneration of the active form of EF-Tu |
| BL1505 | UK; UMP kinase; UMP kinase; PyrH; COG family, uridylate kinase; PFAM_ID, aakinase |
| BL1506 | Ribosome-releasing factor; Frr; COG family, ribosome-recycling factor; PFAM_ID, RRF |
| BL1507 | CDP-diglyceride synthetase; CDP-diglyceride pyrophosphorylase; CDP-diacylglycerol synthase; CdsA; COG family, CDP-diglyceride synthetase; PFAM_ID, Cytidylyltrans |
| BL1545a | RpsO; COG family, ribosomal protein S15p/S13e; PFAM_ID, Ribosomal_S15 |
| BL1546 | Polynucleotide phosphorylase; Pnpase; COG family, polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase); PFAM_ID, RNase_PH; PFAM_ID, RNase_PH; PFAM_ID, KH-domain; PFAM_ID, S1 |
| BL1549 | Binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit |
| BL1550 | RplL; COG family, ribosomal protein L7/L12; PFAM_ID, Ribosomal_L12 |
| BL1558 | GroES; COG family, cochaperonin GroES (Hsp10); PFAM_ID, cpn10 |
| BL1571 | L13 is associated with the antitermination complex |
| BL1572 | RpsI; COG family, ribosomal protein S9; PFAM_ID, Ribosomal_S9 |
| BL1577 | Involved in the binding of tRNA to the ribosomes |
| BL1578 | RplC; COG family, ribosomal protein L3; PFAM_ID, Ribosomal_L3 |
| BL1579 | Subunit important during the early stages of 50S assembly, initially binding near the 5′ end of the 23S rRNA |
| BL1580 | Binds signal recognition particle and trigger factor at the peptide exit area on the 50S ribosome |
| BL1581 | One of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding, and for peptide bond formation |
| BL1582 | RpsS; COG family, ribosomal protein S19; PFAM_ID, Ribosomal_S19 |
| BL1583 | RplV; COG family, ribosomal protein L22; PFAM_ID, Ribosomal_L22 |
| BL1584 | Forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation |
| BL1586 | Located in the peptidyl transferase center and may be involved in peptidyl transferase activity |
| BL1588 | RpmC; COG family, ribosomal protein L29; PFAM_ID, Ribosomal_L29 |
| BL1589 | RpsQ; COG family, ribosomal protein S17; PFAM_ID, Ribosomal_S17 |
| BL1590 | RplN; COG family, ribosomal protein L14; PFAM_ID, Ribosomal_L14 |
| BL1591 | RplX; COG family, ribosomal protein L24; PFAM_ID, Ribosomal_L24 |
| BL1592 | Mediates attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance |
| BL1594 | Binds directly to 16S rRNA central domain, where it helps coordinate assembly of the platform of the 30S subunit |
| BL1595 | RplF; COG family, ribosomal protein L6; PFAM_ID, Ribosomal_L6 |
| BL1596 | RplR; COG family, ribosomal protein L18; PFAM_ID, Ribosomal_L18p |
| BL1597 | Located at the back of the 30S subunit body, where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy |
| BL1599 | Associates with 23S rRNA and is involved in 50S ribosome assembly |
| BL1600 | With SecE and SecG forms a protein conduction channel in the inner membrane |
| BL1604 | Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA |
| BL1604.1 | Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome |
| BL1607 | RplQ; COG family, ribosomal protein L17; PFAM_ID, Ribosomal_L17 |
| BL1615 | Binds to RNA polymerase and RNA; stimulates rho-independent termination by promoting hairpin formation; also interacts with N protein and prevents hairpin formation, thereby preventing termination |
| BL1616 | Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis; also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex |
| BL1618 | tRNA pseudouridine 55 synthase; Psi55 synthase; pseudouridylate synthase; uracil hydrolyase; TruB; COG family, pseudouridine synthase; PFAM_ID, TruB_N |
| BL1619 | Fad pyrophosphorylase; Fad synthetase; RibF; COG family, FAD synthase; PFAM_ID, FAD_Synth |
| BL1777 | Catalyzes formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile) |
| BL0642 | RpmH; COG family, ribosomal protein L34; PFAM_ID, Ribosomal_L34 |
a
The ORF designations refer to those of B. longum biotype longum NCC2705 (384).