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| | proS | Proline--tRNA ligase; Catalyzes the attachment of proline to tRNA(Pro) in a two- step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacy [...] (571 aa) |
| | PP_3994 | Putative tRNA 5-methylaminomethyl-2-thiouridine synthase (tusC-like); Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; enzyme; Centralintermediarymetabolism : Sulfur metabolism; Belongs to the DsrF/TusC family. (119 aa) |
| | tusD | Sulfur transfer protein complex, TusD subunit; Function of homologous gene experimentally demonstrated in an other organism; enzyme; Centralintermediarymetabolism : Sulfur metabolism. (130 aa) |
| | PP_3913 | Protein of unknown function; No homology to any previously reported sequences; Unknown function. (225 aa) |
| | PP_3893 | Putative Phage DNA helicase; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology. (465 aa) |
| | csrA-3 | Carbon storage regulator (csrA-like); A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems. Usually binds in the 5'-UTR; binding at or near the Shine-Dalgarno sequence prevents ribosome-binding, repressing translation, binding elsewhere in the 5'-UTR can activate translation and/or stabilize the mRNA. Its function is antagonized by small RNA(s). (65 aa) |
| | PP_3811 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (294 aa) |
| | fecI | RNA polymerase, sigma 19 factor; Function of homologous gene experimentally demonstrated in an other organism; regulator; Transcription; Belongs to the sigma-70 factor family. ECF subfamily. (170 aa) |
| | trmK | tRNA (adenine(22)-N(1))-methyltransferase; Function of homologous gene experimentally demonstrated in an other organism; enzyme; Biologicalprocesses : Construct biomass (Anabolism). (230 aa) |
| | PP_3307 | Homologs of previously reported genes of unknown function. (126 aa) |
| | paaX | DNA-binding transcriptional repressor PaaX(phenylacetyl-CoA); Function of homologous gene experimentally demonstrated in an other organism; regulator; Energy metabolism. (307 aa) |
| | ligD | DNA ligase D; Function of homologous gene experimentally demonstrated in an other organism; enzyme; DNAmetabolism : DNA replication, recombination, and repair. (833 aa) |
| | PP_3143 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (313 aa) |
| | PP_3086 | Putative RNA polymerase sigma-70 factor; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Belongs to the sigma-70 factor family. ECF subfamily. (168 aa) |
| | PP_3006 | RNA polymerase sigma-70 factor, ECF subfamily. (182 aa) |
| | PP_2952 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (296 aa) |
| | yoeB | Toxin of the YefM-YoeB antitoxin/toxin complex and DNA-binding transcriptional repressor; Function of homologous gene experimentally demonstrated in an other organism; factor; Cellularprocesses : Toxin production and resistance. (84 aa) |
| | PP_2927 | Homologs of previously reported genes of unknown function. (348 aa) |
| | lhgO | L-2-hydroxyglutarate oxidase; Function experimentally demonstrated in the studied genus; enzyme; Energy metabolism. (416 aa) |
| | cysS | Cysteine--tRNA ligase; Belongs to the class-I aminoacyl-tRNA synthetase family. (460 aa) |
| | glnS | Glutamine--tRNA ligase. (567 aa) |
| | PP_2888 | Putative ECF sigma factor PrtI; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Belongs to the sigma-70 factor family. ECF subfamily. (173 aa) |
| | PP_2534 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (299 aa) |
| | PP_2524 | HD domain protein. (218 aa) |
| | PP_2502 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (308 aa) |
| | pheT | Phenylalanine--tRNA ligase beta subunit; Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 1 subfamily. (793 aa) |
| | pheS | Phenylalanine--tRNA ligase alpha subunit; Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. (338 aa) |
| | thrS | Threonine--tRNA ligase; Catalyzes the attachment of threonine to tRNA(Thr) in a two- step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr). (640 aa) |
| | PP_2431 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (307 aa) |
| | PP_2390 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (306 aa) |
| | PP_2270 | Putative DNA primase/helicase protein; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; putative enzyme; Unknownfunction : Enzymes of unknown specificity. (483 aa) |
| | PP_2266 | DNA-directed RNA polymerase, bacteriophage and mitochondrial type. (852 aa) |
| | PP_2188 | Putative tRNA-(Ms(2)io(6)a)-hydroxylase; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology. (205 aa) |
| | PP_2176 | Transcriptional regulator, LysR family; Function of strongly homologous gene; regulator; Regulatory functions; Belongs to the LysR transcriptional regulatory family. (309 aa) |
| | dusA | tRNA-dihydrouridine synthase A; Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U20 and U20a in tRNAs; Belongs to the Dus family. DusA subfamily. (336 aa) |
| | tusA-II | Sulfurtransferase; Sulfur carrier protein which probably makes part of a sulfur- relay system; Belongs to the sulfur carrier protein TusA family. (80 aa) |
| | rlmM | Ribosomal RNA large subunit methyltransferase M; Catalyzes the 2'-O-methylation at nucleotide C2498 in 23S rRNA; Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA methyltransferase RlmE family. RlmM subfamily. (354 aa) |
| | PP_2110 | Putative ribosomal large subunit pseudouridine synthase; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; putative enzyme; Protein synthesis. (301 aa) |
| | rlmKL | Fused 23S rRNA m2G2445 methyltransferase and 23S rRNA m7G2069 methyltransferase; Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA. Belongs to the methyltransferase superfamily. RlmKL family. (745 aa) |
| | PP_2088 | RNA polymerase sigma factor SigX; Belongs to the sigma-70 factor family. ECF subfamily. (196 aa) |
| | truA | tRNA pseudouridine (38-40)synthase; Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. (286 aa) |
| | dusC | tRNA-dihydrouridine synthase C; Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U16 in tRNAs. Belongs to the Dus family. DusC subfamily. (323 aa) |
| | gltX | Glutamate--tRNA ligase; Catalyzes the attachment of glutamate to tRNA(Glu) in a two- step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu); Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily. (493 aa) |
| | rluC | Ribosomal large subunit pseudouridine synthase C; Responsible for synthesis of pseudouridine from uracil. Belongs to the pseudouridine synthase RluA family. (318 aa) |
| | rne | Ribonuclease E; Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs. Belongs to the RNase E/G family. RNase E subfamily. (1091 aa) |
| | deaD | ATP-dependent DEAD-box RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. (559 aa) |
| | PP_1853 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (312 aa) |
| | PP_1758 | Putative sulfurtransferase containing rhodanese-like domain; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; putative enzyme; Unknownfunction : Enzymes of unknown specificity; Belongs to the UPF0176 family. (310 aa) |
| | bolA | DNA-binding transcriptional dual regulator; Function of homologous gene experimentally demonstrated in an other organism; regulator; Regulatory functions; Belongs to the BolA/IbaG family. (98 aa) |
| | mnmC | methyltransferase/FAD-dependent oxidoreductase; Catalyzes the last two steps in the biosynthesis of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34; In the N-terminal section; belongs to the methyltransferase superfamily. tRNA (mnm(5)s(2)U34)-methyltransferase family. (654 aa) |
| | csrA-2 | Putative carbon storage regulator, csrA-like; A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems. Usually binds in the 5'-UTR; binding at or near the Shine-Dalgarno sequence prevents ribosome-binding, repressing translation, binding elsewhere in the 5'-UTR can activate translation and/or stabilize the mRNA. Its function is antagonized by small RNA(s). (59 aa) |
| | rluA | 23S rRNA (746) and tRNA (32) pseudouridine synthase; Responsible for synthesis of pseudouridine from uracil. Belongs to the pseudouridine synthase RluA family. (211 aa) |
| | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD; Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA; Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily. (452 aa) |
| | ttcA | tRNA 2-thiocytidine biosynthesis protein TtcA; Catalyzes the ATP-dependent 2-thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32). The sulfur atoms are provided by the cysteine/cysteine desulfurase (IscS) system. (274 aa) |
| | yfiP | Conserved protein; Homologs of previously reported genes of unknown function; Unknown function. (236 aa) |
| | rpoS | RNA polymerase, sigma S (sigma 38) factor; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response. (335 aa) |
| | truD | tRNA pseudouridine synthase D; Responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs; Belongs to the pseudouridine synthase TruD family. (352 aa) |
| | tilS | tRNA(Ile)-lysidine synthase; Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. Belongs to the tRNA(Ile)-lysidine synthase family. (427 aa) |
| | rnhB | Ribonuclease HII; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids; Belongs to the RNase HII family. (207 aa) |
| | tcdA | tRNA threonylcarbamoyladenosine dehydratase (t(6)A37 dehydratase); Function of homologous gene experimentally demonstrated in an other organism; enzyme; Proteinsynthesis : tRNA and rRNA base modification. (271 aa) |
| | rsmJ | Ribosomal RNA small subunit methyltransferase J; Specifically methylates the guanosine in position 1516 of 16S rRNA. (258 aa) |
| | tsaB | Endopeptidase; Function of homologous gene experimentally demonstrated in an other organism; enzyme; Proteinsynthesis : tRNA and rRNA base modification. (224 aa) |
| | PP_1497 | Transcriptional regulator, TetR family. (238 aa) |
| | lysS | Lysine--tRNA ligase; Belongs to the class-II aminoacyl-tRNA synthetase family. (500 aa) |
| | trmD | tRNA (guanine-N(1)-)-methyltransferase; Specifically methylates guanosine-37 in various tRNAs. Belongs to the RNA methyltransferase TrmD family. (250 aa) |
| | rimM | Ribosome maturation factor RimM; An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes; Belongs to the RimM family. (178 aa) |
| | cmoA | tRNA (cmo5U34)-methyltransferase; Catalyzes the conversion of S-adenosyl-L-methionine (SAM) to carboxy-S-adenosyl-L-methionine (Cx-SAM). (247 aa) |
| | cmoB | tRNA (mo5U34)-methyltransferase; Catalyzes carboxymethyl transfer from carboxy-S-adenosyl-L- methionine (Cx-SAM) to 5-hydroxyuridine (ho5U) to form 5- carboxymethoxyuridine (cmo5U) at position 34 in tRNAs. (318 aa) |
| | rnc | Ribonuclease 3; Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. (229 aa) |
| | rpoE | RNA polymerase sigma E factor; Function of homologous gene experimentally demonstrated in an other organism; factor; Transcription; Belongs to the sigma-70 factor family. ECF subfamily. (193 aa) |
| | rsuA | Ribosomal small subunit pseudouridine synthase A; Function of homologous gene experimentally demonstrated in an other organism; enzyme; Aminoacidbiosynthesis : Glutamate family; Belongs to the pseudouridine synthase RsuA family. (230 aa) |
| | PP_1393 | Putative transcriptional regulator; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; putative regulator; Regulatory functions; Belongs to the LysR transcriptional regulatory family. (291 aa) |
| | sbcB | Function of homologous gene experimentally demonstrated in an other organism; enzyme; DNAmetabolism : DNA replication, recombination, and repair. (477 aa) |
| | rsmH | Ribosomal RNA small subunit methyltransferase H; Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. (315 aa) |
| | rsmI | 16S rRNA 2'-O-ribose C1402 methyltransferase; Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. (294 aa) |
| | trpS | Tryptophan--tRNA ligase; Catalyzes the attachment of tryptophan to tRNA(Trp). Belongs to the class-I aminoacyl-tRNA synthetase family. (449 aa) |
| | rhlB | ATP-dependent RNA helicase RhlB; DEAD-box RNA helicase involved in RNA degradation. Has RNA- dependent ATPase activity and unwinds double-stranded RNA. Belongs to the DEAD box helicase family. RhlB subfamily. (480 aa) |
| | yhaV | Toxin endoribonuclease of toxin antitoxin system SohB(PrlF)-YhaV; Function of homologous gene experimentally demonstrated in an other organism; enzyme; Transcription. (155 aa) |
| | PP_1236 | Putative Glycine cleavage system transcriptional repressor; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology. (186 aa) |
| | aspS | Aspartate--tRNA ligase; Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn); Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily. (591 aa) |
| | PP_3995 | Homologs of previously reported genes of unknown function. (98 aa) |
| | PP_1199 | Toxin-antitoxin system, higB toxin like; Function of strongly homologous gene; enzyme; Cellularprocesses : Toxin production and resistance. (111 aa) |
| | rimO | Ribosomal protein S12 methylthiotransferase; Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12; Belongs to the methylthiotransferase family. RimO subfamily. (443 aa) |
| | PP_1191 | S4 domain protein. (236 aa) |
| | PP_1189 | Conserved hypothetical protein; Homologs of previously reported genes of unknown function; Unknown function. (232 aa) |
| | PP_1164 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (298 aa) |
| | PP_1111 | Putative Synthetase; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology. (262 aa) |
| | metG | Methionine--tRNA ligase; Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. (679 aa) |
| | rnt | Ribonuclease T; Trims short 3' overhangs of a variety of RNA species, leaving a one or two nucleotide 3' overhang. Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A). Also appears to be involved in tRNA biosynthesis. (224 aa) |
| | ybaK | Cys-tRNAPro deacylase; Function of homologous gene experimentally demonstrated in an other organism; enzyme; Biologicalprocesses : Maintain; Belongs to the prolyl-tRNA editing family. YbaK/EbsC subfamily. (156 aa) |
| | tadA | tRNA-specific adenosine deaminase monomer; Catalyzes the deamination of adenosine to inosine at the wobble position 34 of tRNA(Arg2); Belongs to the cytidine and deoxycytidylate deaminase family. (145 aa) |
| | PP_1008 | RNA polymerase subunit sigma-24; Belongs to the sigma-70 factor family. ECF subfamily. (170 aa) |
| | PP_0994 | Putative RNA polymerase sigma factor; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; putative regulator; Belongs to the sigma-70 factor family. ECF subfamily. (178 aa) |
| | valS | valine--tRNA ligase; Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a 'posttransfer' editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA- dependent manner; Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily. (948 aa) |
| | rlmF | Ribosomal RNA large subunit methyltransferase F; Specifically methylates the adenine in position 1618 of 23S rRNA. (317 aa) |
| | rpoN | RNA polymerase sigma-54 factor; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is responsible for the expression of the xylCAB operon and the xylS gene. The open complex (sigma-54 and core RNA polymerase) serves as the receptor for receipt of the melting signal from the remotely bound activator protein XylR for the expression of the xylCAB operon and xylS. (497 aa) |
| | rng | Endoribonuclease G (RNAse G); Function of homologous gene experimentally demonstrated in an other organism; enzyme; Transcription : Degradation of RNA. (485 aa) |
| | PP_0865 | ECF subfamily RNA polymerase sigma-24 factor; Belongs to the sigma-70 factor family. ECF subfamily. (161 aa) |
| | hisS | Histidine--tRNA ligase. (429 aa) |
| | PP_0852 | Transcriptional regulator, Cro/CI family. (335 aa) |
| | pilF | Type IV pili biogenesis protein PilF. (255 aa) |
| | rlmN | Dual-specificity RNA methyltransferase RlmN; Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity; Belongs to the radical SAM superfamily. RlmN family. (381 aa) |
| | trmJ | tRNA Cm32/Um32 methyltransferase; Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA. (251 aa) |
| | tgt | Queuine tRNA-ribosyltransferase; Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form th [...] (371 aa) |
| | selU | tRNA 2-selenouridine synthase; Involved in the post-transcriptional modification of the uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln). Catalyzes the conversion of 2-thiouridine (S2U-RNA) to 2- selenouridine (Se2U-RNA). Acts in a two-step process involving geranylation of 2-thiouridine (S2U) to S-geranyl-2-thiouridine (geS2U) and subsequent selenation of the latter derivative to 2-selenouridine (Se2U) in the tRNA chain. (370 aa) |
| | chpB | mRNA interferase; Function of homologous gene experimentally demonstrated in an other organism; factor; Regulatory functions. (115 aa) |
| | rsmC | Ribosomal RNA small subunit methyltransferase C; Specifically methylates the guanine in position 1207 of 16S rRNA in the 30S particle; Belongs to the methyltransferase superfamily. RsmC family. (332 aa) |
| | PP_0704 | RNA polymerase sigma-70 factor, ECF subfamily. (171 aa) |
| | PP_0698 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (305 aa) |
| | PP_0676 | Putative Transcription elongation factor; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology. (165 aa) |
| | PP_0667 | RNA polymerase sigma-70 factor, ECF subfamily. (178 aa) |
| | PP_0661 | Putative Transcriptional regulator AmpR; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Belongs to the LysR transcriptional regulatory family. (294 aa) |
| | rluD | 23S rRNA pseudouridine(1911,1915,1917) synthase; Responsible for synthesis of pseudouridine from uracil. Belongs to the pseudouridine synthase RluA family. (320 aa) |
| | ileS | Isoleucine--tRNA ligase; Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile). Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily. (943 aa) |
| | cmoM | Putative Methyltransferase; Catalyzes the methylation of 5-carboxymethoxyuridine (cmo5U) to form 5-methoxycarbonylmethoxyuridine (mcmo5U) at position 34 in tRNAs; Belongs to the class I-like SAM-binding methyltransferase superfamily. CmoM family. (249 aa) |
| | nusB | Transcription antitermination protein; Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. (166 aa) |
| | selA | Selenocysteine synthase; Converts seryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis. (475 aa) |
| | rpoA | DNA-directed RNA polymerase subunit alpha; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (333 aa) |
| | rpoC | DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1399 aa) |
| | rpoB | DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1357 aa) |
| | nusG | Transcription antipausing factor NusG; Participates in transcription elongation, termination and antitermination. (177 aa) |
| | tyrS | Tyrosine--tRNA ligase; Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two- step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr); Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 2 subfamily. (399 aa) |
| | crp | DNA-binding transcriptional dual regulator; Function experimentally demonstrated in the studied species; regulator; Transcription. (214 aa) |
| | rsmA | Ribosomal RNA small subunit methyltransferase A; Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. (267 aa) |
| | apaH | Bis(5'-nucleosyl)-tetraphosphatase, symmetrical; Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP; Belongs to the Ap4A hydrolase family. (288 aa) |
| | cca | tRNA nucleotidyltransferase - 2',3'-cyclic phosphodiesterase - 2' nucleotidase and phosphatase; Catalyzes the addition and repair of the essential 3'- terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate. Also shows phosphatase, 2'-nucleotidase and 2',3'-cyclic phosphodiesterase activities. These phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases. (368 aa) |
| | tsaD | tRNA N6-adenosine threonylcarbamoyltransferase; Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction; Belongs to the KAE1 / TsaD family. (341 aa) |
| | dnaG | DNA primase; RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. (660 aa) |
| | rpoD | RNA polymerase, sigma 70 (sigma D) factor; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth. (616 aa) |
| | PP_0357 | ACT domain protein. (172 aa) |
| | PP_0352 | RNA polymerase sigma-70 factor, ECF subfamily. (172 aa) |
| | soxB | Sarcosine oxidase subunit beta; Function experimentally demonstrated in the studied genus; enzyme; Fattyacidandphospholipidmetabolism : Degradation. (416 aa) |
| | PP_0275 | Homologs of previously reported genes of unknown function. (71 aa) |
| | PP_0201 | Homologs of previously reported genes of unknown function. (163 aa) |
| | PP_0162 | RNA polymerase sigma-70 factor, ECF subfamily. (173 aa) |
| | gcdR | Transcriptional activator of gcdH, LysR family; Function of homologous gene experimentally demonstrated in an other organism; regulator; Transcription; Belongs to the LysR transcriptional regulatory family. (305 aa) |
| | trpI | HTH-type transcriptional regulator TrpI; Belongs to the LysR transcriptional regulatory family. (298 aa) |
| | PP_0079 | Putative transcriptional regulator; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; putative regulator; Belongs to the LysR transcriptional regulatory family. (299 aa) |
| | tsaC | Threonylcarbamoyl-AMP synthase; Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, HCO(3)(-)/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of diphosphate. (185 aa) |
| | fmt | Methionyl-tRNA formyltransferase; Attaches a formyl group to the free amino group of methionyl- tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus; Belongs to the Fmt family. (310 aa) |
| | rsmB | Ribosomal RNA small subunit methyltransferase B; Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA. (436 aa) |
| | glyQ | glycine-tRNA ligase alpha subunit; Function of homologous gene experimentally demonstrated in an other organism; enzyme. (315 aa) |
| | glyS | glycine-tRNA ligase beta subunit; Function of homologous gene experimentally demonstrated in an other organism; enzyme. (684 aa) |
| | rnpA | Ribonuclease P protein component; RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. (134 aa) |
| | trmE | GTPase; Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34; Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family. (456 aa) |
| | trmF | tRNA uridine 5-carboxymethylaminomethyl modification enzyme; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family. (631 aa) |
| | rsmG | 16S RNA methyltransferase; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. (216 aa) |
| | PP_5375 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (302 aa) |
| | PP_5311 | Putative signal transduction protein; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; putative factor; Signal transduction. (467 aa) |
| | rpoZ | DNA-directed RNA polymerase subunit omega; Promotes RNA polymerase assembly. Latches the N- and C- terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. (87 aa) |
| | PP_5295 | Homologs of previously reported genes of unknown function; Unknown function. (316 aa) |
| | rph | Ribonuclease PH; Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. (240 aa) |
| | PP_5259 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (296 aa) |
| | rnk | Regulator of nucleotide diphosphokinase; Function of homologous gene experimentally demonstrated in an other organism; regulator. (136 aa) |
| | rho | Transcription termination factor Rho; Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA- dependent ATPase activity, and release of the mRNA from the DNA template. (419 aa) |
| | rppH | RNA pyrophosphohydrolase; Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage; Belongs to the Nudix hydrolase family. RppH subfamily. (159 aa) |
| | yfhL | Putative 4Fe-4S cluster-containing protein; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; carrier; Energymetabolism : Electron transport. (83 aa) |
| | PP_5114 | Putative adenine methyltransferase; Specifically methylates the guanine in position 966 of 16S rRNA in the assembled 30S particle; Belongs to the methyltransferase superfamily. RsmD family. (200 aa) |
| | rpoH | RNA polymerase factor sigma-32; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is involved in regulation of expression of heat shock genes. (284 aa) |
| | trmB | tRNA (guanine-N(7)-)-methyltransferase; Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. (240 aa) |
| | argS | arginyl-tRNA synthetase; Function of homologous gene experimentally demonstrated in an other organism; enzyme. (578 aa) |
| | priA | Primosome assembly protein; Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA; Belongs to the helicase family. PriA subfamily. (739 aa) |
| | trmL | tRNA(Leu) mC34,mU34 2'-O-ribose methyltransferase, AdoMet-dependent; Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide. (157 aa) |
| | thiI | tRNA sulfurtransferase; Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS. (484 aa) |
| | dtd | D-tyrosyl-tRNA(Tyr) deacylase; An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA- based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D- aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl- tRNA entities in vivo and helps enforce protein L-homochirality. Belongs to the DTD family. (145 aa) |
| | PP_5019 | Ribosomal RNA small subunit methyltransferase E; Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit. (235 aa) |
| | PP_4996 | Putative Holliday junction resolvase; Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA; Belongs to the YqgF nuclease family. (141 aa) |
| | rsmE | 16S rRNA m3U1498 methyltransferase; Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit. (239 aa) |
| | dbpA | ATP-dependent RNA helicase, specific for 23S rRNA; Function of homologous gene experimentally demonstrated in an other organism; enzyme; Transcription : RNA processing; Belongs to the DEAD box helicase family. (461 aa) |
| | rlmJ | 23S rRNA m(6)A2030 methyltransferase; Specifically methylates the adenine in position 2030 of 23S rRNA. (278 aa) |
| | orn | Oligoribonuclease; 3'-to-5' exoribonuclease specific for small oligoribonucleotides; Belongs to the oligoribonuclease family. (180 aa) |
| | queG | Epoxyqueuosine reductase; Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr); Belongs to the QueG family. (354 aa) |
| | tsaE | ATPase; Function of strongly homologous gene; enzyme; Unknownfunction : Enzymes of unknown specificity. (157 aa) |
| | miaA | tRNA dimethylallyltransferase; Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A); Belongs to the IPP transferase family. (323 aa) |
| | rnr | Exoribonuclease R; 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs. (857 aa) |
| | rlmB | 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB; Specifically methylates the ribose of guanosine 2251 in 23S rRNA. (248 aa) |
| | dnaB | Replicative DNA helicase (ATPase); Participates in initiation and elongation during chromosome replication; it exhibits DNA-dependent ATPase activity and contains distinct active sites for ATP binding, DNA binding, and interaction with DnaC protein, primase, and other prepriming proteins. Belongs to the helicase family. DnaB subfamily. (465 aa) |
| | dusB | tRNA-dihydrouridine synthase B; Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines; Belongs to the Dus family. DusB subfamily. (337 aa) |
| | rlmH | 23S rRNA m3psi1915 methyltransferase; Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA; Belongs to the RNA methyltransferase RlmH family. (172 aa) |
| | leuS | Leucine--tRNA ligase; Belongs to the class-I aminoacyl-tRNA synthetase family. (868 aa) |
| | ybeY | Endoribonuclease YbeY; Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. (157 aa) |
| | rluE | 23S rRNA pseudouridine 2457 synthase; Function of homologous gene experimentally demonstrated in an other organism; enzyme; Transcription : RNA processing; Belongs to the pseudouridine synthase RsuA family. (210 aa) |
| | hrpB | ATP-dependent helicase HrpB. (842 aa) |
| | PP_4769 | Homologs of previously reported genes of unknown function. (159 aa) |
| | rhlE-I | ATP-dependent RNA helicase; Function of homologous gene experimentally demonstrated in an other organism; enzyme; Belongs to the DEAD box helicase family. (443 aa) |
| | PP_4720 | Putative RNA binding protein; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; putative factor; Unknown function. (102 aa) |
| | rlmE | Ribosomal RNA large subunit methyltransferase E; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit. (207 aa) |
| | nusA | Transcription termination/antitermination L factor; Participates in both transcription termination and antitermination. (493 aa) |
| | rbfA | Ribosome-binding factor A; One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. (132 aa) |
| | truB | tRNA pseudouridine 55 synthase; Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs; Belongs to the pseudouridine synthase TruB family. Type 1 subfamily. (305 aa) |
| | pnp | Polyribonucleotide nucleotidyltransferase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction. (701 aa) |
| | pcnB | poly(A) polymerase; Adds poly(A) tail to the 3' end of many RNAs, which usually targets these RNAs for decay. Plays a significant role in the global control of gene expression, through influencing the rate of transcript degradation, and in the general RNA quality control. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. (460 aa) |
| | gluQ | Glutamyl-Q tRNA(Asp) synthetase; Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto a tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5-dihydroxy-2- cyclopenten-1-yl) moiety of the queuosine in the wobble position of the QUC anticodon; Belongs to the class-I aminoacyl-tRNA synthetase family. GluQ subfamily. (300 aa) |
| | PP_4660 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (298 aa) |
| | trmA | tRNA/tmRNA (uracil-C(5))-methyltransferase; Dual-specificity methyltransferase that catalyzes the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA). (361 aa) |
| | rlmG | Ribosomal RNA large subunit methyltransferase G; Specifically methylates the guanine in position 1835 (m2G1835) of 23S rRNA. (374 aa) |
| | PP_4611 | RNA polymerase sigma-70 factor, ECF subfamily. (170 aa) |
| | PP_4608 | RNA polymerase sigma-70 factor, ECF subfamily. (191 aa) |
| | rnd | Ribonuclease D; Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides; Belongs to the RNase D family. (377 aa) |
| | PP_4585 | RNA methyltransferase, TrmH family. (156 aa) |
| | PP_4553 | RNA polymerase sigma-70 factor, ECF subfamily. (406 aa) |
| | hrpA | ATP-dependent helicase HrpA. (1301 aa) |
| | PP_4520 | Homologs of previously reported genes of unknown function. (199 aa) |
| | PP_4500 | TrpH family protein. (286 aa) |
| | yciO | Putative maturation enzyme; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; putative enzyme; Unknown function; Belongs to the SUA5 family. (221 aa) |
| | rluB | 23S rRNA pseudouridine 2605 synthase; Function of homologous gene experimentally demonstrated in an other organism; enzyme; Transcription : RNA processing; Belongs to the pseudouridine synthase RsuA family. (355 aa) |
| | PP_4494 | Putative LysR-type transcriptional activator protein; Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Belongs to the LysR transcriptional regulatory family. (294 aa) |
| | alaS | Alanine--tRNA ligase; Catalyzes the attachment of alanine to tRNA(Ala) in a two- step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. (874 aa) |
| | csrA | Carbon storage regulator; A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems. Usually binds in the 5'-UTR; binding at or near the Shine-Dalgarno sequence prevents ribosome-binding, repressing translation, binding elsewhere in the 5'-UTR can activate translation and/or stabilize the mRNA. Its function is antagonized by small RNA(s). (62 aa) |
| | fleQ | Transcriptional regulator FleQ. (491 aa) |
| | fliA | RNA polymerase sigma 28 (sigma F) factor for class III flagellar operons; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor controls the expression of flagella-related genes; Belongs to the sigma-70 factor family. FliA subfamily. (246 aa) |
| | pvdS | Alternative sigma factor; Function experimentally demonstrated in the studied genus; regulator; Regulatory functions; Belongs to the sigma-70 factor family. ECF subfamily. (176 aa) |
| | PP_4208 | RNA polymerase sigma-70 factor, ECF subfamily. (158 aa) |
| | rnhA | Ribonuclease H; Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. (148 aa) |
| | PP_4107 | Transcriptional regulator, LysR family; Belongs to the LysR transcriptional regulatory family. (298 aa) |
| | rnz | Ribonuclease Z; Zinc phosphodiesterase, which displays some tRNA 3'- processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA; Belongs to the RNase Z family. (319 aa) |
| | mnmA | tRNA-specific 2-thiouridylase MnmA; Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. (374 aa) |
| | serS | Serine--tRNA ligase; Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L- seryl-tRNA(Sec), which will be further converted into selenocysteinyl- tRNA(Sec). (426 aa) |
| | tusE | Sulfur transfer protein; Part of a sulfur-relay system. (111 aa) |
