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| | pheS | KEGG: cff:CFF8240_1254 phenylalanyl-tRNA synthetase subunit alpha; TIGRFAM: phenylalanyl-tRNA synthetase, alpha subunit; PFAM: phenylalanyl-tRNA synthetase class IIc; aminoacyl tRNA synthetase class II domain protein; Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily. (330 aa) |
| | Sdel_0027 | PFAM: SirA family protein; KEGG: gbm:Gbem_3433 SirA family protein; Belongs to the sulfur carrier protein TusA family. (70 aa) |
| | Sdel_0056 | PFAM: pseudouridine synthase; KEGG: nis:NIS_0055 ribosomal large subunit pseudouridine synthase D. (302 aa) |
| | rlmN | Radical SAM enzyme, Cfr family; 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. (358 aa) |
| | rsmA | Dimethyladenosine transferase; 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. (281 aa) |
| | rnj | Beta-lactamase domain protein; An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay. (664 aa) |
| | Sdel_0065 | PFAM: RNA-binding S4 domain protein; pseudouridine synthase; SMART: RNA-binding S4 domain protein; KEGG: cco:CCC13826_1885 putative peptide ABC transporter, permease protein; Belongs to the pseudouridine synthase RsuA family. (261 aa) |
| | prfA | Peptide chain release factor 1; Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. (355 aa) |
| | rpsT | Ribosomal protein S20; Binds directly to 16S ribosomal RNA. (91 aa) |
| | thrS | TIGRFAM: threonyl-tRNA synthetase; PFAM: tRNA synthetase class II (G H P and S); Anticodon-binding domain protein; Threonyl/alanyl tRNA synthetase SAD; KEGG: cha:CHAB381_0611 threonyl-tRNA synthetase; Belongs to the class-II aminoacyl-tRNA synthetase family. (605 aa) |
| | infC | Translation initiation factor IF-3; IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. (171 aa) |
| | rpmI | TIGRFAM: ribosomal protein L35; PFAM: ribosomal protein L35; KEGG: cff:CFF8240_0114 50S ribosomal protein L35; Belongs to the bacterial ribosomal protein bL35 family. (64 aa) |
| | rplT | Ribosomal protein L20; Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. (117 aa) |
| | rpsU | TIGRFAM: ribosomal protein S21; PFAM: ribosomal protein S21; KEGG: cjd:JJD26997_1587 30S ribosomal protein S21; Belongs to the bacterial ribosomal protein bS21 family. (70 aa) |
| | miaA | tRNA delta(2)-isopentenylpyrophosphate transferase; 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. (298 aa) |
| | Sdel_0162 | Protein of unknown function DUF558; Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit. (222 aa) |
| | rpmE | Ribosomal protein L31; Binds the 23S rRNA. (66 aa) |
| | rsmI | Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase; Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. (270 aa) |
| | Sdel_0165 | TIGRFAM: RNA methyltransferase, TrmH family, group 3; PFAM: tRNA/rRNA methyltransferase (SpoU); RNA 2-O ribose methyltransferase substrate binding; KEGG: ccv:CCV52592_0830 RNA methyltransferase; Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family. (227 aa) |
| | queH | Protein of unknown function DUF208; 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). (362 aa) |
| | Sdel_0190 | KEGG: nam:NAMH_1680 hypothetical protein. (146 aa) |
| | Sdel_0198 | PFAM: UBA/THIF-type NAD/FAD binding protein; KEGG: cco:CCC13826_1574 peptide chain release factor 2. (214 aa) |
| | rplY | Ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5; This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Belongs to the bacterial ribosomal protein bL25 family. CTC subfamily. (178 aa) |
| | pth | peptidyl-tRNA hydrolase; The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. Belongs to the PTH family. (191 aa) |
| | rpmF | TIGRFAM: ribosomal protein L32; PFAM: ribosomal L32p protein; KEGG: cff:CFF8240_0235 50S ribosomal protein L32; Belongs to the bacterial ribosomal protein bL32 family. (50 aa) |
| | infB | Translation initiation factor IF-2; One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex; Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily. (888 aa) |
| | Sdel_0249 | 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. (125 aa) |
| | Sdel_0261 | PFAM: Radical SAM domain protein; protein of unknown function DUF752; SMART: Elongator protein 3/MiaB/NifB; KEGG: glo:Glov_3168 conserved hypothetical radical SAM protein. (564 aa) |
| | Sdel_0296 | TIGRFAM: RNA polymerase sigma factor, FliA/WhiG family; RNA polymerase sigma factor, sigma-70 family; PFAM: sigma-70 region 4 domain protein; sigma-70 region 2 domain protein; Sigma-70 region 4 type 2; KEGG: ccv:CCV52592_0370 flagellar biosynthesis sigma factor. (237 aa) |
| | lepA | GTP-binding protein LepA; Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre- translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP- dependent manner. (597 aa) |
| | Sdel_0316 | PFAM: Radical SAM domain protein; KEGG: nis:NIS_0485 MoaA/NifB/PqqE family protein. (303 aa) |
| | tuf | Translation elongation factor Tu; This protein promotes the GTP-dependent binding of aminoacyl- tRNA to the A-site of ribosomes during protein biosynthesis. (399 aa) |
| | rpmG | TIGRFAM: ribosomal protein L33; PFAM: ribosomal protein L33; KEGG: cff:CFF8240_1324 50S ribosomal protein L33; Belongs to the bacterial ribosomal protein bL33 family. (52 aa) |
| | nusG | Transcription termination/antitermination factor NusG; Participates in transcription elongation, termination and antitermination. (176 aa) |
| | rplK | Ribosomal protein L11; Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. (141 aa) |
| | rplA | Ribosomal protein L1; Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. (234 aa) |
| | rplJ | Ribosomal protein L10; Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. Belongs to the universal ribosomal protein uL10 family. (160 aa) |
| | rplL | Ribosomal protein L7/L12; Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation; Belongs to the bacterial ribosomal protein bL12 family. (124 aa) |
| | rpoB | DNA-directed RNA polymerase, beta subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1385 aa) |
| | rpoC | DNA-directed RNA polymerase, beta' subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1507 aa) |
| | rpsL | Ribosomal protein S12; 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 contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. (125 aa) |
| | rpsG | Ribosomal protein S7; One of the primary rRNA binding proteins, it 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, probably blocks exit of the E-site tRNA; Belongs to the universal ribosomal protein uS7 family. (156 aa) |
| | fusA | Translation elongation factor G; Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome; Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 s [...] (692 aa) |
| | rsmG | Methyltransferase GidB; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. (189 aa) |
| | rpsB | TIGRFAM: ribosomal protein S2; PFAM: ribosomal protein S2; KEGG: ccv:CCV52592_1262 30S ribosomal protein S2; Belongs to the universal ribosomal protein uS2 family. (263 aa) |
| | tsf | Translation elongation factor Ts; Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF- Tu.GTP complex up to the GTP hydrolysis stage on the ribosome. Belongs to the EF-Ts family. (355 aa) |
| | argS | KEGG: nis:NIS_1495 arginyl-tRNA synthetase; TIGRFAM: arginyl-tRNA synthetase. (528 aa) |
| | nusA | Transcription termination factor NusA; Participates in both transcription termination and antitermination. (374 aa) |
| | miaB | tRNA-i(6)A37 thiotransferase enzyme MiaB; Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6- (dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. (438 aa) |
| | tilS | tRNA(Ile)-lysidine synthetase; 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. (331 aa) |
| | rimO | MiaB-like tRNA modifying enzyme YliG; Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12; Belongs to the methylthiotransferase family. RimO subfamily. (436 aa) |
| | prfB | Peptide chain release factor 2; Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA. (364 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. (447 aa) |
| | ileS | isoleucyl-tRNA synthetase; 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. (918 aa) |
| | gatA | glutamyl-tRNA(Gln) amidotransferase, A subunit; Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu- tRNA(Gln). (452 aa) |
| | rplU | Ribosomal protein L21; This protein binds to 23S rRNA in the presence of protein L20; Belongs to the bacterial ribosomal protein bL21 family. (102 aa) |
| | rpmA | TIGRFAM: ribosomal protein L27; PFAM: ribosomal protein L27; KEGG: wsu:WS0504 50S ribosomal protein L27; Belongs to the bacterial ribosomal protein bL27 family. (85 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. (319 aa) |
| | Sdel_0527 | PFAM: PP-loop domain protein; KEGG: cco:CCC13826_0928 PP-loop family protein; Belongs to the TtcA family. (250 aa) |
| | rlmH | Protein of unknown function DUF163; Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA; Belongs to the RNA methyltransferase RlmH family. (151 aa) |
| | Sdel_0536 | Dihydrouridine synthase DuS; 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. (312 aa) |
| | lysS | TIGRFAM: lysyl-tRNA synthetase; PFAM: tRNA synthetase class II (D K and N); nucleic acid binding OB-fold tRNA/helicase-type; KEGG: nis:NIS_1177 lysyl-tRNA synthetase; Belongs to the class-II aminoacyl-tRNA synthetase family. (506 aa) |
| | gatC | glutamyl-tRNA(Gln) amidotransferase, C subunit; Allows the 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. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp- tRNA(Asn) or phospho-Glu-tRNA(Gln); Belongs to the GatC family. (96 aa) |
| | pnp | Polyribonucleotide nucleotidyltransferase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction. (746 aa) |
| | pheT | TIGRFAM: phenylalanyl-tRNA synthetase, beta subunit; KEGG: ccv:CCV52592_0517 phenylalanyl-tRNA synthetase subunit beta. (779 aa) |
| | Sdel_0613 | PFAM: RNA binding S1 domain protein; KEGG: cff:CFF8240_1250 30S ribosomal protein S1. (558 aa) |
| | efp | Translation elongation factor P; Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. (187 aa) |
| | Sdel_0627 | PFAM: HI0933 family protein; FAD-dependent pyridine nucleotide-disulphide oxidoreductase; FAD dependent oxidoreductase; KEGG: sun:SUN_2357 hypothetical protein. (404 aa) |
| | Sdel_0639 | Pseudouridine synthase, RluA family; Responsible for synthesis of pseudouridine from uracil. Belongs to the pseudouridine synthase RluA family. (326 aa) |
| | trmB | tRNA (guanine-N(7)-)-methyltransferase; Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. (392 aa) |
| | rpoZ | DNA-directed RNA polymerase, omega subunit; 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. (71 aa) |
| | tyrS | tyrosyl-tRNA synthetase; 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. (402 aa) |
| | aspS | aspartyl-tRNA synthetase; 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. (582 aa) |
| | ybeY | Protein of unknown function UPF0054; Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. (140 aa) |
| | metG | methionyl-tRNA synthetase; Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. (642 aa) |
| | Sdel_0680 | PFAM: Glutamyl/glutaminyl-tRNA synthetase, class Ic, catalytic domain; KEGG: abu:Abu_1214 glutamylglutaminyl-tRNA synthetase; Belongs to the class-I aminoacyl-tRNA synthetase family. (380 aa) |
| | Sdel_0681 | TIGRFAM: glutaminyl-tRNA synthetase; PFAM: Glutamyl/glutaminyl-tRNA synthetase, class Ic, catalytic domain; Glutamyl/glutaminyl-tRNA synthetase, class Ic, anti-codon binding domain; Asn/Gln amidotransferase; KEGG: sun:SUN_1139 glutaminyl-tRNA synthetase. (748 aa) |
| | Sdel_0844 | KEGG: nis:NIS_0710 signal peptidase I; TIGRFAM: signal peptidase I; PFAM: Peptidase S24/S26A/S26B, conserved region; Belongs to the peptidase S26 family. (276 aa) |
| | rpsR | Ribosomal protein S18; Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit; Belongs to the bacterial ribosomal protein bS18 family. (88 aa) |
| | rpsF | Ribosomal protein S6; Binds together with S18 to 16S ribosomal RNA. (132 aa) |
| | Sdel_0873 | Holliday junction resolvase YqgF; Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA; Belongs to the YqgF HJR family. (135 aa) |
| | Sdel_0896 | TIGRFAM: ybaK/ebsC protein; PFAM: YbaK/prolyl-tRNA synthetase associated region; KEGG: wsu:WS1648 hypothetical protein; Belongs to the prolyl-tRNA editing family. YbaK/EbsC subfamily. (158 aa) |
| | def | Peptide deformylase; Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. (182 aa) |
| | trmA | tRNA (uracil-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). (367 aa) |
| | Sdel_1022 | RNA polymerase sigma-54 factor, RpoN; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. (423 aa) |
| | Sdel_1024 | PFAM: protein of unknown function UPF0079; KEGG: ccv:CCV52592_1981 hypothetical protein. (143 aa) |
| | rplI | Ribosomal protein L9; Binds to the 23S rRNA. (148 aa) |
| | cysS | KEGG: abu:Abu_0245 cysteinyl-tRNA synthetase; TIGRFAM: cysteinyl-tRNA synthetase; PFAM: Cysteinyl-tRNA synthetase class Ia; tRNA synthetase class I (M); Belongs to the class-I aminoacyl-tRNA synthetase family. (466 aa) |
| | hypA | Hydrogenase nickel insertion protein HypA; Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase. (113 aa) |
| | Sdel_1095 | TIGRFAM: hydrogenase expression/formation protein HypE; PFAM: AIR synthase related protein domain protein; AIR synthase related protein; KEGG: shl:Shal_2270 hydrogenase expression/formation protein HypE. (334 aa) |
| | Sdel_1096 | TIGRFAM: hydrogenase expression/formation protein HypD; PFAM: hydrogenase formation HypD protein; KEGG: tcx:Tcr_2041 hydrogenase expression/formation protein HypD; Belongs to the HypD family. (375 aa) |
| | Sdel_1097 | TIGRFAM: hydrogenase assembly chaperone hypC/hupF; PFAM: hydrogenase expression/formation protein (HUPF/HYPC); KEGG: cla:Cla_0790 hydrogenase assembly chaperone HypC. (89 aa) |
| | Sdel_1098 | TIGRFAM: hydrogenase accessory protein HypB; PFAM: cobalamin synthesis protein P47K; KEGG: cco:CCC13826_1096 hydrogenase accessory protein HypB. (278 aa) |
| | truA | tRNA pseudouridine synthase A; Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. (247 aa) |
| | gatB | glutamyl-tRNA(Gln) amidotransferase, B subunit; Allows the 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. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp- tRNA(Asn) or phospho-Glu-tRNA(Gln); Belongs to the GatB/GatE family. GatB subfamily. (476 aa) |
| | Sdel_1144 | TIGRFAM: methyltransferase; PFAM: Protein of unknown function methylase putative; KEGG: nis:NIS_0997 DNA methylase. (191 aa) |
| | Sdel_1170 | PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sun:SUN_1816 ABC transporter, ATP-binding protein. (610 aa) |
| | truD | tRNA pseudouridine synthase D TruD; Responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs; Belongs to the pseudouridine synthase TruD family. (361 aa) |
| | hypA-2 | Hydrogenase nickel insertion protein HypA; Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase. (115 aa) |
| | Sdel_1226 | TIGRFAM: RNA polymerase sigma factor, sigma-70 family; PFAM: Sigma-70 region 4 type 2; sigma-70 region 2 domain protein; KEGG: abu:Abu_1430 ECF subfamily RNA polymerase sigma factor. (155 aa) |
| | Sdel_1263 | KEGG: nis:NIS_1081 tRNA modifying enzyme; TIGRFAM: MiaB-like tRNA modifying enzyme; RNA modification enzyme, MiaB family; PFAM: Protein of unknown function UPF0004; Radical SAM domain protein; SMART: Elongator protein 3/MiaB/NifB. (414 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 t [...] (373 aa) |
| | Sdel_1278 | PFAM: protein of unknown function DUF111; KEGG: wsu:WS0139 hypothetical protein; Belongs to the LarC family. (408 aa) |
| | hisS | KEGG: tdn:Suden_1130 histidyl-tRNA synthetase; TIGRFAM: histidyl-tRNA synthetase; PFAM: tRNA synthetase class II (G H P and S). (402 aa) |
| | Sdel_1304 | TIGRFAM: tRNA 2-selenouridine synthase; SMART: Rhodanese domain protein; KEGG: cco:CCC13826_0142 tRNA 2-selenouridine synthase; Belongs to the SelU family. (342 aa) |
| | proS | prolyl-tRNA synthetase; 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 dea [...] (567 aa) |
| | valS | valyl-tRNA synthetase; 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. (876 aa) |
| | cmoB | Methyltransferase putative; 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. (300 aa) |
| | rpsO | Ribosomal protein S15; Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. (90 aa) |
| | cmoA | Methyltransferase; Catalyzes the conversion of S-adenosyl-L-methionine (SAM) to carboxy-S-adenosyl-L-methionine (Cx-SAM). (234 aa) |
| | Sdel_1370 | KEGG: nam:NAMH_1087 hemolysin A; TIGRFAM: hemolysin A; PFAM: RNA-binding S4 domain protein; ribosomal RNA methyltransferase RrmJ/FtsJ; SMART: RNA-binding S4 domain protein. (238 aa) |
| | rpmH | TIGRFAM: ribosomal protein L34; PFAM: ribosomal protein L34; KEGG: cco:CCC13826_2243 50S ribosomal protein L34; Belongs to the bacterial ribosomal protein bL34 family. (44 aa) |
| | Sdel_1419 | KEGG: tcx:Tcr_0083 hypothetical protein. (1215 aa) |
| | rsmH | S-adenosyl-methyltransferase MraW; Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. (304 aa) |
| | Sdel_1431 | PFAM: peptidase M48 Ste24p; KEGG: abu:Abu_0531 M48 family peptidase. (404 aa) |
| | Sdel_1433 | PFAM: ABC transporter related; SMC domain protein; SMART: AAA ATPase; KEGG: nis:NIS_1038 ABC transport system ATP-binding protein. (649 aa) |
| | Sdel_1483 | PFAM: CMP/dCMP deaminase zinc-binding; KEGG: wsu:WS1357 cytosine deaminase. (146 aa) |
| | Sdel_1495 | TIGRFAM: addiction module toxin, RelE/StbE family; PFAM: plasmid stabilization system; KEGG: rfe:RF_0334 hypothetical protein. (98 aa) |
| | glyS | KEGG: nis:NIS_0732 glycyl-tRNA synthetase subunit beta; TIGRFAM: glycyl-tRNA synthetase, beta subunit; PFAM: glycyl-tRNA synthetase beta subunit. (683 aa) |
| | Sdel_1509 | PFAM: HI0933 family protein; KEGG: sun:SUN_0828 hypothetical protein. (379 aa) |
| | trmL | tRNA/rRNA methyltransferase (SpoU); 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. (156 aa) |
| | Sdel_1513 | PFAM: Polynucleotide adenylyltransferase region; KEGG: nis:NIS_0728 RNA nucleotidyltransferase; Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. (375 aa) |
| | Sdel_1525 | PFAM: pseudouridine synthase; KEGG: sun:SUN_0745 ribosomal small subunit pseudouridine synthase A; Belongs to the pseudouridine synthase RsuA family. (194 aa) |
| | rpoD | RNA polymerase sigma factor RpoD; 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. (617 aa) |
| | rpmB | TIGRFAM: ribosomal protein L28; PFAM: ribosomal protein L28; KEGG: ccv:CCV52592_0722 50S ribosomal protein L28; Belongs to the bacterial ribosomal protein bL28 family. (62 aa) |
| | leuS | TIGRFAM: leucyl-tRNA synthetase; PFAM: aminoacyl-tRNA synthetase class Ia; tRNA synthetase class I (M); KEGG: abu:Abu_0402 leucyl-tRNA synthetase; Belongs to the class-I aminoacyl-tRNA synthetase family. (815 aa) |
| | smpB | SsrA-binding protein; Required for rescue of stalled ribosomes mediated by trans- translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to [...] (154 aa) |
| | Sdel_1632 | PFAM: pseudouridylate synthase TruB domain protein; KEGG: cff:CFF8240_0715 tRNA pseudouridine synthase B; Belongs to the pseudouridine synthase TruB family. (275 aa) |
| | rplS | Ribosomal protein L19; This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. (118 aa) |
| | trmD | tRNA (guanine-N1)-methyltransferase; Specifically methylates guanosine-37 in various tRNAs. Belongs to the RNA methyltransferase TrmD family. (230 aa) |
| | rimM | 16S rRNA processing protein 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. (179 aa) |
| | rpsP | TIGRFAM: ribosomal protein S16; PFAM: ribosomal protein S16; KEGG: cff:CFF8240_1038 30S ribosomal protein S16; Belongs to the bacterial ribosomal protein bS16 family. (76 aa) |
| | Sdel_1651 | PFAM: pseudouridine synthase; KEGG: nis:NIS_1506 ribosomal large subunit pseudouridine synthase D. (242 aa) |
| | glyQ | KEGG: nis:NIS_1511 glycyl-tRNA synthetase subunit alpha; TIGRFAM: glycyl-tRNA synthetase, alpha subunit; PFAM: glycyl-tRNA synthetase alpha subunit. (285 aa) |
| | alaS | alanyl-tRNA synthetase; 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. (846 aa) |
| | Sdel_1695 | PFAM: translation initiation factor SUI1; KEGG: sun:SUN_0118 translation initiation factor SUI1. (119 aa) |
| | Sdel_1696 | PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: sun:SUN_1475 ABC transporter, ATP-binding protein. (531 aa) |
| | nusB | Transcription antitermination factor NusB; 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. (136 aa) |
| | Sdel_1755 | KEGG: cco:CCC13826_0775 tryptophanyl-tRNA synthetase; TIGRFAM: tryptophanyl-tRNA synthetase; PFAM: aminoacyl-tRNA synthetase class Ib. (321 aa) |
| | serS | seryl-tRNA synthetase; 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). (414 aa) |
| | mnmG | Glucose inhibited division protein A; 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. (624 aa) |
| | Sdel_1894 | PFAM: DsrE family protein; KEGG: nam:NAMH_1288 hypothetical protein. (117 aa) |
| | rpsI | PFAM: ribosomal protein S9; KEGG: cjd:JJD26997_1826 30S ribosomal protein S9; Belongs to the universal ribosomal protein uS9 family. (129 aa) |
| | rplM | Ribosomal protein L13; This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly. (142 aa) |
| | rplQ | TIGRFAM: ribosomal protein L17; PFAM: ribosomal protein L17; KEGG: cla:Cla_0096 50S ribosomal protein L17. (116 aa) |
| | rpoA | DNA-directed RNA polymerase, alpha subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (337 aa) |
| | rpsD | Ribosomal protein S4; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. (208 aa) |
| | rpsK | 30S ribosomal protein S11; 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; Belongs to the universal ribosomal protein uS11 family. (130 aa) |
| | rpsM | 30S ribosomal protein S13; Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Belongs to the universal ribosomal protein uS13 family. (122 aa) |
| | rpmJ | TIGRFAM: ribosomal protein L36; PFAM: ribosomal protein L36; KEGG: nis:NIS_0245 50S ribosomal protein L36; Belongs to the bacterial ribosomal protein bL36 family. (37 aa) |
| | infA | Translation initiation factor IF-1; One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. (72 aa) |
| | rplO | Ribosomal protein L15; Binds to the 23S rRNA; Belongs to the universal ribosomal protein uL15 family. (134 aa) |
| | rpsE | Ribosomal protein S5; Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Belongs to the universal ribosomal protein uS5 family. (147 aa) |
| | rplR | Ribosomal protein L18; This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. (118 aa) |
| | rplF | Ribosomal protein L6; This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center; Belongs to the universal ribosomal protein uL6 family. (178 aa) |
| | rpsH | Ribosomal protein S8; One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; Belongs to the universal ribosomal protein uS8 family. (131 aa) |
| | rpsZ | Ribosomal protein S14; Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. (61 aa) |
| | rplE | Ribosomal protein L5; This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. (181 aa) |
| | rplX | Ribosomal protein L24; One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. (78 aa) |
| | rplN | Ribosomal protein L14; Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome; Belongs to the universal ribosomal protein uL14 family. (122 aa) |
| | rpsQ | 30S ribosomal protein S17; One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. (83 aa) |
| | rpmC | TIGRFAM: ribosomal protein L29; PFAM: ribosomal protein L29; KEGG: cff:CFF8240_0042 50S ribosomal protein L29; Belongs to the universal ribosomal protein uL29 family. (62 aa) |
| | rplP | Ribosomal protein L16; Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs; Belongs to the universal ribosomal protein uL16 family. (141 aa) |
| | rpsC | Ribosomal protein S3; Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation; Belongs to the universal ribosomal protein uS3 family. (237 aa) |
| | rplV | Ribosomal protein L22; The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. (110 aa) |
| | rpsS | Ribosomal protein S19; Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. (93 aa) |
| | rplB | Ribosomal protein L2; 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 peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. (276 aa) |
| | rplW | 50S ribosomal protein L23; One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome; Belongs to the universal ribosomal protein uL23 family. (93 aa) |
| | rplD | Ribosomal protein L4/L1e; Forms part of the polypeptide exit tunnel. (204 aa) |
| | Sdel_1968 | TIGRFAM: 50S ribosomal protein L3; PFAM: ribosomal protein L3; KEGG: nis:NIS_0223 50S ribosomal protein L3. (192 aa) |
| | rpsJ | Ribosomal protein S10; Involved in the binding of tRNA to the ribosomes. Belongs to the universal ribosomal protein uS10 family. (103 aa) |
| | rnc | Ribonuclease III; 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. (227 aa) |
| | Sdel_2015 | PFAM: plasmid maintenance system killer; KEGG: nis:NIS_1330 plasmid stabilization system protein. (91 aa) |
| | Sdel_2054 | TIGRFAM: selenium metabolism protein YedF; PFAM: SirA family protein; KEGG: nam:NAMH_1292 hypothetical protein; Belongs to the sulfur carrier protein TusA family. (196 aa) |
| | selA | L-seryl-tRNA selenium transferase; Converts seryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis. (445 aa) |
| | Sdel_2083 | TIGRFAM: selenocysteine-specific translation elongation factor; small GTP-binding protein; PFAM: protein synthesis factor GTP-binding; elongation factor Tu domain 2 protein; KEGG: nam:NAMH_1325 selenocysteine-specific translation elongation factor. (611 aa) |
| | Sdel_2127 | KEGG: abu:Abu_1507 heavy-metal transport protein. (110 aa) |
| | def-2 | Peptide deformylase; Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. (171 aa) |
| | mnmA | tRNA(5-methylaminomethyl-2-thiouridylate)-methyl transferase; Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. (339 aa) |
| | gltX | glutamyl-tRNA synthetase; 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. (463 aa) |
| | tsaD | Metalloendopeptidase, glycoprotease family; 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. (334 aa) |
| | Sdel_2252 | PFAM: protein of unknown function DUF814; Fibronectin-binding A domain protein; KEGG: tdn:Suden_0123 hypothetical protein. (441 aa) |
| | Sdel_2264 | PFAM: RNP-1 like RNA-binding protein; SMART: RNP-1 like RNA-binding protein; KEGG: cff:CFF8240_1240 RNA-binding region RNP-1. (101 aa) |
| | frr | Ribosome recycling factor; Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another; Belongs to the RRF family. (186 aa) |
