-- dump date 20111121_014328 -- class Genbank::CDS -- table cds_note -- id note YP_002916064.1 COG1806 Uncharacterized protein conserved in bacteria YP_002916065.1 COG0526 Thiol-disulfide isomerase and thioredoxins YP_002916066.1 COG1134 ABC-type polysaccharide/polyol phosphate transport system, ATPase component YP_002916067.1 COG1682 ABC-type polysaccharide/polyol phosphate export systems, permease component YP_002916068.1 undetermined function YP_002916069.1 COG2337 Growth inhibitor YP_002916070.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis YP_002916071.1 in Pseudomonas aeruginosa this enzyme is a trimer of dimers; essential for membrane formation; performs third step of type II fatty acid biosynthesis; catalyzes dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP YP_002916072.1 adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis YP_002916073.1 COG1752 Predicted esterase of the alpha-beta hydrolase superfamily YP_002916074.1 COG3022 Uncharacterized protein conserved in bacteria YP_002916075.1 COG0776 Bacterial nucleoid DNA-binding protein YP_002916076.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_002916077.1 COG0608 Single-stranded DNA-specific exonuclease YP_002916078.1 recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1; this protein is similar to release factor 2 YP_002916079.1 COG0508 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes YP_002916080.1 IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits YP_002916081.1 COG5346 Predicted membrane protein YP_002916083.1 COG5448 Uncharacterized conserved protein YP_002916084.1 COG0340 Biotin-(acetyl-CoA carboxylase) ligase YP_002916085.1 COG0605 Superoxide dismutase YP_002916086.1 COG0285 Folylpolyglutamate synthase YP_002916087.1 COG4285 Uncharacterized conserved protein YP_002916088.1 COG0625 Glutathione S-transferase YP_002916089.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_002916091.1 COG0235 Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases YP_002916092.1 COG4113 Predicted nucleic acid-binding protein, contains PIN domain YP_002916093.1 COG4118 Antitoxin of toxin-antitoxin stability system YP_002916094.1 COG0242 N-formylmethionyl-tRNA deformylase YP_002916095.1 COG1496 Uncharacterized conserved protein YP_002916096.1 IPR014746 Glutamine synthetase/guanido kinase, catalytic region YP_002916097.1 COG1295 Predicted membrane protein YP_002916098.1 COG1396 Predicted transcriptional regulators YP_002916100.1 COG3202 ATP/ADP translocase YP_002916101.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; proteins in this cluster have Rickettsial repeat elements (RPE) inserts YP_002916102.1 primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence YP_002916103.1 COG1185 Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) YP_002916104.1 COG0794 Predicted sugar phosphate isomerase involved in capsule formation YP_002916105.1 COG5375 Uncharacterized protein conserved in bacteria YP_002916106.1 COG1934 Uncharacterized protein conserved in bacteria YP_002916107.1 COG1137 ABC-type (unclassified) transport system, ATPase component YP_002916108.1 COG1109 Phosphomannomutase YP_002916110.1 IPP transferase; isopentenyltransferase; involved in tRNA modification; in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity YP_002916111.1 truncated homolog of RrIowa_0780 YP_002916112.1 B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE YP_002916113.1 Catalyzes the rate-limiting step in dNTP synthesis YP_002916114.1 COG3397 Uncharacterized protein conserved in bacteria YP_002916116.1 COG5430 Uncharacterized secreted protein YP_002916117.1 COG3121 P pilus assembly protein, chaperone PapD YP_002916118.1 COG5430 Uncharacterized secreted protein YP_002916119.1 COG0492 Thioredoxin reductase YP_002916120.1 COG2801 Transposase and inactivated derivatives YP_002916121.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate YP_002916122.1 COG0663 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily YP_002916123.1 COG1544 Ribosome-associated protein Y (PSrp-1) YP_002916125.1 COG0466 ATP-dependent Lon protease, bacterial type YP_002916126.1 catalyzes the formation of 2-oxobutanoate from L-threonine YP_002916127.1 COG2801 Transposase and inactivated derivatives YP_002916130.1 COG0210 Superfamily I DNA and RNA helicases YP_002916131.1 COG0463 Glycosyltransferases involved in cell wall biogenesis YP_002916133.1 COG1012 NAD-dependent aldehyde dehydrogenases YP_002916137.1 COG0492 Thioredoxin reductase YP_002916138.1 COG0596 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) YP_002916139.1 COG0679 Predicted permeases YP_002916140.1 COG0595 Predicted hydrolase of the metallo-beta-lactamase superfamily YP_002916141.1 catalyzes the phosphorylation of NAD to NADP YP_002916142.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_002916143.1 COG1714 Predicted membrane protein/domain YP_002916144.1 COG1238 Predicted membrane protein YP_002916145.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_002916146.1 COG4395 Uncharacterized protein conserved in bacteria YP_002916147.1 COG1506 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases YP_002916148.1 COG2002 Regulators of stationary/sporulation gene expression YP_002916149.1 COG5611 Predicted nucleic-acid-binding protein, contains PIN domain YP_002916150.1 catalyzes the interconversion of succinyl-CoA and succinate YP_002916151.1 Catalyzes the only substrate-level phosphorylation in the TCA cycle YP_002916152.1 COG2801 Transposase and inactivated derivatives YP_002916153.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916155.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_002916157.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity YP_002916158.1 COG0163 3-polyprenyl-4-hydroxybenzoate decarboxylase YP_002916159.1 unwinds double stranded DNA YP_002916161.1 COG1187 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases YP_002916162.1 COG1357 Uncharacterized low-complexity proteins YP_002916163.1 COG0742 N6-adenine-specific methylase YP_002916164.1 Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents YP_002916166.1 involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA YP_002916167.1 COG1214 Inactive homolog of metal-dependent proteases, putative molecular chaperone YP_002916169.1 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 YP_002916170.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_002916171.1 COG2801 Transposase and inactivated derivatives YP_002916180.1 COG0042 tRNA-dihydrouridine synthase YP_002916182.1 ATPase YjeE, predicted to have essential role in cell wall biosynthesis YP_002916183.1 COG0803 ABC-type metal ion transport system, periplasmic component/surface adhesin YP_002916184.1 COG0617 tRNA nucleotidyltransferase/poly(A) polymerase YP_002916185.1 COG0658 Predicted membrane metal-binding protein YP_002916186.1 COG2801 Transposase and inactivated derivatives YP_002916187.1 COG1189 Predicted rRNA methylase YP_002916188.1 catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr) YP_002916189.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. YP_002916190.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B' is part of the membrane proton channel. YP_002916191.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0 YP_002916192.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0 YP_002916193.1 COG5336 Uncharacterized protein conserved in bacteria YP_002916194.1 COG1651 Protein-disulfide isomerase YP_002916195.1 COG1329 Transcriptional regulators, similar to M. xanthus CarD YP_002916196.1 COG0500 SAM-dependent methyltransferases YP_002916197.1 Required for DNA replication; binds preferentially to single-stranded, linear DNA YP_002916198.1 COG2801 Transposase and inactivated derivatives YP_002916200.1 COG1678 Putative transcriptional regulator YP_002916201.1 COG1286 Uncharacterized membrane protein, required for colicin V production YP_002916203.1 COG0293 23S rRNA methylase YP_002916204.1 Regulates rRNA biosynthesis by transcriptional antitermination YP_002916205.1 COG0750 Predicted membrane-associated Zn-dependent proteases 1 YP_002916206.1 COG4775 Outer membrane protein/protective antigen OMA87 YP_002916208.1 COG0477 Permeases of the major facilitator superfamily YP_002916209.1 subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_002916210.1 Catalyzes the phosphorylation of UMP to UDP YP_002916211.1 Rrf; Frr; ribosome-recycling factor; release factor 4; RF4; recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G; A GTPase-dependent process results in release of 50S from 70S; inhibited by release factor RF-1; essential for viability; structurally similar to tRNAs YP_002916212.1 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; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain YP_002916213.1 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; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA YP_002916214.1 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; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA YP_002916215.1 COG0834 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain YP_002916216.1 COG1853 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family YP_002916217.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_002916218.1 COG0670 Integral membrane protein, interacts with FtsH YP_002916220.1 COG2801 Transposase and inactivated derivatives YP_002916221.1 COG4625 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain YP_002916222.1 COG0317 Guanosine polyphosphate pyrophosphohydrolases/synthetases YP_002916223.1 COG1472 Beta-glucosidase-related glycosidases YP_002916224.1 COG0776 Bacterial nucleoid DNA-binding protein YP_002916225.1 COG1225 Peroxiredoxin YP_002916226.1 Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA YP_002916227.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate YP_002916228.1 COG0739 Membrane proteins related to metalloendopeptidases YP_002916229.1 COG2961 Protein involved in catabolism of external DNA YP_002916230.1 this protein catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction; essential for DNA replication and repair of damaged DNA; similar to ligase LigB YP_002916231.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_002916234.1 COG1463 ABC-type transport system involved in resistance to organic solvents, periplasmic component YP_002916235.1 COG3761 NADH:ubiquinone oxidoreductase 17.2 kDa subunit YP_002916236.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids YP_002916237.1 COG3814 Uncharacterized protein conserved in bacteria YP_002916238.1 COG3494 Uncharacterized protein conserved in bacteria YP_002916239.1 catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis YP_002916240.1 3'-5' exonuclease of DNA polymerase III YP_002916241.1 COG3346 Uncharacterized conserved protein YP_002916242.1 COG1074 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) YP_002916244.1 COG0331 (acyl-carrier-protein) S-malonyltransferase YP_002916245.1 COG2801 Transposase and inactivated derivatives YP_002916246.1 COG2801 Transposase and inactivated derivatives YP_002916247.1 COG1566 Multidrug resistance efflux pump YP_002916248.1 COG1183 Phosphatidylserine synthase YP_002916249.1 catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine YP_002916251.1 COG0483 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family YP_002916252.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_002916253.1 involved in swarmer-to-stalked cell differentiation in Caulobacter crescentus; catalyzes the condensation of two GTP molecules to form the secondary messenger cyclic di-GMP (c-di-GMP); upon phosphorylation of domain D1 the protein dimerizes; presumably this allows the two GTP-bound GGDEF (diguanylate cyclase) domains to catalyze the condensation reaction; allosterically inhibited by c-di-GMP YP_002916254.1 hydrolyzes diadenosine polyphosphate YP_002916255.1 COG2154 Pterin-4a-carbinolamine dehydratase YP_002916256.1 forms a direct contact with the tRNA during translation YP_002916257.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_002916258.1 COG1520 FOG: WD40-like repeat YP_002916260.1 COG1729 Uncharacterized protein conserved in bacteria YP_002916261.1 COG0642 Signal transduction histidine kinase YP_002916262.1 COG0793 Periplasmic protease YP_002916263.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_002916264.1 COG0666 FOG: Ankyrin repeat YP_002916266.1 COG3827 Uncharacterized protein conserved in bacteria YP_002916267.1 COG1538 Outer membrane protein YP_002916272.1 catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr) YP_002916274.1 catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase YP_002916275.1 COG0612 Predicted Zn-dependent peptidases; similar to mitochondrial protease YP_002916276.1 COG0463 Glycosyltransferases involved in cell wall biogenesis YP_002916277.1 COG4115 Uncharacterized protein conserved in bacteria YP_002916278.1 COG2161 Antitoxin of toxin-antitoxin stability system YP_002916279.1 COG1294 Cytochrome bd-type quinol oxidase, subunit 2 YP_002916280.1 COG1271 Cytochrome bd-type quinol oxidase, subunit 1 YP_002916282.1 COG1132 ABC-type multidrug transport system, ATPase and permease components YP_002916283.1 COG0809 S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) YP_002916284.1 COG2801 Transposase and inactivated derivatives YP_002916285.1 COG4421 Capsular polysaccharide biosynthesis protein YP_002916286.1 COG0147 Anthranilate/para-aminobenzoate synthases component I YP_002916287.1 modifies the free amino group of the aminoacyl moiety of methionyl-tRNA(fMet) which is important in translation initiation; inactivation of this gene in Escherichia coli severely impairs growth YP_002916288.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_002916290.1 negatively supercoils closed circular double-stranded DNA YP_002916292.1 COG0695 Glutaredoxin and related proteins YP_002916293.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion YP_002916294.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids YP_002916295.1 J-type co-chaperone that regulates the ATPase and peptide-binding activity of Hsc66 chaperone; may function in biogenesis of iron-sulfur proteins YP_002916296.1 involved in the maturation of iron-sulfur cluster-containing proteins YP_002916297.1 COG0633 Ferredoxin YP_002916299.1 COG2358 TRAP-type uncharacterized transport system, periplasmic component YP_002916300.1 COG0589 Universal stress protein UspA and related nucleotide-binding proteins YP_002916301.1 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway YP_002916303.1 COG3838 Type IV secretory pathway, VirB2 components (pilins) YP_002916304.1 COG1845 Heme/copper-type cytochrome/quinol oxidase, subunit 3 YP_002916305.1 COG2941 Ubiquinone biosynthesis protein COQ7 YP_002916306.1 required for the assembly and function of the DNAX complex which are required for the assembly of the beta subunit onto primed DNA YP_002916308.1 COG0265 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain YP_002916309.1 heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE; multiple copies in some bacteria YP_002916310.1 chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion YP_002916311.1 COG4105 DNA uptake lipoprotein YP_002916312.1 COG0497 ATPase involved in DNA repair YP_002916313.1 COG2317 Zn-dependent carboxypeptidase YP_002916314.1 SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide YP_002916315.1 component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA YP_002916316.1 COG0720 6-pyruvoyl-tetrahydropterin synthase YP_002916317.1 COG1324 Uncharacterized protein involved in tolerance to divalent cations YP_002916318.1 COG1301 Na+/H+-dicarboxylate symporters YP_002916319.1 COG2801 Transposase and inactivated derivatives YP_002916321.1 COG0271 Stress-induced morphogen (activity unknown) YP_002916322.1 COG2200 FOG: EAL domain YP_002916323.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_002916324.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_002916325.1 D-alanine--D-alanine ligase; DdlA; DdlB; cytoplasmic; catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis; there are two forms of this enzyme in Escherichia coli YP_002916326.1 COG1589 Cell division septal protein YP_002916327.1 COG0849 Actin-like ATPase involved in cell division YP_002916329.1 COG3474 Cytochrome c2 YP_002916331.1 zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis YP_002916333.1 COG1530 Ribonucleases G and E YP_002916334.1 COG1612 Uncharacterized protein required for cytochrome oxidase assembly YP_002916335.1 COG0564 Pseudouridylate synthases, 23S RNA-specific YP_002916336.1 COG1680 Beta-lactamase class C and other penicillin binding proteins YP_002916337.1 COG0708 Exonuclease III YP_002916338.1 COG1071 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit YP_002916339.1 catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acyltransferase within the complex. The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2); it contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase YP_002916340.1 COG1217 Predicted membrane GTPase involved in stress response YP_002916341.1 COG2825 Outer membrane protein YP_002916342.1 catalyzes the formation of 2-oxoglutarate from isocitrate YP_002916343.1 subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport YP_002916344.1 subunit B of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_002916347.1 COG0723 Rieske Fe-S protein YP_002916348.1 COG1290 Cytochrome b subunit of the bc complex YP_002916349.1 COG2857 Cytochrome c1 YP_002916350.1 COG0071 Molecular chaperone (small heat shock protein) YP_002916351.1 recognizes the termination signals UGA and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1 YP_002916352.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_002916353.1 COG2801 Transposase and inactivated derivatives YP_002916354.1 COG0542 ATPases with chaperone activity, ATP-binding subunit YP_002916356.1 in most organisms, only the N-terminal domain is present in a single polypeptide; in some archaea this domain is fused to a kinase domain; this gene is essential for growth in Escherichia coli and Bacillus subtilis; the secreted glycoprotease from Pasteurella haemolytica showed specificity for O-sialoglycosylated proteins; the Pyrococcus structure shows DNA-binding properties, iron-binding, ATP-binding, and AP endonuclease activity YP_002916357.1 COG1398 Fatty-acid desaturase YP_002916358.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_002916359.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_002916360.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_002916361.1 COG0037 Predicted ATPase of the PP-loop superfamily implicated in cell cycle control YP_002916362.1 COG0465 ATP-dependent Zn proteases YP_002916363.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase YP_002916364.1 COG1565 Uncharacterized conserved protein YP_002916365.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_002916366.1 COG0668 Small-conductance mechanosensitive channel YP_002916367.1 functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria YP_002916368.1 COG0558 Phosphatidylglycerophosphate synthase YP_002916370.1 putative prokaryotic lipoprotein YP_002916371.1 COG0242 N-formylmethionyl-tRNA deformylase YP_002916372.1 COG3202 ATP/ADP translocase YP_002916373.1 COG2271 Sugar phosphate permease YP_002916374.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate YP_002916375.1 GidA; glucose-inhibited cell division protein A; involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs YP_002916376.1 glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA YP_002916377.1 COG1192 ATPases involved in chromosome partitioning YP_002916378.1 COG1475 Predicted transcriptional regulators YP_002916379.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence YP_002916380.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_002916381.1 COG0316 Uncharacterized conserved protein YP_002916382.1 dGTPase family type 2 subfamily; presumably hydrolyzes dGTP to deoxyguanosine and triphosphate YP_002916383.1 catalyzes a two-step reaction, first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class-I aminoacyl-tRNA synthetase YP_002916385.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_002916386.1 COG0154 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases YP_002916387.1 Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis YP_002916388.1 molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA YP_002916389.1 COG0745 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain YP_002916390.1 catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in queuosine biosynthesis YP_002916391.1 COG3820 Uncharacterized protein conserved in bacteria YP_002916392.1 COG1282 NAD/NADP transhydrogenase beta subunit. N-terminal truncation of 82 AA's due to frameshift. Rusults in change from nine putative transmembrane domains to six. YP_002916393.1 COG3047 Outer membrane protein W YP_002916394.1 COG0697 Permeases of the drug/metabolite transporter (DMT) superfamily YP_002916395.1 COG0477 Permeases of the major facilitator superfamily YP_002916398.1 catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA YP_002916399.1 one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit YP_002916400.1 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 YP_002916401.1 catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A YP_002916402.1 COG2121 Uncharacterized protein conserved in bacteria YP_002916403.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate YP_002916404.1 COG4115 Uncharacterized protein conserved in bacteria YP_002916405.1 COG2161 Antitoxin of toxin-antitoxin stability system YP_002916406.1 COG0500 SAM-dependent methyltransferases YP_002916407.1 COG2853 Surface lipoprotein YP_002916408.1 COG2854 ABC-type transport system involved in resistance to organic solvents, auxiliary component YP_002916409.1 converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer YP_002916410.1 COG0767 ABC-type transport system involved in resistance to organic solvents, permease component YP_002916411.1 COG1127 ABC-type transport system involved in resistance to organic solvents, ATPase component YP_002916415.1 COG1871 Chemotaxis protein; stimulates methylation of MCP proteins, CheD superfamily YP_002916416.1 required for 70S ribosome assembly YP_002916417.1 RpmE; RpmE2; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome YP_002916418.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_002916419.1 COG0548 Acetylglutamate kinase YP_002916420.1 COG3702 Type IV secretory pathway, VirB3 components YP_002916421.1 COG3451 Type IV secretory pathway, VirB4 components YP_002916422.1 COG3704 Type IV secretory pathway, VirB6 components YP_002916423.1 COG3704 Type IV secretory pathway, VirB6 components YP_002916424.1 COG3704 Type IV secretory pathway, VirB6 components YP_002916425.1 COG3704 Type IV secretory pathway, VirB6 components YP_002916426.1 COG3704 Type IV secretory pathway, VirB6 components YP_002916427.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_002916428.1 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 YP_002916429.1 COG2801 Transposase and inactivated derivatives YP_002916430.1 COG1396 Predicted transcriptional regulators YP_002916431.1 Catalyzes the formation of (d)CDP from ATP and (d)CMP YP_002916432.1 in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins YP_002916433.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates YP_002916435.1 catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate YP_002916436.1 COG2801 Transposase and inactivated derivatives YP_002916437.1 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair YP_002916438.1 COG0552 Signal recognition particle GTPase YP_002916439.1 COG2913 Small protein A (tmRNA-binding) YP_002916440.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not YP_002916441.1 FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs YP_002916442.1 COG2885 Outer membrane protein and related peptidoglycan-associated (lipo)proteins YP_002916443.1 COG0795 Predicted permeases YP_002916444.1 functions in MreBCD complex in some organisms YP_002916445.1 in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall YP_002916446.1 COG1396 Predicted transcriptional regulators YP_002916447.1 COG0194 Guanylate kinase YP_002916448.1 COG1373 Predicted ATPase (AAA+ superfamily) YP_002916450.1 COG0488 ATPase components of ABC transporters with duplicated ATPase domains YP_002916451.1 FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP YP_002916452.1 carries the fatty acid chain in fatty acid biosynthesis YP_002916453.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_002916454.1 catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs YP_002916456.1 in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine, which is found in the wobble position of some tRNAs and affects ribosomal frameshifting; shows potassium-dependent dimerization and GTP hydrolysis; also involved in regulation of glutamate-dependent acid resistance and activation of gadE YP_002916457.1 COG2902 NAD-specific glutamate dehydrogenase YP_002916458.1 COG1426 Uncharacterized protein conserved in bacteria YP_002916459.1 COG0419 ATPase involved in DNA repair YP_002916460.1 COG3027 Uncharacterized protein conserved in bacteria YP_002916461.1 COG0477 Permeases of the major facilitator superfamily YP_002916463.1 COG1396 Predicted transcriptional regulators YP_002916464.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. YP_002916465.1 involved in the peptidyltransferase reaction during translation YP_002916466.1 COG0261 Ribosomal protein L21 YP_002916467.1 COG1267 Phosphatidylglycerophosphatase A and related proteins YP_002916468.1 TatA; similar to TatE that is found in some proteobacteria; part of system that translocates proteins with a conserved twin arginine motif across the inner membrane; capable of translocating folded substrates typically those with bound cofactors; similar to a protein import system in thylakoid membranes YP_002916469.1 COG0683 ABC-type branched-chain amino acid transport systems, periplasmic component YP_002916470.1 COG0313 Predicted methyltransferases YP_002916471.1 COG5510 Predicted small secreted protein YP_002916475.1 COG0177 Predicted EndoIII-related endonuclease YP_002916476.1 COG0278 Glutaredoxin-related protein YP_002916477.1 COG0400 Predicted esterase YP_002916478.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_002916479.1 catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group YP_002916480.1 COG0319 Predicted metal-dependent hydrolase YP_002916481.1 COG1253 Hemolysins and related proteins containing CBS domains YP_002916482.1 COG3202 ATP/ADP translocase YP_002916483.1 COG3243 Poly(3-hydroxyalkanoate) synthetase YP_002916484.1 COG2801 Transposase and inactivated derivatives YP_002916485.1 COG0666 FOG: Ankyrin repeat YP_002916486.1 COG2801 Transposase and inactivated derivatives YP_002916487.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision YP_002916488.1 COG2847 Uncharacterized protein conserved in bacteria YP_002916489.1 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins YP_002916490.1 COG0760 Parvulin-like peptidyl-prolyl isomerase YP_002916491.1 Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids YP_002916492.1 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 YP_002916493.1 adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active YP_002916494.1 negatively supercoils closed circular double-stranded DNA YP_002916495.1 COG0647 Predicted sugar phosphatases of the HAD superfamily YP_002916496.1 COG2239 Mg/Co/Ni transporter MgtE (contains CBS domain) YP_002916497.1 COG4710 Predicted DNA-binding protein with an HTH domain YP_002916498.1 member of preprotein translocase; forms a heterotrimer with SecD and SecF; links the SecD/SecF/YajC/YidC complex with the SecY/SecE/SecG complex YP_002916499.1 part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane YP_002916500.1 COG1999 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems YP_002916501.1 CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane YP_002916502.1 catalyzes the hydrolysis of pyrophosphate to phosphate YP_002916503.1 COG0728 Uncharacterized membrane protein, putative virulence factor YP_002916505.1 COG1200 RecG-like helicase YP_002916506.1 COG2801 Transposase and inactivated derivatives YP_002916507.1 protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus; this enzyme also cleaves other RNA substrates YP_002916508.1 in Escherichia coli transcription of this gene is enhanced by polyamines YP_002916509.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_002916510.1 COG0291 Ribosomal protein L35 YP_002916511.1 COG0602 Organic radical activating enzymes YP_002916512.1 the Ctc family of proteins consists of two types, one that contains the N-terminal ribosomal protein L25 domain only which in Escherichia coli binds the 5S rRNA while a subset of proteins contain a C-terminal extension that is involved in the stress response YP_002916513.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_002916514.1 translation-associated GTPase; the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure (PDB: 1NI3); fluorescence spectroscopy revealed nucleic acid binding; the yeast protein YBR025c interacts with the translation elongation factor eEF1 YP_002916515.1 COG3621 Patatin [General function prediction only]. As a result of a frameshift mutation, protein is truncated relative to most but not all rickettsial patatins, and contains the entire patatin superfamily domain YP_002916516.1 COG0591 Na+/proline symporter YP_002916517.1 COG0666 FOG: Ankyrin repeat YP_002916518.1 MraZ; UPF0040; crystal structure shows similarity to AbrB YP_002916519.1 COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis YP_002916521.1 COG0768 Cell division protein FtsI/penicillin-binding protein 2 YP_002916524.1 COG0768 Cell division protein FtsI/penicillin-binding protein 2 YP_002916525.1 COG1357 Uncharacterized low-complexity proteins YP_002916526.1 COG2204 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains YP_002916527.1 subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_002916528.1 Oxygenase that introduces the hydroxyl group at carbon four of 2-octaprenyl-6-methoxyphenol resulting in the formation of 2-octaprenyl-6-methoxy-1,4-benzoquinone YP_002916529.1 COG0671 Membrane-associated phospholipid phosphatase YP_002916530.1 LRR_RI, Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily YP_002916531.1 COG2801 Transposase and inactivated derivatives YP_002916532.1 catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes YP_002916534.1 COG1192 ATPases involved in chromosome partitioning YP_002916535.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides YP_002916536.1 COG0085 DNA-directed RNA polymerase, beta subunit/140 kDa subunit YP_002916537.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Subunit beta' binds to sigma factor allowing it to bind to the -10 region of the promoter YP_002916538.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme YP_002916539.1 present in two forms; L12 is normal, while L7 is aminoacylated at the N-terminal serine; the only multicopy ribosomal protein; 4:1 ratio of L7/L12 per ribosome; two L12 dimers bind L10; critically important for translation efficiency and fidelity; stimulates GTPase activity of translation factors YP_002916540.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_002916541.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_002916542.1 binds directly to 23S ribosomal RNA YP_002916543.1 Modulates Rho-dependent transcription termination YP_002916544.1 forms a complex with SecY and SecG; SecYEG forms a putative protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force YP_002916545.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_002916546.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_002916547.1 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; mutations in the S12 gene confer streptomycin resistance YP_002916548.1 COG0765 ABC-type amino acid transport system, permease component YP_002916549.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol YP_002916550.1 COG2142 Succinate dehydrogenase, hydrophobic anchor subunit YP_002916551.1 COG2009 Succinate dehydrogenase/fumarate reductase, cytochrome b subunit YP_002916552.1 COG1054 Predicted sulfurtransferase YP_002916553.1 COG0265 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain YP_002916554.1 COG0330 Membrane protease subunits, stomatin/prohibitin homologs YP_002916555.1 COG0330 Membrane protease subunits, stomatin/prohibitin homologs YP_002916556.1 COG0489 ATPases involved in chromosome partitioning YP_002916557.1 COG3660 Predicted nucleoside-diphosphate-sugar epimerase YP_002916559.1 COG0565 rRNA methylase YP_002916560.1 endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity YP_002916561.1 COG1159 GTPase YP_002916562.1 cytoplasmic enzyme involved in processing rRNA and some mRNAs; substrates typically have dsRNA regions; forms a homodimer; have N-terminal nuclease and C-terminal RNA-binding domains; requires magnesium as preferred ion for activity YP_002916563.1 COG0681 Signal peptidase I YP_002916564.1 part of NADH-ubiquinone oxidoreductase complex I; shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH dehydrogenase YP_002916565.1 forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF YP_002916566.1 COG3750 Uncharacterized protein conserved in bacteria YP_002916567.1 COG2801 Transposase and inactivated derivatives YP_002916568.1 binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself. YP_002916569.1 COG0607 Rhodanese-related sulfurtransferase YP_002916570.1 COG2938 Uncharacterized conserved protein YP_002916571.1 COG1197 Transcription-repair coupling factor (superfamily II helicase) YP_002916572.1 involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate YP_002916573.1 COG0770 UDP-N-acetylmuramyl pentapeptide synthase YP_002916574.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_002916575.1 COG2801 Transposase and inactivated derivatives YP_002916577.1 COG0317 Guanosine polyphosphate pyrophosphohydrolases/synthetases YP_002916578.1 COG0772 Bacterial cell division membrane protein YP_002916579.1 COG2801 Transposase and inactivated derivatives YP_002916580.1 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone YP_002916581.1 COG1487 Predicted nucleic acid-binding protein, contains PIN domain YP_002916583.1 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone YP_002916584.1 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone YP_002916585.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_002916586.1 COG3504 Type IV secretory pathway, VirB9 components YP_002916587.1 COG3736 Type IV secretory pathway, component VirB8 YP_002916589.1 COG3736 Type IV secretory pathway, component VirB8 YP_002916590.1 COG3504 Type IV secretory pathway, VirB9 components YP_002916591.1 COG2948 Type IV secretory pathway, VirB10 components YP_002916592.1 COG0630 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis YP_002916593.1 COG3505 Type IV secretory pathway, VirD4 components YP_002916594.1 COG0248 Exopolyphosphatase YP_002916598.1 COG1218 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase YP_002916599.1 This protein performs the mismatch recognition step during the DNA repair process YP_002916600.1 catalyzes the interconversion of ribose 5-phosphate to ribulose 5-phosphate; enzyme from E. coli shows allose 6-phosphate isomerase activity YP_002916601.1 COG0739 Membrane proteins related to metalloendopeptidases YP_002916602.1 COG1451 Predicted metal-dependent hydrolase YP_002916603.1 flavin dependent thymidylate synthase; ThyX; thymidylate synthase complementing protein; catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate; the enzyme from Mycobacterium tuberculosis forms homotetramers; uses FAD as a cofactor YP_002916604.1 forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA YP_002916605.1 binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters YP_002916606.1 involved in the insertion of copper into subunit I of cytochrome C oxidase YP_002916607.1 COG0457 FOG: TPR repeat YP_002916608.1 COG0457 FOG: TPR repeat YP_002916609.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_002916610.1 COG0531 Amino acid transporters YP_002916611.1 catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG YP_002916612.1 COG0811 Biopolymer transport proteins YP_002916613.1 COG0848 Biopolymer transport protein YP_002916614.1 COG0810 Periplasmic protein TonB, links inner and outer membranes YP_002916615.1 COG0317 Guanosine polyphosphate pyrophosphohydrolases/synthetases YP_002916616.1 COG0477 Permeases of the major facilitator superfamily YP_002916617.1 COG0845 Membrane-fusion protein YP_002916618.1 COG4618 ABC-type protease/lipase transport system, ATPase and permease components YP_002916619.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_002916620.1 COG0537 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases YP_002916622.1 heat shock protein involved in degradation of misfolded proteins YP_002916623.1 heat shock protein involved in degradation of misfolded proteins YP_002916625.1 catalyzes the formation of lipid A disaccharide from UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate, lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM YP_002916627.1 COG1559 Predicted periplasmic solute-binding protein YP_002916628.1 defects in the mitochondrial frataxin protein cause Friedreich ataxis which is an autosomal recessive neurodegenerative disease; based on phylogenomic distribution this protein may have a role in iron-sulfur cluster protein assembly YP_002916630.1 catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_002916631.1 COG0204 1-acyl-sn-glycerol-3-phosphate acyltransferase YP_002916632.1 COG5622 Protein required for attachment to host cells YP_002916633.1 COG2945 Predicted hydrolase of the alpha/beta superfamily YP_002916634.1 COG2956 Predicted N-acetylglucosaminyl transferase YP_002916636.1 COG1587 Uroporphyrinogen-III synthase YP_002916637.1 COG1279 Lysine efflux permease YP_002916638.1 COG0477 Permeases of the major facilitator superfamily YP_002916639.1 COG3202 ATP/ADP translocase YP_002916641.1 COG0142 Geranylgeranyl pyrophosphate synthase YP_002916642.1 COG0006 Xaa-Pro aminopeptidase YP_002916643.1 COG0531 Amino acid transporters YP_002916644.1 COG0316 Uncharacterized conserved protein YP_002916645.1 COG0822 NifU homolog involved in Fe-S cluster formation YP_002916646.1 catalyzes the removal of elemental sulfur from cysteine to produce alanine; involved in NAD biosynthesis YP_002916647.1 COG1104 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes YP_002916648.1 COG1959 Predicted transcriptional regulator YP_002916650.1 COG0454 Histone acetyltransferase HPA2 and related acetyltransferases YP_002916651.1 COG2801 Transposase and inactivated derivatives YP_002916652.1 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase YP_002916653.1 COG1004 Predicted UDP-glucose 6-dehydrogenase YP_002916655.1 COG0477 Permeases of the major facilitator superfamily YP_002916656.1 COG0805 Sec-independent protein secretion pathway component TatC YP_002916657.1 catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_002916658.1 COG3451 Type IV secretory pathway, VirB4 components YP_002916660.1 COG0861 Membrane protein TerC, possibly involved in tellurium resistance YP_002916661.1 COG3637 Opacity protein and related surface antigens YP_002916662.1 COG0500 SAM-dependent methyltransferases YP_002916664.1 COG2944 Predicted transcriptional regulator YP_002916665.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916666.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916667.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_002916668.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916669.1 ATP-binding protein; required for proper cytochrome c maturation YP_002916670.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916671.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916672.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916673.1 COG3671 Predicted membrane protein YP_002916674.1 Catalyzes the conversion of citrate to isocitrate YP_002916675.1 part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane YP_002916676.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_002916677.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_002916678.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_002916679.1 Produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex YP_002916680.1 Catalyzes the oxidation of dihydrolipoamide to lipoamide YP_002916681.1 COG0783 DNA-binding ferritin-like protein (oxidative damage protectant) YP_002916682.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_002916683.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine YP_002916684.1 molecular chaperone YP_002916685.1 COG1872 Uncharacterized conserved protein YP_002916687.1 binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA YP_002916688.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate YP_002916689.1 COG1121 ABC-type Mn/Zn transport systems, ATPase component YP_002916690.1 COG1881 Phospholipid-binding protein YP_002916691.1 COG4520 Surface antigen YP_002916692.1 COG0053 Predicted Co/Zn/Cd cation transporters YP_002916693.1 COG0590 Cytosine/adenosine deaminases YP_002916694.1 COG0755 ABC-type transport system involved in cytochrome c biogenesis, permease component YP_002916695.1 COG1146 Ferredoxin YP_002916696.1 COG3637 Opacity protein and related surface antigens YP_002916697.1 COG3637 Opacity protein and related surface antigens YP_002916699.1 COG0472 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N-acetylglucosamine-1-phosphate transferase YP_002916700.1 catalyzes the removal of N-terminal amino acids from peptides and arylamides; generally Co(II) however activity has been shown for some methionine aminopeptidases with Zn, Fe, or Mn YP_002916701.1 COG1674 DNA segregation ATPase FtsK/SpoIIIE and related proteins YP_002916702.1 COG0760 Parvulin-like peptidyl-prolyl isomerase YP_002916703.1 COG0043 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases YP_002916704.1 COG1502 Phosphatidylserine/phosphatidylglycerophosphate/cardiolipi n synthases and related enzymes YP_002916705.1 site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs YP_002916706.1 COG1734 DnaK suppressor protein YP_002916707.1 Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell YP_002916708.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_002916709.1 COG0271 Stress-induced morphogen (activity unknown) YP_002916710.1 COG0799 Uncharacterized homolog of plant Iojap protein YP_002916711.1 COG0475 Kef-type K+ transport systems, membrane components YP_002916712.1 COG3807 Uncharacterized protein conserved in bacteria YP_002916713.1 COG2801 Transposase and inactivated derivatives YP_002916714.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis YP_002916715.1 COG1619 Uncharacterized proteins, homologs of microcin C7 resistance protein MccF YP_002916717.1 COG0354 Predicted aminomethyltransferase related to GcvT YP_002916718.1 COG1723 Uncharacterized conserved protein YP_002916719.1 COG0349 Ribonuclease D YP_002916721.1 COG0212 5-formyltetrahydrofolate cyclo-ligase YP_002916722.1 Catalyzes the oxidation of dihydrolipoamide to lipoamide YP_002916723.1 COG0500 SAM-dependent methyltransferases YP_002916725.1 catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A) YP_002916726.1 COG5009 Membrane carboxypeptidase/penicillin-binding protein YP_002916727.1 COG2801 Transposase and inactivated derivatives YP_002916728.1 COG1207 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) YP_002916729.1 COG0217 Uncharacterized conserved protein YP_002916730.1 smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group do not have the motif YP_002916733.1 COG0741 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) YP_002916735.1 COG2801 Transposase and inactivated derivatives YP_002916736.1 binds to ssrA RNA (tmRNA) and is required for its successful binding to ribosomes; also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site; SmpB protects the tmRNA from RNase R degradation in Caulobacter crescentus; both the tmRNA and SmpB are regulated in cell cycle-dependent manner; functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation YP_002916737.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis YP_002916738.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_002916739.1 COG0745 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain YP_002916740.1 COG0642 Signal transduction histidine kinase YP_002916741.1 COG0020 Undecaprenyl pyrophosphate synthase YP_002916742.1 COG0575 CDP-diglyceride synthetase YP_002916743.1 COG2919 Septum formation initiator YP_002916744.1 COG0349 Ribonuclease D YP_002916746.1 leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase YP_002916748.1 binds the polymerase to DNA and acts as a sliding clamp YP_002916749.1 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 tetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily YP_002916750.1 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 magnesium ions per tetramer; type 1 subfamily YP_002916751.1 COG0621 2-methylthioadenine synthetase YP_002916752.1 involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate YP_002916753.1 COG0438 Glycosyltransferase YP_002916755.1 UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis YP_002916756.1 COG0772 Bacterial cell division membrane protein YP_002916757.1 UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation YP_002916759.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_002916760.1 COG0739 Membrane proteins related to metalloendopeptidases YP_002916761.1 COG0615 Cytidylyltransferase YP_002916762.1 COG1622 Heme/copper-type cytochrome/quinol oxidases, subunit 2 YP_002916763.1 COG0110 Acetyltransferase (isoleucine patch superfamily) YP_002916764.1 COG0843 Heme/copper-type cytochrome/quinol oxidases, subunit 1 YP_002916765.1 COG2071 Predicted glutamine amidotransferases YP_002916767.1 COG2887 RecB family exonuclease YP_002916768.1 COG1619 Uncharacterized proteins, homologs of microcin C7 resistance protein MccF YP_002916770.1 COG0741 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) YP_002916771.1 catalyzes the formation of dUMP from dUTP YP_002916772.1 COG0616 Periplasmic serine proteases (ClpP class) YP_002916773.1 COG0526 Thiol-disulfide isomerase and thioredoxins YP_002916774.1 COG3485 Protocatechuate 3,4-dioxygenase beta subunit YP_002916775.1 COG0545 FKBP-type peptidyl-prolyl cis-trans isomerases 1 YP_002916777.1 COG0672 High-affinity Fe2+/Pb2+ permease YP_002916778.1 Involved in cell division; probably involved in intracellular septation YP_002916779.1 COG2823 Predicted periplasmic or secreted lipoprotein YP_002916780.1 COG0797 Lipoproteins YP_002916781.1 COG1686 D-alanyl-D-alanine carboxypeptidase YP_002916782.1 COG1132 ABC-type multidrug transport system, ATPase and permease components YP_002916783.1 promotes strand exchange during homologous recombination; RuvAB complex promotes branch migration; RuvABC complex scans the DNA during branch migration and resolves Holliday junctions at consensus sequences; forms hexameric rings around opposite DNA arms; requires ATP for branch migration and orientation of RuvAB complex determines direction of migration YP_002916784.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_002916785.1 COG3177 Uncharacterized conserved protein YP_002916786.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_002916787.1 involved in the first step of tetrahydrofolate biosynthesis; catalyzes the formation of formate and 2-amino-4-hydroxy-6-(erythro-1,2, 3-trihydroxypropyl)dihydropteridine triphosphate from GTP and water; forms a homopolymer YP_002916788.1 CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS YP_002916789.1 CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer YP_002916790.1 COG3202 ATP/ADP translocase YP_002916791.1 Catalyzes the reversible oxidation of malate to oxaloacetate YP_002916792.1 COG1495 Disulfide bond formation protein DsbB YP_002916793.1 class I; LysRS1; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine YP_002916794.1 COG0679 Predicted permeases YP_002916795.1 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate YP_002916797.1 COG2801 Transposase and inactivated derivatives YP_002916798.1 COG0477 Permeases of the major facilitator superfamily YP_002916799.1 COG2002 Regulators of stationary/sporulation gene expression YP_002916800.1 COG4374 Uncharacterized protein conserved in bacteria YP_002916801.1 COG2801 Transposase and inactivated derivatives YP_002916802.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_002916803.1 is a component of the macrolide binding site in the peptidyl transferase center YP_002916804.1 catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Dimerization of the alpha subunit is the first step in the sequential assembly of subunits to form the holoenzyme YP_002916805.1 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; interacts with S7 and S18 and IF-3 YP_002916806.1 located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA; makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5; contacts P-site tRNA YP_002916807.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_002916808.1 forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase YP_002916809.1 late assembly protein YP_002916810.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7 YP_002916811.1 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; mutations in this gene result in spectinomycin resistance YP_002916812.1 binds 5S rRNA along with protein L5 and L25 YP_002916813.1 ribosomal protein L6 appears to have arisen as a result of an ancient gene duplication as based on structural comparison of the Bacillus stearothermophilus protein; RNA-binding appears to be in the C-terminal domain; mutations in the L6 gene confer resistance to aminoglycoside antibiotics such as gentamicin and these occur in truncations of the C-terminal domain; it has been localized to a region between the base of the L7/L12 stalk and the central protuberance YP_002916814.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_002916815.1 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif YP_002916816.1 part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13 YP_002916817.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_002916818.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_002916819.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_002916820.1 one of the stabilizing components for the large ribosomal subunit YP_002916821.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_002916822.1 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 YP_002916823.1 binds specifically to 23S rRNA during the early stages of 50S assembly; makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome; mutations in this gene result in erythromycin resistance; located near peptidyl-transferase center YP_002916824.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_002916825.1 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 YP_002916826.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_002916827.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_002916828.1 binds directly near the 3' end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene confer resistance to tiamulin YP_002916829.1 NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex YP_002916831.1 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu YP_002916832.1 COG0566 rRNA methylases YP_002916834.1 class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle YP_002916835.1 COG4118 Antitoxin of toxin-antitoxin stability system YP_002916837.1 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 YP_002916839.1 COG4574 Serine protease inhibitor ecotin YP_002916840.1 COG0694 Thioredoxin-like proteins and domains YP_002916841.1 COG0477 Permeases of the major facilitator superfamily YP_002916842.1 COG0513 Superfamily II DNA and RNA helicases YP_002916843.1 COG1278 Cold shock proteins YP_002916844.1 catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases A1518 and A1519 in 16S rRNA; mutations in ksgA causes resistance to the translation initiation inhibitor kasugamycin YP_002916845.1 COG0760 Parvulin-like peptidyl-prolyl isomerase YP_002916846.1 COG1452 Organic solvent tolerance protein OstA YP_002916847.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides YP_002916848.1 COG0708 Exonuclease III YP_002916849.1 COG4095 Uncharacterized conserved protein YP_002916850.1 EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains YP_002916851.1 COG0661 Predicted unusual protein kinase YP_002916852.1 Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone YP_002916853.1 Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases YP_002916855.1 COG0084 Mg-dependent DNase YP_002916856.1 methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content YP_002916857.1 catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP) YP_002916858.1 COG0477 Permeases of the major facilitator superfamily YP_002916859.1 UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin YP_002916860.1 valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain YP_002916861.1 COG3475 LPS biosynthesis protein YP_002916862.1 COG1322 Uncharacterized protein conserved in bacteria YP_002916863.1 COG5528 Predicted integral membrane protein YP_002916864.1 binds and unfolds substrates as part of the ClpXP protease YP_002916865.1 COG1670 Acetyltransferases, including N-acetylases of ribosomal proteins YP_002916866.1 COG0603 Predicted PP-loop superfamily ATPase YP_002916867.1 COG1598 Uncharacterized conserved protein YP_002916868.1 COG1132 ABC-type multidrug transport system, ATPase and permease components YP_002916870.1 COG0477 Permeases of the major facilitator superfamily YP_002916871.1 COG4591 ABC-type transport system, involved in lipoprotein release, permease component YP_002916872.1 COG1136 ABC-type antimicrobial peptide transport system, ATPase component YP_002916874.1 COG4536 Putative Mg2+ and Co2+ transporter CorB YP_002916875.1 COG1138 Cytochrome c biogenesis factor YP_002916876.1 COG2801 Transposase and inactivated derivatives YP_002916877.1 COG2867 Oligoketide cyclase/lipid transport protein YP_002916878.1 COG5508 Uncharacterized conserved small protein YP_002916879.1 in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase YP_002916880.1 COG2155 Uncharacterized conserved protein YP_002916881.1 As a result of a frameshift mutation, protein is truncated relative to rickettsial homologs but contains the entire acriflavin resistance protein domain YP_002916882.1 COG0776 Bacterial nucleoid DNA-binding protein YP_002916883.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA YP_002916884.1 COG0541 Signal recognition particle GTPase YP_002916885.1 Transfers the fatty acyl group on membrane lipoproteins YP_002916886.1 Catalyzes a key regulatory step in fatty acid biosynthesis YP_002916888.1 site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; XerD specifically exchanges the bottom strands; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs YP_002916889.1 COG4765 Uncharacterized protein conserved in bacteria YP_002916890.1 COG3307 Lipid A core - O-antigen ligase and related enzymes YP_002916891.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916892.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen YP_002916893.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916894.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916895.1 Catalyzes the transfer of electrons from NADH to quinone YP_002916896.1 COG0759 Uncharacterized conserved protein YP_002916897.1 COG2350 Uncharacterized protein conserved in bacteria YP_002916898.1 responsible for recognizing base lesions in the genome and initiating base excision DNA repair YP_002916900.1 catalyzes the bidirectional exonucleolytic cleavage of DNA YP_002916902.1 Essential for efficient processing of 16S rRNA YP_002916903.1 COG2982 Uncharacterized protein involved in outer membrane biogenesis YP_002916904.1 COG0457 FOG: TPR repeat YP_002916906.1 COG1533 DNA repair photolyase YP_002916907.1 converts protoheme IX and farnesyl diphosphate to heme O YP_002916908.1 primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination YP_002916910.1 COG0438 Glycosyltransferase YP_002916911.1 COG0596 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) YP_002916913.1 COG0463 Glycosyltransferases involved in cell wall biogenesis YP_002916914.1 COG0500 SAM-dependent methyltransferases YP_002916915.1 COG0381 UDP-N-acetylglucosamine 2-epimerase YP_002916916.1 COG1086 Predicted nucleoside-diphosphate sugar epimerases YP_002916917.1 COG1091 dTDP-4-dehydrorhamnose reductase YP_002916918.1 COG3093 Plasmid maintenance system antidote protein YP_002916919.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function YP_002916920.1 COG0330 Membrane protease subunits, stomatin/prohibitin homologs YP_002916921.1 COG0450 Peroxiredoxin YP_002916922.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_002916923.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_002916924.1 COG1471: Ribosomal protein S4E YP_002916925.1 COG0598 Mg2+ and Co2+ transporters YP_002916926.1 COG5000 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation YP_002916927.1 a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA YP_002916928.1 COG5590 Uncharacterized conserved protein YP_002916929.1 IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 2 subfamily; some organisms carry two different copies of this enzyme; in some organisms, the type 2 subfamily is associated with resistance to the antibiotic pseudomonic acid (mupirocin) YP_002916930.1 COG4770 Acetyl/propionyl-CoA carboxylase, alpha subunit YP_002916931.1 COG4799 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) YP_002916932.1 Synthesizes thioester adducts of fatty acids enzymatically to the phosphopantetheine group of acyl carrier protein YP_002916933.1 putative COG3070 Regulator of competence-specific genes, TfoX N-terminal domain YP_002916934.1 COG1108 ABC-type Mn2+/Zn2+ transport systems, permease components YP_002916935.1 Involved in ubiquinone biosynthesis YP_002916936.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_002916937.1 COG5342 Invasion protein B, involved in pathogenesis YP_002916938.1 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is essential for growth YP_002916939.1 10 kDa chaperonin; Cpn10; GroES; forms homoheptameric ring; binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it; folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES; release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring YP_002916941.1 RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs YP_002916942.1 with DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins; may act as a thermosensor YP_002916943.1 COG0628 Predicted permease YP_002916944.1 COG0593 ATPase involved in DNA replication initiation YP_002916945.1 COG2801 Transposase and inactivated derivatives YP_002916946.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_002916947.1 type II enzyme; in Escherichia coli this enzyme forms a trimer of dimers which is allosterically inhibited by NADH and competitively inhibited by alpha-ketoglutarate; allosteric inhibition is lost when Cys206 is chemically modified which also affects hexamer formation; forms oxaloacetate and acetyl-CoA and water from citrate and coenzyme A; functions in TCA cycle, glyoxylate cycle and respiration; enzyme from Helicobacter pylori is not inhibited by NADH YP_002916948.1 COG1573 Uracil-DNA glycosylase YP_002916949.1 COG0564 Pseudouridylate synthases, 23S RNA-specific YP_002916950.1 fusion of hemK/trmB; N-terminal HemK domain transfers a methyl group from S-adenosylmethionine to amide nitrogen of specific glutamine residues in protein chain release factors PrfA and PrfB; C-terminal YP_002916951.1 COG0009 Putative translation factor (SUA5) YP_002916952.1 glycine--tRNA ligase beta chain; glyS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA YP_002916953.1 glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA YP_002916954.1 COG1487 Predicted nucleic acid-binding protein, contains PIN domain YP_002916955.1 COG2161 Antitoxin of toxin-antitoxin stability system YP_002916956.1 COG1636 Uncharacterized protein conserved in bacteria YP_002916958.1 COG1474 Cdc6-related protein, AAA superfamily ATPase YP_002916960.1 Catalyzes a two-step reaction, first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_002916961.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_002916962.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria YP_002916963.1 synthesizes RNA primers at the replication forks YP_002916964.1 COG0170 Dolichol kinase YP_002916965.1 necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus YP_002916966.1 COG2834 Outer membrane lipoprotein-sorting protein YP_002916967.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; rhe tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA YP_002916968.1 COG0718 Uncharacterized protein conserved in bacteria YP_002916969.1 COG3577 Predicted aspartyl protease YP_002916970.1 COG2161 Antitoxin of toxin-antitoxin stability system YP_002916971.1 COG1126 ABC-type polar amino acid transport system, ATPase component YP_002916972.1 COG1235 Metal-dependent hydrolases of the beta-lactamase superfamily I YP_002916973.1 COG0671 Membrane-associated phospholipid phosphatase YP_002916974.1 COG3077 DNA-damage-inducible protein J YP_002916975.1 COG0795 Predicted permeases YP_002916976.1 binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB YP_002916977.1 dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica. YP_002916978.1 COG0732 Restriction endonuclease S subunits YP_002916979.1 COG1434 Uncharacterized conserved protein YP_002916980.1 lipoyl/octanoyltransferase; catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein YP_002916981.1 COG3023 Negative regulator of beta-lactamase expression YP_002916982.1 binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity YP_002916983.1 in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif YP_002916984.1 This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. Promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex YP_002916985.1 COG0457 FOG: TPR repeat YP_002916986.1 COG0477 Permeases of the major facilitator superfamily YP_002916987.1 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis YP_002916988.1 COG1981 Predicted membrane protein YP_002916989.1 protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic YP_002916990.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III YP_002921997.1 COG1192 ATPases involved in chromosome partitioning YP_002922000.1 COG0593 ATPase involved in DNA replication initiation YP_002922001.1 COG2801 Transposase and inactivated derivatives YP_002922002.1 COG1044 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase YP_002922003.1 COG4638 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit YP_002922004.1 COG1028 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) YP_002922005.1 COG0332 3-oxoacyl-[acyl-carrier-protein] synthase III YP_002922006.1 COG0236 Acyl carrier protein YP_002922007.1 COG1132 ABC-type multidrug transport system, ATPase and permease components YP_002922008.1 COG0071 Molecular chaperone (small heat shock protein) YP_002922009.1 COG0071 Molecular chaperone (small heat shock protein) YP_002922010.1 COG5464 Uncharacterized conserved protein, transposase like YP_002922011.1 COG2801 Transposase and inactivated derivatives YP_002922012.1 putative lipoprotein YP_002922013.1 COG2076 Membrane transporters of cations and cationic drugs YP_002922014.1 COG0457 FOG: TPR repeat YP_002922015.1 only 5' half of CDS has similarity to part of Sca4 producing apparent chimeric protein YP_002922016.1 COG0419 ATPase involved in DNA repair, truncated relative to rickettsial homologs