-- dump date 20140619_233700 -- class Genbank::CDS -- table cds_note -- id note YP_002128649.1 catalyzes the formation of 3-phospho-D-glycerol phosphate from D-glyceraldehyde 3-phosphate in glycolysis YP_002128653.1 unknown function YP_002128660.1 catalyzes the formation of thymine and 2-deoxy-alpha-D-ribose 1-phosphate from thymidine YP_002128661.1 Catalyzes the formation of PRPP from ATP and ribose 5-phosphate YP_002128689.1 catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate YP_002128718.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP YP_002128735.1 CopA YP_002128771.1 part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum YP_002128828.1 probable dehydrogenase YP_002128847.1 catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis YP_002128872.1 catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP YP_002128876.1 heat shock protein involved in degradation of misfolded proteins YP_002128878.1 heat shock protein involved in degradation of misfolded proteins YP_002128883.1 catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis YP_002128885.1 catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide YP_002128887.1 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis YP_002128891.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming YP_002128896.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase YP_002128898.1 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_002128899.1 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_002128920.1 4-alpha-hydroxytetrahydrobiopterin dehydratase activity; catalyzes the formation of (6R)-6-(L-erythro-1,2-dihydroxypropyl)-7, 8-dihydro-6H-pterin from (6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7, 8-tetrahydro-4a-hydroxypterin; functions in recycling tetrahydrobiopterin (BH4) in phenylalanine hydroxylase reaction YP_002128936.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine YP_002128942.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_002128947.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_002128948.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D YP_002128950.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate YP_002128955.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_002128958.1 Essential for efficient processing of 16S rRNA YP_002128970.1 involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate YP_002128984.1 Catalyzes the conversion of citrate to isocitrate YP_002128994.1 similar to other HIT family hydrolases YP_002128995.1 catalyzes the oxidation of malate to oxaloacetate YP_002129001.1 catalyzes the interconversion of succinyl-CoA and succinate YP_002129003.1 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_002129004.1 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_002129005.1 forms citrate from oxaloacetate and acetyl-CoA; functions in TCA cycle YP_002129008.1 function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain YP_002129009.1 BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell YP_002129021.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma 54 factor is responsible for the expression of enzymes involved in nitrogen assimilation and metabolism; the rhizobia often have 2 copies of this sigma factor; in Rhizobium etli RpoN1 shown to be involved in the assimilation of several nitrogen and carbon sources during free-living aerobic growth and RpoN2 is involved in symbiotic nitrogen fixation; in Bradyrhizobium both RpoN1 and N2 are functional in free-living and symbiotic conditions, rpoN1 gene was regulated in response to oxygen YP_002129031.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis YP_002129033.1 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_002129034.1 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control YP_002129035.1 forms homopentamer; channel that opens in response to pressure or hypoosmotic shock YP_002129037.1 catalyzes the formation of 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate from N-(5-phospho-beta-D-ribosyl)-anthranilate in tryptophan biosynthesis YP_002129038.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_002129039.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis YP_002129046.1 related to Ser/Thr protein kinases YP_002129055.1 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_002129056.1 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_002129078.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_002129079.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_002129080.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_002129081.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex YP_002129089.1 SPOUT methyltransferase; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA YP_002129093.1 similar to plant iojap proteins YP_002129094.1 transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria YP_002129096.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis YP_002129097.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_002129100.1 involved in the peptidyltransferase reaction during translation YP_002129101.1 fusion of ribosomal protein L21 and COG3743 YP_002129110.1 glycosyltransferase; polymerizes glycan strands in the peptidoglycan YP_002129123.1 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z YP_002129146.1 in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media YP_002129147.1 similar to related YP_002129165.1 similar to related YP_002129174.1 functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family YP_002129175.1 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_002129176.1 May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine YP_002129177.1 long form of enzyme; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms active dimers and inactive hexamers which is dependent on concentration of substrates and inhibitors YP_002129182.1 proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the proteins from this group do not and in addition appear to have a truncated C-terminal domain YP_002129184.1 Catalyzes the rate-limiting step in dNTP synthesis YP_002129187.1 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_002129192.1 metalloprotease YP_002129196.1 Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile YP_002129202.1 invasion-associated protein YP_002129204.1 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_002129205.1 catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis YP_002129208.1 YghU; B2989; one of eight glutathione transferases from E. coli YP_002129211.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the 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_002129214.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_002129221.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_002129222.1 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_002129229.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate YP_002129232.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_002129233.1 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_002129235.1 in Escherichia coli transcription of this gene is enhanced by polyamines YP_002129236.1 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 Mnin Bacillus subtilis the protein in this cluster is considered non-essential YP_002129250.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis YP_002129252.1 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_002129259.1 PR-AMP cyclohydrolase; functions in histidine biosynthesis from PRPP; converts 1-(5-phosphoribosyl)-AMP to 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]imidazole-4- carboxyamide during the histidine biosynthesis pathway; binds zinc and magnesium; forms homodimers YP_002129260.1 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_002129261.1 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_002129266.1 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_002129269.1 similar to related YP_002129274.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; in Rhizobia and Ralstonia is involved in PHB biosynthesis YP_002129282.1 Catalyzes the conversion of acetyl-CoA and L-homoserine to CoA and O-acetyl-L-homoserine YP_002129285.1 catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; uses a flavin nucleotide as an essential cofactor; class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus, which plays a role in the membrane association of the enzyme and provides the binding site for the respiratory quinones that serve as physiological electron acceptors YP_002129298.1 similar to related YP_002129300.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_002129304.1 catalyzes the formation of thymine and 2-deoxy-alpha-D-ribose 1-phosphate from thymidine YP_002129307.1 catalyzes the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate YP_002129309.1 catalyzes the degradation of histidine to urocanate and ammmonia YP_002129311.1 catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism YP_002129351.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis YP_002129378.1 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_002129387.1 converts protoheme IX and farnesyl diphosphate to heme O YP_002129388.1 involved in the insertion of copper into subunit I of cytochrome C oxidase YP_002129392.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_002129410.1 thiamine-pyrophosphate requiring enzyme YP_002129411.1 catalyzes the conversion of ferulic acid to feruloyl-CoA YP_002129415.1 Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides YP_002129419.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids YP_002129427.1 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_002129430.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. YP_002129432.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; forms a heterodimer with subunit 1 to form the P protein YP_002129433.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; forms a heterodimer with subunit 2 to form the P protein YP_002129434.1 part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor YP_002129440.1 activates fatty acids by binding to coenzyme A; may be involved in acyclic terpene utilization YP_002129442.1 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_002129448.1 Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates YP_002129478.1 catalyzes the formation of arginine from (N-L-arginino)succinate YP_002129507.1 similar to related YP_002129522.1 similar to related YP_002129523.1 similar to related YP_002129541.1 similar to related YP_002129547.1 upregulated by FixLJ/FixK under oxygen limitation; involved in regulation of genes involved in carbon and amino acid metabolism YP_002129552.1 implicated in the recycling of the 50S subunit (S4 paralog) YP_002129565.1 required for 70S ribosome assembly YP_002129576.1 activates fatty acids by binding to coenzyme A YP_002129586.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis YP_002129587.1 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis YP_002129591.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein YP_002129601.1 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_002129605.1 bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate YP_002129620.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis YP_002129627.1 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_002129634.1 similar to related YP_002129635.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_002129639.1 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_002129662.1 ThyA; catalyzes formation of dTMP and 7,8-dihydrofolate from 5,10-methylenetetrahydrofolate and dUMP; involved in deoxyribonucleotide biosynthesis; there are 2 copies in some Bacilli, one of which appears to be phage-derived YP_002129676.1 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_002129679.1 catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis YP_002129684.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. YP_002129685.1 Involved in ubiquinone biosynthesis YP_002129696.1 involved in type III protein export during flagellum assembly YP_002129700.1 membrane protein involved in the flagellar export apparatus YP_002129702.1 One of three proteins involved in switching the direction of the flagellar rotation YP_002129703.1 binds to and inhibits the function of flagella specific ATPase FliI YP_002129704.1 One of three proteins involved in switching the direction of the flagellar rotation YP_002129705.1 the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod YP_002129710.1 with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit YP_002129717.1 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_002129749.1 similar to related YP_002129753.1 catalyzes the bidirectional exonucleolytic cleavage of DNA YP_002129755.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate YP_002129756.1 part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod YP_002129758.1 makes up the distal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagella YP_002129761.1 with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum YP_002129765.1 FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus YP_002129767.1 with FlgF and C makes up the proximal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum YP_002129768.1 with FlgF and B makes up the proximal portion of the flagellar basal body rod YP_002129769.1 forms a junction between the M-ring and FlgB during flagella biosynthesis; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagella YP_002129773.1 FliQ, with proteins FliP and FliR, forms the core of the central channel in the flagella export apparatus; Bradyrhizobium have one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum YP_002129774.1 FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus YP_002129775.1 membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export YP_002129789.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_002129797.1 similar to related YP_002129828.1 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_002129830.1 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_002129832.1 Converts isocitrate to alpha ketoglutarate YP_002129837.1 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_002129853.1 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis YP_002129856.1 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis YP_002129859.1 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_002129862.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_002129895.1 CopA YP_002129915.1 Regulatory factor involved in maltose metabolism YP_002129924.1 produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine YP_002129938.1 MDM; functions in conversion of succinate to propionate YP_002129941.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation YP_002129951.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_002129953.1 catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine YP_002129998.1 catalyzes the formation of malonyl-CoA from malonate and CoA YP_002130023.1 catalyzes the phosphorylation of NAD to NADP YP_002130050.1 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_002130053.1 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_002130055.1 Modulates Rho-dependent transcription termination YP_002130057.1 binds directly to 23S ribosomal RNA YP_002130058.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_002130059.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_002130060.1 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_002130061.1 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_002130062.1 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_002130067.1 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_002130068.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_002130069.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_002130070.1 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_002130072.1 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_002130073.1 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_002130074.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_002130075.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_002130076.1 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_002130077.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_002130078.1 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_002130079.1 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_002130080.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_002130081.1 one of the stabilizing components for the large ribosomal subunit YP_002130082.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_002130083.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_002130084.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_002130085.1 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_002130086.1 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_002130087.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_002130088.1 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_002130089.1 binds 5S rRNA along with protein L5 and L25 YP_002130090.1 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_002130091.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7 YP_002130092.1 late assembly protein YP_002130093.1 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_002130094.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_002130096.1 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_002130097.1 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_002130098.1 is a component of the macrolide binding site in the peptidyl transferase center YP_002130109.1 may be involved in chromosome condensation; overexpression in Escherichia coli protects against decondensation by camphor; overexpressing the protein results in an increase in supercoiling YP_002130111.1 similar to mitochondrial F1 completex assembly factor 2 YP_002130120.1 this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress YP_002130123.1 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_002130136.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine YP_002130144.1 similar to other HIT family hydrolases YP_002130146.1 involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation; binds to the N-terminal domain of the chaperone ClpA YP_002130147.1 involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function YP_002130153.1 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_002130154.1 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_002130160.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_002130164.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis YP_002130166.1 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_002130167.1 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_002130169.1 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_002130179.1 catalyzes the reversible formation of diaminobutyrate and 2-oxoglutarate from glutamate and L-aspartic beta-semialdehyde YP_002130180.1 N-acetyldiaminobutyrate dehydratase; catalyzes the formation of the osmoprotectant ecotoine from gamma-N-acetyl-alpha,gamma-diaminobutyric acid YP_002130182.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP YP_002130187.1 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_002130202.1 An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis YP_002130207.1 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_002130208.1 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_002130209.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_002130212.1 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_002130218.1 similar to related YP_002130225.1 post-transcriptional repressor of flagellum biosynthesis; promotes degradation of fljK mRNA: Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella YP_002130226.1 acts as an activator of flagellin translation and may be required for filament secretion or assembly; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagellum YP_002130239.1 negatively supercoils closed circular double-stranded DNA YP_002130240.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA YP_002130246.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step YP_002130247.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_002130252.1 phenylalanine 4-hydroxylase; phenylalanine 4-hydroxylase; catalyzes the formation of 4a-hydroxytetrahydrobiopterin and tyrosine from phenylalanine and tetrahydrobiopterin YP_002130260.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_002130284.1 similar to related YP_002130349.1 type IV secretion VirD4 coupling protein family YP_002130355.1 type IV secretion system VirB4 family YP_002130357.1 type IV secretion VirB6 family YP_002130373.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate YP_002130376.1 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_002130379.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_002130381.1 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_002130383.1 unwinds double stranded DNA YP_002130384.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_002130385.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_002130396.1 similar to related YP_002130399.1 carries the fatty acid chain in fatty acid biosynthesis YP_002130400.1 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_002130403.1 Essential for recycling GMP and indirectly, cGMP YP_002130409.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_002130414.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation YP_002130417.1 similar to related YP_002130436.1 functions in degradation of stringent response intracellular messenger ppGpp; in Escherichia coli this gene is co-transcribed with the toxin/antitoxin genes mazEF; activity of MazG is inhibited by MazEF in vitro; ppGpp inhibits mazEF expression; MazG thus works in limiting the toxic activity of the MazF toxin induced during starvation; MazG also interacts with the GTPase Era YP_002130445.1 catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP) YP_002130466.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_002130468.1 CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis YP_002130482.1 type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese YP_002130491.1 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis YP_002130492.1 forms a direct contact with the tRNA during translation YP_002130493.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_002130498.1 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control YP_002130499.1 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_002130500.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY YP_002130504.1 pyrophosphate-energized proton pump; pyrophosphate-energized inorganic pyrophosphatase; H+-PPase; can cleave pyrophosphate to two phosphates; can generate a proton motive force and drive pyrophosphate synthesis when PMF is sufficient YP_002130508.1 Regulates rRNA biosynthesis by transcriptional antitermination YP_002130510.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_002130517.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine YP_002130522.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_002130528.1 Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate YP_002130530.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate YP_002130533.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_002130536.1 catalyzes the coenzyme A-dependent formation of succinyl-CoA from 2-oxoglutarate and ferredoxin YP_002130540.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_002130543.1 binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB YP_002130544.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides YP_002130549.1 catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate) YP_002130550.1 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_002130553.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_002130560.1 with SufCD activates cysteine desulfurase SufS YP_002130566.1 Stimulates the elongation of poly(A) tails YP_002130567.1 catalyzes the transamination of D-amino acids and their alpha-keto acids YP_002130573.1 bifunctional enzyme involved in formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate and 2-C-methyl-D-erythritol 2,4-cyclodiphosphate and CMP from 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; binds divalent cations YP_002130577.1 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_002130583.1 catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acetyltransferase within the complex. The E1 component of 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_002130587.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_002130588.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_002130591.1 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_002130594.1 similar to related YP_002130599.1 TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity YP_002130600.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate YP_002130601.1 involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water YP_002130602.1 Represses a number of genes involved in the response to DNA damage YP_002130604.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_002130608.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis YP_002130609.1 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_002130610.1 adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis YP_002130614.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate YP_002130617.1 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_002130618.1 Catalyzes the phosphorylation of UMP to UDP YP_002130620.1 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_002130622.1 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase YP_002130625.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_002130629.1 type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP YP_002130631.1 Catalyzes the transfer of electrons from NADH to quinone YP_002130632.1 Catalyzes the transfer of electrons from NADH to quinone YP_002130633.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_002130634.1 Catalyzes the transfer of electrons from NADH to quinone YP_002130635.1 Catalyzes the transfer of electrons from NADH to quinone YP_002130636.1 Catalyzes the transfer of electrons from NADH to quinone YP_002130637.1 Catalyzes the transfer of electrons from NADH to quinone YP_002130638.1 Catalyzes the transfer of electrons from NADH to quinone YP_002130639.1 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_002130640.1 Catalyzes the transfer of electrons from NADH to quinone YP_002130642.1 Catalyzes the transfer of electrons from NADH to quinone YP_002130644.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen YP_002130645.1 Catalyzes the transfer of electrons from NADH to quinone YP_002130654.1 binds and unfolds substrates as part of the ClpXP protease YP_002130660.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate YP_002130674.1 catalyzes hydrolysis of 1,6-anhydro bond of anyhydro-N-acetylmuramic acid (anhMurNAc) and phosphorylates anhMurNAc to produce N-acetyl-muramate-6-phosphate; involved in murein recycling YP_002130679.1 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_002130685.1 similar to related YP_002130687.1 functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate YP_002130689.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis YP_002130691.1 an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism YP_002130692.1 leucyltransferase; phenylalanyltransferse; functions in the N-end rule pathway; transfers Leu, Phe, Met, from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys YP_002130694.1 Provides the input to the respiratory chain from the NAD-linked dehydrogenases of the citric acid cycle. The complex couples the oxidation of NADH and the reduction of ubiquinone, to the generation of a proton gradient which is then used for ATP synthesis YP_002130697.1 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_002130698.1 similar to related YP_002130699.1 similar to related YP_002130705.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_002130707.1 involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA YP_002130709.1 Era; Escherichia coli Ras-like protein; Bex; Bacillus Era-complementing segment; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds the cell membrane through apparent C-terminal domain; mutants are arrested during the cell cycle; Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome YP_002130716.1 involved in the de novo synthesis of pyridoxine (Vitamin B6) YP_002130717.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate YP_002130729.1 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_002130730.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis YP_002130771.1 catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers YP_002130774.1 regulator of the sigma 54 transcriptional activator FlbD; represses FlbD when the class II flagellar structure is absent and activates FlbD when the structure is present YP_002130775.1 part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum YP_002130786.1 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_002130789.1 TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine YP_002130794.1 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_002130798.1 catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins YP_002130799.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate YP_002130800.1 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_002130818.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis YP_002130829.1 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway YP_002130830.1 forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis YP_002130843.1 similar to related YP_002130847.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation YP_002130857.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_002130880.1 catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite YP_002130890.1 activates fatty acids by binding to coenzyme A YP_002130914.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate YP_002130917.1 similar to related YP_002130982.1 similar to related YP_002130983.1 subunit A 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 with K+ YP_002130984.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_002130985.1 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_002130993.1 similar to related YP_002131027.1 location of PHZ_c2187 and that of RNA gene PHZ_t0030(tRNA-His) overlap by 58bp YP_002131039.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_002131041.1 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_002131067.1 NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis YP_002131071.1 catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using GTP YP_002131088.1 member of metallo-beta-lactamase; the purified enzyme from Escherichia coli forms dimeric zinc phosphodiesterase; in Bacillus subtilis this protein is a 3'-tRNA processing endoribonuclease and is essential while in Escherichia coli it is not; associates with two zinc ions YP_002131102.1 with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP YP_002131103.1 in Rhizobium meliloti this protein is involved in the synthesis of nodulation factors that are active on the roots of alfalfa; catalyzes formation of activated sulfate intermediate; converts ATP and sulfate to diphosphate and adenylylsulfate and then ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; the activated intermediate is transferred to the nodulation factors by NodH; may interact with NodP and NodQ; similar to the CysD and CysN proteins from EScherichia coli involved in cysteine biosynthesis YP_002131109.1 similar to related YP_002131122.1 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_002131123.1 functions in MreBCD complex in some organisms YP_002131128.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis YP_002131131.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate YP_002131151.1 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_002131152.1 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_002131156.1 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_002131160.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_002131161.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_002131162.1 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_002131164.1 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_002131165.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_002131167.1 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_002131216.1 catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate YP_002131220.1 Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates YP_002131253.1 produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine YP_002131289.1 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase; catalyzes the interconversion of 4-deoxy-L-threo-5-hexosulose uronate to 3-deoxy-D-glycero-2,5-hexodiulosonate YP_002131290.1 catalyzes the interconversion of D-glucuronate to D-fructuronate or D-galacturonate to D-tagaturonate; functions in glucuronic and galacturonic metabolism YP_002131304.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate YP_002131309.1 similar to related YP_002131342.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation YP_002131350.1 activates fatty acids by binding to coenzyme A YP_002131357.1 catalyzes the conversion of ferulic acid to feruloyl-CoA YP_002131374.1 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase; catalyzes radical-mediated transfer of hydroxybenzyl group from 4-hydroxyphenylpyruvate (HPP) to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO); functions in F420 biosynthesis YP_002131376.1 catalyzes the formation of the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) and GMP from actyl (2) diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) YP_002131395.1 catalyzes the conversion of ferulic acid to feruloyl-CoA YP_002131407.1 Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5) YP_002131413.1 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_002131414.1 synthesizes RNA primers at the replication forks YP_002131418.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers YP_002131426.1 four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity YP_002131431.1 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_002131445.1 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate YP_002131446.1 catalyzes the formation of oxaloacetate from L-aspartate YP_002131481.1 similar to related YP_002131495.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence YP_002131503.1 similar to related YP_002131509.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_002131511.1 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia YP_002131515.1 blocks the formation of polar Z-ring septums YP_002131522.1 Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription YP_002131547.1 catalyzes the ATP-dependent formation of a phosphodiester at the site of a single-strand break in duplex DNA; in mycobacteria LigC has weak intrinsic nick joining activities and is not essential for growth YP_002131556.1 activates fatty acids by binding to coenzyme A YP_002131576.1 catalyzes the formation of pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate YP_002131578.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_002131589.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_002131633.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine YP_002131637.1 similar to related YP_002131639.1 similar to related YP_002131651.1 CcoO; FixO YP_002131652.1 CcoN; FixN YP_002131678.1 this tRNA synthetase lacks the tRNA anticodon interaction domain; instead this enzyme modifies tRNA(Asp) with glutamate by esterifying glutamate to the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of queosine generating a modified nucleoside at the first anticodon position of tRNAAsp; the modified tRNA does not bind elongation factor Tu YP_002131696.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_002131699.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP YP_002131701.1 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_002131702.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_002131703.1 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_002131712.1 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis YP_002131726.1 converts 2-oxoglutarate to glutamate; in Escherichia coli this enzyme plays a role in glutamate synthesis when the cell is under energy restriction; uses NADPH; forms a homohexamer YP_002131727.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids YP_002131728.1 catalyzes the formation of O-phospho-L-homoserine from L-homoserine YP_002131733.1 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_002131736.1 similar to related YP_002131747.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine YP_002131750.1 catalyzes the formation of pyruvate from D-cysteine YP_002131773.1 Catalyzes the deamination of dCTP to form dUTP YP_002131775.1 becomes active under oxidative stress; four conserved cysteines bind a zinc atom when they are in the reduced state and the enzyme is inactive; oxidative stress results in oxidized cysteines, release of zinc, and binding of Hsp33 to aggregation-prone proteins; forms dimers and higher order oligomers YP_002131776.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation YP_002131777.1 DapATase; functions in arginine biosynthetic pathway; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine YP_002131782.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides YP_002131800.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_002131801.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source YP_002131810.1 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_002131814.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_002131815.1 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_002131816.1 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_002131819.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_002131829.1 this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress YP_002131848.1 catalyzes the formation of inosine from adenosine YP_002131879.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_002131887.1 similar to related YP_002131917.1 similar to related YP_002131920.1 similar to related YP_002131923.1 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_002131924.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_002131925.1 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_002131930.1 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_002131958.1 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_002131961.1 With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine YP_002131966.1 similar to related YP_002131971.1 similar to related YP_002131978.1 similar to related YP_002131990.1 converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA YP_002131999.1 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; some organisms carry two different copies of this enzyme YP_002132003.1 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_002132020.1 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_002132027.1 catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase YP_002132030.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_002132042.1 RpmE; 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; the proteins in this cluster do not have the CXXC motif; 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_002132048.1 Catalyzes the first step in the glyoxalate cycle, which converts lipids to carbohydrates YP_002132050.1 Catalyzes the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle YP_002132065.1 catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate YP_002132083.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation YP_002132090.1 catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate YP_002132093.1 similar to related YP_002132094.1 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate YP_002132097.1 catalyzes the ATP dependent formation of a phosphodiester at the site of a single-strand break in duplex DNA YP_002132110.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_002132111.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate YP_002132124.1 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway YP_002132138.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_002132151.1 similar to PhoU YP_002132158.1 transforms a conserved lysine residue of initiation factor 5A into deoxyhypusine YP_002132170.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity YP_002132171.1 similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity YP_002132173.1 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_002132181.1 catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine YP_002132183.1 catalyzes the formation of 2-oxobutanoate from L-threonine YP_002132185.1 catalyzes the ATP-dependent formation of a phosphodiester at the site of a single strand break in duplex DNA YP_002132190.1 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_002132208.1 negatively supercoils closed circular double-stranded DNA YP_002132214.1 regulates chemotaxis by demethylation of methyl-accepting chemotaxis proteins YP_002132223.1 Required for DNA replication; binds preferentially to single-stranded, linear DNA YP_002132226.1 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair YP_002132228.1 similar to related YP_002132243.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis YP_002132244.1 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_002132245.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate YP_002132256.1 NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate YP_002132259.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_002132261.1 catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine YP_002132265.1 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_002132268.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_002132269.1 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_002132271.1 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_002132272.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs YP_002132273.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_002132277.1 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_002132279.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_002132280.1 in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins YP_002132284.1 catalyzes the hydrolysis of pyrophosphate to phosphate YP_002132285.1 tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine YP_002132286.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_002132289.1 similar to related YP_002132292.1 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_002132297.1 similar to related YP_002132298.1 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_002132301.1 catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein YP_002132302.1 This protein performs the mismatch recognition step during the DNA repair process YP_002132306.1 binds the polymerase to DNA and acts as a sliding clamp YP_002132307.1 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_002132308.1 Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons YP_002132309.1 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_002132312.1 HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine YP_002132317.1 catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione YP_002132337.1 involved in de novo purine biosynthesis YP_002132355.1 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_002132357.1 required for the assembly and function of the DNAX complex which are required for the assembly of the beta subunit onto primed DNA YP_002132364.1 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_002132365.1 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_002132369.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_002132371.1 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