-- dump date 20140618_191110 -- class Genbank::CDS -- table cds_note -- id note YP_001052714.1 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_001052715.1 binds the polymerase to DNA and acts as a sliding clamp YP_001052716.1 Required for DNA replication; binds preferentially to single-stranded, linear DNA YP_001052718.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_001052720.1 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_001052721.1 SohB; periplasmic protein; member of the peptidase S49 family YP_001052722.1 MraZ; UPF0040; crystal structure shows similarity to AbrB YP_001052726.1 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_001052728.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_001052729.1 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_001052731.1 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_001052732.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_001052733.1 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_001052736.1 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_001052737.1 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_001052743.1 stimulates the release of release factors 1 and 2 from the ribosome after hydrolysis of the ester bond in peptidyl-tRNA has occurred; GDP/GTP-binding protein YP_001052746.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_001052747.1 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_001052752.1 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_001052753.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_001052755.1 Specifically methylates the ribose of guanosine 2251 in 23S rRNA YP_001052756.1 catalyzes de novo synthesis of phosphatidylserine from CDP-diacylglycerol and L-serine which leads eventually to the production of phosphatidylethanolamine; bounds to the ribosome YP_001052757.1 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 1 subfamily; some organisms carry two different copies of this enzyme YP_001052759.1 catalyzes the formation of NAD(+) from nicotinamide ribonucleotide YP_001052767.1 functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase; also involved in reducing some disulfides in a coupled system with glutathione reductase YP_001052768.1 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_001052773.1 catalyzes the N2-methyl guanosine modification of the G2445 residue of 23S rRNA YP_001052780.1 DppD and DppF are the ATP-binding components of the ABC dipeptide transport system DppABCDF YP_001052781.1 Part of the ABC transporter complex DppABCDF involved in the transport of dipeptides YP_001052785.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_001052787.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_001052788.1 pubmed:14742511 YP_001052789.1 pubmed:14742511 YP_001052790.1 pubmed:14742511 YP_001052791.1 pubmed:14742511 YP_001052795.1 with DhaK and DhaM catalyzes the phosphorylation of dihydroxyacetone YP_001052796.1 with DhaL and DhaM forms dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone; DhaK is the dihydroxyacetone binding subunit of the dihydroxyacetone kinase YP_001052798.1 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_001052800.1 can catalyze hydrolysis of broad range of dinucleotide pyrophosphates but prefers reduced form of NADH; requires divalent metal ions such as magnesium and manganese and produces two mononucleoside 5'-phosphates YP_001052804.1 catalyzes the hydrolysis of dipeptides with a proline at the C-terminal; also catalyzes the low efficiency hydrolysis of organophosphate di- and tri-esters YP_001052805.1 TusA; transfers sulfur to TusBCD complex; involved in thiouridation of U34 position of some tRNAs YP_001052807.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_001052810.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis YP_001052813.1 catalyzes the formate-dependent reduction of nitrite to ammonia; cytochrome C552 YP_001052814.1 part of nitrite reductase complex; NrfB is active at high nitrate conditions; NrfA, B, C, and D are essential for the formate-dependent nitrite reduction to ammonia YP_001052819.1 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 protein from Pseudomonas does not have this domain YP_001052825.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III YP_001052828.1 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_001052832.1 affects solute and DNA transport through an unknown mechanism YP_001052833.1 Involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3 YP_001052842.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids YP_001052843.1 EngC; RsgA; CpgA; circularly permuted GTPase; ribosome small subunit-dependent GTPase A; has the pattern G4-G1-G3 as opposed to other GTPases; interacts strongly with 30S ribosome which stimulates GTPase activity YP_001052844.1 Glycine cleavage system transcriptional activator; activates the gcvTHP operon in the presence of glycine and represses the operon in its absence YP_001052845.1 manganese-dependent 5'-nucleotidase; specific for 5'-UMP, 5'-dUMP, and 5'-dTMP; member of haloacid dehalogenase (HAD)-like hydrolase superfamily YP_001052846.1 LysR-type transcriptional regulator; contains helix-turn-helix (HTH) motif; in Escherichia coli this protein regulates cysteine biosynthesis by controlling expression of the cys regulon; autoregulates expression; crystal structure of Klebsiella aerogenes showed tetramer formation YP_001052848.1 catalyzes the formation of aspartate from asparagine, periplasmic; regulated by cyclic AMP receptor protein (CRP) and also induced by anaerobiosis YP_001052849.1 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_001052851.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D YP_001052852.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate YP_001052856.1 catalyzes the hydrolysis of acylphosphate YP_001052861.1 Catalyzes the rate-limiting step in dNTP synthesis YP_001052862.1 cytoplasmic protein that may be involved in the utilization of double-stranded DNA as a carbon source YP_001052863.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_001052864.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_001052865.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_001052866.1 Part of the NQR complex which catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm YP_001052867.1 Part of the NQR complex which consists of NqrA, NqrB, NqrC, NqrD, NqrE and NqrF; NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm; NqrE is probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. YP_001052868.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_001052871.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_001052872.1 putative transporter of 3-phenylpropionate across the inner membrane; member of the major facilitator superfamily of transporters YP_001052874.1 Required for efficient pilin antigenic variation YP_001052876.1 Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates YP_001052879.1 part of membrane-bound complex thought to be involved in electron transport to nitrogen YP_001052880.1 part of membrane-bound complex thought to be involved in electron transport to nitrogen YP_001052882.1 RnfD; RsxD; required for nitrogen fixation in Rhodobacter capsulatus; part of a membrane-bound complex thought to be involved in electron transport to nitrogenase; in Escherichia coli this gene is part of a cluster controlling SoxR-mediated induction of the SoxS transcription factor in the absence of oxidizing agents YP_001052883.1 part of membrane-bound complex hought to be involved in electron transport to nitrogen YP_001052884.1 in Excherichia coli RsxABCDEG reduces SoxR which turns off induction of SoxS transcription factor in the absence of oxidizing agents; similar to the rnfABCDGE operon in Rhodobacter capsulatus involved in transferring electrons to nitrogenase YP_001052885.1 Transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA YP_001052895.1 Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A) YP_001052897.1 catalyzes the formation of prephenate from chorismate and the formation of 4-hydroxyphenylpyruvate from prephenate in tyrosine biosynthesis YP_001052898.1 catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, tyrosine sensitive YP_001052903.1 Stimulates excision of phage lambda; affects Mu development; acts as an activator of rRNA and iRNA transcription YP_001052906.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis YP_001052907.1 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis YP_001052914.1 Regulates rRNA biosynthesis by transcriptional antitermination YP_001052920.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate YP_001052924.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_001052925.1 catalyzes the phosphorylation of NAD to NADP YP_001052932.1 catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); 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 YP_001052938.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_001052944.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function YP_001052946.1 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_001052952.1 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_001052955.1 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis YP_001052956.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate YP_001052957.1 catalyzes the formation of N-acetyl-l-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine YP_001052960.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_001052962.1 catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate YP_001052963.1 multifunctional homotetrameric enzyme that catalyzes the phosphorylation of aspartate to form aspartyl-4-phosphate as well as conversion of aspartate semialdehyde to homoserine; functions in a number of amino acid biosynthetic pathways YP_001052965.1 converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer YP_001052968.1 catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively YP_001052969.1 Essential for recycling GMP and indirectly, cGMP YP_001052973.1 Part of the ABC transporter complex modABC involved in molybdenum import YP_001052974.1 part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE YP_001052978.1 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_001052979.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis YP_001052990.1 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_001052993.1 functions together with PotBCD (A2BCD) in ATP-dependent polyamine transport; PotA is the membrane-associated ATPase YP_001052994.1 can transport spermidine and putrescine but affinity is higher for spermidine; forms a complex of PotA2BCD; PotB is a membrane component YP_001052995.1 can transport spermidine and putrescine but affinity is higher for spermidine; forms a complex of PotA2BCD; PotC is a membrane component YP_001052996.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_001052997.1 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_001052998.1 Involved in ubiquinone biosynthesis YP_001053003.1 Uup; in Escherichia coli this cytoplasmic protein was shown to contain ATPase activity; mutations in this gene affect RecA-independent excision of transposons and affects Mu bacteriophage growth YP_001053010.1 membrane spanning protein in TolA-TolQ-TolR complex; involved in the tonB-independent uptake of group A colicins YP_001053012.1 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_001053013.1 pubmed:8763621 YP_001053015.1 functions as a co-chaperone with DnaK; involved in regulation of colanic acid capsule; inner membrane protein; dimerized via transmembrane domain; J-like domain is cytoplasmic and can functionally substitute for DnaJ; stimulates synthesis of colanic acid mucoid capsule through the RcsB/C signal transduction system YP_001053020.1 ATP-dependent adenylate transferase, transfers adenyl moiety to the MoeD subunit of molybdopterin synthase YP_001053021.1 in Escherichia coli this enzyme catalyzes the SAM-dependent methylation of U1939 in the 23S ribomal RNA; binds an iron-sulfur cluster [4Fe-4S] YP_001053022.1 dGTPase family type 2 subfamily; presumably hydrolyzes dGTP to deoxyguanosine and triphosphate YP_001053023.1 transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA YP_001053027.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate YP_001053029.1 catalyzes the formation of L-homocysteine from cystathionine YP_001053030.1 disulfide oxidoreductase; integral membrane protein; required for perioplasmic disulfide bond formation; oxidizes DsbA protein YP_001053031.1 involved in regulation of intracellular pH under alkaline conditions YP_001053032.1 Multifunctional regulator of fatty acid metabolism YP_001053036.1 catalyzes the formation of selenophosphate from selenide and ATP YP_001053048.1 catalyzes the formation of oxaloacetate from phosphoenolpyruvate YP_001053052.1 Includes: Fructose-specific phosphotransferase enzyme IIB component; Fructose permease IIC component YP_001053053.1 converts fructose-1-phosphate and ATP to fructose-1,6-bisphosphate and ADP; highly specific for fructose-1-phopshate; similar to PfkB; forms homodimers YP_001053054.1 phosphoenolpyruvate (PEP)-dependent, sugar transporting phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIA is phosphorylated by phospho-HP which then transfers the phosphoryl group to the IIB componentr YP_001053055.1 catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain YP_001053057.1 catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate YP_001053058.1 catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose YP_001053061.1 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_001053062.1 catalyzes the dehydration of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid to form O-succinylbenzoate YP_001053064.1 Involved in sulfonamide (sulfathiazole) and bicyclomycin resistance YP_001053067.1 Assists in DNA repair by cleaving phosphodiester bonds at apurinic or apyrimidinic sties to produce new 5' ends that are base-free deoxyribose 5-phosphate residues YP_001053070.1 stress-induced glycyl radical protein that can replace an oxidatively damaged pyruvate formate-lyase subunit YP_001053071.1 Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine YP_001053074.1 involved in the post-transcriptional processing of the daa operon mRNA, which encodes proteins involved in fimbrial biogenesis of an enteropathogenic E. coli strain YP_001053076.1 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_001053080.1 Transfers the fatty acyl group on membrane lipoproteins YP_001053084.1 Converts glycerol and ADP to glycerol-3-phosphate and ADP YP_001053087.1 hydrolyzes deacylated phospholipids to glycerol 3-phosphate and the corresponding alcohols; periplasmic YP_001053088.1 anaerobic, catalyzes the conversion of glycerol 3-phosphate to dihydroxyacetone using fumarate or nitrate as electron acceptor YP_001053089.1 sn-glycerol-3-phosphate dehydrogenase (anaerobic); catalyzes the formation of dihydroxyacetone from glycerol 3-phosphate; part of GlpABC complex; presumably this subunit is responsible for membrane interactions and contains iron-sulfur clusters YP_001053090.1 anaerobic; with GlpAB catalyzes the conversion of glycerol-3-phosphate to dihydroxyacetone phosphate YP_001053091.1 pubmed:8522537; Includes: Diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino)uracil reductase YP_001053092.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_001053093.1 pubmed:8522537; Includes: GTP cyclohydrolase-2; 3,4-dihydroxy-2-butanone 4-phosphate synthase YP_001053094.1 RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not YP_001053095.1 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_001053097.1 catalyzes the removal of an N-terminal amino acid from a peptide or arylamide YP_001053102.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis YP_001053103.1 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; this sigma factor is involved in heat shock and oxidative stress response YP_001053106.1 Activates fatty acids by binding to coenzyme A YP_001053107.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate YP_001053108.1 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_001053110.1 regulates pyrimidine biosynthesis by binding to the mRNA of the pyr genes, also has been shown to have uracil phosphoribosyltransferase activity YP_001053111.1 catalyzes the phosphorylation of D-glycero-D-manno-heptose 7-phosphate to form D,D-heptose-1,7-bisphosphate and catalyzes transfer of ADP to D-glycero-D-manno-heptose 1-phosphate forming ADP-D,D-heptose YP_001053112.1 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_001053113.1 catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins YP_001053115.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate YP_001053116.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis YP_001053117.1 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_001053118.1 adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis YP_001053125.1 catalyzes the formation of N-acetyl-D-glucosamine-6-phosphate from N-acetyl-D-glucosamine YP_001053131.1 catalyzes the formation of arginosuccinate from citrulline and aspartate in arginine biosynthesis YP_001053132.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids YP_001053134.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_001053136.1 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_001053141.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_001053142.1 this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress YP_001053144.1 functions in MreBCD complex in some organisms YP_001053145.1 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_001053150.1 Catalyzes the conversion of acetyl-CoA and L-homoserine to CoA and O-acetyl-L-homoserine YP_001053161.1 catalyzes the interconversion of succinyl-CoA and succinate YP_001053164.1 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_001053173.1 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_001053175.1 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate YP_001053178.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_001053179.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis YP_001053182.1 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair YP_001053183.1 participates with LolB in the incorporation of lipoprotein into the outer membrane YP_001053184.1 When complexed with L-tryptophan it binds the operator region of the trp operon and prevents the initiation of transcription YP_001053192.1 NADPH-dependent; oxygen-insensitive; catalyzes the reduction of nitroaromatic compounds YP_001053196.1 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_001053203.1 Required for efficient pilin antigenic variation YP_001053248.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_001053250.1 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_001053251.1 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_001053252.1 involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA YP_001053273.1 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_001053274.1 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_001053276.1 Catalyzes the phosphorylation of UMP to UDP YP_001053277.1 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_001053279.1 with PdxT forms pyridoxal 5'-phosphate from glutamine, either ribose 5-phosphate or ribulose 5-phosphate, and either glyceraldehyde 3-phosphate or dihydroxyacetone phosphate YP_001053280.1 with PdxST is involved in the biosynthesis of pyridoxal 5'-phosphate; PdxT catalyzes the hydrolysis of glutamine to glutamate and ammonia; PdxS utilizes the ammonia to synthesize pyridoxal 5'-phosphate YP_001053283.1 lipoprotein that appears to be involved in cell division; interacts with the periplasmic protease Prc and may be activated by protease processing YP_001053285.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_001053286.1 acts with MukB and MukE to condense the chromosome and allow for segregation during cell division YP_001053287.1 acts with MukB and MukF to condense the chromosome and allow for segregation during cell division YP_001053288.1 SMC (structural maintenance of chromosomes) family of proteins; involved in chromosome condensatin and partitioning; forms a homodimer and the C-terminal is essential for DNA-binding activity while the purified N-terminal domain binds FtsZ; mutations result in cell division defects YP_001053295.1 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_001053299.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_001053300.1 catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate YP_001053301.1 Specifically methylates the uridine in position 2552 of 23S rRNA in the fully assembled 50S ribosomal subunit YP_001053307.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_001053308.1 forms a direct contact with the tRNA during translation YP_001053315.1 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_001053316.1 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_001053317.1 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_001053321.1 DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium YP_001053324.1 mediates a global response to leucine; acts as a regulator for several genes involved in the high-affinity branched-chain amino acid transport system YP_001053327.1 catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive YP_001053329.1 catalyzes the formation of thymidine 5'-phosphate from thymidine YP_001053331.1 type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese YP_001053338.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits YP_001053344.1 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_001053345.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_001053346.1 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_001053347.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_001053348.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs YP_001053351.1 catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate YP_001053352.1 AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation; utilizes magnesium and ATP; also involved in conversion of acetate to aceyl-CoA YP_001053353.1 periplasmic enzyme; functions during ribonucleic acid degradation; 2',3'-cyclic nucleotides are first converted to 3'-nucleotide and then cleaved to yield a ribonucleotide and a phosphate YP_001053358.1 affects carbohydrate metabolism; has regulatory role in many processes YP_001053359.1 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_001053361.1 Global transcription factor that controls the expression of over 100 target genes in response to anoxia YP_001053366.1 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway YP_001053367.1 catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate YP_001053372.1 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_001053378.1 Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates YP_001053380.1 catalyzes a two-step reaction, first charging an asparagine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_001053383.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_001053384.1 catalyzes a two-step reaction, first charging a glutamine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_001053388.1 catalyzes the formation of cysteine from cystathionine; in B. subtilis also has O-acetylhomoserine thiolyase activity YP_001053389.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_001053392.1 component of the membrane-bound D-lactate oxidase, FAD-binding, NADH independent YP_001053395.1 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z YP_001053401.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_001053403.1 catalyzes the formation of N-acetyl-L-glutamate from L-glutamate and acetyl-CoA in arginine biosynthesis YP_001053404.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis YP_001053405.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_001053407.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine YP_001053415.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; functions in amino acid biosynthesis; lysine sensitive YP_001053428.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_001053432.1 acetolactate synthase large subunit; catalyzes the formation of 2-acetolactate from pyruvate YP_001053433.1 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_001053440.1 involved in start site selection during the initiation of translation YP_001053441.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase YP_001053444.1 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_001053445.1 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_001053449.1 decatenates replicating daughter chromosomes YP_001053450.1 D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm YP_001053451.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_001053452.1 small mechanosensitive ion channel (MscS) that opens in response to stretch forces in the membrane lipid bilayer; maintains cell turgor through accumulation and release of potassium; large protein class of MscS YP_001053453.1 small mechanosensitive ion channel (MscS) that opens in response to stretch forces in the membrane lipid bilayer; maintains cell turgor through accumulation and release of potassium; large protein class of MscS YP_001053455.1 negative modulator of the initiation of chromosome replication YP_001053460.1 Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3' to 5' direction YP_001053463.1 hydrolyzes P(1),P(4)-bis(5'-adenosyl) tetraphosphate to form 2 ADP YP_001053468.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step YP_001053470.1 involved in the import of serine and threonine coupled with the import of sodium YP_001053472.1 catalyzes the degradation of periplasmic UDP-glucose to uridine, glucose-1-phosphate and inorganic phosphate; specific for uridine nucleotides YP_001053474.1 E3 component of pyruvate and 2-oxoglutarate dehydrogenase complex; catalyzes the oxidation of dihydrolipoamide to lipoamide YP_001053475.1 E2 component of pyruvate dehydrogenase multienzyme complex; in Escherichia coli AceF contains three N-terminal lipoyl domains YP_001053476.1 E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC YP_001053477.1 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_001053478.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP YP_001053479.1 An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis YP_001053480.1 Incorporates lipoproteins in the outer membrane after they are released by the LolA protein YP_001053481.1 involved in the transport of lipid A across the inner membrane YP_001053485.1 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_001053486.1 binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA YP_001053499.1 catalyzes the isomerization of sedoheptulose 7-phosphate to D-glycero-D-manno-heptose 7-phosphate YP_001053501.1 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP YP_001053503.1 4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MEP cytidylyltransferase; MCT; catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; forms homodimers YP_001053504.1 catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate YP_001053507.1 catalyzes the bidirectional exonucleolytic cleavage of DNA YP_001053510.1 class II; LysRS2; 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, LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1 YP_001053511.1 involved in the processing of the 5'end of 16S rRNA YP_001053517.1 membrane-bound, lytic; catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine residues YP_001053518.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides YP_001053520.1 binds to the purF operator and coregulates other genes for de novo purine nucleotide synthesis; is involved in regulation of purB, purC, purEK, purHD, purL, purMN and guaBA expression; binds hypoxanthine and guanine as inducers YP_001053523.1 catalyzes the conversion of 4-Hydroxybenzoate into 3-octaprenyl-4-hydroxybenzoate, as part of the ubiquinone biosynthesis pathway YP_001053525.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_001053526.1 HflD; UPF0274; in Escherichia coli this protein is peripherally associated with the membrane and appears to act with lambda CII protein; in Haemophilus influenzae a knockout of the HI0638 gene affected paracytosis YP_001053527.1 in Escherichia coli the CydCD ABC transporter exports cysteine and glutathione into the periplasm in order to maintain redox balance; important for cytochrome bd and c YP_001053528.1 in Escherichia coli the CydCD ABC transporter exports cysteine and glutathione into the periplasm in order to maintain redox balance; important for cytochrome bd and c YP_001053533.1 2,3-bisphosphoglycerate-dependent; catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate YP_001053535.1 functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor YP_001053536.1 Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis YP_001053542.1 catalyzes reversible transfer of hydride ion equivalent between NAD and NADP; membrane-bound proton pump that translocates protons from cytosolic to periplasmic side of the inner membrane; forms a tetramer composed of two alpha and 2 beta subunits; AB-stereospecific enzyme YP_001053543.1 forms a tetramer composed of 2 alpha subunits and 2 beta subunits in the inner membrane; involved in catalyzing transfer of hydride ion equivalents between NAD and NADP; stereospecific (AB-specific); functions as a proton pump by translocating protons from cytoplasm to periplasm YP_001053545.1 catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in queuosine biosynthesis YP_001053546.1 Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate intermediate into D-glycero-beta-D-manno-heptose 1-phosphate YP_001053547.1 bacterioferritin comigratory protein; thiol peroxidase; thioredoxin-dependent; hydroperoxide peroxidase; in Escherichia coli this enzyme preferentially reduces linoleic acid hydroperoxide; contains an active site cysteine YP_001053548.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_001053555.1 MTHFR; catalyzes NADH-linked reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate using FAD as a cofactor YP_001053559.1 catalyzes the formation of 5-methylaminomethyl-2-thiouridine in position 34 of the anticodon of tRNA molecules YP_001053560.1 monomeric bifunctional protein; functions in tryptophan biosynthesis pathway; phosphoribosylanthranilate is rearranged to carboxyphenylaminodeoxyribulosephosphate which is then closed to form indole-3-glycerol phosphate YP_001053563.1 catalyzes formation of pseudouridine at position 65 in tRNA-Ile1 and tRNA-Asp YP_001053568.1 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_001053569.1 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_001053572.1 alpha-aspartyl dipeptidase; catalyzes the hydrolysis of dipeptides with an N-terminal aspartate residue; belongs to peptidase S51 family YP_001053573.1 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_001053575.1 required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA YP_001053577.1 catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis YP_001053578.1 pubmed:14742510 YP_001053579.1 pubmed:14742510 YP_001053580.1 pubmed:14742510 YP_001053581.1 pubmed:14742510 YP_001053582.1 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_001053585.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis YP_001053597.1 required for the formation of active formate dehydrogenase YP_001053598.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate YP_001053600.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis YP_001053601.1 Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA YP_001053603.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_001053604.1 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_001053605.1 catalyzes the phosphorylation of 3-deoxy-D-manno-octulosonic acid at the 4-OH position YP_001053613.1 part of the metNIQ transport system for methionine YP_001053614.1 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_001053616.1 catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template; phosphohydrolase activities include hydrolysis of pyrophosphate, 5'-nucleoside tri- and diphosphates, NADP, and 2'-AMP with the production of Pi, metal-dependent phosphodiesterase activity for 2',3'-cAMP, 2',3'-cGMP, and 2',3'-cCMP, and hydrolysis 2',3'-cyclic substrates with the formation of 2'-nucleotides and 3'-nucleotides; these phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases YP_001053626.1 involved in the maturation of iron-sulfur cluster-containing proteins YP_001053629.1 J-type co-chaperone that regulates the ATPase and peptide-binding activity of Hsc66 chaperone; may function in biogenesis of iron-sulfur proteins YP_001053632.1 catalyzes the removal of elemental sulfur from cysteine to produce alanine; involved in NAD biosynthesis YP_001053639.1 DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium YP_001053642.1 catalyzes the formation of 8-amino-7-oxononanoate from 6-carboxyhexanoyl-CoA and L-alanine YP_001053643.1 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_001053644.1 involved in methylation of ribosomal protein L3 YP_001053645.1 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_001053646.1 penicillin binding protein 4; penicillin sensitive; catalyzes the formation of D-alanine from D-alanyl-D-alanine; one of four, DD-carboxypeptidase low-molecular weight penicillin-binding proteins that remove terminal D-alanine from pentapeptide side chains YP_001053659.1 involved in de novo purine biosynthesis YP_001053661.1 determines N-hexane tolerance and is involved in outer membrane permeability YP_001053662.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_001053668.1 catalyzes the ATP-dependent addition of AMP to a subunit of glutamine synthetase; also catalyzes the reverse reaction - deadenylation; adenylation/deadenylation of glutamine synthetase subunits is important for the regulation of this enzyme YP_001053671.1 Involved in cell division; probably involved in intracellular septation YP_001053674.1 TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs YP_001053676.1 removes the damaged DNA at cytosines and guanines by cleaving on the 3' side of the AP site by a beta-elimination reaction YP_001053677.1 participates in controlling several genes involved in isoleucine and valine biosynthesis; activates the transcription of the ilvC gene in the presence of acetolactate or acetohydroxybutyrate YP_001053681.1 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 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_001053682.1 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_001053686.1 molecular chaperone YP_001053691.1 Catalyzes the rate-limiting step in dNTP synthesis YP_001053692.1 B2 or R2 protein; type 1a enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdA YP_001053693.1 catalyzes the interconversion of UDP-galactose and galactose-1-P with UDP-galactose and glucose-1-P YP_001053694.1 catalyzes the formation of alpha-D-galactose 1-phosphate from D-galactose in galactose metabolism YP_001053697.1 pubmed:10463177 YP_001053704.1 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_001053710.1 Includes: Alcohol dehydrogenase; Acetaldehyde dehydrogenase YP_001053711.1 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_001053712.1 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_001053713.1 catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate YP_001053714.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate YP_001053717.1 catalyzes the formation of pyruvate and glyoxylate from 4-hydroxy-2-oxoglutarate; or pyruvate and D-glyceraldehyde 3-phosphate from 2-dehydro-3-deoxy-D-glyconate 6-phosphate YP_001053731.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity YP_001053732.1 Includes: Chorismate mutase; Prephenate dehydratase YP_001053734.1 activates pyruvate formate-lyase 1 under anaerobic conditions YP_001053738.1 putative metalloprotease YP_001053739.1 involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function YP_001053742.1 broad specificity; family IV; in Corynebacterium glutamicum this protein can use glutamate, 2-aminobutyrate, and aspartate as amino donors and pyruvate as the acceptor YP_001053751.1 catalyzes transfer of adenylyl group of ATP from pyrophosphate to the 3'-hydroxyl group to form cyclic AMP YP_001053752.1 FabB, beta-Ketoacyl-ACP synthase I, KASI; 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_001053763.1 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_001053764.2 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_001053765.1 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_001053771.1 Required for the synthesis of the thiazole moiety YP_001053772.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis YP_001053777.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_001053782.1 catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine in arginine biosynthesis YP_001053788.1 catalyzes the formation of fumarate from aspartate YP_001053792.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_001053798.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides YP_001053802.1 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase YP_001053803.1 non-folate utilizing enzyme, catalyzes the production of beta-formyl glycinamide ribonucleotide from formate, ATP, and beta-GAR and a side reaction producing acetyl phosphate and ADP from acetate and ATP; involved in de novo purine biosynthesis YP_001053804.1 PlsB; catalyzes the formation of 1-acyl-sn-glycerol 3-phosphate by transfering the acyl moiety from acyl-CoA YP_001053805.1 Represses a number of genes involved in the response to DNA damage YP_001053806.1 MutH; Sequence-specific endonuclease that cleaves unmethylated GATC sequences during DNA repair YP_001053808.1 hydrolyzes the terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides YP_001053809.1 RNA uridine methyltransferase B; catalyzes the formation of 5-methyl-uridine at position 747 in 23S rRNA YP_001053810.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_001053814.1 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_001053815.1 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_001053817.1 responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA YP_001053819.1 catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis YP_001053827.1 catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A YP_001053828.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA YP_001053829.1 3'-5' exoribonuclease specific for small oligoribonuclotides YP_001053832.1 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_001053834.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate YP_001053837.1 binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities YP_001053838.1 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_001053840.1 catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine YP_001053842.1 catalyzes the formation of anthranilate from chorismate and glutamine; functions in tryptophan biosynthesis YP_001053844.1 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_001053845.1 converts dATP to dAMP and pyrophosphate YP_001053848.1 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_001053850.1 catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine YP_001053856.1 with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine YP_001053857.1 TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity YP_001053858.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate YP_001053862.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_001053863.1 binds single-stranded DNA at the primosome assembly site YP_001053864.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_001053865.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis YP_001053868.1 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_001053869.1 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_001053872.1 catalyzes the formation of arginine from (N-L-arginino)succinate YP_001053909.1 catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2 YP_001053912.1 An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group YP_001053915.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_001053919.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_001053922.1 putative nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ; the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription YP_001053926.1 porin involved in the transport of maltose and maltodextrins YP_001053927.1 with malEFG is involved in import of maltose/maltodextrin YP_001053928.1 functions in the MalKFGE ABC transporter complex to transport maltose into the cell by using ATP hydrolysis YP_001053929.1 with MalKGE is involved in maltose transport into the cell YP_001053930.1 with MalKFE is involved in the transport of maltose into the cell YP_001053931.1 amylomaltase; acts to release glucose from maltodextrins YP_001053934.1 catalyzes the reduction of 2 glutathione to glutathione disulfide; maintains high levels of reduced glutathione in the cytosol; involved in redox regulation and oxidative defense YP_001053941.1 catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate YP_001053942.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_001053946.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_001053949.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation YP_001053965.1 23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance YP_001053966.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_001053967.1 Antitoxin that counteracts the effect of the YoeB toxin YP_001053969.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate YP_001053970.1 binds and unfolds substrates as part of the ClpXP protease YP_001053971.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates YP_001053974.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence YP_001053977.1 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_001053986.1 regulates arginine biosynthesis when complexed with arginine by binding at site that overlap the promotors of the arginine biosynthesis genes YP_001053987.1 oxidizes malate to oxaloacetate YP_001053989.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_001053993.1 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_001053994.1 interacts with cell division protein FitsZ and may be required to anchor septal ring structure YP_001053995.1 putative role in sulfur assimilation YP_001053996.1 catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate YP_001054000.1 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate YP_001054002.1 ADP-sugar pyrophosphatase; catalyzes the formation of D-ribose 5-phosphate from ADP-ribose; can also act on ADP-mannose and ADP-glucose YP_001054004.1 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_001054005.1 functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to DcuA; DcuA and DcuB function as independent and mutually redundant C4-dicarboxylate (aspartate, malate, fumarate and succinate) transporters YP_001054007.1 reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP YP_001054008.1 Includes: Sucrose-specific phosphotransferase enzyme IIB component; Sucrose permease IIC component YP_001054010.1 permease; with TbpA and ThiQ functions in transport of thiamine and thiamine pyrophosphate into the cell; repressed in presence of exogenous thiamine YP_001054012.1 Phosphotransferase system, enzyme I; transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein; part of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), a major carbohydrate active-transport system YP_001054013.1 functions in phosphoenolpyruvate-(PEP)-dependent phosphotransferase (PTS) system; functions in the transport and phosphorylation of glucose YP_001054014.1 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_001054015.1 unwinds DNA duplexes with 3' to 5' polarity with respect to the bound strand and initiates unwinding most effectively when a single-stranded region is present; involved in the post-incision events of nucleotide excision repair and methyl-directed mismatch repair. YP_001054016.1 GTP hydrolase involved in nickel liganding into hydrogenases YP_001054020.1 involved in hydrogen uptake YP_001054021.1 Fe-S ferrodoxin type component; participates in the periplasmic electron-transferring activity of hydrogenase 2 YP_001054022.1 HybB; cytochrome b subunit of the hydrogenase 2 enzyme, composed of HybA, B, C, and O subunits YP_001054023.1 involved in hydrogen uptake YP_001054024.1 protease responsible for the cleavage of a 15 amino acid peptide from the C-terminal end of the large subunit of hydrogenase 2 (HybC) YP_001054030.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX YP_001054032.1 Reclaims exogenous and endogenous cytidine and 2'-deoxycytidine molecules for UMP synthesis YP_001054033.1 putative ABC transporter, membrane protein YP_001054037.1 highly acidic protein; the structure of the Haemophilus influenzae protein shows similarity to uracil DNA glycosylase inhibitor (Ugi); binds heat-unstable protein (HU-alpha) which is a histone-like protein YP_001054039.1 with TehA confers resistance to tellurite YP_001054040.1 with ArtPQJI acts to transport arginine across the inner membrane YP_001054041.1 with ArtPMJI transports arginine across the inner membrane YP_001054043.1 With ArtMQJI transports arginine across the inner membrane YP_001054048.1 two electrons are transferred from cytoplasmic NADPH to thioredoxin and then to the inner membrane protein DsbD which keeps the disulfide isomerase DsbC in a reduced state in the oxidizing periplasm; DsbC in turns rearranges incorrectly made disulfide bonds in the periplasm YP_001054054.1 pubmed:8461417 YP_001054055.1 YfhD; uncharacterized member of the transglycosylase slt family; part of the rob operon, which plays a role in cellular resistance to antibiotics, bactericidal agents, and organic solvents; unknown function YP_001054057.1 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_001054061.1 ATP-binding protein; required for proper cytochrome c maturation YP_001054062.1 controls initiation of DNA replication by inhibiting re-initiation of replication, promotes hydrolysis of DnaA-bound ATP YP_001054064.1 catalyzes the decarboxylation of oxaloacetate to form pyruvate and carbon dioxide YP_001054065.1 catalyzes the formation of pyruvate from oxaloacetate YP_001054072.1 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_001054073.1 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_001054074.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY YP_001054075.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not YP_001054080.1 Includes: Mannose-specific phosphotransferase enzyme IIA component; Mannose-specific phosphotransferase enzyme IIB component YP_001054082.1 hosphoenolpyruvate-dependent sugar phosphotransferase system catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IID with IIC forms the translocation channel YP_001054087.1 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_001054088.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_001054089.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_001054090.1 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_001054096.1 catalyzes the decarboxylation of phosphatidyl-L-serine to phosphatidylethanoleamine YP_001054097.1 Synthesizes glutathione from L-glutamate and L-cysteine via gamma-L-glutamyl-L-cysteine YP_001054103.1 malate dehydrogenase; catalyzes the oxidation of malate to oxaloacetate YP_001054107.1 ABC transporter; functions in galactose transport; part of MglA2C2B transporter complex YP_001054108.1 with MglBC transports galactose or methyl galactoside into the cell; contains 2 ATP binding domains YP_001054113.1 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_001054116.1 part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA YP_001054117.1 part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; secreted by twin arginine translocation pathway YP_001054118.1 periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC YP_001054129.1 involved in transport of zinc(II) with ZnuA and C YP_001054132.1 pubmed:8181764 YP_001054133.1 pubmed:8359891 YP_001054134.1 pubmed:8359891 YP_001054137.1 Part of the ABC transporter complex FbpABC involved in Fe(3+) ions import YP_001054139.1 catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate YP_001054141.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_001054142.1 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway YP_001054143.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_001054144.1 threonine deaminase; threonine dehydratase; in Escherichia coli, IlvA is part of the isoleucine biosynthetic pathway YP_001054150.1 catalyzes the formation of dimethylmenaquinone from 1,4-dihydroxy-2-naphthoate and octaprenyl diphosphate YP_001054151.1 essential respiratory protein A; may be involved in the transfer of iron-sulfur clusters; essential for growth using oxygen or alternate electron acceptors YP_001054162.1 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_001054163.1 synthesizes RNA primers at the replication forks YP_001054164.1 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_001054165.1 catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr) YP_001054169.1 negatively controls the expression of fabA and fabB, genes involved in the unsaturated fatty acid biosynthesis YP_001054170.1 Activates the expression of a regulon of hydrogen peroxide-inducible genes such as katG, gor, ahpC, ahpF, oxyS, dps, fur and grxA YP_001054174.1 catalyzes the formation of pyridoxal 5'-phosphate from pyridoxal YP_001054175.1 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_001054178.1 antioxidant activity; thioredoxin-dependent thiol peroxidase; forms homodimers in solution; shows substrate specificity to alkyl hydroperoxides; periplasmic protein YP_001054179.1 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_001054181.1 ACT domain-containing protein YP_001054187.1 catalyzes the formation of methylglyoxal from glycerone phosphate YP_001054188.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_001054191.1 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_001054194.1 binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB YP_001054196.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_001054198.1 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_001054199.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate YP_001054200.1 catalyzes the O-acetylation of serine YP_001054201.1 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_001054202.1 catalyzes the formation of (R)-4'-phosphopantothenate in coenzyme A biosynthesis YP_001054206.1 forms a trimer; related to eukaryotic protein gephyrin; functions during molybdenum cofactor biosynthesis YP_001054208.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_001054209.1 catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway YP_001054215.1 in conjunction with FrdC acts to anchor the catalytic components of the fumarate reductase to the cytoplasmic membrane YP_001054216.1 part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; the catalytic subunits are similar to succinate dehydrogenase SdhAB YP_001054217.1 part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; the catalytic subunits are similar to succinate dehydrogenase SdhAB YP_001054218.1 part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; the catalytic subunits are similar to succinate dehydrogenase SdhAB YP_001054219.1 lysine--tRNA ligase beta chain; poxA; class II aminoacyl tRNA synthetase; catalyzes a two-step reaction; first charging a lysine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA YP_001054220.1 involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate YP_001054221.1 functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to dcuB YP_001054224.1 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_001054225.1 catalyzes the cleavage of the lactyl ether moiety of N-acetylmuramic acid-6-phosphate (MurNAc-6-P) to form N-acetylglucosamine-6-phosphate (GlcNAc-6-P) and lactate; involved in MurNAc dissimilation pathway YP_001054226.1 methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype YP_001054231.1 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_001054233.1 enterobacterial common antigen polymerase YP_001054234.1 catalyzes the synthesis of a lipid-linked intermediate involved in ECA synthesis YP_001054235.1 catalyzes the reduction of hydroxylamine to ammonia and water YP_001054238.1 catalyzes the formation of dTDP-D-fucosamine from dTDP-4-oxo-6-deoxy-D-glucose in enterobacterial common antigen biosynthesis YP_001054240.1 catalyzes the oxidation of UDP-N-acetyl-D-mannosamine to UDP-N-acetylmannosaminuronic acid YP_001054244.1 Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway YP_001054247.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_001054248.1 involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain YP_001054251.1 catalyzes the formation of selenocysteinyl-tRNA(Sec) from seryl-tRNA(Sec) and L-selenophosphate in selenoprotein biosynthesis YP_001054252.1 An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group YP_001054260.1 pubmed:14742511 YP_001054266.1 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_001054267.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_001054268.1 pubmed:9632602 YP_001054269.1 pubmed:9632602 YP_001054270.1 pubmed:9632602 YP_001054271.1 pubmed:9169799 YP_001054272.1 pubmed:9169799 YP_001054273.1 pubmed:9169799 YP_001054274.1 pubmed:9169799 YP_001054275.1 contains 2 ATP-binding cassettes; involved in the transport of molybdenum YP_001054276.1 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_001054281.1 forms homopentamer; channel that opens in response to pressure or hypoosmotic shock YP_001054282.1 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_001054283.1 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_001054289.1 SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA YP_001054291.1 This protein performs the mismatch recognition step during the DNA repair process YP_001054303.1 involved in the assembly of the urease metallocenter; possible nickel donor YP_001054305.1 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 ureC (alpha) and 3 ureAB (gamma/beta) subunits YP_001054306.1 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori and Yersinia enterocolitica the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 UreC (alpha) and 3 UreAB (gamma/beta); in Brucella suis the urease encoded by this operon (one of two urease-encoding operons found in its genome) is involved with urease activity, optimum growth, resistance to low-pH killing in-vitro and persistence in-vivo, while the other operon does not seem to be active YP_001054307.1 UreA, with UreB and UreC catalyzes the hydrolysis of urea into ammonia and carbon dioxide; nickel metalloenzyme; accessory proteins UreD, UreE, UreF, and UreG are necessary for assembly of the metallocenter YP_001054311.1 catalyzes the ATP-dependent transport of cobalt YP_001054317.1 Acts as a repressor of the mtlAD operon YP_001054319.1 Includes: Mannitol permease IIC component; Mannitol-specific phosphotransferase enzyme IIB component; Mannitol-specific phosphotransferase enzyme IIA component YP_001054320.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source YP_001054325.1 catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit YP_001054331.1 in Escherichai coli the heterohexameric TusBCD complex is involved in sulfur related that results in thiouridation to U34 position in some tRNAs YP_001054334.1 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_001054335.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_001054336.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_001054337.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_001054338.1 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_001054339.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. YP_001054340.1 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_001054341.1 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_001054342.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit I associates with the membrane and may be involved with cation translocation YP_001054343.1 glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA YP_001054344.1 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_001054351.1 Includes: Mannose-specific phosphotransferase enzyme IIA component; Mannose-specific phosphotransferase enzyme IIB component YP_001054358.1 cytoplasmic mutarotase that catalyzes the conversion between beta-pyran and beta-furan forms of D-ribose; RbsD is required for efficient ribose utilization in E. coli; rbsD-mutant E. coli strains are unable to use ribose as a sole carbon source YP_001054359.1 with RbsBCD acts to import ribose into the cell; RbsA contains 2 ATP-binding domain YP_001054360.1 functions to transport ribose at high affinity; forms a complex with RbsA2C2B YP_001054361.1 periplasmic substrate-binding component of the ATP-dependent ribose transport system YP_001054362.1 catalyzes the formation of D-ribose 5-phosphate from ribose YP_001054366.1 binds to the twin-arginine signal peptides of certain proteins, including dimethylsulfoxide reductase and trimethylamine N-oxide reductase that are translocated to the cytoplasmic membrane YP_001054371.1 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_001054373.1 catalyzes the conversion of the aldose L-fucose into the corresponding ketose L-fuculose YP_001054376.1 catalyzes the formation of glycerone phosphate and (S)-lactaldehyde from L-fuculose 1-phosphate YP_001054383.1 pubmed:10459579 YP_001054387.1 catalyzes the formation of L-xylulose-5-phosphate from 3-keto-L-gulonate-6-phosphate in anaerobic L-ascorbate utilization YP_001054391.1 negative regulator of ulaG and ulaABCDEF YP_001054392.1 L-xylulose 5-phosphate 3-epimerase activity not yet demonstrated; may be involved in the utilization of 2,3-diketo-L-gulonate YP_001054393.1 catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate in the anaerobic catabolism of L-ascorbate; links the arabinose metabolic pathway to the pentose phosphate pathway and allows the bacteria to use arabinose as an energy source YP_001054399.1 catalyzes the interconversion between ADP-D-glycero-beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose YP_001054400.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_001054403.1 membrane component; functions with enzymes IIB (sgaB; ulaB) and IIA (sgaA; ulaC) enzyme I and HPr for anaerobic utilization and uptake of L-ascorbate; sgaTBA are regulated by yifQ as well as Crp and Fnr YP_001054405.1 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_001054406.1 Modulates Rho-dependent transcription termination YP_001054407.1 binds directly to 23S ribosomal RNA YP_001054408.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_001054409.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_001054410.1 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_001054416.1 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_001054417.1 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_001054424.1 heat shock protein involved in degradation of misfolded proteins YP_001054425.1 heat shock protein involved in degradation of misfolded proteins YP_001054426.1 Regulatory factor involved in maltose metabolism YP_001054430.1 Murein hydrolase C; membrane-bound; lytic; catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine residues YP_001054438.1 catalyzes the hydrolysis of the thioester bond in palmitoyl-CoA YP_001054439.1 SEPHCHC synthase; forms 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1- carboxylate from 2-oxoglutarate and isochorismate in menaquinone biosynthesis YP_001054441.1 Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate YP_001054442.1 catalyzes the phosphorylation of the N-acetylmannosamine (ManNAc) liberated from N-acetyl-neuraminic acid by the nanA protein YP_001054443.1 catalyzes the formation of pyruvate and N-acetylmannosamine from N-acetylneuraminic acid YP_001054444.1 catalyzes the reversible formation of fructose 6-phosphate from glucosamine 6-phosphate YP_001054445.1 catalyzes the formation of glucosamine 6-phosphate from N-acetylglucosamine 6-phosphate YP_001054446.1 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_001054449.1 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_001054450.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_001054451.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_001054452.1 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_001054453.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_001054454.1 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_001054455.1 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_001054456.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_001054457.1 one of the stabilizing components for the large ribosomal subunit YP_001054458.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_001054459.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_001054460.1 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_001054461.1 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_001054462.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_001054463.1 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_001054464.1 binds 5S rRNA along with protein L5 and L25 YP_001054465.1 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_001054466.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7 YP_001054467.1 late assembly protein YP_001054468.1 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_001054469.1 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 have the motif YP_001054470.1 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_001054471.1 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_001054472.1 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_001054473.1 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_001054475.1 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_001054476.1 Essential for efficient processing of 16S rRNA YP_001054477.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_001054478.1 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_001054486.1 TorD; involved in the biogenesis of torA; acts on torA before the insertion of the molybdenum cofactor and, as a result, probably favors a conformation of the apoenzyme that is competent for acquiring the cofactor YP_001054489.1 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_001054492.1 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_001054494.1 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_001054497.1 catalyzes the formation of 2,3=diacylglucosamine 1-phosphate from UDP-2,3=diacylglucosamine YP_001054503.1 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_001054504.1 catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP) YP_001054506.1 carries the fatty acid chain in fatty acid biosynthesis YP_001054508.1 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; 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_001054509.1 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_001054511.1 catalyzes the formation of 1,4-dihydroxy-2-naphthoate from O-succinylbenzoyl-CoA YP_001054513.1 promotes RNA polymerase assembly or stability; latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits YP_001054514.1 catalyzes branch migration in Holliday junction intermediates YP_001054517.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_001054518.1 Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor 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_001054519.1 in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase; sulfite oxidase activity not demonstrated; requires inner membrane anchor protein YedZ YP_001054520.1 in Escherichia coli this inner membrane protein was found to anchor the periplasmic catalytic oxidoreductase YedY; sulfite oxidase activity not demonstrated; contains heme YP_001054521.1 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_001054524.1 catalyzes the formation of asparagine from aspartate and ammonia YP_001054525.1 transcriptional repressor of asnA which codes for aspartate-ammonia ligase YP_001054526.1 catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate; involved in the pyrimidine salvage pathway YP_001054528.1 converts L-glutamate to D-glutamate, a component of peptidoglycan YP_001054529.1 hemoprotein; NADPH dependent; with the alpha subunit (a flavoprotein) catalyzes the reduction of sulfite to sulfide YP_001054536.1 flavin mononucleotide-dependent dehydrogenase; functions in aerobic respiration and also has a role in anaerobic nitrate respiration YP_001054538.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_001054540.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis YP_001054544.1 Copper chaperone YP_001054548.1 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway YP_001054549.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis YP_001054552.1 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_001054553.1 in Escherichia coli MobA links a guanosine 5'-phosphate to molydopterin to form molybdopterin guanine dinucleotide during molybdenum cofactor biosynthesis; MobB is not essential but has been found to interact with multiple proteins involved in the molybdopterin guanine dinucleotide cofactor biosynthesis pathway YP_001054560.1 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_001054564.1 catalyzes the transformation of uracil to pseudouracil at nucleotides U955, U2504, and U2580 in 23S rRNA YP_001054574.1 catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP YP_001054578.1 catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate YP_001054580.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_001054582.1 hydrolyzes diadenosine polyphosphate YP_001054584.1 catalyzes the hydrolysis of pyrophosphate to phosphate YP_001054586.1 regulator of RNase E; increases half-life and abundance of RNAs; interacts with RNase E possibly inhibiting catalytic activity YP_001054590.1 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_001054591.1 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_001054593.1 catalyzes the interconversion of D-xylose to D-xylulose YP_001054594.1 periplasmic substrate-binding component of the ATP-dependent xylose transport system; high affinity YP_001054595.1 with XylFH is part of the high affinity xylose ABC transporter YP_001054600.1 mediates high affinitiy panthothenate transport which is stimulated by the presence of sodium ions; member of SSS family of sodium/solute symporters; the imported panthothenate is phosphorylated by panthothenate kinase YP_001054602.1 when combined with S-adenosylmethionine represses the expression of the methionine regulon and of proteins involved in S-adenosylmethionine synthesis YP_001054608.1 predicted polysaccharide polymerase involved in biofilm formation; required for the synthesis of the beta-1,6-N-acetylglucosamine polysaccharide; PgaC; in Yersinia the HmsR protein is an inner membrane protein YP_001054610.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate YP_001054611.1 catalyzes the modification of U13 in tRNA(Glu) YP_001054612.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate YP_001054621.1 in Escherichia coli transcription of this gene is enhanced by polyamines YP_001054622.1 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_001054630.1 exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH YP_001054632.1 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine YP_001054633.1 RNase BN; required for 3' maturation of certain phage T4-encoded tRNAs; forms a dimer; specific for immature tRNA substrates containing incorrect residues within the universal CCA sequence; 3' to 5' exoribonuclease YP_001054634.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway YP_001054637.1 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_001054638.1 similar to zinc-dependent eukaryotic ADH enzymes and distinct from fermentative ADHs YP_001054639.1 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_001054644.1 complexes with cyclic AMP and binds to specific DNA sites near the promoter to regulate the transcription of several catabolite-sensitive operons YP_001054646.1 FtsZ binding protein; synthetically lethal with a defect in the Min system; this protein is the first identified nucleoid occlusion factor which works along with the Min system to properly position the FtsZ ring assembly YP_001054647.1 catalyzes the formation of dUMP from dUTP YP_001054648.1 catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine YP_001054649.1 Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase YP_001054650.1 required for 70S ribosome assembly YP_001054651.1 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_001054653.1 catalyzes the reversible formation of diaminobutyrate and 2-oxoglutarate from glutamate and L-aspartic beta-semialdehyde YP_001054658.1 catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs YP_001054660.1 responsible for the influx of magnesium ions YP_001054664.1 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_001054665.1 mediates the export of protein precursors bearing twin-arginine signal peptides YP_001054667.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_001054669.1 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_001054671.1 catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_001054679.1 involved in the peptidyltransferase reaction during translation YP_001054684.1 16S rRNA M2G1207 methyltransferase; one of many enzymes that modify bases of the ribosomal RNA; this enzyme methylates the G at position 1207 of the small ribosomal subunit YP_001054685.1 with the chi subunit binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB YP_001054686.1 alanine acetyltransferase that specifically acetylates ribosomal protein S18 YP_001054687.1 facilitates an early step in the assembly of the 50S subunit of the ribosome YP_001054688.1 catalyzes the formation of pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate YP_001054693.1 similar to Haemophilus parasuis FhuD YP_001054694.1 part of the FhuBCD ATP-dependent iron (III) hydroxamate transporter involved in the high-affinity transport of Fe(3+)-ferrichrome YP_001054697.1 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_001054698.1 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_001054699.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_001054700.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_001054702.1 catalyzes the formation of 3-(imidazol-4-yl)-2-oxopropyl phosphate from D-ethythro-1-(imidazol-4-yl)glycerol 3-phosphate and histidinol from histidinol phosphate YP_001054704.1 with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide YP_001054705.1 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_001054707.1 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribosyl)-ATP and the subsequent formation of 1-(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide from 1-(5-phosphoribosyl)-AMP in histidine biosynthesis YP_001054709.1 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_001054713.1 phosphorylates aminoimidazole ribotide (AIR) which forms 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P); synthesis of HMP-P from AIR is complex and requires the product of thiC gene at least YP_001054715.1 part of the ATP-dependent transport system LolCDE; responsible for the localization of lipoproteins to the periplasmic surface of the outer membrane YP_001054718.1 Catalyzes the reduction of hydroxypyruvate to form D-glycerate, using NADH as an electron donor YP_001054719.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_001054721.1 similar to M.PmuHemKP YP_001054723.1 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