-- dump date 20140619_120234 -- class Genbank::CDS -- table cds_note -- id note YP_512166.1 MobA/MobL family protein YP_507943.1 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_507944.1 binds the polymerase to DNA and acts as a sliding clamp YP_507945.1 Required for DNA replication; binds preferentially to single-stranded, linear DNA YP_507946.1 negatively supercoils closed circular double-stranded DNA YP_507964.1 catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate YP_507970.1 catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate YP_507973.1 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_507975.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis YP_507980.1 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_507982.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_507983.1 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_508004.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis YP_508009.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming YP_508011.1 catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic YP_508030.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate YP_508036.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_508056.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_508065.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D YP_508070.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_508077.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate YP_508079.1 catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; also known as acetolactate synthase large subunit YP_508087.1 involved in chelation of magnesium into protoporphyrin IX; involved in bacteriochlorophyll biosynthesis; part of a complex with BchI, BchD, and BchH YP_508088.1 involved in chelation of magnesium into protoporphyrin IX; involved in bacteriochlorophyll biosynthesis; part of a complex with BchI, BchD, and BchH YP_508091.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine YP_508093.1 oxidative; catalyzes the formation of divinylprotochlorophyllide from magnesium-protoporphyrin IX 13-monomethyl ester in isocyclic ring formation in chlorophyll biosynthesis YP_508099.1 catalyzes the formation of Mg-protoporphyrin IX methyl ester and S-adenosyl-L-homocysteine from Mg-protoporphyrin IX and S-adenosyl-L-methionine YP_508100.1 light-independent; with chlN(bchN) and chlB(bchB) reduces ring D of protochlorophyllide to form chlorophyllide a in chlorophyll/bacteriochlorophyll production YP_508101.1 involved in chelation of magnesium into protoporphyrin IX; involved in bacteriochlorophyll biosynthesis; the enzyme from Rhodobacter capsulatus contains an Fe-S cluster; part of a complex with BchI, BchD, and BchH YP_508102.1 light-independent reduction of protochlorophyllide to form chlorophyllide a YP_508103.1 light-independent reduction of protochlorophyllide to form chlorophyllide a YP_508112.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate YP_508127.1 heat shock protein involved in degradation of misfolded proteins YP_508129.1 heat shock protein involved in degradation of misfolded proteins YP_508135.1 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_508138.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate YP_508140.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_508141.1 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_508142.1 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_508146.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_508147.1 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_508149.1 Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons YP_508151.1 This protein performs the mismatch recognition step during the DNA repair process YP_508152.1 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate YP_508153.1 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_508154.1 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_508158.1 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_508189.1 BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell YP_508190.1 function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain YP_508202.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate YP_508203.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_508204.1 catalyzes the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA YP_508226.1 Regulatory factor involved in maltose metabolism YP_508228.1 Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase YP_508231.1 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_508233.1 bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate YP_508235.1 protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic YP_508240.1 Involved in ubiquinone biosynthesis YP_508243.1 involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan YP_508271.1 permease; with TbpA and ThiQ functions in transport of thiamine and thiamine pyrophosphate into the cell; repressed in presence of exogenous thiamine YP_508272.1 part of the thiamine and TPP transport system tbpA-thiPQ YP_508273.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_508279.1 Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile YP_508286.1 D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm YP_508291.1 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway YP_508296.1 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_508312.1 CobD; CbiD in Salmonella; converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group YP_508321.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate YP_508341.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate YP_508353.1 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_508393.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_508394.1 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_508396.1 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_508399.1 homopentamer; channel that opens in response to pressure or hypoosmotic shock YP_508415.1 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_508433.1 Glycine cleavage system transcriptional activator; activates the gcvTHP operon in the presence of glycine and represses the operon in its absence YP_508435.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; in Rhizobia and Ralstonia is involved in PHB biosynthesis YP_508439.1 catalyzes the formation of arginine from (N-L-arginino)succinate YP_508440.1 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_508444.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids YP_508449.1 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_508455.1 Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits YP_508458.1 involved in the de novo synthesis of pyridoxine (Vitamin B6) YP_508462.1 Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids YP_508466.1 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_508469.1 involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA YP_508477.1 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP YP_508485.1 converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA YP_508495.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_508497.1 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_508505.1 binds directly to 23S ribosomal RNA YP_508506.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_508508.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_508509.1 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_508510.2 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_508511.1 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_508517.1 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_508518.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_508519.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_508520.1 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_508524.1 NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex YP_508525.1 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_508526.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_508527.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_508530.1 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_508531.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_508532.1 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_508533.1 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_508534.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_508541.1 one of the stabilizing components for the large ribosomal subunit YP_508542.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_508543.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_508544.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_508545.1 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_508546.1 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_508547.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_508548.1 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_508549.1 binds 5S rRNA along with protein L5 and L25 YP_508550.1 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_508551.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7 YP_508553.1 late assembly protein YP_508554.1 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_508555.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_508557.1 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_508558.1 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_508559.1 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_508560.1 is a component of the macrolide binding site in the peptidyl transferase center YP_508575.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate YP_508576.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_508579.1 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_508584.1 in Escherichia coli transcription of this gene is enhanced by polyamines YP_508590.1 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_508596.1 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation YP_508597.1 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA YP_508600.1 catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA YP_508609.1 catalyzes the conversion of ferulic acid to feruloyl-CoA YP_508613.1 cleaves the ring of 2,3-dihydro-2,3-dihydroxybenzoyl-CoA forming 6-hydroxy-3-hexenoyl-CoA YP_508617.1 consists of N-terminal helix-turn-helix domain and C-terminal shikimate kinase-like domain which may bind benzoyl-CoA; controls inducible expression of the bzd catabolic operon that is involved in the anaerobic catabolism of benzoate YP_508639.1 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_508648.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_508649.1 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_508650.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis YP_508657.1 Catalyzes the formation of (d)CDP from ATP and (d)CMP YP_508663.1 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_508683.1 RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome YP_508684.1 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_508690.1 Essential for efficient processing of 16S rRNA YP_508691.1 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_508692.1 catalyzes the interconversion of chorismate to prephenate YP_508709.1 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_508710.1 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_508711.1 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B' is part of the membrane proton channel. YP_508712.1 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel. YP_508716.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_508725.1 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_508741.1 catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate YP_508746.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase YP_508751.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol YP_508760.1 Catalyzes the reversible oxidation of malate to oxaloacetate YP_508763.1 catalyzes the interconversion of succinyl-CoA and succinate YP_508773.1 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_508774.1 component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA YP_508797.1 catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine YP_508836.1 catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_508839.1 catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein YP_508843.1 catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione YP_508848.1 binds with the catalytic core of RNA polymerase to produce the holoenzyme; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma-32 is responsible for the expression of heat shock promoters; there are paralogs in Rhizobium and Sinorhizobium; the proteins in this cluster act as secondary heat shock sigma factors; the Rhizobium sigma-32 factor may also be involved in exopolysaccharide production YP_508849.1 catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine YP_508882.2 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase YP_508887.1 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_508888.1 May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine YP_508889.1 short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ YP_508896.1 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_508906.1 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_508907.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_508908.1 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_508917.1 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_508923.1 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate YP_508925.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate YP_508929.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate YP_508957.1 catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit YP_508965.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation YP_508966.1 DapATase; functions in arginine biosynthetic pathway; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine YP_508972.1 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_508974.1 similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity YP_508975.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity YP_508976.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_508977.1 dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate YP_508989.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_508990.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_508991.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_509000.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate YP_509002.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_509005.1 four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity YP_509010.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate YP_509012.1 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_509014.1 unwinds double stranded DNA YP_509026.1 part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane YP_509027.1 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_509033.1 flavin dependent thymidylate synthase; ThyX; thymidylate synthase complementing protein; catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate; the enzyme from Mycobacterium tuberculosis forms homotetramers; uses FAD as a cofactor YP_509040.1 catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr) YP_509046.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_509091.1 catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA YP_509092.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_509096.1 Catalyzes the transfer of electrons from NADH to quinone YP_509112.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen YP_509113.1 Catalyzes the transfer of electrons from NADH to quinone YP_509115.1 Catalyzes the transfer of electrons from NADH to quinone YP_509118.1 catalyzes the transfer of electrons from NADH to ubiquinone YP_509121.1 part of NADH-ubiquinone oxidoreductase complex I; shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH dehydrogenase YP_509125.1 Catalyzes the transfer of electrons from NADH to quinone YP_509127.1 Catalyzes the transfer of electrons from NADH to quinone YP_509129.1 Catalyzes the transfer of electrons from NADH to quinone YP_509132.1 Catalyzes the transfer of electrons from NADH to quinone YP_509135.1 Catalyzes the transfer of electrons from NADH to quinone YP_509136.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_509137.1 Catalyzes the transfer of electrons from NADH to quinone YP_509138.1 Catalyzes the transfer of electrons from NADH to quinone YP_509140.1 type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP YP_509163.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA YP_509164.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain YP_509167.1 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_509176.1 catalyzes the transformation of hydroxyatrazine to N-isopropylammelide and ethylamine in the atrazine degradation pathway. YP_509180.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis YP_509188.2 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers YP_509194.1 lipoyl-[acyl-carrier protein]-protein-N-lipoyltransferse; lipoate-protein ligase B; transfers lipoate to apolipoproteins; involved in lipoate metabolism YP_509218.1 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_509248.1 Catalyzes the deamination of cytosine to uracil and ammonia YP_509265.1 catalyzes the conversion of salicylyl-CoA to gentisyl-CoA YP_509268.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_509275.1 Involved in the incorporation of exogenous aryl acids in the biosynthesis of aromatic amino acids: catalysis of the ferredoxin-dependent oxidative decarboxylation of arylpyruvates. YP_509299.1 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_509340.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_509381.1 An oxygenase that acts to open the ring of homogentisate formingmaleylacetoacetate as part of the catabolism of L-tyrosine and L-phenylalanine YP_509389.1 catalyzes the oxidative ring opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate semialdehyde in the final enzymatic step of quinolinate biosynthesis YP_509393.1 catalyzes the formation of L-aspartate to iminoaspartate in NAD(+) biosynthesis YP_509416.1 Catalyzes the deamination of cytosine to uracil and ammonia YP_509434.1 catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine YP_509435.1 catalyzes the formation of betaine from betaine aldehyde YP_509449.1 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_509485.1 MobA/MobL family protein YP_509521.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine YP_509555.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_509562.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_509563.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_509564.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_509569.1 carries the fatty acid chain in fatty acid biosynthesis YP_509571.1 FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP YP_509595.1 catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP YP_509625.1 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair YP_509632.1 catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acetyltransferase within the complex. The E1 component of the pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase(E2) and lipoamide dehydrogenase YP_509635.1 catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis YP_509636.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_509642.1 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_509649.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_509654.1 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_509659.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step YP_509662.1 E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide YP_509665.1 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_509682.1 unwinds double stranded DNA YP_509683.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate YP_509684.1 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis YP_509694.1 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_509710.1 IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits YP_509723.1 Catalyzes the deamination of dCTP to form dUTP YP_509725.1 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_509727.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY YP_509728.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not YP_509735.1 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_509739.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_509748.1 recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1; this protein is similar to release factor 2 YP_509751.1 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_509752.1 catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate) YP_509757.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides YP_509758.1 binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB YP_509778.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_509784.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_509787.1 catalyzes the formation of malate from glyoxylate and acetyl-CoA YP_509798.1 Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group YP_509799.1 similar protein in Methanocaldococcus converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate as the first step in methanopterin biosynthesis YP_509808.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA YP_509816.1 Represses a number of genes involved in the response to DNA damage YP_509818.1 MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis YP_509821.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate YP_509824.1 with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine YP_509835.1 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_509845.1 Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate YP_509853.1 ATP-dependent carboxylate-amine ligase YP_509858.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA YP_509867.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_509875.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine YP_509877.1 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_509895.1 catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate YP_509911.1 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate YP_509913.1 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_509915.1 catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate YP_509918.1 catalyzes the transfer of the N5-methyl group from (6S)-methyl tetrahydrofolate to the cobalt center of a corrinoid iron-sulfur protein YP_509928.1 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_509929.1 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_509935.1 CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis YP_510014.1 catalyzes the formation of methylglyoxal from glycerone phosphate YP_510020.1 part of the UgpABCE glycerol-3-phosphate uptake system YP_510078.1 with HmuTU is involved in the transport of hemin YP_510084.1 this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress YP_510085.1 this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress YP_510111.1 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_510115.1 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_510118.1 Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates YP_510163.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_510168.1 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_510184.1 involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain YP_510186.1 Stimulates the elongation of poly(A) tails YP_510222.1 fusion of ribosomal protein L21 and COG3743 YP_510223.1 involved in the peptidyltransferase reaction during translation YP_510225.2 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_510226.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis YP_510227.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway YP_510234.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation YP_510242.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis YP_510247.1 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_510248.1 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_510266.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_510277.1 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_510278.1 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate YP_510282.1 catalyzes the formation of putrescine from agmatine YP_510286.1 functions in degradation of stringent response intracellular messenger ppGpp; in Escherichia coli this gene is co-transcribed with the toxin/antitoxin genes mazEF; activity of MazG is inhibited by MazEF in vitro; ppGpp inhibits mazEF expression; MazG thus works in limiting the toxic activity of the MazF toxin induced during starvation; MazG also interacts with the GTPase protein Era YP_510293.1 catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis YP_510306.1 with SufCD activates cysteine desulfurase SufS YP_510314.1 Converts isocitrate to alpha ketoglutarate YP_510321.1 DmdA; DMSP demethylase; in Silicibacter knockout of this gene results in an inability to convert DMSP to methanethiol which is restored with a cloned copy of the gene YP_510336.1 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_510337.1 related to arylsulfate sulfotransferase involved in siderophore biosynthesis YP_510367.1 forms a direct contact with the tRNA during translation YP_510368.2 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_510372.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_510382.1 Essential for recycling GMP and indirectly, cGMP YP_510392.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis YP_510393.1 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_510397.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate YP_510402.1 Catalyzes the phosphorylation of UMP to UDP YP_510403.1 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_510411.1 part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE YP_510414.1 Catalyzes the rate-limiting step in dNTP synthesis YP_510418.1 Catalyzes a key regulatory step in fatty acid biosynthesis YP_510419.1 catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively YP_510429.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis YP_510436.1 negatively supercoils closed circular double-stranded DNA YP_510440.1 TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine YP_510445.1 catalyzes branch migration in Holliday junction intermediates YP_510449.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_510462.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_510474.1 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia YP_510475.1 recognizes the termination signals UGA and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1 YP_510487.1 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_510489.1 catalyzes the formation of methionine from L-homocysteine and S-adenosyl-L-methionine YP_510499.1 involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth YP_510518.1 catalyzes the formation of acetaldehyde from ethanolamine YP_510533.1 catalyzes the formation of L-rhamnulose from L-rhamnose YP_510549.1 catalyzes the formation of glyoxylate from (S)-ureidoglycolate YP_510562.1 catalyzes the cleavage of carbon-halogen bonds in aliphatic compounds forming a primary alcohol and a halide YP_510588.1 Catalyzes the conversion of citrate to isocitrate YP_510589.1 ATP-binding protein; required for proper cytochrome c maturation YP_510596.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate YP_510605.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_510609.1 catalyzes the ATP-dependent formation of a phosphodiester at the site of a single strand break in duplex DNA YP_510617.1 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine YP_510647.1 catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position YP_510649.1 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide YP_510651.1 catalyzes the formation of pyruvate and beta-alanine from L-alanine and 3-oxopropanoate YP_510654.1 catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines YP_510655.1 function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain YP_510657.1 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_510659.1 leucyltransferase; phenylalanyltransferse; functions in the N-end rule pathway; transfers Leu, Phe, Met, from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys YP_510662.1 Provides the input to the respiratory chain from the NAD-linked dehydrogenases of the citric acid cycle. The complex couples the oxidation of NADH and the reduction of ubiquinone, to the generation of a proton gradient which is then used for ATP synthesis YP_510666.1 Catalyzes the deamination of guanine YP_510667.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_510672.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_510673.1 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_510675.1 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_510680.1 catalyzes the formation of 2-oxobutanoate from L-threonine YP_510691.1 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_510692.1 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_510695.1 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_510696.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_510701.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_510702.1 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_510705.1 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_510706.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_510708.1 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_510723.1 biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate YP_510730.1 catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis YP_510731.1 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_510734.1 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_510737.1 catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase YP_510738.1 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis YP_510749.1 binds and unfolds substrates as part of the ClpXP protease YP_510788.1 catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source YP_510790.1 catalyzes the formation of pyruvate and beta-alanine from L-alanine and 3-oxopropanoate YP_510814.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_510818.1 catalyzes the formation of pyruvate from D-cysteine YP_510825.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_510828.1 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_510848.1 Converts D-sorbitol to L-sorbose YP_510850.1 catalyzes the formation of catechol from salicylate YP_510855.1 activates fatty acids by binding to coenzyme A YP_510862.1 catalyzes the formation of precorrin 6x from precorrin 5 YP_510863.1 catalyzes 2 sequential methylations, the formation of precorrin-1 and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and uroporphyrin III, and the formation of precorrin-2 and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and precorrin-1 YP_510864.1 responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid YP_510871.1 catalyzes the interconversion of precorrin-8X and hydrogenobyrinate YP_510873.1 with CobST catalyzes the formation of cobyrinic acid a,c-diamide from hydrogenobyrinic acid a,c-diamide in an ATP-dependent manner; involved in porphyrin and chlorophyll metabolism; vitamin B12 metabolism YP_510879.1 catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation YP_510905.1 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_510917.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation YP_510925.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate YP_510926.1 catalyzes the formation of inosine from adenosine YP_510927.1 catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose YP_510928.1 Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate YP_510931.1 NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate YP_510932.1 catalyzes the phosphorylation of NAD to NADP YP_510933.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_510940.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine YP_510942.1 type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese YP_511009.1 Transcriptional repressor of the nan operon that encodes proteins involved in sialic acid utilization YP_511055.1 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_511056.1 catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate YP_511057.1 catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose YP_511059.1 catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate YP_511061.1 catalyzes the formation of malonyl-CoA from malonate and CoA YP_511076.1 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_511087.1 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_511091.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_511094.1 involved in the insertion of copper into subunit I of cytochrome C oxidase YP_511096.1 converts protoheme IX and farnesyl diphosphate to heme O YP_511102.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_511108.1 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_511117.1 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway YP_511121.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis YP_511123.1 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_511127.1 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_511128.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source YP_511141.1 necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space YP_511142.1 involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan YP_511149.1 Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate YP_511154.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis YP_511184.1 Involved in nucleotide synthesis and salvage YP_511186.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_511194.1 catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate YP_511196.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_511224.1 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_511229.1 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z YP_511233.1 catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine YP_511244.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis YP_511247.1 catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole YP_511262.1 catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs YP_511266.1 catalyzes the formation of thymidine 5'-phosphate from thymidine YP_511270.1 catalyzes the formation of L-proline from pyrroline-5-carboxylate YP_511275.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_511288.1 NH(3)-dependent; catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers YP_511295.1 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway YP_511300.1 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 not essential for growth YP_511301.1 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_511303.1 catalyzes the hydrolysis of pyrophosphate to phosphate YP_511309.1 MDM; functions in conversion of succinate to propionate YP_511342.1 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_511355.1 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_511359.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_511366.1 required for 70S ribosome assembly YP_511373.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_511391.1 synthesizes RNA primers at the replication forks YP_511392.1 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_511399.1 functions in transport of arginine/ornithine; inner membrane ATPase that cleaves ATP and phosphorylates two periplasmic proteins that function as two distinct transport systems, the AO (arginine and ornithine) and LAO (lysine, arginine, and ornithine) periplasmic binding proteins YP_511404.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_511409.1 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_511410.1 YghU; B2989; one of eight putative glutathione transferase proteins from E. coli YP_511415.1 catalyzes the formation of histidinol phosphate and 2-oxoglutarate from glutamate and imidazole acetol-phosphate YP_511419.1 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_511420.1 catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA YP_511436.1 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_511507.1 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_511508.1 in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media YP_511524.1 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_511526.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis YP_511527.1 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_511529.1 catalyzes the formation of 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate from N-(5-phospho-beta-D-ribosyl)-anthranilate in tryptophan biosynthesis YP_511531.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_511534.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_511538.1 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_511544.1 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_511559.1 class I; LysRS1; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine YP_511563.1 part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor YP_511564.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine YP_511569.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence YP_511571.1 transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria YP_511578.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_511585.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis YP_511587.1 functions in MreBCD complex in some organisms YP_511588.1 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_511600.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_511626.1 in Escherichia coli this homodimeric enzyme is expressed under aerobic conditions; anaerobic expression is repressed by the arcAB system; converts sn-glycerol-3-phosphate and ubiquinone-8 to dihydroxy acetone phosphate and ubiquinol-8; associates with the cytoplasmic membrane YP_511635.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_511637.1 subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved with K+ YP_511657.1 subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved with K+ YP_511658.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_511659.1 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone YP_511660.1 subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport YP_511687.1 proposed role in polysaccahride synthesis YP_511703.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate YP_511745.1 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_511751.1 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_511766.1 catalyzes the dehydration of L-carnitinyl-CoA to crotonobetainyl-CoA YP_511769.1 Converts (S)-3-hydroxyacyl-CoA to 3-oxyacyl-CoA; may also act as a thioesterase YP_511774.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-galactonate 6-phosphate; functions in galactonate metabolism YP_511787.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis YP_511788.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III YP_511790.1 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis YP_511799.1 CcoN; FixN YP_511801.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_511807.1 catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis YP_511818.1 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_511820.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_511833.1 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_511844.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis YP_511854.1 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_511855.1 UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin YP_511861.1 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_511872.1 catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_511921.1 in Escherichia coli this inner membrane protein was found to anchor the periplasmic catalytic oxidoreductase YedY; sulfite oxidase activity not demonstrated; contains heme YP_511923.1 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_511931.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase YP_511937.1 involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function YP_511939.1 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_511972.1 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_511976.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs YP_511978.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_511979.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_511984.1 involved in de novo purine biosynthesis YP_511989.1 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_512016.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine YP_512021.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate YP_512022.1 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_512103.1 catalyzes the formation of protocatechuate from 4-hydroxybenzoate YP_512116.1 with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook YP_512118.1 part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum YP_512120.1 FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus YP_512122.1 the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod YP_512126.1 With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine YP_512128.1 membrane protein involved in the flagellar export apparatus YP_512130.1 membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export YP_512133.1 part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod YP_512134.1 required for the assembly of the flagellar basal body P-ring YP_512135.1 makes up the distal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagella YP_512136.1 FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod; Rhodobacter sphaeroides has 2 copies of this and other flagella genes YP_512138.1 forms a junction between the M-ring and FlgB during flagella biosynthesis; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella YP_512139.1 with FlgF and B makes up the proximal portion of the flagellar basal body rod YP_512140.1 with FlgF and C makes up the proximal portion of the flagellar basal body rod YP_512143.1 post-transcriptional repressor of flagellum biosynthesis; promotes degradation of fljK mRNA: Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella YP_512144.1 acts as an activator of flagellin translation and may be required for filament secretion or assembly; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagellum YP_512149.1 acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod; Rhodobacter sphaeroides has 2 copies of many flagellar genes; the Rhodobacter protein in this cluster is associated with a set of flagellar genes acquired by lateral gene transfer; these genes are not normally expressed YP_512152.1 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_512154.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase