-- dump date 20140618_185941 -- class Genbank::CDS -- table cds_note -- id note YP_002317416.1 catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr) YP_002317417.1 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_002317419.1 essential respiratory protein A; may be involved in the transfer of iron-sulfur clusters; essential for growth using oxygen or alternate electron acceptors YP_002317433.1 Required for DNA replication; binds preferentially to single-stranded, linear DNA YP_002317435.1 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_002317436.1 in Escherichia coli transcription of this gene is enhanced by polyamines YP_002317439.1 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_002317441.1 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_002317448.1 Catalyzes the deamination of guanine YP_002317463.1 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_002317474.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_002317475.1 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_002317482.1 catalyzes the release of sulfite from alkanesulfonates YP_002317485.1 catalyzes the formation of N-acetyl-L-glutamate from L-glutamate and acetyl-CoA in arginine biosynthesis YP_002317490.1 Involved in ubiquinone biosynthesis YP_002317496.1 RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs YP_002317527.1 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_002317531.1 represses the lctPRD operon YP_002317532.1 flavin mononucleotide-dependent dehydrogenase; functions in aerobic respiration and also has a role in anaerobic nitrate respiration YP_002317533.1 component of the membrane-bound D-lactate oxidase, FAD-binding, NADH independent YP_002317534.1 catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate YP_002317536.1 catalyzes the formation of pyruvate and succinate from 2-methylisocitrate YP_002317537.1 catalyzes the synthesis of 2-methylcitrate from propionyl-CoA and oxaloacetate; also catalyzes the condensation of oxaloacetate with acetyl-CoA but with a lower specificity YP_002317538.1 Catalyzes the conversion of citrate to isocitrate YP_002317552.1 catalyzes the oxidative deamination of D-amino acids YP_002317584.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_002317592.1 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_002317593.1 malic enzyme; oxaloacetate-decarboxylating; NAD-dependent; catalyzes the formation of pyruvate form malate YP_002317601.1 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_002317603.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. YP_002317604.1 Produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex YP_002317605.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_002317606.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_002317607.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the beta chain is a regulatory subunit YP_002317608.1 part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane YP_002317618.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_002317635.1 involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function YP_002317642.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_002317646.1 catalyzes the hydrolysis of pyrophosphate to phosphate YP_002317668.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_002317702.1 streptomycin 3'-adenyltransferase YP_002317711.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_002317723.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_002317727.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides YP_002317730.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate YP_002317736.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_002317737.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine YP_002317743.1 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_002317749.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine YP_002317756.1 catalyzes the formation of arginine from (N-L-arginino)succinate YP_002317759.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis YP_002317771.1 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_002317772.1 forms a complex with SecY and SecG; SecYEG forms a putative protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force YP_002317774.1 binds directly to 23S ribosomal RNA YP_002317775.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_002317776.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_002317777.1 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_002317778.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme YP_002317779.1 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_002317787.1 molecular chaperone YP_002317795.1 FadA; fatty acid oxidation complex component beta; functions in a heterotetramer with FadB; similar to FadI2J2 complex; functions in beta-oxidation of fatty acids YP_002317796.1 includes enoyl-CoA hydratase, delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase, and 3-hydroxybutyryl-CoA epimerase; catalyzes the formation of an hydroxyacyl-CoA by addition of water on enoyl-CoA; also exhibits 3-hydroxyacyl-CoA epimerase and 3-hydroxyacyl-CoA dehydrogenase activities; forms a heterotetramer with FadA; similar to FadI2J2 complex; functions in beta-oxidation of fatty acids YP_002317800.1 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_002317809.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function YP_002317816.1 catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis YP_002317820.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate YP_002317823.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_002317824.1 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_002317825.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_002317826.1 subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport YP_002317829.1 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_002317830.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_002317831.1 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_002317845.1 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_002317866.1 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_002317872.1 may be involved in chromosome condensation; overexpression in Escherichia coli protects against decondensation by camphor; overexpressing the protein results in an increase in supercoiling YP_002317874.1 RpmE2; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome YP_002317883.1 activates fatty acids by binding to coenzyme A; may be involved in acyclic terpene utilization YP_002317891.1 activator of 3-phenylpropionic acid catabolism YP_002317895.1 hydrolyzes diadenosine polyphosphate YP_002317899.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate YP_002317900.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D YP_002317902.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_002317904.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_002317906.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_002317911.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_002317913.1 carrier protein part of the Na(+)-independent, binding-protein-independent glutamate-aspartate transport system YP_002317925.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_002317934.1 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_002317935.1 required for 70S ribosome assembly YP_002317945.1 ThyA; catalyzes formation of dTMP and 7,8-dihydrofolate from 5,10-methylenetetrahydrofolate and dUMP; involved in deoxyribonucleotide biosynthesis; there are 2 copies in some Bacilli, one of which appears to be phage-derived YP_002317948.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_002317976.1 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_002317979.1 Catalyzes the conversion of acetyl-CoA and L-homoserine to CoA and O-acetyl-L-homoserine YP_002317983.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_002317984.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates YP_002317985.1 binds and unfolds substrates as part of the ClpXP protease YP_002317989.1 catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate YP_002317991.1 catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate YP_002317996.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway YP_002317999.1 hydrolyzes the terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides YP_002318004.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate YP_002318008.1 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_002318009.1 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_002318012.1 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_002318014.1 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_002318018.1 3'-5' exoribonuclease specific for small oligoribonuclotides YP_002318026.1 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_002318028.1 catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; also known as acetolactate synthase large subunit YP_002318029.1 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_002318030.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis YP_002318035.1 stimulates the release of release factors 1 and 2 from the ribosome after hydrolysis of the ester bond in peptidyl-tRNA has occurred; GDP/GTP-binding protein YP_002318080.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_002318083.1 catalyzes the formation of cysteine from 3-O-acetyl-L-serine and hydrogen sulfide YP_002318085.1 in Escherichia coli this enzyme catalyzes the SAM-dependent methylation of U1939 in the 23S ribomal RNA; binds an iron-sulfur cluster [4Fe-4S] YP_002318088.1 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_002318092.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate YP_002318093.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine YP_002318097.1 activates fatty acids by binding to coenzyme A YP_002318098.1 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_002318104.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_002318106.1 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_002318107.1 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_002318108.1 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_002318110.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_002318130.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma 54 factor is responsible for the expression of enzymes involved in nitrogen assimilation and metabolism; the rhizobia often have 2 copies of this sigma factor; in Rhizobium etli RpoN1 shown to be involved in the assimilation of several nitrogen and carbon sources during free-living aerobic growth and RpoN2 is involved in symbiotic nitrogen fixation; in Bradyrhizobium both RpoN1 and N2 are functional in free-living and symbiotic conditions, rpoN1 gene was regulated in response to oxygen YP_002318133.1 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_002318134.1 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_002318135.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_002318159.1 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_002318160.1 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate YP_002318161.1 catalyzes the formation of inosine from adenosine YP_002318168.1 catalyzes the oxidation of tricarballylate to cis-aconitate; FAD-dependent; required for the utilization of tricarballylate as a carbon and energy source by S. enterica YP_002318180.1 catalyzes the formation of tetrahydropteroyl-L-glutamate and methionine from L-homocysteine and 5-methyltetrahydropteroyltri-L-glutamate YP_002318190.1 Catalyzes the rate-limiting step in dNTP synthesis YP_002318192.1 Catalyzes the rate-limiting step in dNTP synthesis YP_002318198.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen YP_002318199.1 NuoCD; NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; subunits NuoCD, E, F, and G constitute the peripheral sector of the complex; in Escherichia coli this gene encodes a fusion protein of NuoC and NuoD that are found separate in other organisms YP_002318200.1 Catalyzes the transfer of electrons from NADH to quinone YP_002318202.1 Catalyzes the transfer of electrons from NADH to quinone YP_002318203.1 Catalyzes the transfer of electrons from NADH to quinone YP_002318204.1 Catalyzes the transfer of electrons from NADH to quinone YP_002318207.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_002318208.1 Catalyzes the transfer of electrons from NADH to quinone YP_002318210.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate YP_002318226.1 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_002318232.1 Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis YP_002318242.1 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_002318256.1 DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium YP_002318262.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not YP_002318265.1 carries the fatty acid chain in fatty acid biosynthesis YP_002318272.1 Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5) YP_002318273.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_002318274.1 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_002318275.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP YP_002318276.1 An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis YP_002318279.1 catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins YP_002318285.1 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_002318291.1 member of the betaine, carnitine, choline transporter (BCCT) family; unknown function YP_002318302.1 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_002318303.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_002318304.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_002318305.1 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_002318311.1 Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate YP_002318312.1 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_002318325.1 catalyzes the formation of dUMP from dUTP YP_002318327.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate YP_002318345.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_002318392.1 malate dehydrogenase; catalyzes the oxidation of malate to oxaloacetate YP_002318393.1 catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine YP_002318394.1 catalyzes the formation of betaine from betaine aldehyde YP_002318395.1 HTH-type; bet1; Repressor involved in choline regulation of the bet genes YP_002318397.1 proton-motive-force-driven choline transporter YP_002318406.1 predicted polysaccharide polymerase involved in biofilm formation; required for the synthesis of the beta-1,6-N-acetylglucosamine polysaccharide; PgaC; in Yersinia the HmsR protein is an inner membrane protein YP_002318408.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_002318422.1 catalyzes the formation of L-aspartate to iminoaspartate in NAD(+) biosynthesis YP_002318428.1 catalyzes the formation of glutamate from glutamine YP_002318438.1 one of two methionine synthases in Escherichia coli; MetH catalyzes a methyl transfer reaction from methyltetrahydrofolate to homocysteine to create methionine; requires zinc for activity YP_002318440.1 catalyzes the formation of pyruvate from serine YP_002318447.1 Fep; Cbt; Cbr; FeuB; FepA; PfeA; IroN; BfeA; outer membrane receptor of ferric enterobactin and colicins B and D; interacts with the TonB-ExbBD complex which catalyzes the translocation of the siderophore to the periplasmic space YP_002318455.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate YP_002318463.1 class II; LysRS2; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri, LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1 YP_002318465.1 with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP YP_002318472.1 Catalyzes the first step in the glyoxalate cycle, which converts lipids to carbohydrates YP_002318476.1 UreA, with UreB and UreC catalyzes the hydrolysis of urea into ammonia and carbon dioxide; nickel metalloenzyme; accessory proteins UreD, UreE, UreF, and UreG are necessary for assembly of the metallocenter YP_002318478.1 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_002318479.1 involved in the assembly of the urease metallocenter; possible nickel donor YP_002318487.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_002318491.1 converts 2-oxoglutarate to glutamate; in Escherichia coli this enzyme plays a role in glutamate synthesis when the cell is under energy restriction; uses NADPH; forms a homohexamer YP_002318509.1 specific inhibitor of chromosomal initiation of replication in vitro; binds the three 13-mers in the origin (oriC) to block initiation of replication; also controls genes involved in arginine transport YP_002318531.1 Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A) YP_002318532.1 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis YP_002318534.1 catalyzes the formation of arginosuccinate from citrulline and aspartate in arginine biosynthesis YP_002318555.1 catalyzes the transamination of 2-N-succinylornithine and alpha-ketoglutarate into 2-N-succinylglutamate semialdehyde and glutamate; also functions as the catabolic acetylornithine aminotransferase catalyzing the formation of 2-N-acetylglutamate semialdehyde and glutamate from 2-N-acetylornithine and alpha-ketoglutarate YP_002318566.1 catalyzes the formation of 2,5-dioxopentanoate from 5-dehydro-4-deoxy-D-glucarate YP_002318574.1 catalyzes the conversion of ferulic acid to feruloyl-CoA YP_002318576.1 catalyzes the conversion of feruloyl-CoA to vanillin and acetyl-CoA YP_002318600.1 catalyzes the formation of inosine from adenosine YP_002318603.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids YP_002318605.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. YP_002318692.1 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_002318694.1 Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine YP_002318695.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis YP_002318698.1 complexes with cyclic AMP and binds to specific DNA sites near the promoter to regulate the transcription of several catabolite-sensitive operons YP_002318705.1 catalyzes the N2-methyl guanosine modification of the G2445 residue of 23S rRNA YP_002318707.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis YP_002318711.1 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_002318721.1 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_002318725.1 catalyzes the degradation of 2-hydro-1,2-dihydroxy benzoate to catechol YP_002318739.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides YP_002318784.1 catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA YP_002318800.1 This protein performs the mismatch recognition step during the DNA repair process YP_002318892.1 catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA YP_002318893.1 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA YP_002318894.1 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation YP_002318940.1 catalyzes the formation of protocatechuate from 4-hydroxybenzoate YP_002318947.1 catalyzes the degradation of phosphonoacetaldehyde to acetaldehyde and phosphate YP_002318956.1 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_002318957.1 converts 3-hydroxyadipyl-CoA to beta-ketoadipyl-CoA in phenylacetate degradation YP_002318958.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_002318959.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_002318969.1 Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates YP_002319024.1 catalyzes the reversible formation of 2'-(5''-triphosphoribosyl)-3'dephospho-CoA from 3-dephospho-CoA YP_002319025.1 acyl carrier protein of malonate decarboxylase YP_002319026.1 The beta subunit catalyzes the decarboxylation of the malonyl moiety on coenzyme A YP_002319028.1 Catalyzes the transfer of 2-(5''-triphosphoribosyl)-3'-dephosphocoenzyme-A to the apo-acyl carrier protein of malonate dehydrogenase to form holo-acyl carrier protein YP_002319044.1 catalyzes the conversion of taurine (2-aminoethanesulfonate) to sulfite and aminoacetaldehyde concurrently with the conversion of alpha-ketoglutarate to succinate and carbon dioxide; non-heme iron oxidase; allows the use of taurine as an alternative sulfur source; forms homodimers YP_002319066.1 broad specificity; family IV; in Corynebacterium glutamicum this protein can use glutamate, 2-aminobutyrate, and aspartate as amino donors and pyruvate as the acceptor YP_002319071.1 catalyzes the formation of succinyldiaminopimelate from N-succinyl-2-amino-6-ketopimelate YP_002319073.1 non-folate utilizing enzyme, catalyzes the production of beta-formyl glycinamide ribonucleotide from formate, ATP, and beta-GAR and a side reaction producing acetyl phosphate and ADP from acetate and ATP; involved in de novo purine biosynthesis YP_002319081.1 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_002319118.1 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_002319125.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_002319126.1 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_002319132.1 catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs YP_002319134.1 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_002319138.1 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_002319143.1 involved in the import of serine and threonine coupled with the import of sodium YP_002319149.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_002319151.1 class II aldolase; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis and gluconeogenesis YP_002319156.1 glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA YP_002319174.1 Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine YP_002319178.1 Catalyzes the formation of (d)CDP from ATP and (d)CMP YP_002319179.1 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_002319182.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase YP_002319187.1 catalyzes the formation of malate from glyoxylate and acetyl-CoA YP_002319204.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_002319206.1 regulator of RNase E; increases half-life and abundance of RNAs; interacts with RNase E possibly inhibiting catalytic activity YP_002319214.1 involved in the maturation of iron-sulfur cluster-containing proteins YP_002319251.1 catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive YP_002319255.1 catalyzes the formation of lipid A disaccharide from UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate, lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM YP_002319268.1 catalyzes the conversion of O-succinylhomoserine into homocysteine YP_002319271.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_002319279.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_002319280.1 involved in methylation of ribosomal protein L3 YP_002319281.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_002319285.1 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_002319313.1 catalyzes the formation of fumarate from aspartate YP_002319323.1 catalyzes the formation of acetoacetate from 3-hydroxybutyrate YP_002319332.1 catalyzes the formation of catechol from anthranilate YP_002319343.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate YP_002319345.1 possibly involved in transport of pyrroloquinoline quinone transport YP_002319346.1 Required in the synthesis of PPQ, but its exact function is unknown YP_002319347.1 with PqqC converts a biosynthetic intermediate to pyrroloquinoline quinone YP_002319479.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate YP_002319531.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate YP_002319540.1 catalyzes the thiolytic cleavage of beta-ketoadipyl-CoA to succinate and acetyl-CoA YP_002319545.1 catalyzes the formation of phenylacetaldehyde from 2-phenylethylamine YP_002319573.1 catalyzes the dehydration of 3-dehydroquinate to form 3-dehydroshikimate in aromatic amino acid biosynthesis YP_002319580.1 catalyzes the thiolytic cleavage of beta-ketoadipyl-CoA to succinate and acetyl-CoA YP_002319583.1 4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MEP cytidylyltransferase; MCT; catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; forms homodimers YP_002319586.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_002319587.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_002319588.1 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_002319596.1 catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, tyrosine sensitive YP_002319599.1 involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation; binds to the N-terminal domain of the chaperone ClpA YP_002319601.1 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_002319604.1 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway YP_002319605.1 threonine deaminase; threonine dehydratase; in Escherichia coli, IlvA is part of the isoleucine biosynthetic pathway YP_002319626.1 catalyzes the formation of N-acetyl-l-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine YP_002319659.1 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_002319662.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis YP_002319663.1 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_002319664.1 adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis YP_002319668.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate YP_002319671.1 Rrf; Frr; ribosome-recycling factor; release factor 4; RF4; recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G; A GTPase-dependent process results in release of 50S from 70S; inhibited by release factor RF-1; essential for viability; structurally similar to tRNAs YP_002319672.1 Catalyzes the phosphorylation of UMP to UDP YP_002319673.1 catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit YP_002319677.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation YP_002319679.1 catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate YP_002319681.1 catalyzes the oxidative deamination of D-amino acids YP_002319684.1 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_002319695.1 MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis YP_002319708.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis YP_002319720.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_002319731.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_002319732.1 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_002319740.1 P-type ATPase involved in magnesium influx YP_002319765.1 catalyzes the interconversion of chorismate to prephenate YP_002319786.1 Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group YP_002319788.1 catalyzes a two-step reaction, first charging a glutamine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_002319790.1 catalyzes the formation of 2,3=diacylglucosamine 1-phosphate from UDP-2,3=diacylglucosamine YP_002319791.1 catalyzes the reduction of nitroaromatic compounds such as nitrofurazone, quinones and the anti-tumor agent CB1954; NAD(P)H-dependent; oxygen insensitive YP_002319794.1 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_002319809.1 catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate YP_002319820.1 One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions YP_002319821.1 catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions YP_002319834.1 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_002319847.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_002319853.1 converts protoheme IX and farnesyl diphosphate to heme O YP_002319854.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_002319855.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_002319856.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_002319864.1 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_002319866.1 methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype YP_002319869.1 involved in de novo purine biosynthesis YP_002319870.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis YP_002319938.1 catalyzes the formation of pyruvate and beta-alanine from L-alanine and 3-oxopropanoate YP_002319944.1 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_002319945.1 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_002319951.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_002319953.1 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_002319958.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate YP_002319961.1 enables ATP-dependent unwinding of double stranded RNA as a component of the RNA degradosome, a multi-enzyme complex important in RNA processing and messenger RNA degradation YP_002319964.1 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_002319967.1 functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate YP_002319974.1 catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate and catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis YP_002319978.1 involved in the transport of C4-dicarboxylates across the membrane YP_002319981.1 catalyzes the phosphorylation of NAD to NADP YP_002320005.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_002320086.1 catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in queuosine biosynthesis YP_002320095.1 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_002320096.1 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_002320101.1 catalyzes the conversion of NADPH to NADH YP_002320102.1 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_002320103.1 functions in fatty acid oxidation; converts acyl-CoA and FAD to FADH2 and delta2-enoyl-CoA YP_002320106.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine YP_002320112.1 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate YP_002320113.1 catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template; phosphohydrolase activities include hydrolysis of pyrophosphate, 5'-nucleoside tri- and diphosphates, NADP, and 2'-AMP with the production of Pi, metal-dependent phosphodiesterase activity for 2',3'-cAMP, 2',3'-cGMP, and 2',3'-cCMP, and hydrolysis 2',3'-cyclic substrates with the formation of 2'-nucleotides and 3'-nucleotides; these phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases YP_002320120.1 catalyzes the conversion of 4-Hydroxybenzoate into 3-octaprenyl-4-hydroxybenzoate, as part of the ubiquinone biosynthesis pathway YP_002320128.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate YP_002320129.1 involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water YP_002320139.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III YP_002320147.1 catalyzes the formation of histamine from L-histidine YP_002320149.1 bifunctional 2,3-dihydroxybenzoate-AMP ligase/S-dihydroxybenzoyltransferase; activates the carboxylate group of 2,3-dihydroxy-benzoate forming (2,3-dihydroxybenzoyl)adenylate then catalyzes the acylation of holo-entB with 2,3-dihydroxy-benzoate adenylate YP_002320187.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_002320190.1 RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome YP_002320203.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_002320204.1 HflD; UPF0274; in Escherichia coli this protein is peripherally associated with the membrane and appears to act with lambda CII protein; in Haemophilus influenzae a knockout of the HI0638 gene affected paracytosis YP_002320205.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_002320208.1 SohB; periplasmic protein; member of the peptidase S49 family YP_002320209.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation YP_002320218.1 catalyzes the reversible formation of diaminobutyrate and 2-oxoglutarate from glutamate and L-aspartic beta-semialdehyde YP_002320226.1 transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA YP_002320229.1 Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway YP_002320239.1 Yersinia-type crispr-associated helicase YP_002320272.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis YP_002320273.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_002320276.1 catalyzes the formation of 3-phospho-D-glyceroyl phosphate from D-glyceraldehyde 3-phosphate; involved in growth under gluconeogenic conditions and in glycolytic activity at high ATP concentrations in Corynebacterium; NAD and NADP dependent YP_002320279.1 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_002320289.1 involved in the de novo synthesis of pyridoxine (Vitamin B6) YP_002320292.1 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_002320296.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_002320299.1 catalyzes the formation of oxaloacetate from L-aspartate YP_002320301.1 catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP) YP_002320311.1 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway YP_002320322.1 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_002320323.1 dGTPase family type 3 subfamily, presumably hydrolyzes dGTP to deoxyguanosine and triphosphate YP_002320324.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_002320325.1 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_002320330.1 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_002320333.1 catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate YP_002320335.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates YP_002320342.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_002320352.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine YP_002320367.1 involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate YP_002320371.1 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_002320394.1 putative metalloprotease YP_002320400.1 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is essential for growth YP_002320401.1 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_002320406.1 catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using GTP YP_002320407.1 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_002320412.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate YP_002320422.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers YP_002320424.1 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_002320439.1 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_002320443.1 Catalyzes the only substrate-level phosphorylation in the TCA cycle YP_002320444.1 catalyzes the interconversion of succinyl-CoA and succinate YP_002320445.1 E3 component of pyruvate and 2-oxoglutarate dehydrogenase complex; catalyzes the oxidation of dihydrolipoamide to lipoamide YP_002320447.1 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_002320448.1 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_002320449.1 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_002320459.1 lipoyl/octanoyltransferase; catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein YP_002320467.1 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_002320470.1 involved in the peptidyltransferase reaction during translation YP_002320483.1 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_002320582.1 Hsp31 stabilizes early unfolding protein intermediates under severe heat stress YP_002320585.1 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_002320590.1 catalyzes the formation of serine from phosphoserine; also has phosphoserine:homoserine phosphotransferase activity YP_002320591.1 catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite YP_002320595.1 Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell YP_002320597.1 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_002320598.1 functions in MreBCD complex in some organisms YP_002320600.1 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_002320601.1 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_002320606.1 in Escherichia coli SbmA is involved in uptake of microcin J25; functions along with FhuA, TonB, and ExbB/D in this capacity; in Sinorhizobium meliloti, BacA is essential and required for symbiosis; defects appear to affect the cell envelope YP_002320621.1 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_002320633.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_002320647.1 homopentamer; channel that opens in response to pressure or hypoosmotic shock YP_002320666.1 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_002320674.1 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_002320681.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis YP_002320685.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_002320704.1 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_002320715.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_002320716.1 catalyzes the ATP-dependent addition of AMP to a subunit of glutamine synthetase; also catalyzes the reverse reaction - deadenylation; adenylation/deadenylation of glutamine synthetase subunits is important for the regulation of this enzyme YP_002320718.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step YP_002320721.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_002320723.1 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_002320724.1 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_002320734.1 putative nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ; the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription YP_002320741.1 Catalyzes the oxidation of dihydrolipoamide to lipoamide YP_002320752.1 hydrolyzes P(1),P(4)-bis(5'-adenosyl) tetraphosphate to form 2 ADP YP_002320753.1 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_002320755.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_002320777.1 catalyzes the oxidation of malate to oxaloacetate YP_002320780.1 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_002320786.1 Catalyzes the transfer of the phosphoribosyl moiety from 5-phospho--D-ribosyl-1-pyrophosphate (PRib-PP) to the 6-oxo-guanine and -xanthine YP_002320807.1 is a component of the macrolide binding site in the peptidyl transferase center YP_002320808.1 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_002320809.1 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_002320810.1 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_002320811.1 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_002320812.1 smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group have the motif YP_002320813.1 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_002320814.1 late assembly protein YP_002320815.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7 YP_002320816.1 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_002320817.1 binds 5S rRNA along with protein L5 and L25 YP_002320818.1 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_002320819.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_002320820.1 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_002320821.1 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_002320822.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_002320823.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_002320824.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_002320825.1 one of the stabilizing components for the large ribosomal subunit YP_002320826.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_002320827.1 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_002320828.1 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_002320829.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_002320830.1 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_002320831.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_002320832.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_002320833.1 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_002320834.1 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_002320840.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_002320844.1 PlsB; catalyzes the formation of 1-acyl-sn-glycerol 3-phosphate by transfering the acyl moiety from acyl-CoA YP_002320847.1 catalyzes branch migration in Holliday junction intermediates YP_002320859.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate YP_002320860.1 catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate YP_002320861.1 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis YP_002320862.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate YP_002320870.1 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_002320871.1 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_002320882.1 catalyzes the formation of succinate and glutamate from N(2)-succinylglutamate in arginine catabolism YP_002320883.1 catalyzes the hydrolysis of 2-N-succinylarginine into 2-N-succinylornithine, ammonia and carbon dioxide in arginine degradation YP_002320886.1 catalyzes the transamination of 2-N-succinylornithine and alpha-ketoglutarate into 2-N-succinylglutamate semialdehyde and glutamate; also functions as the catabolic acetylornithine aminotransferase catalyzing the formation of 2-N-acetylglutamate semialdehyde and glutamate from 2-N-acetylornithine and alpha-ketoglutarate YP_002320904.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_002320909.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs YP_002320910.1 acts as a molecular chaperone to fold and export lipase A YP_002320912.1 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_002320913.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_002320914.1 Essential for efficient processing of 16S rRNA YP_002320915.1 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_002320923.1 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_002320924.1 Essential for recycling GMP and indirectly, cGMP YP_002320925.1 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_002320936.1 glutamate synthase is composed of subunits alpha and beta; beta subunit is a flavin adenine dinucleotide-NADPH dependent oxidoreductase; provides electrons to the alpha subunit, which binds L-glutamine and 2-oxoglutarate and forms L-glutamate YP_002320937.1 catalyzes the formation of glutamate from glutamine and alpha-ketoglutarate YP_002320939.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis YP_002320940.1 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis YP_002320949.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_002320957.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_002320968.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence YP_002320973.1 part of two-component system EnvZ/OmpR; regulates transcription of outer membrane porin genes ompC/F; under high osmolarity EnvZ functions as kinase/phosphotransferase and phosphorylates OmpR; the result is increased expression of ompC and repression of ompF; also functions in regulation of other genes; forms dimers upon phosphorylation YP_002320978.1 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_002320979.1 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_002320981.1 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_002320986.1 catalyzes the formation of O-phospho-L-homoserine from L-homoserine YP_002320987.1 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_002321037.1 member of the sodium:solute symporter family; cotranscribed with the acs gene which encodes acetyl coenzyme A synthase; mutations affect acetate uptake YP_002321049.1 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_002321057.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_002321065.1 E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC YP_002321070.1 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_002321073.1 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_002321074.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_002321075.1 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_002321076.1 catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione YP_002321079.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate YP_002321095.1 catalyzes the formation of S-ureidoglycolate and urea from allantoate YP_002321096.1 catalyzes the formation of glyoxylate from (S)-ureidoglycolate YP_002321097.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_002321111.1 catalyzes the transfer of an amino moiety YP_002321118.1 catalyzes the decarboxylation of phosphatidyl-L-serine to phosphatidylethanoleamine YP_002321120.1 catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate YP_002321121.1 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine YP_002321127.1 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_002321128.1 Regulates rRNA biosynthesis by transcriptional antitermination YP_002321132.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source YP_002321144.1 catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway YP_002321146.1 catalyzes the degradation of histidine to urocanate and ammmonia YP_002321147.1 catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism YP_002321165.1 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_002321183.1 catalyzes the reduction of 2,5-diketo-D-gluconic acid to 2-keto-L-gulonic acid YP_002321186.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_002321188.1 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_002321193.1 catalyzes the formation of oxaloacetate from phosphoenolpyruvate YP_002321198.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis