-- dump date 20140619_011305 -- class Genbank::CDS -- table cds_note -- id note YP_003104817.1 catalyzes the formation of 2,3-dihydroxybenzoate from 2,3-dihydro-2,3-dihydroxybenzoate; involved in the biosynthesis of siderophores, enterobactin, bacillibactin or vibriobactin YP_003104819.1 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_003104860.1 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_003104881.1 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_003104885.1 catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine YP_003104888.1 catalyzes the formation of pyruvate and glyoxylate from 4-hydroxy-2-oxoglutarate; or pyruvate and D-glyceraldehyde 3-phosphate from 2-dehydro-3-deoxy-D-glyconate 6-phosphate YP_003104893.1 part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE YP_003104900.1 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia YP_003104912.1 catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate YP_003104920.1 membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export YP_003104921.1 One of three proteins involved in switching the direction of the flagellar rotation YP_003104925.1 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_003104927.1 FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod; Bradyrhizobium have one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella YP_003104928.1 involved in type III protein export during flagellum assembly YP_003104948.1 with FlgF and C makes up the proximal portion of the flagellar basal body rod; Bradyrhizobium have one thick flagellum and several thin flagella; the proteins in this cluster are associated with the thin flagella YP_003104949.1 with FlgF and B makes up the proximal portion of the flagellar basal body rod YP_003104950.1 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_003104951.1 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_003104952.1 required for the assembly of the flagellar basal body P-ring; Bradyrhizobium japonicum has two types of flagella, a single thick flagella and a few thin flagella; the protein in this cluster is associated with the thin flagella YP_003104953.1 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_003104955.1 part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod YP_003104957.1 FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus YP_003104982.1 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_003104983.1 May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine YP_003104984.1 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_003104987.1 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_003104990.1 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_003104991.1 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_003104995.1 catalyzes the formation of FMN from riboflavin and the formation of FAD from FMN; in Bacillus the ribC gene has both flavokinase and FAD synthetase activities YP_003104996.1 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; some organisms carry two different copies of this enzyme YP_003105010.1 catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A YP_003105011.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate YP_003105013.1 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_003105017.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_003105018.1 converts 3-hydroxyadipyl-CoA to beta-ketoadipyl-CoA in phenylacetate degradation YP_003105068.1 reduces nitrous oxide to nitrogen YP_003105085.1 catalyzes the formation of 2-octaprenylphenol from 3-octaprenyl-4-hydroxybenzoate YP_003105093.1 upregulated by FixLJ/FixK under oxygen limitation; involved in regulation of genes involved in carbon and amino acid metabolism YP_003105107.1 in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF YP_003105108.1 Catalyzes the rate-limiting step in dNTP synthesis YP_003105109.1 B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE YP_003105113.1 blocks the formation of polar Z-ring septums YP_003105115.1 works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell YP_003105132.1 catalyzes the formation of glutamate from glutamine YP_003105133.1 inactive form YP_003105143.1 catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate YP_003105151.1 Enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine YP_003105152.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_003105179.1 Enables the production of acetyl-CoA by phosphorylating acetate in the presence of ATP and a divalent cation YP_003105189.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_003105225.1 catalyzes the formation of 5-aminovulinate from (S)-4-amino-5-oxopentanoate YP_003105238.1 this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress YP_003105245.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_003105246.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_003105276.1 catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis YP_003105278.1 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_003105279.1 catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate YP_003105280.1 DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium YP_003105281.1 catalyzes the formation of 8-amino-7-oxononanoate from 6-carboxyhexanoyl-CoA and L-alanine YP_003105286.1 forms a trimer; related to eukaryotic protein gephyrin; functions during molybdenum cofactor biosynthesis YP_003105289.1 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_003105290.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_003105291.1 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_003105292.1 subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_003105293.1 subunit F 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_003105294.1 subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_003105315.1 E3 component of the branched-chain alpha-keto acid dehydrogenase complex; catalyzes the oxidation of dihydrolipoamide to lipoamide YP_003105347.1 rhizobial iron regulator; in Sinorhizobium meliloti mutations in this gene affect the expression of a number of iron-responsive operons YP_003105351.1 catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit YP_003105366.1 catalyzes branch migration in Holliday junction intermediates YP_003105367.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source YP_003105368.1 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_003105375.1 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_003105377.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_003105380.1 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_003105381.1 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_003105382.1 catalyzes the opening and hydrolysis of the beta-lactam ring of beta-lactam antibiotics such as penicillins and cephalosporins YP_003105383.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function YP_003105385.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis YP_003105386.1 Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides YP_003105387.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX YP_003105390.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_003105395.1 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_003105396.1 involved in swarmer-to-stalked cell differentiation in Caulobacter crescentus; catalyzes the condensation of two GTP molecules to form the secondary messenger cyclic di-GMP (c-di-GMP); upon phosphorylation of domain D1 the protein dimerizes; presumably this allows the two GTP-bound GGDEF (diguanylate cyclase) domains to catalyze the condensation reaction; allosterically inhibited by c-di-GMP YP_003105400.1 Regulates the synthesis of nucleoside triphosphates for nucleic acid synthesis, CTP for lipid synthesis, and GTP for protein elongation YP_003105401.1 involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function YP_003105421.1 catalyzes the thiolytic cleavage of beta-ketoadipyl-CoA to succinate and acetyl-CoA YP_003105426.1 catalyzes the formation of protocatechuate from 4-hydroxybenzoate YP_003105430.1 Catalyzes the cycloisomerization of cis,cis-muconate YP_003105440.1 part of the UgpABCE glycerol-3-phosphate uptake system YP_003105451.1 proposed role in polysaccahride synthesis YP_003105472.1 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_003105473.1 involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth YP_003105480.1 laccase; copper-stimulated phenoloxidase and ferroxidase which may be involved in copper detoxification YP_003105495.1 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_003105498.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine YP_003105499.1 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_003105500.1 catalyzes the transfer of a methylene carbon from the methylamine-loaded GcvH protein to tetrahydrofolate, causing the release of ammonia and the generation of reduced GcvH protein YP_003105535.1 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_003105537.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides YP_003105542.1 crystal structure of protein from Xanthomonas shows pentameric toroidal structure; physiological function is unknown YP_003105550.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_003105551.1 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate YP_003105553.1 catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate YP_003105554.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate YP_003105555.1 catalyzes the formation of L-proline from pyrroline-5-carboxylate YP_003105564.1 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_003105568.1 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_003105574.1 with NikABCD is involved with nickel transport into the cell YP_003105575.1 with NikABCE is involved in nickel transport into the cell YP_003105576.1 with NikABDE is involved in nickel transport into the cell YP_003105577.1 with NikACDE is involved in nickel transport into the cell YP_003105579.1 Inhibits transcription at high concentrations of nickel YP_003105586.1 catalyzes the interconversion of D-glucuronate to D-fructuronate or D-galacturonate to D-tagaturonate; functions in glucuronic and galacturonic metabolism YP_003105588.1 catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate YP_003105591.1 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_003105592.1 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_003105637.1 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_003105641.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate YP_003105642.1 catalyzes the interconversion of ribose 5-phosphate to ribulose 5-phosphate; enzyme from E. coli shows allose 6-phosphate isomerase activity YP_003105643.1 class II aldolase; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis and gluconeogenesis YP_003105644.1 catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate YP_003105655.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D YP_003105659.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_003105661.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_003105669.1 catalyzes the formation of L-proline from L-ornithine YP_003105679.1 produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine YP_003105694.1 catalyzes the oxidative deamination of D-amino acids YP_003105696.1 catalyzes the formation of pyruvate and beta-alanine from L-alanine and 3-oxopropanoate YP_003105698.1 catalyzes the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate YP_003105699.1 catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway YP_003105700.1 catalyzes the degradation of histidine to urocanate and ammmonia YP_003105702.1 catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism YP_003105704.1 catalyzes the transamination of D-amino acids and their alpha-keto acids YP_003105708.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-galactonate 6-phosphate; functions in galactonate metabolism YP_003105710.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate YP_003105717.1 intracellular enzymes acting on low molecular weight D-amino acid amides, esters and oligopeptides containing D-amino acids; these proteases release the N-terminal D-amino acid from a peptide, and show higher affinity for D-Ala, D-Ser or D-Thr; no preference for the stereochemistry of the second amino acid YP_003105736.1 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_003105754.1 MarR family transcriptionnal regulator absent in other brucella, but present in ochrobactrum. YP_003105759.1 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_003105760.1 in Escherichia coli this inner membrane protein was found to anchor the periplasmic catalytic oxidoreductase YedY; sulfite oxidase activity not demonstrated; contains heme YP_003105774.1 catalyzed the formation of 2-ketoglutarate from 2-hydroxyglutarate YP_003105775.1 3'-5' exonuclease of DNA polymerase III YP_003105781.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_003105789.1 in Escherichia coli transcription of this gene is enhanced by polyamines YP_003105790.1 protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus; this enzyme also cleaves other RNA substrates YP_003105791.1 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_003105792.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_003105793.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate YP_003105796.1 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway YP_003105799.1 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_003105801.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_003105802.1 modifies the free amino group of the aminoacyl moiety of methionyl-tRNA(fMet) which is important in translation initiation; inactivation of this gene in Escherichia coli severely impairs growth YP_003105803.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_003105807.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_003105810.1 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_003105815.1 D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm YP_003105816.1 catalyzes the formation of methylglyoxal from glycerone phosphate YP_003105817.1 catalyzes the conversion of ATP and D-glucose to ADP and D-glucose 6-phosphate YP_003105819.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_003105820.1 catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate YP_003105821.1 likely pseudogene YP_003105823.1 in integrase region YP_003105824.1 in integrase region YP_003105825.1 in integrase region YP_003105836.1 catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine YP_003105838.1 Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone YP_003105839.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate YP_003105841.1 this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress YP_003105857.1 converts 3-hydroxyadipyl-CoA to beta-ketoadipyl-CoA in phenylacetate degradation YP_003105858.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_003105874.1 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia YP_003105899.1 FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus YP_003105900.1 membrane protein involved in the flagellar export apparatus YP_003105901.1 FliQ, with proteins FliP and FliR, forms the core of the central channel in the flagella export apparatus; Bradyrhizobium have one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum YP_003105902.1 acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod; Yersinia, Vibrio parahaemolyticus, Bradyrhizobium and other organisms have 2 copies of some flagellar genes; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella YP_003105903.1 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_003105904.1 acts as an activator or flagellin translation and may be required for filament secretion or assembly; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella YP_003105905.1 with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thin flagella YP_003105906.1 with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook YP_003105907.1 the hook connects flagellar basal body to the flagellar filament YP_003105911.1 a periplasmic protein that interacts with and stabilizes MotB; in Rhizobium, interactions between MotB and MotC at the periplasmic surface of the motor control the energy flux or the energy coupling that drives flagellar rotation YP_003105912.1 with MotA 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_003105914.1 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_003105919.1 with XylFH is part of the high affinity xylose ABC transporter YP_003105967.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_003105972.1 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_003105973.1 binds the polymerase to DNA and acts as a sliding clamp YP_003105974.1 Required for DNA replication; binds preferentially to single-stranded, linear DNA YP_003105975.1 ATP-dependent adenylate transferase, transfers adenyl moiety to the MoeD subunit of molybdopterin synthase YP_003105987.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_003105988.1 catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA YP_003105992.1 AcsA; in Sinorhizobium meliloti this enzyme is required for acetoacetate activation; similar to acetyl-CoA synthase YP_003105996.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis YP_003105997.1 Catalyzes the formation of (d)CDP from ATP and (d)CMP YP_003105998.1 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_003106005.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_003106006.1 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_003106009.1 catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis YP_003106010.1 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_003106030.1 catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate YP_003106041.1 DNA polymerase involved in damage-induced mutagenesis and translesion synthesis. It is not the major replicative DNA polymerase. YP_003106046.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming YP_003106054.1 4-alpha-hydroxytetrahydrobiopterin dehydratase activity; catalyzes the formation of (6R)-6-(L-erythro-1,2-dihydroxypropyl)-7, 8-dihydro-6H-pterin from (6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7, 8-tetrahydro-4a-hydroxypterin; functions in recycling tetrahydrobiopterin (BH4) in phenylalanine hydroxylase reaction YP_003106065.1 Catalyzes the conversion of citrate to isocitrate YP_003106066.1 ATP-binding protein; required for proper cytochrome c maturation YP_003106071.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis YP_003106083.1 catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate YP_003106093.1 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair YP_003106095.1 negatively supercoils closed circular double-stranded DNA YP_003106112.1 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_003106114.1 catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein YP_003106116.1 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate YP_003106117.1 This protein performs the mismatch recognition step during the DNA repair process YP_003106119.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_003106123.1 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_003106128.1 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_003106137.1 putative role in sulfur assimilation YP_003106141.1 with DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins; may act as a thermosensor YP_003106142.1 Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons YP_003106143.1 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_003106145.1 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_003106146.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_003106152.1 catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite YP_003106158.1 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_003106162.1 with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP YP_003106163.1 in Rhizobium meliloti this protein is involved in the synthesis of nodulation factors that are active on the roots of alfalfa; catalyzes formation of activated sulfate intermediate; converts ATP and sulfate to diphosphate and adenylylsulfate and then ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; the activated intermediate is transferred to the nodulation factors by NodH; may interact with NodP and NodQ; similar to the CysD and CysN proteins from EScherichia coli involved in cysteine biosynthesis YP_003106168.1 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_003106181.1 Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate YP_003106182.1 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_003106215.1 Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell YP_003106216.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_003106219.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_003106221.1 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_003106235.1 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_003106236.1 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori and Yersinia enterocolitica the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 UreC (alpha) and 3 UreAB (gamma/beta); in Brucella suis the urease encoded by this operon (one of two urease-encoding operons found in its genome) is involved with urease activity, optimum growth, resistance to low-pH killing in-vitro and persistence in-vivo, while the other operon does not seem to be active YP_003106237.1 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_003106238.1 involved in the assembly of the urease metallocenter; possible nickel donor YP_003106245.1 catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position YP_003106246.1 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_003106249.1 catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines YP_003106250.1 function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain YP_003106252.1 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_003106256.1 activates fatty acids by binding to coenzyme A YP_003106268.1 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_003106269.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation YP_003106270.1 becomes active under oxidative stress; four conserved cysteines bind a zinc atom when they are in the reduced state and the enzyme is inactive; oxidative stress results in oxidized cysteines, release of zinc, and binding of Hsp33 to aggregation-prone proteins; forms dimers and higher order oligomers YP_003106271.1 protein associated with Co2+ and Mg2+ efflux YP_003106272.1 catalyzes the conversion of O-succinylhomoserine and sulfide to homocysteine; second step in methionine biosynthesis YP_003106273.1 Catalyzes the deamination of dCTP to form dUTP YP_003106277.1 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_003106283.1 homopentamer; channel that opens in response to pressure or hypoosmotic shock YP_003106284.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine YP_003106294.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine YP_003106295.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate YP_003106317.1 Catalyzes the deamination of guanine YP_003106325.1 CcoO; FixO YP_003106326.1 CcoN; FixN YP_003106335.1 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_003106338.1 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_003106344.1 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_003106345.1 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_003106346.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B' is part of the membrane proton channel. YP_003106347.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. YP_003106348.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids YP_003106356.1 An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis YP_003106359.1 exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH YP_003106365.1 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_003106366.1 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_003106373.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_003106376.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis YP_003106377.1 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_003106378.1 catalyzes the formation of pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate YP_003106382.1 Catalyzes a key regulatory step in fatty acid biosynthesis YP_003106389.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_003106392.1 catalyzes the bidirectional exonucleolytic cleavage of DNA YP_003106397.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate YP_003106404.1 catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine YP_003106407.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_003106409.1 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_003106410.1 unwinds double stranded DNA YP_003106412.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_003106413.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_003106414.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_003106417.1 catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_003106418.1 carries the fatty acid chain in fatty acid biosynthesis YP_003106420.1 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_003106423.1 Essential for recycling GMP and indirectly, cGMP YP_003106428.1 converts protoheme IX and farnesyl diphosphate to heme O YP_003106430.1 involved in the insertion of copper into subunit I of cytochrome C oxidase YP_003106434.1 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_003106435.1 catalyzes the formation of O-phospho-L-homoserine from L-homoserine YP_003106436.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids YP_003106443.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_003106459.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_003106463.1 catalyzes the formation of glyoxylate from (S)-ureidoglycolate YP_003106495.1 catalyzes the interconversion of D-xylose to D-xylulose YP_003106500.1 catalyzes the formation of betaine from betaine aldehyde YP_003106501.1 catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine YP_003106502.1 HTH-type; bet1; Repressor involved in choline regulation of the bet genes YP_003106521.1 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia YP_003106555.1 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_003106561.1 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_003106570.1 Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile YP_003106582.1 catalyzes the formation of histidinol phosphate and 2-oxoglutarate from glutamate and imidazole acetol-phosphate YP_003106592.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis YP_003106593.1 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_003106597.1 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_003106599.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate YP_003106601.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_003106605.1 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_003106607.1 cytoplasmic enzyme involved in processing rRNA and some mRNAs; substrates typically have dsRNA regions; forms a homodimer; have N-terminal nuclease and C-terminal RNA-binding domains; requires magnesium as preferred ion for activity YP_003106608.1 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_003106609.1 involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA YP_003106613.1 Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides YP_003106621.1 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_003106625.1 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_003106626.1 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_003106631.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides YP_003106632.1 binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB YP_003106636.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate YP_003106641.1 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_003106651.1 glycinamide ribonucleotide transformylase; GAR Tfase; catalyzes the synthesis of 5'-phosphoribosylformylglycinamide from 5'-phosphoribosylglycinamide and 10-formyltetrahydrofolate; PurN requires formyl folate for the reaction unlike PurT which uses formate YP_003106652.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_003106680.1 catalyzes the formation of L-homocysteine from cystathionine YP_003106687.1 catalyzes the formation of catechol from salicylate YP_003106689.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate YP_003106692.1 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_003106695.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_003106696.1 Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate YP_003106698.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_003106699.1 catalyzes the formation of 3-hydroxy-2-methylpropanoate from 3-hydroxy-2-methylpropanoyl-CoA YP_003106705.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_003106708.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_003106709.1 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_003106710.1 Regulates rRNA biosynthesis by transcriptional antitermination YP_003106711.1 pyrophosphate-energized proton pump; pyrophosphate-energized inorganic pyrophosphatase; H+-PPase; can cleave pyrophosphate to two phosphates; can generate a proton motive force and drive pyrophosphate synthesis when PMF is sufficient YP_003106716.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY YP_003106717.1 FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs YP_003106718.1 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_003106730.1 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis YP_003106731.1 catalyzes the formation of putrescine from agmatine YP_003106732.1 forms a direct contact with the tRNA during translation YP_003106733.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_003106735.1 catalyzes the formation of L-methionine and acetate from O-acetyl-L-homoserine and methanethiol YP_003106742.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106743.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen YP_003106744.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106745.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106746.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106747.1 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_003106748.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106749.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106750.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106751.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106752.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106753.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_003106754.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106755.1 Catalyzes the transfer of electrons from NADH to quinone YP_003106761.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_003106764.1 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase YP_003106768.1 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_003106775.1 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_003106778.1 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_003106779.1 With PurL and PurQ catalyzes the conversion of formylglycinamide ribonucleotide, ATP, and glutamine to formylglycinamidine ribonucleotide, ADP, and glutamate in the fourth step of the purine biosynthetic pathway YP_003106780.1 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_003106785.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_003106787.1 Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA YP_003106789.1 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_003106790.1 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_003106791.1 Involved in the biosynthetic pathways of fatty acids, phospholipids, lipopolysaccharides, and oligosaccharides YP_003106802.1 catalyzes the formation of adenosylcobalamin from Ado-cobinamide-GDP and alpha-ribazole YP_003106803.1 catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole YP_003106812.1 dGTPase family type 2 subfamily; presumably hydrolyzes dGTP to deoxyguanosine and triphosphate YP_003106813.1 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_003106817.1 TatA; similar to TatE that is found in some proteobacteria; part of system that translocates proteins with a conserved twin arginine motif across the inner membrane; capable of translocating folded substrates typically those with bound cofactors; similar to a protein import system in thylakoid membranes YP_003106818.1 mediates the export of protein precursors bearing twin-arginine signal peptides YP_003106820.1 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_003106821.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate YP_003106822.1 catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins YP_003106827.1 part of the preprotein secretory system; forms a complex with protein 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_003106830.1 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_003106834.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_003106835.1 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_003106838.1 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_003106841.1 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_003106842.1 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_003106843.1 composes the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase complex, the enzyme that catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, which in turn controls the rate of fatty acid metabolism YP_003106844.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis YP_003106853.1 catalyzes the release of newly synthesized polypeptide chains at the stop codons UAA and UGA YP_003106860.1 catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr) YP_003106861.1 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_003106865.1 with SufCD activates cysteine desulfurase SufS YP_003106871.1 catalyzes the phosphorylation of NAD to NADP YP_003106881.1 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_003106891.1 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z YP_003106922.1 catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP) YP_003106923.1 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_003106925.1 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_003106928.1 responsible for transport of beta-1,2-glucans from the cytoplasm to periplasm; inner membrane ABC transporter permease component; Cgt; ChvA; NdvA YP_003106939.1 catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate YP_003106941.1 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway YP_003106943.1 catalyzes the reduction of 2 glutathione to glutathione disulfide; maintains high levels of reduced glutathione in the cytosol; involved in redox regulation and oxidative defense YP_003106946.1 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_003106947.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_003106949.1 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate YP_003106975.1 Catalyzes the rate-limiting step in dNTP synthesis YP_003106978.1 catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively YP_003106982.1 stationary phase protein that binds TrpR repressor YP_003106984.1 catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic YP_003106986.1 CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis YP_003107000.1 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_003107004.1 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_003107010.1 involved in the first step of tetrahydrofolate biosynthesis; catalyzes the formation of formate and 2-amino-4-hydroxy-6-(erythro-1,2, 3-trihydroxypropyl)dihydropteridine triphosphate from GTP and water; forms a homopolymer YP_003107011.1 PR-AMP cyclohydrolase; functions in histidine biosynthesis from PRPP; converts 1-(5-phosphoribosyl)-AMP to 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]imidazole-4- carboxyamide during the histidine biosynthesis pathway; binds zinc and magnesium; forms homodimers YP_003107028.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_003107029.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step YP_003107032.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA YP_003107034.1 negatively supercoils closed circular double-stranded DNA YP_003107041.1 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_003107045.1 binds and unfolds substrates as part of the ClpXP protease YP_003107046.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates YP_003107048.1 Stimulates the elongation of poly(A) tails YP_003107051.1 involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain YP_003107057.1 bifunctional enzyme involved in formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate and 2-C-methyl-D-erythritol 2,4-cyclodiphosphate and CMP from 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; binds divalent cations YP_003107061.1 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_003107063.1 E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide YP_003107064.1 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_003107068.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_003107069.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_003107070.1 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_003107074.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate YP_003107076.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate YP_003107077.1 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_003107078.1 MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis YP_003107080.1 Represses a number of genes involved in the response to DNA damage YP_003107082.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_003107083.1 type II enzyme; in Escherichia coli this enzyme forms a trimer of dimers which is allosterically inhibited by NADH and competitively inhibited by alpha-ketoglutarate; allosteric inhibition is lost when Cys206 is chemically modified which also affects hexamer formation; forms oxaloacetate and acetyl-CoA and water from citrate and coenzyme A; functions in TCA cycle, glyoxylate cycle and respiration; enzyme from Helicobacter pylori is not inhibited by NADH YP_003107084.1 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_003107086.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis YP_003107087.1 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_003107088.1 adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis YP_003107093.1 catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate YP_003107094.1 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_003107095.1 Catalyzes the phosphorylation of UMP to UDP YP_003107096.1 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_003107097.1 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_003107105.1 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_003107118.1 NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis YP_003107124.1 MDM; functions in conversion of succinate to propionate YP_003107129.1 converts L-glutamate to D-glutamate, a component of peptidoglycan YP_003107133.1 Converts isocitrate to alpha ketoglutarate YP_003107135.1 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_003107136.1 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_003107142.1 is a component of the macrolide binding site in the peptidyl transferase center YP_003107143.1 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_003107144.1 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_003107145.1 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_003107146.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_003107147.1 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_003107148.1 late assembly protein YP_003107149.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7 YP_003107150.1 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_003107151.1 binds 5S rRNA along with protein L5 and L25 YP_003107152.1 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_003107153.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_003107154.1 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_003107155.1 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_003107156.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_003107157.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_003107158.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_003107159.1 one of the stabilizing components for the large ribosomal subunit YP_003107160.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_003107161.1 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_003107162.1 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_003107163.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_003107164.1 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_003107165.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_003107166.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_003107167.1 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_003107168.1 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_003107169.1 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_003107170.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_003107171.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_003107172.1 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_003107175.1 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_003107176.1 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_003107177.1 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_003107178.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_003107179.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_003107180.1 binds directly to 23S ribosomal RNA YP_003107181.1 Modulates Rho-dependent transcription termination YP_003107182.1 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_003107183.1 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_003107202.1 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_003107204.1 type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese YP_003107205.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine YP_003107210.1 Regulatory factor involved in maltose metabolism YP_003107211.1 catalyzes the removal of N-terminal amino acids from peptides and arylamides; generally Co(II) however activity has been shown for some methionine aminopeptidases with Zn, Fe, or Mn YP_003107212.1 Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase YP_003107218.1 catalyzes the interconversion of precorrin-8X and hydrogenobyrinate YP_003107219.1 catalyzes the formation of precorrin-3 from precorrin-2 YP_003107225.1 CobD; CbiD in Salmonella; converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group YP_003107227.1 responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid YP_003107229.1 Catalyzes the methylation of C-1 in cobalt-precorrin-5 and the subsequent extrusion of acetic acid from the resulting intermediate to form cobalt-precorrin-6A YP_003107230.1 CobK/CbiJ; there are 2 pathways for cobalamin (vitamin B12) production, one aerobic (ex. P. denitrificans), the other anaerobic (ex. S. typhimurium); the CobK/CbiJ perform similar reactions in both; the anaerobic pathway includes the use of a chelated cobalt ion in order for ring contraction to occur; CobK thus converts precorrin 6 into dihydro-precorrin 6 while CbiJ converts cobalt-precorrin 6 into cobalt-deihydro-precorrin 6 YP_003107236.1 catalyzes the formation of adenosylcob(III)yrinic acid a,c-diamide from cob(I)yrinic acid a,c-diamide YP_003107237.1 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_003107239.1 catalyzes ATP-dependent phosphorylation of adenosylcobinamide to form adenosylcobinamide phosphate and the addition of guanosine monophosphate to adenosylcobinamide phosphate to form adenosylcobinamide-GDP YP_003107242.1 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_003107254.1 part of the preprotein secretory system; forms a complex with protein 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_003107283.1 UreA, with UreB and UreC, catalyzes the hydrolysis of urea to ammonia and carbon dioxide; nickel metalloenzyme; accessory proteins UreD, UreE, UreF, and UreG are necessary for assembly of the metallocenter YP_003107284.1 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori and Yersinia enterocolitica the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 UreC (alpha) and 3 UreAB (gamma/beta); in Brucella suis the urease encoded by this operon (one of two urease-encoding operons found in its genome) does not seem to be involved with urease activity, optimum growth, resistance to low-pH killing in-vitro and persistence in-vivo YP_003107285.1 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Yersinia enterocolitica the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 ureC (alpha) and 3 ureAB (gamma/beta) subunits YP_003107286.1 involved in the assembly of the urease metallocenter; possible nickel donor YP_003107292.1 catalyzes the ATP-dependent transport of cobalt YP_003107306.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis YP_003107311.1 involved in the de novo synthesis of pyridoxine (Vitamin B6) YP_003107315.1 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_003107317.1 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_003107326.1 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_003107344.1 methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype YP_003107347.1 this protein catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction; essential for DNA replication and repair of damaged DNA; similar to ligase LigB YP_003107351.1 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_003107352.1 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_003107355.1 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_003107356.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_003107357.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_003107358.1 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_003107360.1 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_003107361.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_003107363.1 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_003107382.1 catalyzes the formation of (E)-3-(methoxycarbonyl)pent-2-enedioate and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and trans-aconitate YP_003107383.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence YP_003107397.1 likely pseudogene YP_003107407.1 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_003107408.1 synthesizes RNA primers at the replication forks YP_003107411.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers YP_003107416.1 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_003107423.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate YP_003107431.1 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_003107439.1 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_003107455.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_003107460.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP YP_003107462.1 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_003107463.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_003107464.1 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_003107467.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis YP_003107477.1 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis YP_003107496.1 trpE(G); catalyzes the formation of anthranilate from chorismate and glutamine; contains both component I and II YP_003107515.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_003107543.1 Acts on the hydroxyl group at position 7 of the steroid frame YP_003107570.1 this tRNA synthetase lacks the tRNA anticodon interaction domain; instead this enzyme modifies tRNA(Asp) with glutamate by esterifying glutamate to the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of queosine generating a modified nucleoside at the first anticodon position of tRNAAsp; the modified tRNA does not bind elongation factor Tu YP_003107571.1 catalyzes the formation of malate from glyoxylate and acetyl-CoA YP_003107573.1 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_003107580.1 in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media YP_003107582.1 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_003107596.1 catalyzes the formation of dUMP from dUTP YP_003107604.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis YP_003107606.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_003107607.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate YP_003107610.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_003107617.1 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_003107622.1 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_003107623.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_003107624.1 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_003107626.1 catalyzes the formation of thiamine monophosphate from 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate and 4-methyl-5-(2-phosphono-oxyethyl)-thiazole YP_003107628.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_003107634.1 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_003107645.1 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_003107647.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_003107663.1 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway YP_003107664.1 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_003107666.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_003107675.1 part of the thiamine and TPP transport system tbpA-thiPQ YP_003107676.1 permease; with TbpA and ThiQ functions in transport of thiamine and thiamine pyrophosphate into the cell; repressed in presence of exogenous thiamine YP_003107680.1 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_003107689.1 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_003107692.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not YP_003107693.1 glycosyltransferase; polymerizes glycan strands in the peptidoglycan YP_003107695.1 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_003107698.1 biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate YP_003107713.1 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_003107714.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_003107715.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_003107716.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_003107717.1 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_003107719.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity YP_003107720.1 similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity YP_003107722.1 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_003107726.1 Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA YP_003107728.1 putative metalloprotease YP_003107731.1 involved in de novo purine biosynthesis YP_003107739.1 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_003107740.1 catalyzes the interconversion of chorismate to prephenate YP_003107745.1 catalyzes the formation of pyridoxal 5'-phosphate from pyridoxal YP_003107751.1 hydrolyzes diadenosine polyphosphate YP_003107755.1 SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA YP_003107757.1 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_003107758.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway YP_003107759.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis YP_003107760.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_003107764.1 involved in the peptidyltransferase reaction during translation YP_003107780.1 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_003107782.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. YP_003107783.1 Involved in ubiquinone biosynthesis YP_003107798.1 catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane YP_003107799.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis YP_003107800.1 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_003107801.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate YP_003107802.1 unknown function; YciI from Haemophilus influenzae presents crystal structure similarity to a muconolactone isomerase, but does not seem to catalyze any of the predicted reactions based on sequence and structure similarity YP_003107814.1 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_003107815.1 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_003107819.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate YP_003107820.1 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_003107827.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_003107828.1 Essential for efficient processing of 16S rRNA YP_003107829.1 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_003107831.1 Catalyzes the oxidation of dihydrolipoamide to lipoamide YP_003107835.1 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_003107836.1 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_003107838.1 Catalyzes the only substrate-level phosphorylation in the TCA cycle YP_003107839.1 catalyzes the interconversion of succinyl-CoA and succinate YP_003107840.1 Catalyzes the reversible oxidation of malate to oxaloacetate YP_003107845.1 involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate YP_003107848.1 Involved in cell division; probably involved in intracellular septation YP_003107854.1 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_003107858.1 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_003107870.1 catalyzes the formation of fumarate from aspartate YP_003107877.1 catalyzes the formation of methanethiol and 2-ocobutanoate from L-methionine YP_003107881.1 converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA YP_003107894.1 catalyzes the formation of arginine from (N-L-arginino)succinate YP_003107900.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_003107901.1 dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate YP_003107906.1 catalyzes the hydrolysis of pyrophosphate to phosphate YP_003107913.1 porin involved in osmoregulation allowing water to move into and out of the cell in response to osmotic pressure YP_003107926.1 required for 70S ribosome assembly YP_003107938.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis YP_003107939.1 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis YP_003107941.1 site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; XerD specifically exchanges the bottom strands; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs YP_003107942.1 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_003107952.1 catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_003107966.1 required for the assembly and function of the DNAX complex which are required for the assembly of the beta subunit onto primed DNA YP_003107969.1 glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA YP_003107970.1 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_003107971.1 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_003107973.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_003107975.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III YP_003107977.1 Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell YP_003107978.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate YP_003107979.1 catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis YP_003107980.1 3'-5' exonuclease of DNA polymerase III YP_003107981.1 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_003107982.1 F exclusion of bacteriophage T7; overproduction of this protein in Escherichia coli inhibits the F plasmid-mediated exclusion of bacteriophage T7; interacts with the F plasmid-encoded PifA protein; inner membrane protein YP_003107988.1 heat shock protein involved in degradation of misfolded proteins YP_003107989.1 heat shock protein involved in degradation of misfolded proteins YP_003107990.1 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_003107992.1 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_003107993.1 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_003107994.1 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_003107995.1 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis YP_003107996.1 catalyzes the formation of (R)-4'-phosphopantothenate in coenzyme A biosynthesis YP_003107998.1 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP YP_003108006.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine YP_003108016.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits YP_003108017.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis YP_003108019.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_003108020.1 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_003108026.1 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_003108029.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_003108031.1 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_003108032.1 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_003108034.1 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_003108035.1 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_003108037.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase YP_003108040.1 catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione YP_003108048.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation YP_003108056.1 binds DNA in a non-sequence-specific manner and is abundant during stationary phase; forms a DNA-protein crystal that protects DNA from damage; required for normal starvation response and long-term stationary viability; forms a homododecameric complex and sequesters iron which provides protection against oxidative damage YP_003108064.1 Transfers the fatty acyl group on membrane lipoproteins YP_003108066.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_003108067.1 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_003108068.1 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_003108069.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_003108071.1 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_003108072.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_003108073.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs YP_003108074.1 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_003108077.1 Catalyzes a key regulatory step in fatty acid biosynthesis YP_003108078.1 FabB, beta-Ketoacyl-ACP synthase I, KASI; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP YP_003108079.1 catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP YP_003108089.1 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_003108090.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_003108091.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase