-- dump date   	20140620_063718
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_561021.1	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_561023.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_561028.1	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_561029.1	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_561033.1	TusA; transfers sulfur to TusBCD complex; involved in thiouridation of U34 position of some tRNAs
YP_561034.1	FadA; fatty acid oxidation complex component beta; functions in a heterotetramer with FadB; similar to FadI2J2 complex; functions in beta-oxidation of fatty acids
YP_561035.2	includes enoyl-CoA hydratase, delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase, and 3-hydroxybutyryl-CoA epimerase; catalyzes the formation of an hydroxyacyl-CoA by addition of water on enoyl-CoA; also exhibits 3-hydroxyacyl-CoA epimerase and 3-hydroxyacyl-CoA dehydrogenase activities; forms a heterotetramer with FadA; similar to FadI2J2 complex; functions in beta-oxidation of fatty acids
YP_561036.1	catalyzes the hydrolysis of dipeptides with a proline at the C-terminal; also catalyzes the low efficiency hydrolysis of organophosphate di- and tri-esters
YP_561041.1	involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain
YP_561044.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_561050.1	catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis
YP_561054.1	AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate
YP_561069.1	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_561083.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_561101.1	catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway
YP_561103.1	catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism
YP_561104.1	catalyzes the degradation of histidine to urocanate and ammmonia
YP_561121.1	together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z
YP_561122.1	MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis
YP_561133.1	ATP-dependent adenylate transferase, transfers adenyl moiety to the MoeD subunit of molybdopterin synthase
YP_561137.1	PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP
YP_561138.1	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_561170.1	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_561173.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_561174.1	catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon
YP_561176.1	catalyzes the formation of (R)-4'-phosphopantothenate in coenzyme A biosynthesis
YP_561177.1	forms a complex with SecY and SecG; SecYEG forms a 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_561179.1	binds directly to 23S ribosomal RNA
YP_561180.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_561181.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_561182.1	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_561183.1	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_561184.1	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_561185.1	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_561186.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_561187.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_561188.1	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_561189.1	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_561190.1	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_561191.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_561192.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_561193.1	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_561194.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_561195.1	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_561196.1	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_561197.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_561198.1	one of the stabilizing components for the large ribosomal subunit
YP_561200.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_561201.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_561202.1	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_561203.1	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_561204.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_561205.1	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_561206.1	binds 5S rRNA along with protein L5 and L25
YP_561207.1	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_561208.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_561209.1	late assembly protein
YP_561210.1	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_561212.1	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_561213.1	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_561214.1	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_561215.1	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_561216.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_561228.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_561230.1	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_561237.1	Catalyzes the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle
YP_561244.1	ADP-sugar pyrophosphatase; catalyzes the formation of D-ribose 5-phosphate from ADP-ribose; can also act on ADP-mannose and ADP-glucose
YP_561247.1	catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA
YP_561248.1	catalyzes the formation of selenophosphate from selenide and ATP
YP_561250.1	negatively controls the expression of fabA and fabB, genes involved in the unsaturated fatty acid biosynthesis
YP_561251.1	catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs
YP_561252.1	converts L-glutamate to D-glutamate, a component of peptidoglycan
YP_561267.1	catalyzes the formation of oxaloacetate from phosphoenolpyruvate
YP_561269.1	catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate
YP_561270.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate
YP_561271.1	catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation
YP_561272.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_561273.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_561280.1	type I enzyme similar to type II but differentially regulated; major shikimate kinase in fully repressed cells; catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis
YP_561288.1	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_561303.1	catalyzes the phosphorylation of protein substrates at serine and threonine residues in vitro; specific substrate in vivo has not been identified yet; plays a role in long-term cell survival and expression of surface appendages
YP_561308.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_561321.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_561337.1	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_561338.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_561339.1	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_561341.1	FtsZ binding protein; synthetically lethal with a defect in the Min system; this protein is the first identified nucleoid occlusion factor which works along with the Min system to properly position the FtsZ ring assembly
YP_561342.1	catalyzes the formation of dUMP from dUTP
YP_561344.1	Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase
YP_561346.1	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_561347.1	catalyzes the formation of N-acetyl-L-glutamate from L-glutamate and acetyl-CoA in arginine biosynthesis
YP_561352.1	catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis
YP_561353.1	catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis
YP_561354.1	dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate
YP_561355.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D
YP_561364.1	MraZ; UPF0040; crystal structure shows similarity to AbrB
YP_561368.1	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_561370.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_561371.1	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_561373.1	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_561374.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_561377.1	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_561378.1	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_561381.1	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_561406.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_561409.1	involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate
YP_561432.1	two electrons are transferred from cytoplasmic NADPH to thioredoxin and then to the inner membrane protein DsbD which keeps the disulfide isomerase DsbC in a reduced state in the oxidizing periplasm; DsbC in turns rearranges incorrectly made disulfide bonds in the periplasm
YP_561437.1	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_561438.1	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_561459.1	Stimulates excision of phage lambda; affects Mu development; acts as an activator of rRNA and iRNA transcription
YP_561461.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_561462.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_561464.1	enables ATP-dependent unwinding of double stranded RNA as a component of the RNA degradosome, a multi-enzyme complex important in RNA processing and messenger RNA degradation
YP_561467.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_561478.1	regulator of RNase E; increases half-life and abundance of RNAs; interacts with RNase E possibly inhibiting catalytic activity
YP_561482.1	binds specifically to the major sigma factor sigma 70; active in stationary phase
YP_561483.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III
YP_561493.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_561498.1	catalyzes the conversion of 4-Hydroxybenzoate into 3-octaprenyl-4-hydroxybenzoate, as part of the ubiquinone biosynthesis pathway
YP_561499.1	unwinds DNA duplexes with 3' to 5' polarity with respect to the bound strand and initiates unwinding most effectively when a single-stranded region is present; involved in the post-incision events of nucleotide excision repair and methyl-directed mismatch repair.
YP_561504.1	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_561508.1	forms homotetramers; catalyzes hydrolysis of KDO 8-P to KDO and inorganic phosphate; functions in lipopolysaccharide biosynthesis
YP_561517.1	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_561521.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_561522.1	forms a direct contact with the tRNA during translation
YP_561524.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_561527.1	Specifically methylates the ribose of guanosine 2251 in 23S rRNA
YP_561530.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_561531.1	binds single-stranded DNA at the primosome assembly site
YP_561532.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_561533.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_561537.1	converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer
YP_561549.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_561551.1	transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA
YP_561556.1	catalyzes the S-adenosylmethionine-dependent transmethylation of thiopurine compounds; may be involved in selenium cycling by forming dimethylselenide and/or dimethyldiselenide
YP_561627.1	when combined with S-adenosylmethionine represses the expression of the methionine regulon and of proteins involved in S-adenosylmethionine synthesis
YP_561629.1	multifunctional homodimeric enzyme that catalyzes the phosphorylation of aspartate to form aspartyl-4-phosphate as well as conversion of aspartate semialdehyde to homoserine; functions in a number of amino acid biosynthetic pathways
YP_561648.1	YghU; B2989; one of eight  glutathione transferase proteins from E. coli
YP_561655.1	MTHFR; catalyzes NADH-linked reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate using FAD as a cofactor
YP_561702.1	proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the proteins from this group do not and in addition appear to have a truncated C-terminal domain
YP_561712.1	catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine
YP_561715.1	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_561722.1	catalyzes the phosphorylation of D-glycero-D-manno-heptose 7-phosphate to form D,D-heptose-1,7-bisphosphate and catalyzes transfer of ADP to D-glycero-D-manno-heptose 1-phosphate forming ADP-D,D-heptose
YP_561726.1	HTH-type; bet1; Repressor involved in choline regulation of the bet genes
YP_561727.1	catalyzes the formation of betaine from betaine aldehyde
YP_561728.1	catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine
YP_561745.1	catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine
YP_561749.1	malic enzyme; oxaloacetate-decarboxylating; NAD-dependent; catalyzes the formation of pyruvate form malate
YP_561757.1	facilitates an early step in the assembly of the 50S subunit of the ribosome
YP_561769.1	pyrophosphatase; has activity against dUTP and dITP; the crystal structure of the Vibrio protein showed similarity to Methanococcus janaschii Mj0226; in Vibrio cholerae this gene is part of the Mba operon that is involved in regulation and maintenance of biofilms; in Escherichia coli overexpression of this gene leads to resistance to an HMP analog
YP_561783.1	nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ; the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription
YP_561797.1	with HmuTU is involved in the transport of hemin
YP_561810.1	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_561823.1	Transfers the fatty acyl group on membrane lipoproteins
YP_561827.1	catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A)
YP_561830.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_561831.1	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_561837.1	regulates arginine biosynthesis when complexed with arginine by binding at site that overlap the promotors of the arginine biosynthesis genes
YP_561838.1	oxidizes malate to oxaloacetate
YP_561845.1	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_561846.1	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_561847.1	acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine
YP_561867.1	SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA
YP_561870.1	in Escherichia coli the CydCD ABC transporter exports cysteine and glutathione into the periplasm in order to maintain redox balance; important for cytochrome bd and c
YP_561871.1	in Escherichia coli the CydCD ABC transporter exports cysteine and glutathione into the periplasm in order to maintain redox balance; important for cytochrome bd and c
YP_561878.1	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_561879.1	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_561882.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_561909.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_561921.1	catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate
YP_561927.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_561928.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_561930.1	catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins
YP_561931.1	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_561936.1	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_561941.1	catalyzes reversible transfer of hydride ion equivalent between NAD and NADP; membrane-bound proton pump that translocates protons from cytosolic to periplasmic side of the inner membrane; forms a tetramer composed of two alpha and 2 beta subunits; AB-stereospecific enzyme
YP_561942.1	forms a tetramer composed of 2 alpha subunits and 2 beta subunits in the inner membrane; involved in catalyzing transfer of hydride ion equivalents between NAD and NADP; stereospecific (AB-specific); functions as a proton pump by translocating protons from cytoplasm to periplasm
YP_561944.1	hemoprotein; NADPH dependent; with the alpha subunit (a flavoprotein) catalyzes the reduction of sulfite to sulfide
YP_561945.1	catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite
YP_561950.1	catalyzes the formation of D-ribose 5-phosphate from ribose
YP_561951.2	Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively; pyrimidine-specific
YP_561970.1	with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP
YP_561971.1	may be GTPase that regulates ATP sulfurylase activity that is involved in converting ATP and sulfate to diphosphate and adenylylsulfate; in Escherichia coli this enzyme functions in cysteine biosynthesis in the first step; forms a heterodimer with CysD; part of the GTP-binding elongation factor family CysN/NodQ
YP_561973.1	converts ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; in Escherichia coli this enzyme functions in cysteine biosynthesis
YP_561992.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_561993.1	uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm
YP_561994.1	uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm
YP_561995.1	uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm
YP_561996.1	Part of the NQR complex which catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm
YP_561997.1	Part of the NQR complex which consists of NqrA, NqrB, NqrC, NqrD, NqrE and NqrF; NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm; NqrE is probably involved in the second step, the conversion of ubisemiquinone to ubiquinol.
YP_561998.1	uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm
YP_562005.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_562006.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_562007.1	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_562010.1	Specifically methylates the uridine in position 2552 of 23S rRNA in the fully assembled 50S ribosomal subunit
YP_562013.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_562014.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_562016.1	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_562017.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_562018.1	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_562019.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_562020.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_562021.1	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_562031.1	lipoprotein that appears to be involved in cell division; interacts with the periplasmic protease Prc and may be activated by protease processing
YP_562032.1	stimulates the release of release factors 1 and 2 from the ribosome after hydrolysis of the ester bond in peptidyl-tRNA has occurred; GDP/GTP-binding protein
YP_562036.1	catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate
YP_562037.1	Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate
YP_562038.1	catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose
YP_562039.1	catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate
YP_562041.1	GbpA; plays a role mediating bacterial attachment and colonization of zooplankton and/or intestinal epithelium; in Vibrio cholerae this protein probably binds directly N-acetylglucosamine residues in chitin, glycoproteins and lipids on intestinal epithelial cells
YP_562046.1	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_562065.1	DapATase; bifunctional enzyme that functions in arginine and lysine biosynthetic pathways; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine or N-succinyl-2-L-amino-6-oxoheptanedioate from 2-oxoglutarate and N-succinyl-L-2,6-diaminoheptanedioate
YP_562067.1	a high throughput screen identified this enzyme as an aldehyde dehydrogenase with broad substrate specificity; converts succinylglutamate semialdehyde and NAD to succinylglutamate and NADH
YP_562083.1	catalyzes the formation of acetaldehyde from ethanolamine
YP_562090.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_562093.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_562094.1	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_562095.2	NAD-dependent; catalyzes the formation of 4-phosphoerythronate from erythrose 4-phosphate in the biosynthesis of pyridoxine 5'-phosphate
YP_562096.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_562097.1	class II aldolase; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis and gluconeogenesis
YP_562103.1	Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_562106.1	specifically hydrolyze the DD-diaminopimelate-alanine bonds in high-molecular-mass murein sacculi; Penicillin-binding protein 7
YP_562126.1	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_562129.1	catalyzes the formation of adenosylcobalamin from Ado-cobinamide-GDP and alpha-ribazole
YP_562150.1	ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence
YP_562151.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_562154.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_562156.1	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_562157.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_562165.1	glycosyltransferase; polymerizes glycan strands in the peptidoglycan
YP_562189.1	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_562191.1	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_562192.1	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_562194.1	involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function
YP_562200.2	part of the two-component regulatory system with UvrY; involved in the regulation of carbon metabolism via the csrA/csrB regulatory system
YP_562201.1	in Escherichia coli this enzyme catalyzes the SAM-dependent methylation of U1939 in the 23S ribomal RNA; binds an iron-sulfur cluster [4Fe-4S]
YP_562203.1	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_562204.1	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_562205.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_562207.1	4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MEP cytidylyltransferase; MCT; catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; forms homodimers
YP_562208.1	catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate
YP_562210.1	catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate
YP_562216.1	This protein performs the mismatch recognition step during the DNA repair process
YP_562217.1	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_562222.1	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_562228.1	involved in the first step of glutathione biosynthesis
YP_562232.1	With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway
YP_562248.1	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_562254.1	Catalyzes the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle
YP_562262.1	23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance
YP_562265.1	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_562266.1	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_562268.1	with YaeT, YfiO, and NlpB forms a complex involved in outer membrane protein biogenesis
YP_562269.1	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_562277.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_562278.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_562279.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_562281.1	YfhD; uncharacterized member of the transglycosylase slt family; part of the rob operon, which plays a role in cellular resistance to antibiotics, bactericidal agents, and organic solvents; unknown function
YP_562282.1	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_562309.1	required for the assembly of the flagellar basal body P-ring
YP_562312.1	with FlgF and C makes up the proximal portion of the flagellar basal body rod
YP_562313.1	with FlgF and B makes up the proximal portion of the flagellar basal body rod
YP_562314.1	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; in V. parahaemolyticus one set used for lateral flagella production and the other is used for the polar flagella production
YP_562315.1	the hook connects flagellar basal body to the flagellar filament
YP_562316.1	FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod
YP_562317.1	makes up the distal portion of the flagellar basal body rod
YP_562318.1	part of the basal body which consists of four rings L, P, S, and M mounted on a central rod
YP_562319.1	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_562320.1	Flagellum-specific muramidase which hydrolyzes the peptidoglycan layer to assemble the rod structure in the periplasmic space
YP_562322.1	with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook; Yersinia, Vibrio parahaemolyticus, Bradyrhizobium and other organisms have 2 copies of this and other flagellar genes.
YP_562328.1	flagellin specific chaperone
YP_562333.1	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_562334.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_562335.1	binds to and inhibits the function of flagella specific ATPase FliI
YP_562336.1	involved in type III protein export during flagellum assembly
YP_562339.2	interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring
YP_562343.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_562345.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_562347.1	FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus
YP_562348.1	membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export
YP_562349.1	membrane protein involved in the flagellar export apparatus
YP_562350.1	positive regulator of class III flagellar genes
YP_562352.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor directs late flagellar biosynthesis genes
YP_562356.1	regulates chemotaxis by demethylation of methyl-accepting chemotaxis proteins
YP_562378.1	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_562380.1	Catalyzes the specific recognition and activation of amino acids during peptide synthesis
YP_562390.1	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; in Pseudomonas this protein is involved in quinolone signal biosynthesis
YP_562392.1	Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate intermediate into D-glycero-beta-D-manno-heptose 1-phosphate
YP_562403.1	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_562406.1	Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A)
YP_562409.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_562410.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_562411.1	member of preprotein translocase; forms a heterotrimer with SecD and SecF; links the SecD/SecF/YajC/YidC complex with the SecY/SecE/SecG complex
YP_562412.1	part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane
YP_562413.1	forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF
YP_562428.1	Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates
YP_562429.1	activates anaerobic ribonucleoside-triphosphate reductase under anaerobic conditions
YP_562436.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_562437.1	molecular chaperone
YP_562439.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_562441.1	catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers
YP_562445.1	in Escherichia coli the protein UvrY is part of a two-component system along with BarA that is needed for efficient switching between glycolytic and gluconeogenic carbon sources possibly by regulating the Csr system; in Salmonella SirA and BarA regulate virulence gene expression also via the Csr system
YP_562446.1	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_562455.1	catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate
YP_562466.1	catalyzes the removal of elemental sulfur from cysteine to produce alanine; involved in NAD biosynthesis
YP_562469.1	J-type co-chaperone that regulates the ATPase and peptide-binding activity of Hsc66 chaperone; may function in biogenesis of iron-sulfur proteins
YP_562470.1	involved in the maturation of iron-sulfur cluster-containing proteins
YP_562473.1	removes the damaged DNA at cytosines and guanines by cleaving on the 3' side of the AP site by a beta-elimination reaction
YP_562474.1	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_562475.1	Involved in cell division; probably involved in intracellular septation
YP_562494.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_562498.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_562505.1	periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC
YP_562511.1	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_562521.1	catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in queuosine biosynthesis
YP_562522.1	SecY regulator that either chelates excess SecY or negatively regulates the SecYE translocase function
YP_562530.1	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_562537.1	FadI; fatty acid oxidation complex component beta; functions in a heterotetramer with FadJ; similar to FadA2B2 complex; functions in beta-oxidation of fatty acids during anaerobic growth
YP_562538.1	multifunctional enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase/3-hydroxybutyryl-CoA epimerase; catalyzes the formation of an hydroxyacyl-CoA by addition of water on enoyl-CoA; exhibits 3-hydroxyacyl-CoA epimerase and 3-hydroxyacyl-CoA dehydrogenase activities: forms a heterotetramer with FadI; similar to FadA2B2 complex; involved in the anaerobic degradation of long and medium-chain fatty acids in the presence of nitrate
YP_562544.1	involved in methylation of ribosomal protein L3
YP_562545.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_562555.1	An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group
YP_562557.1	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_562559.1	catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway
YP_562560.1	catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein
YP_562561.1	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_562562.1	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_562563.1	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_562564.1	Catalyzes the phosphorylation of UMP to UDP
YP_562565.1	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_562568.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_562572.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_562573.1	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_562574.1	catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis
YP_562575.1	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_562576.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_562577.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_562600.1	negatively regulates a number of operons that encode enzymes involved in iron transport; activated by manganese; forms a homodimer
YP_562601.1	Modulates the activities of several enzymes which are inactive in their acetylated form
YP_562603.1	periplasmic enzyme; functions during ribonucleic acid degradation; 2',3'-cyclic nucleotides are first converted to 3'-nucleotide and then cleaved to yield a ribonucleotide and a phosphate
YP_562609.1	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_562610.1	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_562611.1	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_562612.1	Transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA
YP_562618.1	catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribosyl)-ATP and the subsequent formation of 1-(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide from 1-(5-phosphoribosyl)-AMP in histidine biosynthesis
YP_562619.1	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_562620.1	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_562621.1	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_562622.1	catalyzes the formation of 3-(imidazol-4-yl)-2-oxopropyl phosphate from D-ethythro-1-(imidazol-4-yl)glycerol 3-phosphate and histidinol from histidinol phosphate
YP_562623.1	catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis
YP_562624.1	catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer
YP_562625.1	long form of enzyme; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms active dimers and inactive hexamers which is dependent on concentration of substrates and inhibitors
YP_562632.1	Activates fatty acids by binding to coenzyme A
YP_562634.1	works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell
YP_562636.1	blocks the formation of polar Z-ring septums
YP_562641.1	involved in regulation of intracellular pH under alkaline conditions
YP_562642.1	Multifunctional regulator of fatty acid metabolism
YP_562650.1	controls initiation of DNA replication by inhibiting re-initiation of replication, promotes hydrolysis of DnaA-bound ATP
YP_562657.1	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_562668.1	DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium
YP_562671.1	catalyzes the formation of pyruvate and succinate from 2-methylisocitrate
YP_562673.1	Catalyzes the conversion of citrate to isocitrate
YP_562675.1	catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate
YP_562686.1	catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis
YP_562710.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_562712.1	catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_562715.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_562728.1	affects solute and DNA transport through an unknown mechanism
YP_562729.1	Involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3
YP_562737.1	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_562740.1	bacterioferritin comigratory protein; thiol peroxidase; thioredoxin-dependent; hydroperoxide peroxidase; in Escherichia coli this enzyme preferentially reduces linoleic acid hydroperoxide; contains an active site cysteine
YP_562742.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_562749.1	mediates a global response to leucine; acts as a regulator for several genes involved in the high-affinity branched-chain amino acid transport system
YP_562753.1	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_562754.1	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_562755.1	catalyzes the synthesis of pseudouridine from U-2604 in the 23S ribosomal RNA
YP_562757.1	catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate
YP_562758.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_562759.1	Catalyzes the formation of (d)CDP from ATP and (d)CMP
YP_562760.2	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_562761.1	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_562764.1	type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase
YP_562771.1	functions in fatty acid oxidation; converts acyl-CoA and FAD to FADH2 and delta2-enoyl-CoA
YP_562777.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_562781.1	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_562782.1	in Escherichia coli this enzyme functions in thiamine biosynthesis along with thiFSGI and iscS; with ThiFSG catalyzes the formation of thiazole phosphate from tyrosine, cysteine and 1-deoxy-D-xylulose-5-phosphate; forms a complex with ThiG; contains an iron-sulfur center
YP_562786.1	catalyzes de novo synthesis of phosphatidylserine from CDP-diacylglycerol and L-serine which leads eventually to the production of phosphatidylethanolamine; bounds to the ribosome
YP_562792.1	catalyzes the formation of succinate and glutamate from N(2)-succinylglutamate in arginine catabolism
YP_562796.1	3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate
YP_562800.1	catalyzes the formation of 3-phospho-D-glyceroyl phosphate from D-glyceraldehyde 3-phosphate; involved in growth under gluconeogenic conditions and in glycolytic activity at high ATP concentrations in Corynebacterium; NAD and NADP dependent
YP_562804.1	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_562821.1	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_562823.1	functions in phosphoenolpyruvate-(PEP)-dependent phosphotransferase (PTS) system; functions in the transport and phosphorylation of glucose
YP_562833.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_562834.1	HflD; UPF0274; in Escherichia coli this protein is peripherally associated with the membrane and appears to act with lambda CII protein; in Haemophilus influenzae a knockout of the HI0638 gene affected paracytosis
YP_562835.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_562840.1	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_562842.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_562843.1	Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate
YP_562844.1	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_562848.1	TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs
YP_562849.1	with UspC and UspD is involved in resistance to UV irradiation
YP_562850.1	Global transcription factor that controls the expression of over 100 target genes in response to anoxia
YP_562858.1	CcoN; FixN
YP_562870.1	part of membrane-bound complex thought to be involved in electron transport to nitrogen
YP_562871.1	part of membrane-bound complex thought to be involved in electron transport to nitrogen
YP_562872.1	RnfD; RsxD; required for nitrogen fixation in Rhodobacter capsulatus; part of a membrane-bound complex thought to be involved in electron transport to nitrogenase; in Escherichia coli this gene is part of a cluster controlling SoxR-mediated induction of the SoxS transcription factor in the absence of oxidizing agents
YP_562874.1	in Excherichia coli RsxABCDEG reduces SoxR which turns off induction of SoxS transcription factor in the absence of oxidizing agents; similar to the rnfABCDGE operon in Rhodobacter capsulatus involved in transferring electrons to nitrogenase
YP_562889.1	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_562890.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_562891.1	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_562893.1	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_562908.1	converts asparagine to aspartate and ammonia
YP_562941.1	catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate
YP_562943.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_562946.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_562951.1	hydrolyzes the terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
YP_562953.1	catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine
YP_562955.1	Involved in ubiquinone biosynthesis
YP_562958.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_562959.1	B2 or R2 protein; type 1a enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdA
YP_562964.1	catalyzes a two-step reaction, first charging an asparagine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_562976.1	Required for the expression of anaerobic nitric oxide (NO) reductase; acts as a transcriptional activator for the norVW operon
YP_562991.1	catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate
YP_562992.1	negative modulator of the initiation of chromosome replication
YP_562996.1	An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group
YP_562998.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_562999.1	broad specificity; family IV; in Corynebacterium glutamicum this protein can use glutamate, 2-aminobutyrate, and aspartate as amino donors and pyruvate as the acceptor
YP_563001.1	dGTPase family type 2 subfamily; presumably hydrolyzes dGTP to deoxyguanosine and triphosphate
YP_563015.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_563017.1	tryptophan sensitive; catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate
YP_563021.1	YbaX; catalyzes the transformation of GTP to 7-cyano-7-deazaguanine (preQ0), as one of the early reactions of quenosine biosynthesis; quenosine is a modified nucleoside that occurs at the wobble position of GUN anticodons in tRNAs for Asn, Asp, Tyr, and His
YP_563025.1	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_563031.1	regulator of RNase E; increases half-life and abundance of RNAs; interacts with RNase E possibly inhibiting catalytic activity
YP_563049.1	Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA
YP_563051.1	in Escherichia coli this enzyme specifically methylates C1407 of the 16S rRNA
YP_563056.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_563059.1	functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor
YP_563061.1	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_563080.1	functions in asparagine biosynthesis; converts glutamine, aspartate, ATP, and water to glutamate, asparagine, pyrophosphate and AMP
YP_563081.1	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_563082.1	catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate
YP_563084.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_563085.1	Represses the expression of the zwf, eda, glp and gap
YP_563095.1	functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase; also involved in reducing some disulfides in a coupled system with glutathione reductase
YP_563098.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_563099.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_563100.1	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_563101.1	LysR-type transcriptional regulator; contains helix-turn-helix (HTH) motif; in Escherichia coli this protein regulates cysteine biosynthesis by controlling expression of the cys regulon; autoregulates expression; crystal structure of Klebsiella aerogenes showed tetramer formation
YP_563120.1	functions in fatty acid oxidation; converts acyl-CoA and FAD to FADH2 and delta2-enoyl-CoA
YP_563128.1	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_563135.1	metalloprotease
YP_563136.1	alpha-aspartyl dipeptidase; catalyzes the hydrolysis of dipeptides with an N-terminal aspartate residue; belongs to peptidase S51 family
YP_563139.1	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_563142.1	catalyzes the degradation of periplasmic UDP-glucose to uridine, glucose-1-phosphate and inorganic phosphate; specific for uridine nucleotides
YP_563186.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_563188.1	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_563189.1	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_563190.1	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_563193.1	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_563202.1	transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate
YP_563222.1	reduces nitrous oxide to nitrogen
YP_563280.1	catalyzes the formation of pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate
YP_563281.1	catalyzes the formation of putrescine from agmatine
YP_563283.1	catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis
YP_563289.1	methylates the guanosine in position 745 of 23S rRNA; required for translation and cell growth
YP_563290.1	Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
YP_563291.1	Reclaims exogenous and endogenous cytidine and 2'-deoxycytidine molecules for UMP synthesis
YP_563295.1	carries the fatty acid chain in fatty acid biosynthesis
YP_563298.1	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_563299.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_563300.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_563307.1	this fusion consists of methionine sulfoxide B reductase at the N-terminus and A at the C-terminus; A and B are stereospecific enzymes that recognize the damaged produces of oxidative stress, S and R epimers of methionine sulfoxide, respectively; a fusion protein of these enzymes with thioredoxin provides protection against oxidative stress in Neisseria gonorrhoeae
YP_563309.1	essential GTPase; functions in ribosome assembly; binds a unique part of the 23S rRNA; interacts with ribosomal protein L25(Ctc)
YP_563316.1	catalyzes the formation of L-homocysteine from cystathionine
YP_563331.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_563332.1	catalyzes the hydrolysis of 2-N-succinylarginine into 2-N-succinylornithine, ammonia and carbon dioxide in arginine degradation
YP_563347.1	in Escherichia coli this inner membrane protein was found to anchor the periplasmic catalytic oxidoreductase YedY; sulfite oxidase activity not demonstrated; contains heme
YP_563348.1	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_563357.1	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_563364.1	catalyzes the formation of dihydromonapterin triphosphate from dihydroneopterin triphosphate
YP_563385.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_563393.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_563403.1	decatenates replicating daughter chromosomes
YP_563410.1	activates pyruvate formate-lyase 1 under anaerobic conditions
YP_563412.1	AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation; utilizes magnesium and ATP; also involved in conversion of acetate to aceyl-CoA
YP_563413.1	catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate
YP_563416.1	catalyzes a two-step reaction, first charging a glutamine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_563431.1	Has polymerase, DNA-binding and 3'-5' exonuclease activities. In Aeropyrum pernix this protein is sensitive to aphidicolin and stable at 95#C
YP_563432.1	helicase involved in DNA repair and perhaps also replication
YP_563453.1	with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine
YP_563454.1	TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity
YP_563455.1	Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_563456.1	monomeric bifunctional protein; functions in tryptophan biosynthesis pathway; phosphoribosylanthranilate is rearranged to carboxyphenylaminodeoxyribulosephosphate which is then closed to form indole-3-glycerol phosphate
YP_563457.1	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_563458.1	catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis
YP_563468.1	catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP
YP_563471.1	Uup; in Escherichia coli this cytoplasmic protein was shown to contain ATPase activity; mutations in this gene affect RecA-independent excision of transposons and affects Mu bacteriophage growth
YP_563473.1	catalyzes the N2-methyl guanosine modification of the G2445 residue of 23S rRNA
YP_563474.1	SohB; periplasmic protein; member of the peptidase S49 family
YP_563482.1	acts together with PspC to induce psp operon during infection with phage, exposure to ethanol or osmotic shock; forms a complex with PspA and C; PspC is required for PspAB binding
YP_563490.1	enzyme from Treponema denticola exhibits NADH-dependent trans-2-enoyl-CoA reductase activity
YP_563497.1	binds and unfolds substrates as part of the ClpXP protease
YP_563498.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_563499.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_563500.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_563501.1	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_563503.1	catalyzes the formation of 2,3=diacylglucosamine 1-phosphate from UDP-2,3=diacylglucosamine
YP_563509.1	with SbcC cleaves DNA hairpin structure, also has 5' single-strand endonuclease activity
YP_563520.1	role in sulfur assimilation
YP_563522.1	catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs
YP_563528.1	involved in the import of serine and threonine coupled with the import of sodium
YP_563536.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_563538.1	catalyzes the formation of thymidine 5'-phosphate from thymidine
YP_563546.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_563560.1	has 3'-5' exonuclease activity that preferentially acts on ssDNA; also 3'-phosphodiesterase activity at sites with 3' incised apurinic/apyrimidinic sites; can remove 3' phosphoglycolate groups
YP_563563.1	catalyzes the formation of 2-oxoglutarate from isocitrate
YP_563567.1	Glycine cleavage system transcriptional activator; activates the gcvTHP operon in the presence of glycine and represses the operon in its absence
YP_563568.1	Required for the synthesis of the thiazole moiety
YP_563569.1	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; Vibrio parahaemolyticus protein is associated with the polar flagella
YP_563570.1	Homologous to MotA in E. coli and Salmonella. With PomB forms the ion channels that couple flagellar rotation to sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine.
YP_563573.1	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_563574.1	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_563575.1	catalyzes the phosphorylation of NAD to NADP
YP_563583.1	regulates several genes involved in high affinity phosphate uptake; under conditions of high phosphate concentrations downregulates the PHO regulon
YP_563584.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_563590.1	catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis
YP_563591.1	receptor for colicin S4
YP_563596.1	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_563597.1	phenylalanine 4-hydroxylase; phenylalanine 4-hydroxylase; catalyzes the formation of 4a-hydroxytetrahydrobiopterin and tyrosine from phenylalanine and tetrahydrobiopterin
YP_563605.1	catalyzes phosphorylation of fructose; cytosolic enzyme
YP_563665.1	NAD(P) binding; catalyzes the formation of dTDP-4-dehydro-6-deoxy-D-glucose from dTDP-glucose
YP_563668.1	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_563672.1	crystal structure of protein from Xanthomonas shows pentameric toroidal structure; physiological function is unknown
YP_563675.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_563677.1	involved in start site selection during the initiation of translation
YP_563688.1	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_563693.1	Required for efficient pilin antigenic variation
YP_563697.1	catalyzes the formation of glutamate from glutamine
YP_563699.1	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_563722.1	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_563724.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_563725.1	IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme
YP_563728.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_563737.1	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_563740.1	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_563741.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_563742.1	multifunctional homotetrameric enzyme that catalyzes the phosphorylation of aspartate to form aspartyl-4-phosphate as well as conversion of aspartate semialdehyde to homoserine; functions in a number of amino acid biosynthetic pathways
YP_563751.1	catalyzes the formation of prephenate from chorismate and the formation of 4-hydroxyphenylpyruvate from prephenate in tyrosine biosynthesis
YP_563752.1	catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, tyrosine sensitive
YP_563753.1	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_563754.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_563755.1	Essential for efficient processing of 16S rRNA
YP_563756.1	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_563757.1	with 4.5S RNA forms a signal recognition particle involved in targeting and integration of inner membrane proteins
YP_563764.1	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_563765.1	involved in the de novo synthesis of pyridoxine (Vitamin B6)
YP_563767.1	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_563768.1	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_563770.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_563774.1	Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor regulates genes involved in alginate biosynthesis
YP_563775.1	catalyzes the formation of oxaloacetate from L-aspartate
YP_563778.1	Na+/H+ antiporter regulatory protein; activates the genes nhaA and osmC
YP_563780.1	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_563781.1	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_563784.1	hydrolyzes diadenosine polyphosphate
YP_563785.1	MutH; Sequence-specific endonuclease that cleaves unmethylated GATC sequences during DNA repair
YP_563792.1	catalyzes the formation of glutamate from glutamine and alpha-ketoglutarate
YP_563793.1	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_563812.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_563814.1	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_563817.1	essential respiratory protein A; may be involved in the transfer of iron-sulfur clusters; essential for growth using oxygen or alternate electron acceptors
YP_563820.1	Catalyzes the conversion of carbamoyl phosphate and l-aspartate to yield orthophosphate and n-carbamoyl-l-aspartate
YP_563821.1	Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway
YP_563828.1	BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters UDP disphosphate which reduces the pool of lipid carrier available to the cell
YP_563831.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX
YP_563832.1	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_563833.1	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_563869.1	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_563884.1	functions as a co-chaperone with DnaK; involved in regulation of colanic acid capsule; inner membrane protein; dimerized via transmembrane domain; J-like domain is cytoplasmic and can functionally substitute for DnaJ; stimulates synthesis of colanic acid mucoid capsule through the RcsB/C signal transduction system
YP_563889.1	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_563890.1	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_563891.1	protein associated with Co2+ and Mg2+ efflux
YP_563892.1	hydrolyzes P(1),P(4)-bis(5'-adenosyl) tetraphosphate to form 2 ADP
YP_563902.1	catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive
YP_563926.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_563927.1	involved in the peptidyltransferase reaction during translation
YP_563943.1	specifically modifies tRNA at position G18
YP_563950.1	exhibits an RNA-dependent ATPase activity, specifically stimulated by bacterial 23S rRNA
YP_563959.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_563975.1	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_563976.1	catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
YP_563983.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; functions in amino acid biosynthesis; lysine sensitive
YP_563987.1	catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate
YP_564050.1	transcriptional repressor of asnA which codes for aspartate-ammonia ligase
YP_564059.1	NAD(P)H-flavin reductase; catalyzes the reversible oxidation/reduction of NAD(P) and flavine mononucleotide; in Salmonella and E. coli this protein also reduces aquacob(III)alamin to cob(II)alamin
YP_564064.1	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_564075.1	catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate; involved in the pyrimidine salvage pathway
YP_564097.1	catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate
YP_564127.1	class II; LysRS2; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri, LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1
YP_564167.1	catalyzes the removal of an N-terminal amino acid from a peptide or arylamide
YP_564168.1	Regulatory factor involved in maltose metabolism
YP_564173.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_564174.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_564189.1	complexes with cyclic AMP and binds to specific DNA sites near the promoter to regulate the transcription of several catabolite-sensitive operons
YP_564190.1	a high throughput screen identified this enzyme as an aldehyde dehydrogenase with broad substrate specificity; converts succinylglutamate semialdehyde and NAD to succinylglutamate and NADH
YP_564192.1	DapATase; bifunctional enzyme that functions in arginine and lysine biosynthetic pathways; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine or N-succinyl-2-L-amino-6-oxoheptanedioate from 2-oxoglutarate and N-succinyl-L-2,6-diaminoheptanedioate
YP_564197.1	transcriptional activator; required for activation of bacteriophage P1 late promoter; induced by starvation
YP_564205.1	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_564206.1	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_564211.1	3'-5' exoribonuclease specific for small oligoribonuclotides
YP_564212.1	EngC; RsgA; CpgA; circularly permuted GTPase; ribosome small subunit-dependent GTPase A; has the pattern G4-G1-G3 as opposed to other GTPases; interacts strongly with 30S ribosome which stimulates GTPase activity
YP_564213.1	catalyzes the decarboxylation of phosphatidyl-L-serine to phosphatidylethanoleamine
YP_564217.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_564219.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_564224.1	trimeric outer membrane protein involved in efflux of hydrophobic/amphipathic molecules; functions with a number of efflux systems in the inner membrane to transport molecules out of the cell
YP_564284.1	catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis
YP_564299.1	catalyzes the conversion of glutamine residues to glutamate on methyl-accepting chemotaxis receptors
YP_564329.1	involved in the processing of the 5'end of 16S rRNA
YP_564332.1	in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall
YP_564333.1	functions in MreBCD complex in some organisms
YP_564351.1	regulates the degradation of the small RNAs CsrB and CsrC; may function to targate RNase E to specific RNA molecules
YP_564353.1	RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome
YP_564356.1	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_564360.1	heat shock protein involved in degradation of misfolded proteins
YP_564361.1	heat shock protein involved in degradation of misfolded proteins
YP_564373.1	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_564376.1	catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate
YP_564377.1	YniC; catalyzes the dephosphorylation of 2-deoxyglucose 6-phosphate, mannose 6-phosphate and p-nitrophenyl phosphate
YP_564380.1	E3 component of pyruvate and 2-oxoglutarate dehydrogenase complex; catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_564381.1	E2 component of pyruvate dehydrogenase multienzyme complex; in Escherichia coli AceF contains three N-terminal lipoyl domains
YP_564382.1	E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC
YP_564383.1	activates lctPRD operon; autoregulates itself through repression of pdhR-aceEF-lpdA operon; regulates pyruvate dehydrogenase complex
YP_564384.1	involved in regulation of beta-lactamase; signaling protein
YP_564391.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_564404.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_564405.1	involved in de novo purine biosynthesis
YP_564406.1	mediates expression of the zinc export protein ZntA in response to high levels of zinc; member of MerR family of transcriptional regulators
YP_564409.1	threonine deaminase; threonine dehydratase; in Escherichia coli, IlvA is part of the isoleucine biosynthetic pathway
YP_564410.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_564412.1	catalyzes the formation of 2-acetolactate from pyruvate; also known as acetolactate synthase large subunit
YP_564413.1	catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis
YP_564414.1	participates in controlling several genes involved in isoleucine and valine biosynthesis; activates the transcription of the ilvC gene in the presence of acetolactate or acetohydroxybutyrate
YP_564425.1	manganese-dependent 5'-nucleotidase; specific for 5'-UMP, 5'-dUMP, and 5'-dTMP; member of haloacid dehalogenase (HAD)-like hydrolase superfamily
YP_564431.1	Essential for recycling GMP and indirectly, cGMP
YP_564432.1	promotes RNA polymerase assembly or stability; latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits
YP_564445.1	hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine
YP_564446.1	RNase BN; required for 3' maturation of certain phage T4-encoded tRNAs; forms a dimer; specific for immature tRNA substrates containing incorrect residues within the universal CCA sequence; 3' to 5' exoribonuclease
YP_564452.1	forms a homododecamer; forms glutamine from ammonia and glutamate with the conversion of ATP to ADP and phosphate; also functions in the assimilation of ammonia; highly regulated protein controlled by the addition/removal of adenylyl groups by adenylyltransferase from specific tyrosine residues; addition of adenylyl groups results in inactivation of the enzyme
YP_564474.1	catalyzes branch migration in Holliday junction intermediates
YP_564476.1	FMN-dependent; requires NADH; catalyzes the cleavage of azo bond in aromatic azo compounds
YP_564498.1	uncharacterized member of the APC superfamily of amino acid transporters; unknown function
YP_564500.1	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_564512.1	PlsB; catalyzes the formation of 1-acyl-sn-glycerol 3-phosphate by transfering the acyl moiety from acyl-CoA
YP_564513.1	Represses a number of genes involved in the response to DNA damage
YP_564517.1	involved in the insertion of copper into subunit I of cytochrome C oxidase
YP_564522.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_564526.1	cytoplasmic protein that may be involved in the utilization of double-stranded DNA as a carbon source
YP_564536.1	part of two-component system EnvZ/OmpR; regulates transcription of outer membrane porin genes ompC/F; under high osmolarity EnvZ functions as kinase/phosphotransferase and phosphorylates OmpR; the result is increased expression of ompC and repression of ompF; also functions in regulation of other genes; forms dimers upon phosphorylation
YP_564537.1	membrane-localized osmosensor; histidine kinase; in high osmolarity EnvZ autophosphorylates itself and transfers phosphoryl group to OmpR
YP_564549.1	catalyzes the formation of 3-phospho-D-glyceroyl phosphate from D-glyceraldehyde 3-phosphate
YP_564567.1	ATP-binding protein; required for proper cytochrome c maturation
YP_564571.1	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_564590.1	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_564610.1	catalyzes the phosphorylation of 3-deoxy-D-manno-octulosonic acid at the 4-OH position
YP_564613.1	catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine
YP_564614.1	converts threonine and NAD to 1,2-amino-3-oxobutanoate and NADH; functions in threonine catabolism
YP_564619.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_564624.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_564625.1	catalyzes the formation of inosine from adenosine
YP_564631.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor directs late flagellar biosynthesis genes
YP_564641.1	FlgJ; flagellum-specific muramidase which hydrolyzes the peptidoglycan layer to assemble the rod structure in the periplasmic space; like the lateral flagella FlgJ in Vibrio parahaemolyticus this protein does not contains a C-terminal muramidase domain
YP_564642.1	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_564643.1	part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod
YP_564646.1	the hook connects flagellar basal body to the flagellar filament; Vibrio parahaemolyticus protein is associated with the lateral flagella
YP_564649.1	with FlgF and C makes up the proximal portion of the flagellar basal body rod; Vibrio parahaemolyticus protein is associated with the lateral flagella
YP_564655.1	binds to and inhibits the function of flagella specific ATPase FliI
YP_564656.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_564657.1	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; the Vibrio parahaemolyticus protein is associated with the lateral flagella
YP_564662.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_564684.1	forms a trimer; related to eukaryotic protein gephyrin; functions during molybdenum cofactor biosynthesis
YP_564691.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_564692.1	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_564694.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_564739.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_564747.1	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_564748.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_564749.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_564750.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_564751.1	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_564752.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_564753.1	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_564754.1	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_564758.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_564759.1	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_564760.1	An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group
YP_564770.1	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_564773.1	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_564774.1	in Escherichia coli transcription of this gene is enhanced by polyamines