-- dump date   	20140620_074715
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_415519.1	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_415520.1	binds the polymerase to DNA and acts as a sliding clamp
YP_415522.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_415526.1	catalyzes the degradation of histidine to urocanate and ammmonia
YP_415527.1	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_415533.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_415535.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_415542.1	SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA
YP_415562.1	in group A Streptococci this protein was found to cross react with anti myosin antibodies and may play a role in rheumatic fever
YP_415587.1	[Mn/Fe]
YP_415590.1	catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate
YP_415592.1	catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate
YP_415593.1	catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose
YP_415629.1	Catalyzes the reversible two-electron oxidation of formate to carbon dioxide. It allows the assimilation of carbon dioxide and provides energy for growth through oxidative phosphorylation coupled to the reduction of oxygen, nitrate, sulphate or fumarate
YP_415635.1	bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate
YP_415642.1	catalyzes the cleavage of the lactyl ether moiety of N-acetylmuramic acid-6-phosphate (MurNAc-6-P) to form N-acetylglucosamine-6-phosphate (GlcNAc-6-P) and lactate; involved in MurNAc dissimilation pathway
YP_415659.2	FMN-dependent; requires NADH; catalyzes the cleavage of azo bond in aromatic azo compounds
YP_415670.1	cytoplasmic membrane protein that functions as a monomer; catalyzes the active transport of sugar-phosphates such as glucose-6-phosphate with the obligatory exchange of inorganic phosphate or organophosphate
YP_415673.1	similar to S. epidermidis BitC protein
YP_415698.1	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_415701.1	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_415705.1	involved in peptidoglycan cross-linking
YP_415708.1	negatively regulates murein hydrolase activity
YP_415709.1	in conjunction with LrgA this protein inhibits the expression or activity of extracellular murein hydrolases
YP_415716.1	cytoplasmic mutarotase that catalyzes the conversion between beta-pyran and beta-furan forms of D-ribose; RbsD is required for efficient ribose utilization in E. coli; rbsD-mutant E. coli strains are unable to use ribose as a sole carbon source
YP_415756.1	catalyzes the formation of pyruvate and N-acetylmannosamine from N-acetylneuraminic acid
YP_415759.1	Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate
YP_415781.1	membrane component; functions with enzymes IIB (sgaB; ulaB) and IIA (sgaA; ulaC) enzyme I and HPr for anaerobic utilization and uptake of L-ascorbate; sgaTBA are regulated by yifQ as well as Crp and Fnr
YP_415808.1	catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine
YP_415809.1	catalyzes the formation of 5,10-methylenetetrahydrofolate from 5-methyltetrahydrofolate and S-adenosyl-L-homocysteine and methionine from S-adenosyl-L-methionine and L-homocysteine; expressed in B. subtilis under methionine starvation conditions
YP_415816.1	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_415818.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_415820.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_415840.1	Catalyzes the transfer of the phosphoribosyl moiety from 5-phospho--D-ribosyl-1-pyrophosphate (PRib-PP) to the 6-oxo-guanine and -xanthine
YP_415843.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_415877.1	these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_415878.1	these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_415879.1	these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_415880.1	SSL5, SET3, SET10; bind P-selectin glycoprotein ligand-1 and inhibit P-selectin-mediated neutrophil rolling along the endothelium; these proteins share structural homology to known superantigens but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_415881.1	SSL7, SET1; blocks IgA-FcR interactions and inhibits complement, leading to increased survival of a sensitive bacterium in blood
YP_415882.1	these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_415883.1	these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_415884.1	these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_415886.1	these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_415901.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_415921.1	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_415928.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_415930.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_415934.1	in Bacillus subtilis this protein is involved in the negative regulation of DNA replication initiation; interacts with DnaN and DnaA
YP_415938.1	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_415941.1	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_415943.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_415946.1	stage V sporulation protein G; essential for spore formation and a negative regulator of asymmetric septation in Bacillus; involved in methicillin-resistance, biofilm formation and capsular polysaccharide synthesis in Staphylococcus
YP_415947.1	forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis
YP_415948.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_415949.1	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_415950.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_415960.1	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_415965.1	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_415967.1	with PdxT forms pyridoxal 5'-phosphate from glutamine, either ribose 5-phosphate or ribulose 5-phosphate, and either glyceraldehyde 3-phosphate or dihydroxyacetone phosphate
YP_415968.1	with PdxST is involved in the biosynthesis of pyridoxal 5'-phosphate; PdxT catalyzes the hydrolysis of glutamine to glutamate and ammonia; PdxS utilizes the ammonia to synthesize pyridoxal 5'-phosphate
YP_415974.1	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_415976.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_415978.1	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_415983.1	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 have the CXXC motif
YP_415984.1	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_415986.1	binds directly to 23S ribosomal RNA
YP_415987.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_415988.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_415991.1	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_415992.1	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_415993.1	in Bacillus subtilis this non-essential protein associates with the ribosome
YP_415994.1	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_415995.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_415996.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_415997.1	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_415999.1	catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine
YP_416000.1	Hsp31 stabilizes early unfolding protein intermediates under severe heat stress
YP_416001.1	catalyzes the phosphorylation of ribulose to ribulose 5-phosphate
YP_416003.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_416012.1	similar protein in Methanocaldococcus converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate as the first step in methanopterin biosynthesis
YP_416027.1	Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine
YP_416034.1	in Salmonella this enzyme is required for ethanolamine catabolism; has higher affinity for CoA than Pta
YP_416053.1	similar to zinc-dependent eukaryotic ADH enzymes and distinct from fermentative ADHs
YP_416055.1	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_416057.1	similar to Bacillus spp. YvrC protein
YP_416058.1	similar to Bacillus spp. YvrB protein
YP_416067.1	subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_416068.1	subunit B of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_416069.1	subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_416070.1	subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone; in S. meliloti it is known to be involved specifically with K+ transport
YP_416071.1	subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport
YP_416072.1	subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_416073.1	subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_416081.1	with TagG is involved in the export of teichoic acids
YP_416093.1	with DhaL and DhaM forms dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone; DhaK is the dihydroxyacetone binding subunit of the dihydroxyacetone kinase
YP_416126.1	BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell
YP_416167.1	catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis
YP_416172.1	NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis
YP_416175.1	in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF
YP_416176.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_416177.1	B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE
YP_416183.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_416188.1	catalyzes the release of the N-terminal amino acid from a tripeptide
YP_416198.1	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_416199.1	recognizes the termination signals UGA and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1
YP_416200.1	similar to S. epidermidis transposase sequence
YP_416204.1	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_416205.1	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate
YP_416206.1	catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system
YP_416207.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_416215.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_416216.1	malic enzyme; oxaloacetate-decarboxylating; NAD-dependent; catalyzes the formation of pyruvate form malate
YP_416222.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_416223.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_416224.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_416225.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_416230.1	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_416253.1	catalyzes the dehydration of 3-dehydroquinate to form 3-dehydroshikimate in aromatic amino acid biosynthesis
YP_416257.1	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_416263.1	sigmaB-regulated
YP_416281.1	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_416288.1	transfers D-alanine to the D-alanyl carrier protein during the incorporation of D-alanine into lipoteichoic acid
YP_416290.1	D-alanyl carrier protein subunit; involved in the incorporation of D-alanine into membrane-associated D-alanyl-lipoteichoic acid; D-alanyl carrier protein is the acceptor of activated D-alanine which it donates to a membrane acceptor(D-alanyl transferase) for incorporation into membrane lipoteichoic acid
YP_416302.1	subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_416303.1	subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_416304.1	subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_416305.1	subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone
YP_416306.1	subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_416307.1	subunit B of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in the case of S. meliloti it was proved to be involved specifically with K+ transport
YP_416308.1	subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_416317.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_416318.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_416319.1	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_416328.1	NADPH-dependent; catalyzes the reduction of coenzyme A disulfide
YP_416336.1	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_416350.1	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_416351.2	the anti-alpha factor Spx interacts with RNA polymerase alpha subunit C-terminal domain in a region that interacts with the sigma 70 subunit and may interfere with activation of promoters; in Bacillus subtilis this protein is a substrate for ClpXP protease; blocks transcription of the competence regulatory gene encoded by the srf operon; regulates a number of genes involved in thiol homeostasis including trxA and trxB; monomeric member of ArsC family of proteins; does not bind DNA; contains a disulfide bond between C10 and C13 which may sense disulfide stress
YP_416352.1	enables recognition and targeting of proteins for proteolysis, involved in negative regulation of competence
YP_416360.1	catalyzes the phosphorylation of NAD to NADP
YP_416364.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_416368.1	similar to 2'-5' RNA ligase
YP_416370.1	processive; catalyzes the formation of mono-, di- and tri-glucosyldiacylglycerol by the progressive transfer of glucosyl residues to diacylglycerol; involved in the formation of membrane glycolipids
YP_416371.1	involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of lysine to UDP-N-acetylmuramoyl-L-alanyl-D-glutamate forming UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine
YP_416373.1	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_416394.1	catalyzes the formation of dimethylmenaquinone from 1,4-dihydroxy-2-naphthoate and octaprenyl diphosphate
YP_416398.1	catalyzes the formation of 1,4-dihydroxy-2-naphthoate from O-succinylbenzoyl-CoA
YP_416415.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_416417.1	With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway
YP_416418.1	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_416420.1	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_416421.1	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_416422.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_416423.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_416425.1	involved in de novo purine biosynthesis
YP_416426.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_416442.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_416447.1	E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_416461.1	depletion of this protein in Bacillus subtilis results in defects in cell morphology; crystal structure of Staphylococcus protein shows homodimer; ligand binding protein
YP_416463.1	biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate
YP_416465.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_416473.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_416476.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_416484.1	iron regulated; catalyzes the release of heme from hemoglobin allowing bacterial pathogens to use the host heme as an iron source
YP_416486.1	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_416487.1	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_416488.2	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_416492.1	MutS2; MutS-II; involved in blocking homologous and homeologous recombination; has ATPase activity stimulated by recombination intermediates; inhibits DNA strand exchange
YP_416494.1	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_416496.1	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_416497.1	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_416498.1	converts L-glutamate to D-glutamate, a component of peptidoglycan
YP_416499.1	hydrolyzes non-standard nucleotides such as xanthine and inosine
YP_416503.1	FLIPr; secreted protein that blocks the formyl peptide receptor-like 1 (FPRL1) found in neutrophils, monocytes, B cells, and NK cells; inhibits the binding of chemoattractants (such as formylated peptides) to FPRL1, which initiates the phagocyte mobilization towards the infection site
YP_416514.1	these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_416515.1	these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_416516.1	these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation
YP_416517.1	catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation
YP_416518.1	catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP
YP_416526.1	MraZ; UPF0040; crystal structure shows similarity to AbrB
YP_416530.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_416531.1	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_416534.1	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_416540.1	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_416542.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_416544.1	regulates pyrimidine biosynthesis by binding to the mRNA of the pyr genes, also has been shown to have uracil phosphoribosyltransferase activity
YP_416546.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_416547.1	catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis
YP_416548.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_416549.1	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_416550.1	type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase
YP_416551.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_416555.1	Essential for recycling GMP and indirectly, cGMP
YP_416556.1	Promotes RNA polymerase assembly; latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits
YP_416560.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_416563.1	23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance
YP_416569.1	required for 70S ribosome assembly
YP_416572.1	catalyzes branch migration in Holliday junction intermediates
YP_416573.1	negative regulator of genes involved in fatty acid and phospholipid biosynthesis for gram positive bacteria
YP_416574.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_416577.1	carries the fatty acid chain in fatty acid biosynthesis
YP_416578.1	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_416583.1	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_416584.1	Essential for efficient processing of 16S rRNA
YP_416585.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_416586.1	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_416587.1	essential GTPase; functions in ribosome assembly; binds a unique part of the 23S rRNA; interacts with ribosomal protein L25(Ctc)
YP_416588.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_416589.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_416590.1	Catalyzes the only substrate-level phosphorylation in the TCA cycle
YP_416592.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_416593.1	TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine
YP_416595.1	heat shock protein involved in degradation of misfolded proteins
YP_416596.1	heat shock protein involved in degradation of misfolded proteins
YP_416597.1	CodY; DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase (By similarity). It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor
YP_416598.1	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_416599.1	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_416600.1	Catalyzes the phosphorylation of UMP to UDP
YP_416601.1	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_416602.1	catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate
YP_416605.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_416606.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; required for leading strand synthesis; PolC exhibits 3' to 5' exonuclease activity
YP_416607.1	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_416608.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_416611.1	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_416612.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_416613.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_416615.1	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_416626.1	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_416627.1	protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP
YP_416631.1	catalyzes the coenzyme A dependent formation of succinyl-CoA from 2-oxoglutarate and ferredoxin
YP_416633.1	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_416636.1	This protein performs the mismatch recognition step during the DNA repair process
YP_416639.1	Converts glycerol and ADP to glycerol-3-phosphate and ADP
YP_416642.1	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_416663.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; lysine and threonine sensitive
YP_416664.1	catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine
YP_416665.1	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_416666.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_416671.2	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_416672.1	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_416674.1	Represses a number of genes involved in the response to DNA damage
YP_416682.1	forms homopentamer; channel that opens in response to pressure or hypoosmotic shock
YP_416684.1	Catalyzes the conversion of citrate to isocitrate
YP_416688.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_416689.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_416694.1	this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress
YP_416697.1	catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate
YP_416699.1	with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine
YP_416701.1	Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_416702.1	involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water
YP_416703.1	catalyzes the formation of 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate from N-(5-phospho-beta-D-ribosyl)-anthranilate in tryptophan biosynthesis
YP_416704.1	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_416705.1	catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis
YP_416719.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_416725.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.
YP_416727.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_416728.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_416737.1	catalyzes the hydrolysis of acylphosphate
YP_416745.1	component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA
YP_416746.1	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_416750.1	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_416755.1	this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress
YP_416756.1	this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress
YP_416759.1	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_416789.1	functions in homologous recombination, DNA repair, and chromosome segregation; binds preferentially to three- and four-stranded DNA intermediates; introduces specific nick sites in four-stranded DNA substrates; functions similarly to Escherichia coli RuvC
YP_416794.1	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_416797.1	catalyzes the addition and repair of the 3'-terminal CCA sequence in tRNA; these proteins belong to the CCA-adding enzyme subfamily 2 which does not have phosphohydrolase activity
YP_416804.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_416805.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_416806.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_416807.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_416809.1	Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone
YP_416812.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_416813.1	in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins
YP_416815.1	Catalyzes the formation of (d)CDP from ATP and (d)CMP
YP_416839.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_416857.1	catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate
YP_416866.1	regulates arginine biosynthesis when complexed with arginine by binding at site that overlap the promotors of the arginine biosynthesis genes
YP_416868.1	catalyzes the bidirectional exonucleolytic cleavage of DNA
YP_416869.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_416870.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_416872.1	an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism
YP_416874.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_416880.1	acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; forms a heterodimer with subunit 1 to form the P protein
YP_416881.1	acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; forms a heterodimer with subunit 2 to form the P protein
YP_416882.1	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_416895.1	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_416901.1	Assists in DNA repair by cleaving phosphodiester bonds at apurinic or apyrimidinic sties to produce new 5' ends that are base-free deoxyribose 5-phosphate residues
YP_416905.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; primary sigma factor of bacterium
YP_416909.1	Catalyzes a two-step reaction, first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_416911.1	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_416919.1	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_416921.1	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_416922.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_416923.1	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_416924.1	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_416925.1	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_416927.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_416929.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_416930.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_416931.1	required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA
YP_416940.1	in Bacillus subtilis this enzyme appears to be involved in 30S ribosomal RNA subunit biogenesis
YP_416951.1	necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus
YP_416952.1	functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor
YP_416957.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_416959.1	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_416962.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_416963.1	similar to B. subtilis yrvO protein
YP_416969.1	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_416970.1	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_416972.1	hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine
YP_416974.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_416976.1	part of the preprotein secretory system; forms a complex with protein YajC; SecDFyajC stimulates the proton motive force-driven protein translocation, seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF
YP_416978.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_416979.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_416980.1	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_416981.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_416983.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_416984.1	involved in the peptidyltransferase reaction during translation
YP_416988.1	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_416991.1	Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase
YP_416994.1	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_416997.1	Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway
YP_416998.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_417000.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_417002.1	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_417003.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_417004.1	binds and unfolds substrates as part of the ClpXP protease
YP_417005.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_417008.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_417010.1	IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits
YP_417012.1	catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr)
YP_417013.1	Primosomal protein that may act to load helicase DnaC during DNA replication
YP_417017.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_417023.1	Converts isocitrate to alpha ketoglutarate
YP_417024.1	catalyzes the formation of citrate from acetyl-CoA and oxaloacetate
YP_417027.1	catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis
YP_417028.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein
YP_417029.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits
YP_417036.1	catalyzes the opening and hydrolysis of the beta-lactam ring of beta-lactam antibiotics such as penicillins and cephalosporins
YP_417040.1	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_417042.1	antioxidant activity; thioredoxin-dependent thiol peroxidase; forms homodimers in solution; shows substrate specificity to alkyl hydroperoxides; periplasmic protein
YP_417044.1	Required for the synthesis of the thiazole moiety
YP_417046.1	acts to negatively regulates ftsZ ring formation by modulating the frequency and position of the ftsZ ring formation
YP_417048.1	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_417052.1	catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate
YP_417062.1	catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate
YP_417063.1	Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA
YP_417067.1	catalyzes the formation of 3-deoxy-D-aribino-hept-2-ulosonate 7-phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate and the formation of prephenate from chorismate
YP_417070.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_417078.1	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_417081.1	divalent metal ion-dependent extracellular dipeptidase; able to hydrolyze a broad range of dipeptides but no tri-, tetra-, or larger oligopeptides; differences in the amino acid specificity of the cleavage site varies between species; similar to succinyl-diaminopimelate desuccinylases
YP_417087.1	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_417094.1	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_417096.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_417101.1	catalyzes the reduction of arsenate to arsenite; also can dephosphorylate tyrosine phosphorylated proteins, aryl phosphates, and acyl phosphates
YP_417107.1	similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity
YP_417109.1	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_417113.2	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_417114.1	PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP
YP_417225.1	catalyzes the formation of protoporphyrin IX from protoporphyrinogen IX
YP_417226.1	protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic
YP_417227.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III
YP_417237.1	catalyzes the exonucleic cleavage of mRNA yielding nucleioside 5'-phosphates
YP_417246.1	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_417259.1	converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate
YP_417267.1	binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities
YP_417268.1	monofunctional; catalyzes the elongation of glycan strands in cell wall biosynthesis
YP_417282.1	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_417289.1	involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function
YP_417292.1	similar to YegS from E. coli
YP_417294.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA
YP_417295.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA
YP_417296.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain
YP_417303.1	PcrB-like protein; GGGP synthase; member of prenyltransferases that transfer isoprenoid groups to nonisoprenoid acceptors; functions in form GGGP from glycerol-1-phosphate (G-1-P) and geranylgeranyl pyrophosphate (GGPP); important in lipid metabolism and especially important as the ether linkages in archaea are different than those in bacteria; GGGP synthase lies at the branch point for membrane lipid biosynthesis; cytosolic; T acidophilum protein acts as a homodimer while M thermoautotrophicum protein has been reported to function as a pentamer
YP_417305.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_417311.1	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_417312.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate
YP_417318.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_417339.1	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_417342.1	catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine
YP_417372.1	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_417373.1	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_417389.1	modulates transcription in response to the NADH/NAD(+) redox state
YP_417393.1	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_417397.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_417399.1	with IlvI catalyzes the formation of 2-acetolactate from pyruvate, this subunit subunit is required for full activity and valine sensitivity; also known as acetolactate synthase small
YP_417400.1	catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis
YP_417401.1	catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis
YP_417402.1	catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis
YP_417403.1	dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate
YP_417404.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D
YP_417405.1	catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic
YP_417408.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma B is not essential for sporulation; rather it is required for maximal expression of ctc and csbA which are transcribed in the early stationary phase under conditions inimical to sporulation; induced by heat shock, salt stress, oxidative stress, glucose limitation, oxygen limitation and entry into stationary phase
YP_417409.1	binds to sigma-B preventing the formation of an RNA polymerase holoenzyme
YP_417415.1	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_417419.1	one of the components of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; the C subunit may be involved in assembly of the KDP complex
YP_417420.1	One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions
YP_417421.1	catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions
YP_417426.1	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_417434.1	Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate
YP_417435.1	catalyzes the formation of 4-methyl-5-(2-phosphoethyl)-thiazole and ADP from 4-methyl-5-(2-hydroxyethyl)-thiazole and ATP
YP_417441.1	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_417442.1	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_417444.1	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_417445.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_417446.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_417447.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_417448.1	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_417449.1	produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel
YP_417450.1	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_417451.1	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_417454.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_417455.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_417460.1	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_417461.1	catalyzes the formation of thymidine 5'-phosphate from thymidine
YP_417462.1	RpmE2; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome
YP_417463.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_417466.1	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_417467.1	catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate; induced by anaerobic conditions in Bacillus subtilis
YP_417469.1	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_417470.1	participates in both the initiation and recycling phases of transcription; in the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling
YP_417472.1	catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type II pantothenate kinases are not regulated by feedback inhibition by coenzyme A
YP_417476.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_417478.1	Catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway
YP_417479.1	catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate
YP_417480.1	catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate
YP_417492.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_417499.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_417528.1	catalyzes the formation of 6-phospho-galactose from a 6-phospho-beta-galactoside
YP_417531.1	catalyzes the reversible reaction of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate; in Streptococcus pyogenes there are two paralogs of tagatose-bisphosphate aldolase, encoded by lacD1 and lacD2; expression of lacD1 is highly regulated by environmental conditions while lacD2 specializes in an efficient utilization of carbohydrate sources
YP_417532.1	catalyzes the formation of tagatose 1,6-bisphosphate from tagatose 6-phosphate and ATP
YP_417533.1	catalyzes the interconversion of galactose 6-phosphate to tagatose 6-phosphate
YP_417534.1	catalyzes the interconversion of galactose 6-phosphate to tagatose 6-phosphate; tagatose pathway for galactose utilization
YP_417536.1	Modulates the activities of several enzymes which are inactive in their acetylated form
YP_417545.1	catalyzes the formation of 2-acetolactate from pyruvate in stationary phase
YP_417548.1	forms a direct contact with the tRNA during translation
YP_417549.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_417550.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_417552.1	with CbiNQ forms the ABC transporter for cobalt import; Staphylococcus has two adjacent copies of this gene
YP_417553.1	with CbiNQ forms the ABC transporter for cobalt import; Staphylococcus has two adjacent copies of this gene
YP_417554.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_417555.1	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_417556.1	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_417557.1	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_417558.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_417559.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_417560.1	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_417561.1	late assembly protein
YP_417562.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_417563.1	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_417564.1	binds 5S rRNA along with protein L5 and L25
YP_417565.1	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_417566.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_417567.2	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 appear to contain the zinc-binding motif
YP_417568.1	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_417569.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_417570.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_417571.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_417572.1	one of the stabilizing components for the large ribosomal subunit
YP_417573.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_417574.1	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_417575.1	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_417576.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_417577.1	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_417578.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_417579.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_417580.1	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_417581.1	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_417598.1	in Escherichia coli MobA links a guanosine 5'-phosphate to molydopterin to form molybdopterin guanine dinucleotide during molybdenum cofactor biosynthesis
YP_417603.1	MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis
YP_417609.1	involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth
YP_417617.1	UreA, with UreB and UreC catalyzes the hydrolysis of urea into ammonia and carbon dioxide; nickel metalloenzyme; accessory proteins UreD, UreE, UreF, and UreG are necessary for assembly of the metallocenter
YP_417618.1	ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori and Yersinia enterocolitica the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 UreC (alpha) and 3 UreAB (gamma/beta); in Staphylococcus saprophyticus plays a role in bladder invasiveness and may induce the formation of kidney and bladder stones due to the alkalization of urine
YP_417619.1	ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 ureC (alpha) and 3 ureAB (gamma/beta) subunits
YP_417620.1	involved in the assembly of the urease metallocenter; possible nickel donor
YP_417664.1	catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway
YP_417665.1	catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism
YP_417668.1	catalyzes the formation of glutamate and formamide from N-formimidoyl-L-glutamate
YP_417670.1	catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_417682.1	catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate
YP_417701.2	malate dehydrogenase; catalyzes the oxidation of malate to oxaloacetate
YP_417752.1	2,3-bisphosphoglycerate-dependent; catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate
YP_417760.1	catalyzes the formation of pimeloyl-CoA from pimelate and coenzyme A
YP_417762.1	catalyzes the formation of biotin from dethiobiotin and sulfur 2 S-adenosyl-L-methionine
YP_417780.1	ketopantoate reductase; catalyzes the NADPH reduction of ketopantoate to pantoate; functions in pantothenate (vitamin B5) biosynthesis
YP_417863.1	catalyzes the formation of acetyl phosphate from pyruvate
YP_417870.1	similar to streptococcal exotoxin G
YP_417877.1	catalyzes the conversion of 1-proline-5-carboxylate dehydrogenase to L-glutamate
YP_417881.1	catalyzes the formation of pyruvate from lactate
YP_417912.1	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_417918.1	Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5)
YP_417919.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_417920.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_417926.1	catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis
YP_417927.1	malate dehydrogenase; catalyzes the oxidation of malate to oxaloacetate
YP_417933.1	catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine
YP_417938.1	Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates
YP_417940.1	catalyzes the formation of siroheme from precorrin-2
YP_417954.2	catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP
YP_417956.1	catalyzes the formation of ornithine and carbamylphosphate from citrulline in the arginine catabolic pathway
YP_417957.1	catalyzes the degradation of arginine to citruline and ammonia
YP_417979.1	this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; a fusion protein of this enzyme with MsrB provides protection against oxidative stress in Neisseria gonorrhoeae
YP_417985.1	predicted polysaccharide polymerase involved in biofilm formation; required for the synthesis of the beta-1,6-N-acetylglucosamine polysaccharide; PgaC; in Yersinia the HmsR protein is an inner membrane protein
YP_417992.1	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_417993.1	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_417994.1	catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-hosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide
YP_417995.1	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_417996.1	catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis
YP_417997.1	catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer
YP_417998.1	short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ
YP_417999.1	May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine
YP_418009.1	catalyzes the removal of 5-oxoproline from various penultimate amino acid residues except L-proline
YP_418029.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_418030.1	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_418031.1	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_418032.1	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_418033.1	in Escherichia coli transcription of this gene is enhanced by polyamines