-- dump date   	20140619_044403
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_003216515.1	catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA
YP_003216520.1	biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate
YP_003216526.1	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_003216527.1	non-specific DNA-binding; scans chromosomes during sporulation for DNA-damage; delays initiation of sporulation; participates in a checkpoint signaling cascade for cell-cycle progression and DNA repair
YP_003216548.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_003216549.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_003216550.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_003216560.1	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
YP_003216561.1	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_003216562.1	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_003216565.1	binds directly to 23S ribosomal RNA
YP_003216567.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_003216570.1	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_003216571.1	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_003216572.2	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_003216573.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_003216574.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_003216575.1	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_003216577.1	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_003216578.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_003216580.1	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_003216582.1	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_003216584.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_003216588.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_003216591.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_003216592.1	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_003216595.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_003216598.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_003216602.1	smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group have the motif
YP_003216603.1	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_003216604.1	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_003216606.1	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_003216607.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_003216609.1	with CbiNQ forms the ABC transporter for cobalt import; Clostridia have two adjacent copies of this gene
YP_003216616.1	Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates
YP_003216621.1	catalyzes the synthesis of butanoylphosphate from butanoyl-CoA and inorganic phosphate
YP_003216622.1	catalyzes the phosphorylation of 2-butanoate to butanoyl phosphate
YP_003216625.1	catalyzes the coenzyme A-dependent oxidation of 3-methyl-2-oxobutanoate coupled to the reduction of ferredoxin producing S-(2-methylpropanoyl)-CoA
YP_003216632.1	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_003216637.1	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_003216661.1	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_003216681.1	modulates transcription in response to the NADH/NAD(+) redox state
YP_003216695.1	responsible for channeling the electrons from the oxidation of dihydroorotate from the FMN redox center in the pyrD subunit to the ultimate electron acceptor NAD(+)
YP_003216696.1	catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway, using a flavin nucleotide as an essential cofactor; subclass 1B is a heterotetramer consisting of two PyrDB subunits, similar to the PyrDA subunits and two PyrK subunits
YP_003216697.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_003216706.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_003216716.1	FrwC with FrwB, FrwD and PtsA forms a PEP-dependent sugar phosphotransferase system permease which may phosphorylate and transport sugars into the cell; forms translocation channel and contains the specific substrate-binding site
YP_003216717.1	FrwB with FrwC, FrwD and PtsA forms a PEP-dependent sugar phosphotransferase system (PTS) permease which may phosphorylate and transport sugars into the cell; cytoplasmic protein that interacts with complex EIIA; contains the second phosphorylation site of the PTS
YP_003216724.1	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_003216728.1	involved in de novo purine biosynthesis
YP_003216758.1	forms a junction between the M-ring and FlgB during flagella biosynthesis
YP_003216759.1	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_003216772.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_003216774.1	FlhB is a membrane protein responsible for substrate specificity in switching from rod/hook-type export to filament-type export; FliR is required for export of flagellar proteins, although a specific role has not yet been determined
YP_003216775.1	membrane protein involved in the flagellar export apparatus
YP_003216776.1	positive regulator of class III flagellar genes
YP_003216780.1	makes up the distal portion of the flagellar basal body rod; the Clostridia have two adjacent copies of the FlgG gene
YP_003216781.1	makes up the distal portion of the flagellar basal body rod; the Clostridia have 2 adjacent copies of the FlgG gene
YP_003216785.1	molecular chaperone
YP_003216842.1	catalyzes the removal of amino acids from the N termini of peptides
YP_003216845.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_003216976.1	catalyzes the formation of L-proline from L-ornithine
YP_003216990.1	catalyzes the formation of glutamate from glutamine
YP_003217005.1	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_003217128.1	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_003217129.1	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_003217140.1	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_003217147.1	catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate
YP_003217154.1	part of a complex that catalyzes the cleavage of acetyl-CoA
YP_003217155.1	part of a complex that catalyzes the cleavage of acetyl-CoA
YP_003217157.1	in acetogenic organisms, this enzyme complex converts carbon dioxide to acetyl-CoA while in methanogenic organisms this enzyme is used to degrade acetyl-CoA to form methane and carbon dioxide; part of an enzyme complex
YP_003217158.1	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_003217166.1	catalyzes the formation of L-histidinol from L-histidinol phosphate
YP_003217183.1	Required for the synthesis of the thiazole moiety
YP_003217197.1	catalyzes the conversion of sorbitol 6-phosphate into fructose 6-phosphate
YP_003217201.1	binds to sigma F preventing its association with RNA polymerase during sporulation
YP_003217263.1	in Methanococcus jannaschii this protein catalyzes the condensation of alpha-ketoglutarate and acetyl-CoA to form trans-homoaconitate; functions in alphaketosuberate synthesis which is a precursor in coenzyme B and biotin synthesis
YP_003217264.1	Catalyzes the conversion of citrate to isocitrate
YP_003217272.1	Catalyzes the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate
YP_003217321.1	catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine
YP_003217334.1	oxidoreductase
YP_003217336.1	catalyzes the formation of decaprenylphosphoryl-5-phosphoribose from phosphoribose diphosphate and decaprenyl phosphate
YP_003217357.1	Catalyzes the reversible hydration of fumaric acid to yield I-malic acid
YP_003217401.1	catalyzes the release of the N-terminal amino acid from a tripeptide
YP_003217430.1	catalyzes the removal of amino acids from the N termini of peptides
YP_003217448.1	two-component sensor histidine kinase
YP_003217463.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_003217487.1	works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell
YP_003217499.1	involved in the peptidyltransferase reaction during translation
YP_003217513.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_003217514.1	negative regulator of genes involved in fatty acid and phospholipid biosynthesis for gram positive bacteria
YP_003217515.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_003217560.1	catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose
YP_003217583.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_003217585.1	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_003217600.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_003217613.1	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_003217620.1	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_003217638.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_003217642.1	Modulates the activities of several enzymes which are inactive in their acetylated form
YP_003217661.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; diaminopimelate sensitive
YP_003217664.1	catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA
YP_003217668.1	protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP
YP_003217673.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_003217678.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_003217753.1	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_003217796.1	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_003217801.1	synthesizes RNA primers at the replication forks
YP_003217847.1	catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate
YP_003217858.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_003217859.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_003217867.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_003217872.1	catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis
YP_003217883.1	function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain
YP_003217896.1	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_003217897.1	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_003217923.1	subname: full=phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
YP_003217985.1	catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions
YP_003217986.1	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_003217987.1	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_003218052.1	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_003218069.1	catalyzes the removal of 5-oxoproline from various penultimate amino acid residues except L-proline
YP_003218088.1	arsenical pump membrane protein precursor
YP_003218092.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_003218095.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_003218099.1	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_003218108.1	MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis
YP_003218136.1	catalyzes the formation of inosine from adenosine
YP_003218173.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_003218174.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_003218198.1	multi-drug resistance efflux pump
YP_003218207.1	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_003218221.1	catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate
YP_003218222.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_003218223.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_003218224.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_003218320.1	ethanolamine utilization protein EutA
YP_003218322.1	catalyzes the formation of acetaldehyde from ethanolamine
YP_003218384.1	RNA-binding protein (host factor-I protein)
YP_003218386.1	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_003218430.1	catalyzes the formation of ornithine and carbamylphosphate from citrulline in the arginine catabolic pathway
YP_003218434.1	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_003218453.1	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_003218454.1	similar to YegS from E. coli
YP_003218478.1	Zn-dependent extracellular dipeptidase; similar to succinyl-diaminopimelate desuccinylases
YP_003218479.1	catalyzes the formation of pyruvate from 2,3-diaminopropionate
YP_003218512.1	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_003218513.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_003218524.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_003218531.1	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_003218540.1	mutations in this gene result in a compromised ability for drug-inducible mexXY expression; expression is inducible by the same ribosome-targeting agents that induce mexXY
YP_003218548.1	catalyzes the formation of biotin from dethiobiotin and sulfur
YP_003218549.1	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; in Thermotoga this enzyme has an extra C-terminal domain
YP_003218561.1	catalyzes the reduction of hydroxylamine to ammonia and water
YP_003218595.1	sugar transporter
YP_003218618.1	with AsrAC catalyzes the reduction of sulfite to hydrogen sulfide
YP_003218626.1	catalyzes the formation of pyruvate and N-acetylmannosamine from N-acetylneuraminic acid
YP_003218627.1	Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate
YP_003218631.1	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_003218659.1	decatenates replicating daughter chromosomes
YP_003218662.1	catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate in the anaerobic catabolism of L-ascorbate; links the arabinose metabolic pathway to the pentose phosphate pathway and allows the bacteria to use arabinose as an energy source
YP_003218702.1	similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity
YP_003218703.1	Catalyzes the transfer of the phosphoribosyl moiety from 5-phospho--D-ribosyl-1-pyrophosphate (PRib-PP) to the 6-oxo-guanine and -xanthine
YP_003218708.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_003218724.1	GrdA accepts a carboxymethylselenoether from protein B and transfers it to protein C forming a protein C-bound acetyl-thioester; oxidized GrdA is then reduced by thioredoxin
YP_003218741.1	catalyzes the formation of oxaloacetate from L-aspartate
YP_003218742.1	3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate
YP_003218749.1	catalyzes the phosphorylation of 2-butanoate to butanoyl phosphate
YP_003218750.1	Involved in the incorporation of exogenous aryl acids in the biosynthesis of aromatic amino acids: catalysis of the ferredoxin-dependent oxidative decarboxylation of arylpyruvates.
YP_003218775.1	catalyzes the formation of dUMP from dUTP
YP_003218783.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_003218799.1	catalyzes the phosphorylation of 2-butanoate to butanoyl phosphate
YP_003218807.1	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_003218825.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_003218836.1	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_003218842.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_003218845.1	Initiates the rapid degradation of small, acid-soluble proteins during spore germination
YP_003218848.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_003218868.1	catalyzes the formation of selenocysteinyl-tRNA(Sec) from seryl-tRNA(Sec) and L-selenophosphate in selenoprotein biosynthesis
YP_003218873.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_003218888.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_003218906.1	member of metallo-beta-lactamase family; the purified enzyme from Escherichia coli forms dimeric zinc phosphodiesterase; in Bacillus subtilis this protein is a 3'-tRNA processing endoribonuclease and is essential while in Escherichia coli it is not; associates with two zinc ions
YP_003218907.1	CoADR; specific for coenzyme A disulfide; requires NADH; involved in protecting cells against reactive oxygen species by recycling coenzyme A disulfide which can reduce hydrogen peroxide
YP_003218919.1	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_003218925.1	catalyzes branch migration in Holliday junction intermediates
YP_003218928.1	required for 70S ribosome assembly
YP_003218955.1	Essential for recycling GMP and indirectly, cGMP
YP_003218964.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_003218973.1	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_003218982.1	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 2 subfamily; some organisms carry two different copies of this enzyme; in some organisms, the type 2 subfamily is associated with resistance to the antibiotic pseudomonic acid (mupirocin)
YP_003218991.1	ACT domain-containing protein
YP_003219000.1	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_003219010.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor is responsible for the expression of sporulation specific genes and is expressed after engulfment; this factor is involved in the transcription of small acid-soluble proteins involved in protecting the forespore chromatin
YP_003219011.1	sigma-29; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor is responsible for the expression of sporulation specific genes and is expressed in the mother cell at the onset of sporulation
YP_003219022.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_003219027.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_003219032.1	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_003219046.1	catalyzes the formation of acetoacetate from 3-hydroxybutyrate
YP_003219062.1	catalyzes the formation of asparagine from aspartate and ammonia
YP_003219075.1	catalyzes the conversion of shikimate to 3-dehydroshikimate
YP_003219109.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_003219111.1	hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine
YP_003219172.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_003219173.1	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_003219174.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_003219175.1	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_003219181.1	catalyzes the reduction of tartronate semialdehyde to glycerate
YP_003219198.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_003219245.1	transports degraded pectin products into the bacterial cell
YP_003219266.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the D subunit is part of the catalytic core of the ATP synthase complex
YP_003219267.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the B subunit is part of the catalytic core of the ATP synthase complex
YP_003219268.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the A subunit is part of the catalytic core of the ATP synthase complex
YP_003219269.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the F subunit is part of the catalytic core of the ATP synthase complex
YP_003219270.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the C subunit is part of the catalytic core of the ATP synthase complex
YP_003219272.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the K subunit is a nonenzymatic component which binds the dimeric form by interacting with the G and E subunits
YP_003219281.1	involved in production of dipicolinic acid (pyridine-2,6-dicarboxylic acid, DPA) which is synthesized late in sporulation in the mother cell and accumulates in the spore; mutations in this gene result in a lack of DPA synthesis; presumably functions with SpoVFA to form the synthase enzyme
YP_003219282.1	catalyzes the synthesis of dipicolinic acid from dihydroxydipicolinic acid; plays a role in spore heat resistance
YP_003219299.1	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_003219317.1	transports degraded pectin products into the bacterial cell
YP_003219357.1	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_003219362.1	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_003219389.1	catalyzes the reversible reaction of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate; in enteric bacteria there are two D-tagatose 1,6-bisphosphate-specific aldolases: KbaY (also called AgaY), involved in catabolism of N-acetyl-galactosamine and D-galactosamine, and GatY which is part of the galactitol catabolism pathway
YP_003219401.1	involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake
YP_003219419.1	alcohol dehydrogenase
YP_003219424.1	catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis
YP_003219429.1	6-phospho-beta-glucosidase BglA
YP_003219486.1	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_003219502.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_003219503.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_003219504.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_003219512.1	in Escherichia coli expression is induced in response to phase-specific signals and controlled by RpoS
YP_003219514.1	Zn-dependent extracellular dipeptidase; similar to succinyl-diaminopimelate desuccinylases
YP_003219515.1	catalyzes the formation of pyruvate from 2,3-diaminopropionate
YP_003219553.1	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_003219570.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_003219594.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_003219605.1	pz-peptidase
YP_003219636.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_003219640.1	binds and unfolds substrates as part of the ClpXP protease
YP_003219642.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_003219693.1	catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time. Proposed to be responsible for the synthesis of the lagging strand. In the low GC gram positive bacteria this enzyme is less processive and more error prone than its counterpart in other bacteria.
YP_003219699.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_003219706.1	catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system
YP_003219707.1	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_003219709.1	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_003219716.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_003219718.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_003219720.1	precorrin-6x reductase
YP_003219722.1	catalyzes the formation of cobalt-precorrin 4 from cobalt-precorrin 3
YP_003219724.1	catalyzes the methylation of either C-15 or C-5 in cobalt-precorrin-6Y to form cobalt-precorrin-7W; decarboxylating
YP_003219725.1	catalyzes the methylation of C-5 in cobalt-precorrin-6Y to form cobalt-precorrin-7W-a
YP_003219726.1	Catalyzes the methylation of C-1 in cobalt-precorrin-5 and the subsequent extrusion of acetic acid from the resulting intermediate to form cobalt-precorrin-6A
YP_003219727.1	catalyzes the interconversion of cobalt-precorrin-8X and cobyrinic acid in the anaerobic biosynthesis of cobalamin
YP_003219731.1	responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid
YP_003219732.1	catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation
YP_003219743.1	metalloprotein
YP_003219745.1	catalyzes the reversible reaction of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate; in enteric bacteria there are two D-tagatose 1,6-bisphosphate-specific aldolases: KbaY (also called AgaY), involved in catabolism of N-acetyl-galactosamine and D-galactosamine, and GatY which is part of the galactitol catabolism pathway
YP_003219777.1	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_003219779.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_003219784.1	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_003219790.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_003219795.1	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_003219799.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_003219814.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_003219827.1	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_003219830.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_003219835.1	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_003219865.1	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_003219867.1	type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP
YP_003219878.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_003219901.1	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_003219902.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_003219903.1	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_003219904.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_003219911.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_003219952.1	the Vibrio parahaemolyticus gene VP2867 was found to be a potassium/proton antiporter; can rapidly extrude potassium against a potassium gradient at alkaline pH when cloned and expressed in Escherichia coli
YP_003219965.1	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_003219977.1	Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides
YP_003219983.1	SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA
YP_003219988.1	acts to load the DnaB helicase onto the initiation site during DNA replication
YP_003219989.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_003220009.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_003220010.1	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_003220011.1	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_003220015.1	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