-- dump date   	20140619_044239
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_003213056.1	binds the polymerase to DNA and acts as a sliding clamp
YP_003213070.1	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_003213075.1	biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate
YP_003213081.1	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_003213082.1	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_003213103.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_003213104.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_003213105.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_003213114.1	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
YP_003213115.1	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_003213116.1	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_003213119.1	binds directly to 23S ribosomal RNA
YP_003213121.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_003213124.1	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_003213125.1	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_003213126.2	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_003213127.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_003213128.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_003213129.1	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_003213131.1	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_003213132.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_003213134.1	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_003213136.1	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_003213138.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_003213142.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_003213145.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_003213146.1	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_003213149.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_003213152.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_003213156.1	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_003213157.1	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_003213158.1	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_003213160.1	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_003213161.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_003213163.1	with CbiNQ forms the ABC transporter for cobalt import; Clostridia have two adjacent copies of this gene
YP_003213166.1	truncated
YP_003213170.1	Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates
YP_003213175.1	catalyzes the synthesis of butanoylphosphate from butanoyl-CoA and inorganic phosphate
YP_003213176.1	catalyzes the phosphorylation of 2-butanoate to butanoyl phosphate
YP_003213179.1	catalyzes the coenzyme A-dependent oxidation of 3-methyl-2-oxobutanoate coupled to the reduction of ferredoxin producing S-(2-methylpropanoyl)-CoA
YP_003213183.1	[isomerizing]
YP_003213186.1	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_003213191.1	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_003213215.1	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_003213235.1	modulates transcription in response to the NADH/NAD(+) redox state
YP_003213249.1	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_003213250.1	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_003213251.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_003213260.1	[glutamine-hydrolyzing]; contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_003213270.1	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_003213271.1	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_003213278.1	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_003213282.1	involved in de novo purine biosynthesis
YP_003213312.1	forms a junction between the M-ring and FlgB during flagella biosynthesis
YP_003213313.1	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_003213326.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_003213328.1	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_003213329.1	membrane protein involved in the flagellar export apparatus
YP_003213330.1	positive regulator of class III flagellar genes
YP_003213334.1	makes up the distal portion of the flagellar basal body rod; the Clostridia have two adjacent copies of the FlgG gene
YP_003213335.1	makes up the distal portion of the flagellar basal body rod; the Clostridia have 2 adjacent copies of the FlgG gene
YP_003213339.1	molecular chaperone
YP_003213396.1	catalyzes the removal of amino acids from the N termini of peptides
YP_003213399.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_003213423.1	[glutamine-hydrolyzing]
YP_003213511.1	aminobenzoyl-glutamate transporter
YP_003213529.1	catalyzes the formation of L-proline from L-ornithine
YP_003213543.1	catalyzes the formation of glutamate from glutamine
YP_003213558.1	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_003213681.1	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_003213682.1	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_003213693.1	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_003213700.1	catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate
YP_003213707.1	part of a complex that catalyzes the cleavage of acetyl-CoA
YP_003213708.1	part of a complex that catalyzes the cleavage of acetyl-CoA
YP_003213710.1	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_003213711.1	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_003213719.1	catalyzes the formation of L-histidinol from L-histidinol phosphate
YP_003213736.1	Required for the synthesis of the thiazole moiety
YP_003213750.1	catalyzes the conversion of sorbitol 6-phosphate into fructose 6-phosphate
YP_003213754.1	binds to sigma F preventing its association with RNA polymerase during sporulation
YP_003213816.1	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_003213817.1	Catalyzes the conversion of citrate to isocitrate
YP_003213825.1	Catalyzes the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate
YP_003213873.1	catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine
YP_003213886.1	oxidoreductase
YP_003213888.1	catalyzes the formation of decaprenylphosphoryl-5-phosphoribose from phosphoribose diphosphate and decaprenyl phosphate
YP_003213909.1	Catalyzes the reversible hydration of fumaric acid to yield I-malic acid
YP_003213955.1	catalyzes the release of the N-terminal amino acid from a tripeptide
YP_003213984.1	catalyzes the removal of amino acids from the N termini of peptides
YP_003214002.1	two-component sensor histidine kinase
YP_003214017.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_003214041.1	works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell
YP_003214053.1	involved in the peptidyltransferase reaction during translation
YP_003214067.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_003214068.1	negative regulator of genes involved in fatty acid and phospholipid biosynthesis for gram positive bacteria
YP_003214069.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_003214114.1	catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose
YP_003214137.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_003214139.1	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_003214154.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_003214167.1	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_003214174.1	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_003214192.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_003214196.1	Modulates the activities of several enzymes which are inactive in their acetylated form
YP_003214215.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; diaminopimelate sensitive
YP_003214218.1	catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA
YP_003214222.1	protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP
YP_003214227.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_003214232.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_003214307.1	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_003214350.1	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_003214355.1	synthesizes RNA primers at the replication forks
YP_003214401.1	catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate
YP_003214412.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_003214413.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_003214421.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_003214426.1	catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis
YP_003214437.1	function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain
YP_003214450.1	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_003214451.1	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_003214479.1	snf2-related protein
YP_003214541.1	catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions
YP_003214542.1	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_003214543.1	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_003214581.1	[Mn]
YP_003214608.1	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_003214625.1	catalyzes the removal of 5-oxoproline from various penultimate amino acid residues except L-proline
YP_003214645.1	arsenical pump membrane protein precursor
YP_003214649.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_003214652.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_003214656.1	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_003214665.1	MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis
YP_003214692.1	catalyzes the formation of inosine from adenosine
YP_003214729.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_003214730.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_003214763.1	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_003214777.1	catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate
YP_003214778.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_003214779.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_003214780.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_003214789.1	cell surface protein (bnr/asp-box repeat protein); conserved repeat domain protein
YP_003214811.1	ethanolamine utilization protein EutA
YP_003214813.1	catalyzes the formation of acetaldehyde from ethanolamine
YP_003214875.1	RNA-binding protein (host factor-I protein)
YP_003214877.1	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_003214921.1	catalyzes the formation of ornithine and carbamylphosphate from citrulline in the arginine catabolic pathway
YP_003214925.1	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_003214944.1	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_003214945.1	similar to YegS from E. coli
YP_003214969.1	Zn-dependent extracellular dipeptidase; similar to succinyl-diaminopimelate desuccinylases
YP_003214970.1	catalyzes the formation of pyruvate from 2,3-diaminopropionate
YP_003215003.1	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_003215004.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_003215015.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_003215022.1	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_003215031.1	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_003215039.1	catalyzes the formation of biotin from dethiobiotin and sulfur
YP_003215040.1	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_003215052.1	catalyzes the reduction of hydroxylamine to ammonia and water
YP_003215086.1	sugar transporter
YP_003215109.1	with AsrAC catalyzes the reduction of sulfite to hydrogen sulfide
YP_003215117.1	catalyzes the formation of pyruvate and N-acetylmannosamine from N-acetylneuraminic acid
YP_003215118.1	Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate
YP_003215122.1	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_003215150.1	decatenates replicating daughter chromosomes
YP_003215153.1	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_003215193.1	similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity
YP_003215194.1	Catalyzes the transfer of the phosphoribosyl moiety from 5-phospho--D-ribosyl-1-pyrophosphate (PRib-PP) to the 6-oxo-guanine and -xanthine
YP_003215199.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_003215215.1	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_003215231.1	[carboxylating]
YP_003215232.1	catalyzes the formation of oxaloacetate from L-aspartate
YP_003215233.1	3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate
YP_003215240.1	catalyzes the phosphorylation of 2-butanoate to butanoyl phosphate
YP_003215241.1	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_003215266.1	catalyzes the formation of dUMP from dUTP
YP_003215274.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_003215290.1	catalyzes the phosphorylation of 2-butanoate to butanoyl phosphate
YP_003215298.1	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_003215316.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_003215327.1	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_003215333.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_003215336.1	Initiates the rapid degradation of small, acid-soluble proteins during spore germination
YP_003215339.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_003215360.1	catalyzes the formation of selenocysteinyl-tRNA(Sec) from seryl-tRNA(Sec) and L-selenophosphate in selenoprotein biosynthesis
YP_003215365.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_003215380.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_003215387.1	binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities
YP_003215399.1	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_003215400.1	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_003215404.1	[UDP-forming]
YP_003215411.1	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_003215417.1	catalyzes branch migration in Holliday junction intermediates
YP_003215420.1	required for 70S ribosome assembly
YP_003215447.1	Essential for recycling GMP and indirectly, cGMP
YP_003215456.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_003215465.1	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_003215474.1	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_003215483.1	ACT domain-containing protein
YP_003215492.1	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_003215502.1	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_003215503.1	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_003215514.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_003215519.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_003215524.1	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_003215538.1	catalyzes the formation of acetoacetate from 3-hydroxybutyrate
YP_003215554.1	catalyzes the formation of asparagine from aspartate and ammonia
YP_003215567.1	catalyzes the conversion of shikimate to 3-dehydroshikimate
YP_003215601.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_003215603.1	hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine
YP_003215664.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_003215665.1	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_003215666.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_003215667.1	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_003215673.1	catalyzes the reduction of tartronate semialdehyde to glycerate
YP_003215690.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_003215737.1	transports degraded pectin products into the bacterial cell
YP_003215758.1	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_003215759.1	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_003215760.1	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_003215761.1	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_003215762.1	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_003215764.1	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_003215773.1	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_003215774.1	catalyzes the synthesis of dipicolinic acid from dihydroxydipicolinic acid; plays a role in spore heat resistance
YP_003215792.1	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_003215810.1	transports degraded pectin products into the bacterial cell
YP_003215850.1	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_003215855.1	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_003215882.1	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_003215894.1	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_003215912.1	alcohol dehydrogenase
YP_003215917.1	catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis
YP_003215922.1	6-phospho-beta-glucosidase BglA
YP_003215979.1	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_003215995.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_003215996.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_003215997.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_003216005.1	in Escherichia coli expression is induced in response to phase-specific signals and controlled by RpoS
YP_003216007.1	Zn-dependent extracellular dipeptidase; similar to succinyl-diaminopimelate desuccinylases
YP_003216008.1	catalyzes the formation of pyruvate from 2,3-diaminopropionate
YP_003216046.1	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_003216063.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_003216087.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_003216098.1	pz-peptidase
YP_003216129.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_003216133.1	binds and unfolds substrates as part of the ClpXP protease
YP_003216135.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_003216186.1	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_003216192.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_003216199.1	catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system
YP_003216200.1	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_003216202.1	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_003216209.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_003216211.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_003216213.1	precorrin-6x reductase
YP_003216215.1	catalyzes the formation of cobalt-precorrin 4 from cobalt-precorrin 3
YP_003216217.1	catalyzes the methylation of either C-15 or C-5 in cobalt-precorrin-6Y to form cobalt-precorrin-7W; decarboxylating
YP_003216218.1	catalyzes the methylation of C-5 in cobalt-precorrin-6Y to form cobalt-precorrin-7W-a
YP_003216219.1	[deacetylating]; 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_003216220.1	catalyzes the interconversion of cobalt-precorrin-8X and cobyrinic acid in the anaerobic biosynthesis of cobalamin
YP_003216224.1	responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid
YP_003216225.1	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_003216236.1	metalloprotein
YP_003216238.1	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_003216270.1	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_003216272.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_003216277.1	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_003216283.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_003216288.1	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_003216292.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_003216302.1	(Corrin/Porphyrin)
YP_003216307.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_003216320.1	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_003216323.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_003216328.1	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_003216358.1	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_003216360.1	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_003216371.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_003216394.1	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_003216395.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_003216396.1	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_003216397.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_003216404.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_003216457.1	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_003216469.1	Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides
YP_003216475.1	SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA
YP_003216480.1	acts to load the DnaB helicase onto the initiation site during DNA replication
YP_003216481.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_003216501.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_003216502.1	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_003216503.1	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_003216507.1	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