-- dump date   	20140619_122512
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_794209.1	binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself.
YP_794212.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_794215.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_794226.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_794242.1	SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA
YP_794273.1	catalyzes the formation of 1,4-dihydroxy-2-naphthoate from O-succinylbenzoyl-CoA
YP_794277.1	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_794285.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_794296.1	catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate
YP_794306.1	has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF
YP_794328.1	4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase; catalyzes the interconversion of 4-deoxy-L-threo-5-hexosulose uronate to 3-deoxy-D-glycero-2,5-hexodiulosonate
YP_794336.1	catalyzes the interconversion of D-glucuronate to D-fructuronate or D-galacturonate to D-tagaturonate; functions in glucuronic and galacturonic metabolism
YP_794345.1	similar to full-length Gnd, these proteins seems to have a truncated C-terminal 6PGD domainin; in Methylobacillus flagellatus this gene is essential for NAD+-dependent oxidation of 6-phosphogluconate
YP_794347.1	catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate
YP_794351.1	catalyzes the interconversion of D-glucuronate to D-fructuronate or D-galacturonate to D-tagaturonate; functions in glucuronic and galacturonic metabolism
YP_794361.1	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_794380.1	catalyzes the interconversion of D-xylose to D-xylulose
YP_794443.1	enzyme from Treponema denticola exhibits NADH-dependent trans-2-enoyl-CoA reductase activity
YP_794450.1	dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.
YP_794451.1	similar to zinc-dependent eukaryotic ADH enzymes and distinct from fermentative ADHs
YP_794478.1	in group A Streptococci this protein was found to cross react with anti myosin antibodies and may play a role in rheumatic fever
YP_794521.1	catalyzes the formation of pyruvate and glyoxylate from 4-hydroxy-2-oxoglutarate; or pyruvate and D-glyceraldehyde 3-phosphate from 2-dehydro-3-deoxy-D-glyconate 6-phosphate
YP_794523.1	Involved in the metabolism of 2-deoxyglucose
YP_794537.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_794572.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_794637.1	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_794641.1	Modulates the activities of several enzymes which are inactive in their acetylated form
YP_794647.1	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_794649.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_794651.1	catalyzes the transfer of alpha-xylosyl residue from alpha-xyloside to xylose, glucose, mannose, fructose, maltose, isomaltose, nigerose, kojibiose, sucrose, and trehalose; shows higher activity against alpha-xylosyl fluoride, isoprimeverose (6-O-alpha-xylopyranosyl-glucopyranose), and alpha-xyloside in xyloglucan oligosaccharides
YP_794664.1	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_794665.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_794675.1	participates in both the initiation and recycling phases of transcription; in the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling
YP_794676.1	CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer
YP_794680.1	catalyzes the formation of 2-acetolactate from pyruvate in stationary phase
YP_794683.1	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_794690.1	metalloprotease
YP_794696.1	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_794704.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_794713.1	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_794723.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate
YP_794724.1	catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers
YP_794728.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_794751.1	Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_794754.1	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_794757.1	catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA
YP_794762.1	forms a complex with SecY and SecG; SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force
YP_794764.1	binds directly to 23S ribosomal RNA
YP_794765.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_794766.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_794767.1	present in two forms; L12 is normal, while L7 is aminoacylated at the N-terminal serine; the only multicopy ribosomal protein; 4:1 ratio of L7/L12 per ribosome; two L12 dimers bind L10; critically important for translation efficiency and fidelity; stimulates GTPase activity of translation factors
YP_794770.1	converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA
YP_794771.1	B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE
YP_794772.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_794778.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_794780.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_794782.1	catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA
YP_794788.1	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_794792.1	modulates transcription in response to the NADH/NAD(+) redox state
YP_794793.1	10 kDa chaperonin; Cpn10; GroES; forms homoheptameric ring; binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it; folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES; release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring
YP_794794.1	60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is essential for growth
YP_794803.1	functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; in some organisms, there are paralogous proteins that have been found to be nonessential but do function in secretion of a subset of exported proteins
YP_794812.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_794813.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_794817.1	catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system
YP_794818.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_794824.1	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_794825.1	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate
YP_794830.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_794836.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_794837.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_794838.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_794844.1	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_794847.1	Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine
YP_794848.1	in Salmonella this enzyme is required for ethanolamine catabolism; has higher affinity for CoA than Pta
YP_794855.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_794860.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_794861.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_794877.1	catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate
YP_794888.1	class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle
YP_794897.1	forms homopentamer; channel that opens in response to pressure or hypoosmotic shock
YP_794899.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_794909.1	catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG
YP_794910.1	catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes
YP_794916.1	Assists in DNA repair by cleaving phosphodiester bonds at apurinic or apyrimidinic sties to produce new 5' ends that are base-free deoxyribose 5-phosphate residues
YP_794927.1	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_794928.1	glycine--tRNA ligase beta chain; glyS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA
YP_794935.1	catalyzes the release of the N-terminal amino acid from a tripeptide
YP_794938.1	similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity
YP_794950.1	Catalyzes the formation of (d)CDP from ATP and (d)CMP
YP_794951.1	in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins
YP_794952.1	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_794958.1	ThyA; catalyzes formation of dTMP and 7,8-dihydrofolate from 5,10-methylenetetrahydrofolate and dUMP; involved in deoxyribonucleotide biosynthesis; there are 2 copies in some Bacilli, one of which appears to be phage-derived
YP_794972.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_794974.1	heat shock protein involved in degradation of misfolded proteins
YP_794975.1	heat shock protein involved in degradation of misfolded proteins
YP_794978.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_794979.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_794981.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_794986.1	site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; cell division protein FtsK may regulate the XerS
YP_795004.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_795007.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_795008.1	catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate
YP_795021.1	GpsB; guiding PBP1 shuttling; similar to DivIVA
YP_795023.1	functions in homologous recombination, DNA repair, and chromosome segregation; binds preferentially to three- and four-stranded DNA intermediates; introduces specific nick sites in four-stranded DNA substrates; functions similarly to Escherichia coli RuvC
YP_795034.1	catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate
YP_795037.1	dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.
YP_795065.1	4-OT; member of subfamily 5; forms a dimer; the function in the Escherichia coli cell is unknown
YP_795091.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_795101.1	FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs
YP_795105.1	this protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site
YP_795106.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_795107.1	Essential for efficient processing of 16S rRNA
YP_795109.1	binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity
YP_795117.1	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_795118.1	carries the fatty acid chain in fatty acid biosynthesis
YP_795119.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_795120.1	catalyzes branch migration in Holliday junction intermediates
YP_795140.1	catalyzes the bidirectional exonucleolytic cleavage of DNA
YP_795141.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_795143.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_795147.1	involved in the peptidyltransferase reaction during translation
YP_795171.1	functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor
YP_795173.1	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_795174.1	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_795183.1	similar to zinc-dependent eukaryotic ADH enzymes and distinct from fermentative ADHs
YP_795187.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_795193.1	transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria
YP_795195.1	in Bacillus subtilis this enzyme appears to be involved in 30S ribosomal RNA subunit biogenesis
YP_795199.1	IF-3
YP_795201.1	Primosomal protein that may act to load helicase DnaC during DNA replication
YP_795205.1	Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases
YP_795211.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_795219.1	divalent metal ion-dependent extracellular dipeptidase; able to hydrolyze a broad range of dipeptides but no tri-, tetra-, or larger oligopeptides; differences in the amino acid specificity of the cleavage site varies between species; similar to succinyl-diaminopimelate desuccinylases
YP_795226.1	leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase
YP_795306.1	enables recognition and targeting of proteins for proteolysis, involved in negative regulation of competence
YP_795358.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_795360.1	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_795366.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_795367.1	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_795369.1	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_795370.1	This protein performs the mismatch recognition step during the DNA repair process
YP_795374.1	catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs
YP_795385.1	in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall
YP_795386.1	functions in MreBCD complex in some organisms
YP_795389.1	valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain
YP_795393.1	acts to negatively regulates ftsZ ring formation by modulating the frequency and position of the ftsZ ring formation
YP_795395.1	primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination
YP_795404.1	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_795412.1	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_795414.1	part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane
YP_795415.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_795418.1	Produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex
YP_795419.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_795420.1	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_795422.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_795423.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_795426.1	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_795427.1	catalyzes the formation of thymidine 5'-phosphate from thymidine
YP_795455.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_795459.1	transfers D-alanine to the D-alanyl carrier protein during the incorporation of D-alanine into lipoteichoic acid
YP_795461.1	chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion
YP_795464.1	Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons
YP_795466.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_795467.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_795468.1	IF-2: GTPase
YP_795471.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_795472.1	in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins
YP_795474.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; required for leading strand synthesis; PolC exhibits 3' to 5' exonuclease activity
YP_795475.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_795478.1	catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate
YP_795480.1	Catalyzes the phosphorylation of UMP to UDP
YP_795505.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_795511.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_795512.1	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_795515.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_795516.1	binds and unfolds substrates as part of the ClpXP protease
YP_795517.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_795518.1	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_795521.1	primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence
YP_795522.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_795523.1	required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA
YP_795528.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_795536.1	E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_795540.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_795553.1	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_795563.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_795570.1	IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme
YP_795575.1	GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function
YP_795579.1	UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation
YP_795580.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_795584.1	MraZ; UPF0040; crystal structure shows similarity to AbrB
YP_795600.1	catalyzes the phosphorylation of NAD to NADP
YP_795612.1	cis/trans isomerase of peptidylprolyl; PPIase; membrane-bound lipoprotein
YP_795649.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_795670.1	stimulates the release of release factors 1 and 2 from the ribosome after hydrolysis of the ester bond in peptidyl-tRNA has occurred; GDP/GTP-binding protein
YP_795679.1	binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities
YP_795697.1	cytoplasmic mutarotase that catalyzes the conversion between beta-pyran and beta-furan forms of D-ribose; RbsD is required for efficient ribose utilization in E. coli; rbsD-mutant E. coli strains are unable to use ribose as a sole carbon source
YP_795701.1	catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate
YP_795702.1	catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose
YP_795703.1	catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate
YP_795714.1	similar to carboxysome shell protein CcmL
YP_795717.1	similar to carboxysome shell protein CcmK
YP_795718.1	similar to carboxysome shell protein CcmK
YP_795725.1	similar to carboxysome shell protein CcmK
YP_795735.1	similar to YegS from E. coli
YP_795736.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA
YP_795737.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA
YP_795738.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain
YP_795755.1	catalyzes the formation of asparagine from aspartate and ammonia
YP_795758.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_795763.1	forms a direct contact with the tRNA during translation
YP_795764.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_795768.1	with CbiNQ forms the ABC transporter for cobalt import; Bacillus spp. have two adjacent copies of this gene
YP_795770.1	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_795771.1	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_795772.1	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_795773.1	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_795774.1	IF-1
YP_795776.1	forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase
YP_795778.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_795779.1	located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance
YP_795782.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_795784.1	part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13
YP_795785.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_795788.1	one of the stabilizing components for the large ribosomal subunit
YP_795789.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_795790.1	forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation
YP_795791.1	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_795792.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_795793.1	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_795795.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_795796.1	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_795797.1	NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex
YP_795799.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_795800.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_795801.1	interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance
YP_795803.1	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_795804.1	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_795808.1	catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_795838.1	catalyzes the formation of L-ribulose from L-arabinose in L-arabinose catabolism
YP_795839.1	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_795857.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_795859.1	catalyzes the formation of (R)-4'-phosphopantothenate in coenzyme A biosynthesis
YP_795878.1	catalyzes the removal of N-terminal dipeptides when proline is the penultimate residue
YP_795993.1	catalyzes the formation of alpha-D-glucose 1-phosphate and UDP-galactose from UDP-glucose and alpha-D-galactose 1-phosphate in galactose metabolism
YP_795995.1	catalyzes the formation of alpha-D-galactose 1-phosphate from D-galactose in galactose metabolism
YP_796079.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_796106.1	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_796111.1	catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP
YP_796112.1	associated with arginine deiminase pathway genes; probably functions in arginine catabolism
YP_796114.1	catalyzes the formation of ornithine and carbamylphosphate from citrulline in the arginine catabolic pathway
YP_796115.1	catalyzes the degradation of arginine to citruline and ammonia
YP_796130.1	2,3-bisphosphoglycerate-dependent; catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate
YP_796148.1	translation-associated GTPase; the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure (PDB: 1NI3); fluorescence spectroscopy revealed nucleic acid binding; the yeast protein YBR025c interacts with the translation elongation factor eEF1
YP_796153.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_796156.1	catalyzes the hydrolysis of both purine and pyrimidine ribonucleosides
YP_796184.1	catalyzes the formation of 4-methyl-5-(2-phosphoethyl)-thiazole and ADP from 4-methyl-5-(2-hydroxyethyl)-thiazole and ATP
YP_796222.1	ketopantoate reductase; catalyzes the NADPH reduction of ketopantoate to pantoate; functions in pantothenate (vitamin B5) biosynthesis
YP_796269.1	Hydrolyzes cytidine or uridine to ribose and cytosine or uracil, respectively
YP_796270.1	activator of nucleoside metabolism
YP_796284.1	malic enzyme; oxaloacetate-decarboxylating; NAD-dependent; catalyzes the formation of pyruvate form malate
YP_796288.1	catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP
YP_796289.1	catalyzes the formation of carbamoylputrescine from agmatine in the arginine decarboxylase pathway of putrescine biosynthesis
YP_796291.1	catalyzes the formation of putrescine from carbamoyl-putrescine during agmatine degradation
YP_796348.1	dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.
YP_796388.1	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_796389.1	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_796392.1	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