-- dump date   	20140619_095709
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_001121138.1	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_001121140.1	ORF00005 has a programmed ribosomal frameshift 'aaaaaaag' which permits frameshifting to ORF00004 to produce a single ORF with high sequence similarity to IS630 family of insertion elements; programmed frameshift
YP_001121144.1	Acts as an electrical shunt for an outwardly-directed proton pump that is linked to amino acid decarboxylation
YP_001121146.1	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_001121147.1	catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis
YP_001121150.1	non-folate utilizing enzyme, catalyzes the production of beta-formyl glycinamide ribonucleotide from formate, ATP, and beta-GAR and a side reaction producing acetyl phosphate and ADP from acetate and ATP; involved in de novo purine biosynthesis
YP_001121157.1	exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH
YP_001121160.1	programmed frameshift
YP_001121178.1	programmed frameshift
YP_001121179.1	catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions
YP_001121185.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_001121194.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_001121195.1	catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis
YP_001121196.1	programmed frameshift
YP_001121200.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_001121205.1	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_001121206.1	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_001121215.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_001121217.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001121220.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_001121222.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001121229.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III
YP_001121231.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_001121232.1	Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex
YP_001121234.1	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_001121240.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0
YP_001121241.1	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_001121242.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_001121243.1	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_001121244.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_001121245.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the gamma chain is a regulatory subunit
YP_001121246.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_001121247.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex
YP_001121257.1	part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase
YP_001121258.1	SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide
YP_001121260.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_001121261.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_001121262.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_001121270.1	Catalyzes the conversion of citrate to isocitrate
YP_001121279.1	programmed frameshift
YP_001121287.1	catalyzes the addition and repair of the 3'-terminal CCA sequence in tRNA; these proteins belong to the CCA-adding enzyme subfamily 2 which does not have phosphohydrolase activity
YP_001121289.1	transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate
YP_001121291.1	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_001121292.1	catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose
YP_001121296.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_001121297.1	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_001121308.1	programmed frameshift
YP_001121314.1	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_001121315.2	forms a complex with SecY and SecG; SecYEG forms a putative 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_001121317.1	binds directly to 23S ribosomal RNA
YP_001121318.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_001121319.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_001121320.1	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_001121321.1	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_001121324.1	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_001121326.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_001121327.1	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_001121328.1	Essential for efficient processing of 16S rRNA
YP_001121329.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_001121330.1	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_001121335.1	hydrolyzes diadenosine polyphosphate
YP_001121338.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_001121342.1	catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins
YP_001121343.1	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_001121345.1	programmed frameshift
YP_001121346.1	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_001121347.1	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_001121350.1	programmed frameshift
YP_001121361.1	type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese
YP_001121371.1	programmed frameshift
YP_001121373.1	involved in methylation of ribosomal protein L3
YP_001121374.1	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_001121375.1	programmed frameshift
YP_001121380.1	Involved in ubiquinone biosynthesis
YP_001121387.1	programmed frameshift
YP_001121395.1	works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell
YP_001121398.1	in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif
YP_001121399.1	required for 70S ribosome assembly
YP_001121405.1	programmed frameshift
YP_001121409.1	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_001121413.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_001121416.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_001121417.1	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_001121418.1	catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis
YP_001121419.1	catalyzes the formation of lipid A disaccharide from UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate, lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM
YP_001121426.1	HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine
YP_001121431.1	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_001121432.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_001121438.1	programmed frameshift
YP_001121449.1	catalyzes the formation of L-proline from L-ornithine
YP_001121453.1	Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation
YP_001121455.1	functions in fatty acid oxidation; converts acyl-CoA and FAD to FADH2 and delta2-enoyl-CoA
YP_001121460.1	component of putative O antigen gene cluster
YP_001121461.1	component of putative O antigen gene cluster
YP_001121462.1	component of putative O antigen gen cluster
YP_001121463.1	component of putative O antigen gene cluster
YP_001121464.1	component of putative O antigen gene cluster
YP_001121465.1	component of putative O antigen gene cluster
YP_001121466.1	component of putative O antigen gene cluster
YP_001121467.1	component of putative O antigen gene cluster
YP_001121468.1	component of putative antigen O gene complex
YP_001121469.1	component of putative O antigen gene complex
YP_001121470.1	component of putative O antigen gene complex
YP_001121471.1	component of putative O antigen gene complex
YP_001121472.1	component of putative O antigen gene complex
YP_001121473.1	component of putative O antigen gene complex
YP_001121476.1	programmed frameshift
YP_001121488.1	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_001121493.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_001121496.1	programmed frameshift
YP_001121511.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_001121535.1	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_001121536.1	Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5)
YP_001121538.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_001121541.1	programmed frameshift
YP_001121549.1	component of fatty acid biosynthesis gene cluster
YP_001121550.1	carries the fatty acid chain in fatty acid biosynthesis
YP_001121551.1	component of fatty acid biosynthesis gene cluster
YP_001121552.1	component of fatty acid biosynthesis gene cluster
YP_001121553.1	component of fatty acid biosynthesis gene cluster
YP_001121554.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_001121555.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_001121557.1	catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase
YP_001121559.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_001121561.1	class II aldolase; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis and gluconeogenesis
YP_001121562.1	programmed frameshift
YP_001121563.1	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_001121586.1	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_001121591.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_001121593.1	inferred from sequence similarity with MglB protein from F. novicida, function derived from mutation phenotype. PMID: 9701818
YP_001121594.1	inferred from sequence similarity with MglB protein from F. novicida, function derived from mutation phenotype. PMID: 9701818
YP_001121595.1	forms a direct contact with the tRNA during translation
YP_001121596.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_001121599.1	with DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins; may act as a thermosensor
YP_001121600.1	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_001121601.1	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_001121604.1	programmed frameshift
YP_001121607.1	more than 60% identity to characterized protein from P. aeruginosa PMID: 10464225
YP_001121634.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_001121636.1	UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis
YP_001121640.1	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_001121643.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_001121645.1	programmed frameshift
YP_001121647.1	CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS
YP_001121650.1	catalyzes the interconversion of UDP-galactose and galactose-1-P with UDP-galactose and glucose-1-P
YP_001121655.1	Essential for recycling GMP and indirectly, cGMP
YP_001121656.1	3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate
YP_001121678.1	a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA
YP_001121689.1	programmed frameshift
YP_001121691.1	programmed frameshift
YP_001121700.1	in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase
YP_001121709.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_001121717.1	programmed frameshift
YP_001121719.1	catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate
YP_001121720.1	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_001121721.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_001121734.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_001121739.1	programmed frameshift
YP_001121742.1	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_001121758.1	methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content
YP_001121763.1	converts 2-oxoglutarate to glutamate; in Escherichia coli this enzyme plays a role in glutamate synthesis when the cell is under energy restriction; uses NADPH; forms a homohexamer
YP_001121783.1	molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA
YP_001121784.1	This protein performs the mismatch recognition step during the DNA repair process
YP_001121785.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein
YP_001121789.1	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_001121797.1	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_001121798.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_001121800.1	E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC
YP_001121801.1	E2 component of pyruvate dehydrogenase multienzyme complex; in Escherichia coli AceF contains three N-terminal lipoyl domains
YP_001121803.1	programmed frameshift
YP_001121806.1	catalyzes the N2-methyl guanosine modification of the G2445 residue of 23S rRNA
YP_001121809.1	catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
YP_001121810.1	Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway
YP_001121814.1	inferred from blast alignment with NRAA database
YP_001121819.1	catalyzes the formation of inosine from adenosine
YP_001121829.1	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_001121833.1	catalyzes the reduction of 2 glutathione to glutathione disulfide; maintains high levels of reduced glutathione in the cytosol; involved in redox regulation and oxidative defense
YP_001121840.1	catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive
YP_001121843.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_001121845.1	involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain
YP_001121847.1	with SufCD activates cysteine desulfurase SufS
YP_001121863.1	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_001121866.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_001121874.1	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_001121875.1	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_001121882.1	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_001121887.1	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_001121888.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_001121890.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_001121900.1	lipoyl/octanoyltransferase; catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein
YP_001121905.1	a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA
YP_001121909.1	TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs
YP_001121927.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_001121928.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_001121929.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_001121931.1	catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis
YP_001121932.1	programmed frameshift
YP_001121933.1	catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine
YP_001121957.1	Catalyzes the reversible oxidation of malate to oxaloacetate
YP_001121958.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_001121974.1	Transposase, member of the IS630 Tc-1 mariner family. This gene contains a programmed ribosomal frameshifting motif, 5'-AAAAAAAG-3' which permits frameshifting to produce a single ORF; programmed frameshift
YP_001121975.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_001121978.1	heat shock protein involved in degradation of misfolded proteins
YP_001121979.1	heat shock protein involved in degradation of misfolded proteins
YP_001121981.1	catalyzes the conversion of NADPH to NADH
YP_001121985.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_001121986.1	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_001121990.1	the Ctc family of proteins consists of two types, one that contains the N-terminal ribosomal protein L25 domain only which in Escherichia coli binds the 5S rRNA while a subset of proteins contain a C-terminal extension that is involved in the stress response
YP_001122001.1	catalyzes the formation of histamine from L-histidine
YP_001122007.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_001122009.1	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_001122012.1	catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group
YP_001122014.1	cofactor involved in the reduction of disulfides
YP_001122023.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_001122026.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_001122033.1	IPP transferase; isopentenyltransferase; involved in tRNA modification; in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity
YP_001122037.1	binds and unfolds substrates as part of the ClpXP protease
YP_001122038.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_001122039.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_001122040.1	catalyzes the formation of thymidine 5'-phosphate from thymidine
YP_001122043.1	catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A)
YP_001122054.1	catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis
YP_001122071.1	binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters
YP_001122073.1	forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF
YP_001122074.1	part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane
YP_001122080.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_001122088.1	catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate
YP_001122090.1	catalyze the formation of cyanophycin which may act to store excess nitrogen
YP_001122097.1	protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic
YP_001122101.1	programmed frameshift
YP_001122107.1	proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the protein from Pseudomonas does not have this domain
YP_001122111.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_001122112.1	type I enzyme similar to type II but differentially regulated; major shikimate kinase in fully repressed cells; catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis
YP_001122118.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_001122120.1	Era; Escherichia coli Ras-like protein; Bex; Bacillus Era-complementing segment; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds the cell membrane through apparent C-terminal domain; mutants are arrested during the cell cycle; Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome
YP_001122136.1	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_001122137.1	TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs
YP_001122141.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_001122148.1	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_001122154.1	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_001122157.1	Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_001122158.1	Transposase, member of the IS630 Tc-1 mariner family. This gene contains a programmed ribosomal frameshifting motif, 5'-AAAAAAAG-3' which permits frameshifting to produce a single ORF; programmed frameshift
YP_001122161.1	malic enzyme; oxaloacetate-decarboxylating; NAD-dependent; catalyzes the formation of pyruvate form malate
YP_001122163.1	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_001122164.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_001122172.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining; maintains net negative superhelicity
YP_001122181.1	With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway
YP_001122185.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_001122186.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_001122192.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_001122197.1	this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress
YP_001122199.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_001122202.1	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_001122204.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_001122211.1	putative metalloprotease
YP_001122213.1	RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs
YP_001122215.1	UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin
YP_001122234.1	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_001122239.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_001122245.1	programmed frameshift
YP_001122253.1	programmed frameshift
YP_001122261.1	Required for efficient pilin antigenic variation
YP_001122273.1	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_001122280.1	this fusion consists of methionine sulfoxide B reductase at the N-terminus and A at the C-terminus; A and B are stereospecific enzymes that recognize the damaged produces of oxidative stress, S and R epimers of methionine sulfoxide, respectively; a fusion protein of these enzymes with thioredoxin provides protection against oxidative stress in Neisseria gonorrhoeae
YP_001122290.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_001122304.1	Transposase, member of the IS630 Tc-1 mariner family. This gene contains a programmed ribosomal frameshifting motif, 5'-AAAAAAAG-3' which permits frameshifting to produce a single ORF; programmed frameshift
YP_001122310.1	programmed frameshift
YP_001122312.1	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_001122316.1	involved in the peptidyltransferase reaction during translation
YP_001122318.1	functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins
YP_001122320.1	programmed frameshift
YP_001122324.1	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_001122326.1	functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family
YP_001122340.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_001122341.1	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_001122346.1	in Escherichia coli the CydCD ABC transporter exports cysteine and glutathione into the periplasm in order to maintain redox balance; important for cytochrome bd and c
YP_001122347.1	in Escherichia coli the CydCD ABC transporter exports cysteine and glutathione into the periplasm in order to maintain redox balance; important for cytochrome bd and c
YP_001122357.1	ISFtu1. Transposase, member of the IS630 Tc-1 mariner family. This gene contains a programmed ribosomal frameshifting motif, 5'-AAAAAAAG-3' which permits frameshifting to produce a single ORF; programmed frameshift
YP_001122362.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_001122363.1	catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine
YP_001122364.1	converts threonine and NAD to 1,2-amino-3-oxobutanoate and NADH; functions in threonine catabolism
YP_001122367.1	cell division protein; COG2919; contain pfam profile PF04977:Septum formation initiator
YP_001122368.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_001122372.1	in Escherichia coli this enzyme catalyzes the SAM-dependent methylation of U1939 in the 23S ribomal RNA; binds an iron-sulfur cluster [4Fe-4S]
YP_001122374.1	Contains equivalog HMM TIGR00690: DNA-directed RNA polymerase, omega subunit
YP_001122375.1	functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor
YP_001122376.1	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_001122377.1	essential respiratory protein A; may be involved in the transfer of iron-sulfur clusters; essential for growth using oxygen or alternate electron acceptors
YP_001122378.1	Similar to RNA binding S1:KH [Halorhodospira halophila SL1] GI:88948524 and Polyribonucleotide nucleotidyltransferase [Nitrococcus mobilis Nb-231] GI:88812956
YP_001122379.1	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_001122380.1	Similar to Peptidoglycan glycosyltransferase [Oceanospirillum sp. MED92](GI:89095265) that has experimental mRNA evidence
YP_001122381.1	Contains TIGR equivalog HMM TIGR02209: cell division protein FtsL
YP_001122382.1	Contains TIGR equivalog HMM TIGR00006: S-adenosyl-methyltransferase MraW
YP_001122383.1	Contains HMM profile PF00501: AMP-binding enzyme. Similar to 2-acyl-glycerophospho-ethanolamine acyltransferase [Oceanospirillum sp. MED92](GI:89092511) that has experiment mRNA evidence
YP_001122384.1	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_001122385.1	This gene contains a programmed ribosomal frameshifting motif, 5'-AAAAAAAG-3' which permits frameshifting to produce a single ORF; programmed frameshift
YP_001122386.1	with PdxST is involved in the biosynthesis of pyridoxal 5'-phosphate; PdxT catalyzes the hydrolysis of glutamine to glutamate and ammonia; PdxS utilizes the ammonia to synthesize pyridoxal 5'-phosphate
YP_001122387.1	with PdxT forms pyridoxal 5'-phosphate from glutamine, either ribose 5-phosphate or ribulose 5-phosphate, and either glyceraldehyde 3-phosphate or dihydroxyacetone phosphate
YP_001122388.1	Contains equivalog HMM TIGR01059: DNA gyrase, B subunit
YP_001122390.1	Contains HMM profile PF01207: Dihydrouridine synthase (Dus). Similar to tRNA-dihydrouridine synthase A [Escherichia coli K12]GI:16131875
YP_001122391.1	Mapped to COG1651: Protein-disulfide isomerase
YP_001122394.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_001122395.1	Contains subfamily HMM TIGR01019: succinyl-CoA synthetase, alpha subunit
YP_001122400.1	Contains PFAM profile PF03932: CutC family
YP_001122401.1	Contains Pfam profiles PF03466: LysR substrate binding domain and PF00126: transcriptional regulator, LysR family. Map to COG0583 Transcriptional regulator
YP_001122404.1	Contains TIGR equivalog HMM TIGR01292: thioredoxin-disulfide reductase
YP_001122406.1	Contains TIGR superfamily HMM TIGR00585: DNA mismatch repair protein MutL
YP_001122409.1	Contains equivalog HMM TIGR00157: ribosome small subunit-dependent GTPase A
YP_001122411.1	Mapped to COG0687 Spermidine/putrescine-binding periplasmic protein
YP_001122414.1	Mapped to equivalog HMM TIGR00644: single-stranded-DNA-specific exonuclease
YP_001122415.1	Contains equivalog domain HMM TIGR00121: biotin-[acetyl-CoA-carboxylase] ligase. Maps to COG0340 Biotin-(acetyl-CoA carboxylase) ligase
YP_001122416.1	Contains hypoth_equivalog HMM TIGR00462: lysyl-tRNA synthetase homolog GenX. Maps to COG2269 Truncated, possibly inactive, lysyl-tRNA synthetase (class II)
YP_001122417.1	Contains pfam profile PF00924: transporter, small conductance mechanosensitive ion channel (MscS) family. Maps to COG0668 Small-conductance mechanosensitive channel
YP_001122419.1	Maps to equivalog HMM TIGR00514: acetyl-CoA carboxylase, biotin carboxylase. Maps to COG0439 Biotin carboxylase
YP_001122420.1	Maps to equivalog HMM TIGR00531: acetyl-CoA carboxylase, biotin carboxyl carrier protein. Maps to COG0511 Biotin carboxyl carrier protein
YP_001122421.1	catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis
YP_001122422.1	hydrolyzes P(1),P(4)-bis(5'-adenosyl) tetraphosphate to form 2 ADP
YP_001122423.1	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_001122425.1	Contains Pfam profile PF04453: Organic solvent tolerance protein. Maps to COG1452 Organic solvent tolerance protein OstA
YP_001122426.1	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_001122428.1	Maps to subfamily HMM TIGR00520: L-asparaginases, type II
YP_001122430.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_001122431.1	Maps to COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein
YP_001122433.1	SohB; periplasmic protein; member of the peptidase S49 family
YP_001122435.1	Maps to pfam profile PF04358: DsrC like protein
YP_001122436.1	Maps to pfam profile PF04362: Protein of unknown function (DUF495), this is a family of bacterial Fe(2+) trafficking proteins
YP_001122437.1	Maps to pfam profile PF02366: dolichyl-phosphate-mannose-protein mannosyltransferase
YP_001122438.1	Maps to pfam profile PF00535: glycosyl transferase, group 2 family protein
YP_001122439.1	Maps to pfam profile PF04794: YdjC-like protein. This region is possibly involved in the the cleavage of cellobiose-phosphate
YP_001122440.1	Maps to equivalog HMM TIGR02614: cell division protein FtsW
YP_001122441.1	Maps to equivalog HMM TIGR01087: UDP-N-acetylmuramoylalanine--D-glutamate ligase
YP_001122442.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_001122443.1	PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP
YP_001122444.1	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_001122446.1	Maps to pfam profile PF00005: ABC transporter, ATP-binding protein
YP_001122447.1	Maps to pfam profile PF07690: transporter, major facilitator family. Also maps to COG0477 Permeases of the major facilitator superfamily
YP_001122449.1	Maps to subfamily HMM TIGR00710: drug resistance transporter, Bcr/CflA subfamily
YP_001122451.1	ISFtu1. Transposase, member of the IS630 Tc-1 mariner family. This gene contains a programmed ribosomal frameshifting motif, 5'-AAAAAAAG-3' which permits frameshifting to produce a single ORF; programmed frameshift
YP_001122452.1	Maps to equivalog HMM TIGR01081: UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso- diaminopimelate ligase
YP_001122453.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_001122454.1	catalyzes the formation of 2,3=diacylglucosamine 1-phosphate from UDP-2,3=diacylglucosamine
YP_001122455.1	Maps to HMM profile PF00795: hydrolase, carbon-nitrogen family
YP_001122456.1	Maps to pfam profile PF04371: Porphyromonas-type peptidyl-arginine deiminase
YP_001122457.1	catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine
YP_001122458.1	Maps to pfam profile PF02675: S-adenosylmethionine decarboxylase
YP_001122460.1	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_001122461.1	Maps to equivalog HMM TIGR00191: homoserine kinase
YP_001122463.1	catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde
YP_001122465.1	Maps to subfamily HMM profile TIGR01143: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
YP_001122467.1	Maps to subfamily HMM profile TIGR01085: UDP-N-acetylmuramyl-tripeptide synthetases
YP_001122468.1	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_001122469.1	amylomaltase; acts to release glucose from maltodextrins
YP_001122471.1	catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose
YP_001122472.1	catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate
YP_001122473.1	catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate
YP_001122474.1	catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain
YP_001122477.1	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_001122478.1	acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; forms a heterodimer with subunit 2 to form the P protein
YP_001122480.1	catalyzes the transfer of a methylene carbon from the methylamine-loaded GcvH protein to tetrahydrofolate, causing the release of ammonia and the generation of reduced GcvH protein
YP_001122482.1	pfam03550
YP_001122490.1	enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine
YP_001122491.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_001122496.1	Ribonuclease B OB domain protein
YP_001122497.1	a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA
YP_001122498.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_001122500.1	NadM-Nudix subfamily; involved in creation of nicotanimide adenine dinucleotide NAD from either biosynthetic or salvage pathways
YP_001122502.1	catalyzes the decarboxylation of phosphatidyl-L-serine to phosphatidylethanoleamine
YP_001122504.1	programmed frameshift
YP_001122507.2	RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome
YP_001122509.1	conserved virulence factor
YP_001122511.1	ATPase
YP_001122512.1	presence of both enzymatic activities needs to be experiementally confirmed, protein not always bifunctional
YP_001122514.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_001122515.1	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_001122517.1	programmed frameshift
YP_001122519.1	programmed frameshift
YP_001122524.1	predicted flavoproteins
YP_001122525.1	programmed frameshift
YP_001122527.1	programmed frameshift
YP_001122528.1	molecular chaperone
YP_001122529.1	programmed frameshift
YP_001122530.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_001122531.1	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_001122532.1	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_001122533.1	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_001122534.1	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_001122535.1	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_001122536.1	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_001122537.1	late assembly protein
YP_001122538.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_001122539.1	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_001122540.1	binds 5S rRNA along with protein L5 and L25
YP_001122541.1	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_001122542.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_001122543.1	located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif
YP_001122544.1	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_001122545.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_001122546.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_001122547.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_001122548.1	one of the stabilizing components for the large ribosomal subunit
YP_001122549.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_001122550.1	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_001122551.1	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_001122552.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_001122553.1	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_001122554.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_001122555.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_001122556.1	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_001122557.1	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_001122558.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_001122559.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_001122560.1	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_001122562.1	catalyzes the formation of dUMP from dUTP
YP_001122564.1	catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate
YP_001122565.1	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_001122566.1	Catalyzes the phosphorylation of UMP to UDP
YP_001122567.1	EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP resulting in regeneration of the active form of EF-Tu
YP_001122568.1	one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit
YP_001122571.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_001122572.1	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_001122574.1	catalyzes the reduction of nitroaromatic compounds such as nitrofurazone, quinones and the anti-tumor agent CB1954; NAD(P)H-dependent; oxygen insensitive
YP_001122576.1	cell envelope
YP_001122579.1	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_001122584.1	Uncharacterized protein containing a von Willebrand factor type A (vWA) domain
YP_001122586.1	contains a von Willebrand factor type A (vWA) domain
YP_001122588.1	Possibly located in cell envelope
YP_001122592.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_001122601.1	programmed frameshift
YP_001122606.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_001122607.1	may be involved in chromosome condensation; overexpression in Escherichia coli protects against decondensation by camphor; overexpressing the protein results in an increase in supercoiling
YP_001122610.1	Maps HMM profile PF00528: ABC transporter, permease protein
YP_001122611.1	Maps to pfam profile PF00005: ABC transporter, ATP-binding protein
YP_001122613.1	Maps to pfam profile PF00999: transporter, monovalent cation:proton antiporter-2 (CPA2) family. Also maps to COG0025 NhaP-type Na+/H+ and K+/H+ antiporters
YP_001122615.1	Maps to pfam profile PF03550: Outer membrane lipoprotein LolB
YP_001122616.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_001122618.1	ISFtu1. Transposase, member of the IS630 Tc-1 mariner family. This gene contains a programmed ribosomal frameshifting motif, 5'-AAAAAAAG-3' which permits frameshifting to produce a single ORF; programmed frameshift
YP_001122620.1	Maps to pfam profile PF01384: Phosphate transporter family
YP_001122621.1	Maps to COG1392 Phosphate transport regulator
YP_001122622.1	Maps to pfam profile PF04185: Phosphoesterase family
YP_001122623.1	Maps to COG1984 Allophanate hydrolase subunit 2
YP_001122624.1	Maps to pfam profile PF03746: LamB/YcsF family
YP_001122625.1	Maps to COG2049 Allophanate hydrolase subunit 1
YP_001122626.1	ISFtu1. Transposase, member of the IS630 Tc-1 mariner family. This gene contains a programmed ribosomal frameshifting motif, 5'-AAAAAAAG-3' which permits frameshifting to produce a single ORF; programmed frameshift
YP_001122627.1	Maps to pfam profile PF00582: universal stress protein family
YP_001122632.1	Maps to pfam profile PF00590: Tetrapyrrole (Corrin/Porphyrin) Methylases
YP_001122633.1	Maps to equivalog HMM TIGR01082: UDP-N-acetylmuramate--alanine ligase
YP_001122636.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_001122637.1	Maps to pfam PF02096: 60Kd inner membrane protein
YP_001122638.1	Maps to pfam PF03279: Bacterial lipid A biosynthesis acyltransferase
YP_001122639.1	Mmaps to pfam PF03279: Bacterial lipid A biosynthesis acyltransferase
YP_001122641.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_001122642.1	3'-5' exoribonuclease specific for small oligoribonuclotides
YP_001122643.1	ISFtu1. Transposase, member of the IS630 Tc-1 mariner family. This gene contains a programmed ribosomal frameshifting motif, 5'-AAAAAAAG-3' which permits frameshifting to produce a single ORF; programmed frameshift
YP_001122644.1	Maps to equivalog HMM TIGR00437: ferrous iron transport protein B
YP_001122645.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_001122646.1	Maps to equivalog HMM TIGR01122: branched-chain amino acid aminotransferase
YP_001122648.1	programmed frameshift
YP_001122659.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_001122660.1	involved in de novo purine biosynthesis
YP_001122671.1	zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis
YP_001122672.1	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_001122675.1	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_001122677.1	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_001122687.1	programmed frameshift
YP_001122694.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_001122701.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_001122702.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_001122703.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_001122708.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_001122710.1	programmed frameshift
YP_001122716.1	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_001122717.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_001122719.1	Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides
YP_001122732.1	hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine
YP_001122735.1	programmed frameshift
YP_001122742.1	molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA
YP_001122743.1	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_001122747.1	catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate
YP_001122748.1	programmed frameshift
YP_001122749.1	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_001122750.1	programmed frameshift
YP_001122752.1	ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence
YP_001122757.1	specific inhibitor of chromosomal initiation of replication in vitro; binds the three 13-mers in the origin (oriC) to block initiation of replication; also controls genes involved in arginine transport
YP_001122761.1	monomeric bifunctional protein; functions in tryptophan biosynthesis pathway; phosphoribosylanthranilate is rearranged to carboxyphenylaminodeoxyribulosephosphate which is then closed to form indole-3-glycerol phosphate
YP_001122767.1	Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_001122769.1	with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine