-- dump date   	20140618_205145
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_003915161.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915165.1	identified by match to protein family PF03551
YP_003915166.1	identified by match to protein family PF03432: Relaxase/Mobilisation nuclease domain. Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation
YP_003915167.1	identified by match to protein family PF05713: bacterial mobilisation protein (MobC). This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region
YP_003915169.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.621 between position 22 and 23. 2 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003915170.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.879) with cleavage site probability 0.323 between position 19 and 20. 2 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003915172.1	match to PF00239. Possibly involved in site-specific recombination of DNA
YP_003915173.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.983) with cleavage site probability 0.615 between position 21 and 22
YP_003915174.1	identified by match to PF00436. The Escherichia coli single-strand binding protein binds tightly to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids
YP_003915175.1	similar to protein SP:Q9X550 (Corynebacterium glutamicum plasmid R-plasmid pAG1). Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.700 between position 26 and 27
YP_003915176.1	similar to protein SP:Q9X549 (Corynebacterium glutamicum plasmid R-plasmid pAG1). Match to PS51257: prokaryotic membrane lipoprotein lipid attachment site profile
YP_003915177.1	similar to protein SP:Q9X548 (Corynebacterium glutamicum plasmid R-plasmid pAG1)
YP_003915178.1	match to PF00376: MerR family regulatory protein
YP_003915179.1	identified by match to protein family PF00817. In Escherichia coli, the gene products of the umuDC operon play important roles in the ability to tolerate damage to its DNA
YP_003915180.1	in Escherichia coli, the gene products of the umuDC operon play important roles in the ability to tolerate damage to its DNA
YP_003915181.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits: subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003915182.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits: subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003915183.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits: subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003915187.1	match to PF00239. Possibly involved in site-specific recombination of DNA
YP_003915193.1	identified by match to PF02661: Fic protein family. cAMP may be a regulation factor in cell division of some bacteria. The Fic (filamentation induced by cAMP) protein is involved in the synthesis of PAB or folate. It would appear that the Fic protein and cAMP are involved in a regulatory mechanism of cell division via folate metabolism and in these organisms cell division could be controlled by coordination of cAMP, Fic and Fts proteins
YP_003915194.1	match to PF00239 and PF02796. Possibly involved in site-specific recombination of DNA
YP_003915196.1	identified by match to protein family PF05713: bacterial mobilisation protein (MobC). This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region
YP_003915197.1	identified by match to protein family PF03432: Relaxase/Mobilisation nuclease domain. Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation
YP_003915199.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915201.1	identified by match to protein family PF02534. The TraG family are bacterial conjugation proteins. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome although the exact mechanism of action is unknown
YP_003915203.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915204.1	6 transmembrane helices predicted by TMHMM2.0
YP_003915205.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915206.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915209.1	match to protein family TIGR01764
YP_003915210.1	similar to protein SP:Q9X549 (Corynebacterium glutamicum plasmid R-plasmid pAG1). Match to PS51257: prokaryotic membrane lipoprotein lipid attachment site profile
YP_003915211.1	identified by match to protein family PF01551. Members of this family are zinc metallopeptidases with a range of specificities. Peptidase family M23 are also endopeptidases. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0. 661 between position 37 and 38
YP_003915213.1	match to SSF47598: Ribbon-helix-helix superfamily
YP_003915219.1	identified by match to protein family PF00462
YP_003915221.1	plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication
YP_003915222.1	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication once it is clamped onto DNA. DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII complex. PolIII associates with the gamma complex (composed of gamma, delta, delta, psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex
YP_003915223.1	RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task.
YP_003915224.1	match to protein family PF05258. This family contains several actinomycete proteins of unknown function
YP_003915225.1	DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings. Made up of two chains. The A chain is responsible for DNA breakage and rejoining; the B chain catalyzes ATP hydrolysis
YP_003915226.1	DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings. Made up of two chains. The A chain is responsible for DNA breakage and rejoining; the B chain catalyzes ATP hydrolysis
YP_003915227.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915228.1	match to PF00534: Glycosyl transferases group 1. Proteins containing this domain transfer UDP, ADP, GDP or CMP linked sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. The bacterial enzymes are involved in various biosynthetic processes that include exopolysaccharide biosynthesis, lipopolysaccharide core biosynthesis and the biosynthesis of the slime polysaccaride colanic acid
YP_003915229.1	identified by match to protein family PF01758. Bile acid:Na+ symporter (BASS) family (TC 2.A.28.y.z): these symporters exhibit broad specificity, taking up a variety of non bile organic compounds as well as taurocholate and other bile salts
YP_003915230.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.973) with cleavage site probability 0.306 between position 22 and 23. 8 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003915232.1	identified by match to protein family PF00160: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD. Peptidylprolyl isomerase is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides
YP_003915233.1	identified by match to protein family PF01694. This group of proteins contain serine peptidases belonging to the MEROPS peptidase family S54 (Rhomboid, clan S-). They are integral membrane proteins related to the Drosophila melanogaster (Fruit fly) rhomboid protein. 7 transmembrane helices predicted by TMHMM2.0
YP_003915234.1	L-lysine exporter (LysE) family, L-lysine exporter (TC 2.A.75.1.1). Identified by match to protein family PF01810. In Corynebacterium glutamicum, LysE appears to catalyze unidirectional efflux of L-lysine (and other basic amino acids such as L-arginine). The physiological function of the exporter is to excrete excess l-Lysine as a result of natural flux imbalances
YP_003915235.1	probable transcriptional regulator of lysE. Identified by similarity to protein SP: P94632 (Corynebacterium glutamicum)
YP_003915236.1	drug/metabolite transporter (DMT) superfamily, small multidrug resistance (SMR) family, quaternary ammonium compound (cetylpyridinium, cetyldimethyl ethylammonium, hexadecyltrimethyl ammonium) efflux pump (TC 2.A.7.1.4). Confers resistance to cetylpyridinium, cetyldimethylethyl ammonium and cetrimide cations
YP_003915237.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915238.1	identified by match to protein family PF04203. Sortase is a transpeptidase that attaches surface proteins by the threonine of an LPXTG motif to the cell wall
YP_003915240.1	anthranilate synthase is the first enzyme in the branch pathway in tryptophane biosynthesis. It catalyzes the biosynthesis of anthranilate from chorismate and glutamine
YP_003915241.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003915243.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003915245.1	identified by match to PF00903: glyoxalase/bleomycin resistance protein/dioxygenase superfamily
YP_003915246.1	identified by match to protein domain PD000001. Match to PS00108 pattern. Protein kinases are a group of enzymes that possess a catalytic subunit which transfers the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. They play a role in a mulititude of cellular processes, including division, proliferation, apoptosis, and differentiation
YP_003915247.1	identified by match to protein domain PD000001. Match to PS00108 pattern. Protein kinases are a group of enzymes that possess a catalytic subunit which transfers the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. They play a role in a mulititude of cellular processes, including division, proliferation, apoptosis, and differentiation
YP_003915248.1	match to PF00905. The large number of penicillin binding proteins, which are represented in this group of sequences, are responsible for the final stages of peptidoglycan biosynthesis for cell wall formation. The proteins synthesise cross-linked peptidoglycan from lipid intermediates, and contain a penicillin-sensitive transpeptidase carboxy-terminal domain
YP_003915249.1	plays a role in the stabilization of the FtsZ ring during cell division
YP_003915250.1	match to PF00481: protein phosphatase 2C
YP_003915251.1	match to PF00498. The forkhead-associated (FHA) domain is a phosphopeptide recognition domain found in many regulatory proteins
YP_003915252.1	match to PF00498. The forkhead-associated (FHA) domain is a phosphopeptide recognition domain found in many regulatory proteins
YP_003915256.1	match to protein domain PF00356. Numerous bacterial transcription regulatory proteins bind DNA via a helix- turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR. Within this family, the HTH motif is situated towards the N-terminus
YP_003915257.1	catalyzes the hydrolysis of all of the commonly occuring purine and pyrimidine nucleosides into ribose and the associated base, but has a preference for inosine and uridine as substrates
YP_003915258.1	identified by match to PF01738: dienelactone hydrolase family. Carboxymethylenebutenolidases play a crucial role in chlorocatechol degradation via the modified ortho cleavage pathway
YP_003915259.1	identified by match to PF00582: universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general stress endurance activity
YP_003915261.1	match to protein family PF00378. This family contains a diverse set of enzymes including: Enoyl-CoA hydratase, Napthoate synthase, Carnitate racemase, 3- hydoxybutyryl-CoA dehydratase, Dodecanoyl-CoA delta- isomerase
YP_003915263.1	fructokinase catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into glucose-6-phosphate
YP_003915264.1	match to protein family PF08282: haloacid dehalogenase-like hydrolase. The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P- type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification
YP_003915265.1	glycerophosphoryl diester phosphodiesterases display broad specificity for glycerophosphodiesters; glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol, and bis(glycerophosphoglycerol)
YP_003915268.1	major facilitator superfamily, sugar porter family (TC 2.A.1.1.z)
YP_003915269.1	nucleobase:cation symporter-2 (NCS2) Family (TC 2.A. 40.y.z). Identified by match to protein family PF00860
YP_003915270.1	involved in thiamin biosynthesis. Catalyzes the phosphorylation of HMP-P to HMP-PP
YP_003915271.1	catalyses the following reaction: 2-methyl-4-amino- 5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-(2- phosphono-oxyethyl)thiazole <=> diphosphate + thiamine phosphate
YP_003915272.1	catalyses the following reaction : ATP + 4-methyl-5- (2-hydroxyethyl)thiazole <=> ADP + 4-methyl-5-(2- phosphonooxyethyl)thiazole
YP_003915274.1	12 transmembrane helices predicted by TMHMM2.0
YP_003915275.1	identified by match to protein family PF00171
YP_003915276.1	amino acid-polyamine-organocation (APC) superfamily, amino acid transporter (AAT) family, lysine:H+ symporter (TC 2.A.3.1.2). Identified by similarity to protein SP:P25737 (Escherichia coli)
YP_003915277.1	catalyzes the interconversion of alpha-D-glucose 1- phosphate to alpha-D-glucose 6-phosphate
YP_003915278.1	proton-dependent oligopeptide transporter (POT) family (TC 2.A.17), di- or tripeptide:H+ symporter (TC 2.A. 17.1.1). Identified by match to protein family PF00854
YP_003915280.1	identified by match to protein domain PF00581. Rhodanese has an internal duplication. This HMM represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases
YP_003915281.1	catalyzes the decarboxylation of prephenate into phenylpyruvate. Involved in phenylalanine biosynthesis
YP_003915282.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.999) with cleavage site probability 0.916 between position 19 and 20
YP_003915283.1	activates serine and transfers it to tRNA(Ser) as the first step in protein biosynthesis
YP_003915284.1	match to protein family PF08282: haloacid dehalogenase-like hydrolase. The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P- type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification
YP_003915286.1	selectively removes pyroglutamate (pGlu) from the N- terminus of proteins and peptides. The enzyme appears to play an important role in the activation and inactivation of many N-terminal pyroglutamyl-terminating peptides
YP_003915287.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915289.1	responsible for the hydrolysis of pyrophosphate (PPi) which is formed principally as the product of the many biosynthetic reactions that utilize ATP
YP_003915290.1	identified by match to protein family PF02113. Is involved in the metabolism of cell components; it is synthesised with a leader peptide to target it to the cell membrane. Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D- Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine
YP_003915292.1	ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine
YP_003915293.1	catalyses the formation of IMP and diphosphate from hypoxanthine and 5-phospho-alpha-D-ribose 1-diphosphate. Guanine and 6-mercaptopurine can replace hypoxanthine. This enzyme is essential for salvaging exogenous purine bases
YP_003915294.1	FtsH is a membrane-anchored ATP-dependent protease that degrades misfolded or misassembled membrane proteins as well as a subset of cytoplasmic regulatory proteins. 2 transmembrane helices predicted by TMHMM2.0
YP_003915295.1	catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP : GTP + H2O <=> formate + 2-amino-4-hydroxy-6-(erythro-1,2,3- trihydroxypropyl)- dihydropteridine triphosphate
YP_003915296.1	catalyzes the condensation of 6-hydroxymethyl-7,8- dihydropteridine pyrophosphate to para-aminobenzoic acid to form 7,8-dihydropteroate. This is the second step in the three steps pathway leading from 6-hydroxymethyl-7,8- dihydropterin to 7,8-dihydrofolate. It is the target of sulfonamides which are substrates analog that compete with para-aminobenzoic acid
YP_003915297.1	EC 4.1.2.25 catalyzes the following reaction: 2- amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7, 8- dihydropteridine <=> 2-amino-4-hydroxy-6-hydroxymethyl-7, 8- dihydropteridine + glycolaldehyde. EC 2.7.6.3 catalyses the following reaction: ATP + 2-amino-4-hydroxy-6- hydroxymethyl-7,8-dihydropteridine <=> AMP + (2-amino-4- hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate
YP_003915298.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.991) with cleavage site probability 0.734 between position 31 and 32. 3 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003915299.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915300.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915302.1	catalyzes the formation of pantothenate from pantoate and beta-alanine
YP_003915303.1	identified by match to protein family PF03060: 2- nitropropane dioxygenase
YP_003915305.1	match to PF01381: helix-turn-helix. This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003915306.1	identified by match to PF07804 (HipA-like C- terminal domain) and PF07805 (HipA-like N-terminal domain). The HipA protein is known to be involved in high- frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis. When expressed alone, it is toxic to bacterial cells but it is usually tightly associated with HipB and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products
YP_003915308.1	identified by match to PF05649 and PF01431
YP_003915312.1	ATP-dependent Clp proteases act as chaperones to target the proteases to substrates
YP_003915313.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915315.1	identified by match to PF00903: glyoxalase/bleomycin resistance protein/dioxygenase superfamily
YP_003915316.1	identified by match to protein domain PF00165: bacterial regulatory helix-turn-helix proteins, AraC family
YP_003915317.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003915318.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003915319.1	6 transmembrane helices predicted by TMHMM2.0
YP_003915320.1	identified by match to protein domain PF00730. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C terminal iron-sulphur cluster loop (FCL)
YP_003915321.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915322.1	participates in a DNA-damage check-point that is active prior to asymmetric division when DNA is damaged
YP_003915323.1	may play a role in the repair of endogenous alkylation damage
YP_003915325.1	TCDB: ATP-binding cassette (ABC) superfamily, phosphate uptake transporter (PhoT) family, phosphate transporter (TC 3.A.1.7.2). ABCISSE: ABC transporter, binding protein (BP), MOI-family, phosphate import. Part of the ABC transporter complex PstSACB involved in phosphate import. The complex is composed of two ATP- binding proteins (PstB), two transmembrane proteins (PstC and PstA) and a solute-binding protein (PstS)
YP_003915326.1	TCDB: ATP-binding cassette (ABC) superfamily, phosphate uptake transporter (PhoT) family, phosphate transporter (TC 3.A.1.7.2). ABCISSE: ABC transporter, permease (IM), MOI-family, phosphate import. Part of the ABC transporter complex pstSACB involved in phosphate import. The complex is composed of two ATP-binding proteins (pstB), two transmembrane proteins (pstC and pstA) and a solute-binding protein (pstS)
YP_003915327.1	TCDB: ATP-binding cassette (ABC) superfamily, phosphate uptake transporter (PhoT) family, phosphate transporter (TC 3.A.1.7.2). ABCISSE: ABC transporter, permease (IM), MOI-family, phosphate import. Part of the ABC transporter complex pstSACB involved in phosphate import. The complex is composed of two ATP-binding proteins (pstB), two transmembrane proteins (pstC and pstA) and a solute-binding protein (pstS)
YP_003915328.1	TCDB: ATP-binding cassette (ABC) superfamily, phosphate uptake transporter (PhoT) family, phosphate transporter (TC 3.A.1.7.2). ABCISSE: ABC transporter, ATP- binding protein (ABC), MOI-family, phosphate import. Part of the ABC transporter complex pstSACB involved in phosphate import. The complex is composed of two ATP- binding proteins (pstB), two transmembrane proteins (pstC and pstA) and a solute-binding protein (pstS)
YP_003915330.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915331.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915332.1	match to protein domain PF01381: helix-turn-helix
YP_003915333.1	inorganic phosphate transporter (PiT) family (TC 2. A.20.y.z). Identified by match to protein family PF01384
YP_003915339.1	identified by match to PF01738: dienelactone hydrolase family
YP_003915341.1	TCDB: ATP-binding cassette (ABC) superfamily, () drug resistance ATPase-1 (Drug RA1) family (TC 3.A.1.120.z). ABCISSE: fused ATP-binding protein (ABC2), ART-family. Duplicated ATPase domains (PF00005)
YP_003915342.1	identified by match to protein family PF02517: CAAX amino terminal protease family. Members of this family are probably proteases (after a prenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein, the AAX tripeptide is removed by one of the CAAX prenyl proteases). The family contains the Q03530 CAAX prenyl protease. Signal peptide predicted by SignalP 3.0 HMM (probability: 0.755) with cleavage site probability 0.459 between position 27 and 28. 5 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003915343.1	converts dimethylmenaquinone (DMKH2) to menaquinone (MKH2) and converts 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4- benzoquinol (DMQH2)
YP_003915345.1	identified by match to PF01022. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003915347.1	catalyses the following reaction: an aldehyde + NAD(+) + H(2)O <=> an acid + NADH
YP_003915348.1	catalyses the following reaction: an alcohol + NAD(+) <=> an aldehyde or ketone + NADH
YP_003915350.1	identified by similarity to protein SP:P94957 (Micrococcus luteus). It is a DNA excision repair enzyme. Also named UV endonuclease (cyclobutane pyrimidine dimer- DNA glycosylase/abasic lyase)
YP_003915351.1	catalyses the following reaction: L-2-amino-6- oxoheptanedioate + NH(3) + NADPH <=> meso-2,6- diaminoheptanedioate + H(2)O + NADP(+). Involved in lysine biosynthesis
YP_003915354.1	serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of 2 cysteine thiol groups to a disulphide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulphide and a dithiol
YP_003915355.1	8 transmembrane helices predicted by TMHMM2.0
YP_003915356.1	identified by match to protein domain PF00581. Rhodanese has an internal duplication. This HMM represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases
YP_003915357.1	identified by match to PF00753: metallo-beta- lactamase superfamily. Apart from the beta-lactamases, a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl- glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake
YP_003915359.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003915360.1	identified by match to protein family PF02566: OsmC, OsmC-like protein. Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. This family also contains an organic hydroperoxide detoxification protein that has a novel pattern of oxidative stress regulation
YP_003915361.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003915362.1	identified by match to PF02913 and PF01565
YP_003915363.1	identified by match to SM00507
YP_003915364.1	amino acid-polyamine-organocation (APC) Superfamily (TC 2.A.3.y.z)
YP_003915367.1	gluconokinase catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product, gluconate-6- phoshate, is an important precursor of gluconate metabolism
YP_003915369.1	identified by match to protein domain PF00205. Thiamine pyrophosphate binding domains are present in enzymes such as acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase and phosphonopyruvate decarboxylase
YP_003915370.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1) with cleavage site probability 0.973 between position 26 and 27
YP_003915374.1	match to protein domain PF01872. This domain is found in the C-terminus of the bifunctional deaminase- reductase in combination with PF00383 as well as in isolation in some archaebacterial proteins
YP_003915375.1	mannitol 2-dehydrogenase catalyzes the NAD- dependent reduction of mannitol to fructose
YP_003915376.1	major facilitator superfamily, polyol porter (PP) family (TC 2.A.1.18.z). Possible mannitol transporter
YP_003915377.1	DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway
YP_003915378.1	catalyses the following reaction: ATP + D-xylulose <=> ADP + D-xylulose 5-phosphate. Involved in the catabolism of xylose
YP_003915379.1	glycerophosphoryl diester phosphodiesterases display broad specificity for glycerophosphodiesters; glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol, and bis(glycerophosphoglycerol)
YP_003915381.1	identified by match to protein family PF03591
YP_003915382.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915384.1	match to PF01596. This family includes catechol o- methyltransferase, caffeoyl-CoA O-methyltransferase and a family of bacterial O-methyltransferases that may be involved in antibiotic production
YP_003915385.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915386.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003915389.1	major facilitator superfamily, AzgA family purine transporter (TC 2.A.1.40.z)
YP_003915390.1	identified by match to PF00582: universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general stress endurance activity
YP_003915391.1	Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.432 between position 29 and 30
YP_003915392.1	match to PS00142 pattern: neutral zinc metallopeptidases, zinc-binding region signature
YP_003915394.1	removes the damaged DNA at cytosines and guanines by cleaving on the 3 -side of the apurinic/apyrimidinic sites
YP_003915395.1	enoyl-CoA hydratase catalyzes the hydratation of 2- trans-enoyl-CoA into 3-hydroxyacyl-CoA
YP_003915396.1	catalyzes the NAD-dependent, reversible oxidation of 3-hydroxbutyrate to methylmalonate. Involved in the catabolism of valine
YP_003915397.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003915399.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915400.1	identified by match to PF01022: bacterial regulatory protein, ArsR family. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003915401.1	catalyses the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide
YP_003915403.1	catalyses the formation of orotidine-5-phosphate from orotate and PRPP. Involved in pyrimidine biosynthesis
YP_003915404.1	match to protein domain PF00356. Numerous bacterial transcription regulatory proteins bind DNA via a helix- turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR. Within this family, the HTH motif is situated towards the N-terminus
YP_003915405.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family, xylobiose porter (TC 3.A.1.1.21). ABCISSE: ABC transporter, binding protein (BP), OSP-family (oligosaccharides or polyols)
YP_003915406.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family, xylobiose porter (TC 3.A.1.1.21). ABCISSE: ABC transporter, permease (IM), OSP-family (oligosaccharides or polyols)
YP_003915407.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family, xylobiose porter (TC 3.A.1.1.21). ABCISSE: ABC transporter, permease (IM), OSP-family (oligosaccharides or polyols)
YP_003915408.1	hydrolysis of 1,4-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini. Also hydrolyzes xylobiose. Identified by similarity to protein SP: Q76BU6 (Streptomyces thermoviolaceus), involved in degradation of xylans
YP_003915409.1	TCDB: ATP-binding cassette (ABC) superfamily (TC 3. A.1.y.z), DRI-family. Inverted organization, in which the permease component (IM) is C-terminal with respect to the ABC domain (ABC-IM)
YP_003915411.1	in E. coli, NagD is shown to be a nucleotide phosphatase. Its exact function has not been established, but it play a role in cell wall construction or disassembly (N-acetyl-glucosamine metabolism) or involved in NDP / NMP hydrolysis
YP_003915412.1	identified by match to protein family PF00588: SpoU rRNA Methylase family. Possible role in rRNA modification
YP_003915413.1	identified by match to protein family PF01551. Members of this family are zinc metallopeptidases with a range of specificities. Peptidase family M23 are also endopeptidases. 1 transmembrane helice predicted by TMHMM2. 0
YP_003915414.1	catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6-bisphosphate
YP_003915416.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915418.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915419.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915420.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.998) with cleavage site probability 0.527 between position 29 and 30
YP_003915421.1	identified by match to protein family PF01037
YP_003915422.1	identified by match to protein family PTHR14084. Kynureninase catalyzes the hydrolytic cleavage of L- kynurenine to anthranilic acid and L-alanine. Kynurinine is a Trp breakdown product and a precursor for NAD. This reaction is a key step in the catabolism of L-tryptophan by Pseudomonas fluorescens and some other bacteria
YP_003915423.1	amino acid-polyamine-organocation (APC) superfamily, amino acid transporter (AAT) family (TC 2.A.3.1.z)
YP_003915424.1	catalyzes the formation of thymidine 5-phosphate from thymidine
YP_003915425.1	identified by match to PF00440: bacterial regulatory proteins, tetR family
YP_003915426.1	xylitol oxidase catalyzes the following reaction: xylitol + O(2) <=> xylose + H(2)O(2)
YP_003915427.1	catalyses the following reaction: ATP + D-xylulose <=> ADP + D-xylulose 5-phosphate. Involved in the catabolism of xylose
YP_003915428.1	catalyzes the interconversion of D-xylose to D- xylulose. It can also isomerize D-ribose to D-ribulose and D-glucose to D-fructose
YP_003915429.1	match to PF00480: ROK family
YP_003915430.1	identified by match to PF00376. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA
YP_003915431.1	catalyzes the first step in the conversion of IMP to AMP in de novo purine nucleotide metabolism
YP_003915432.1	PRK08199: acetolactate synthase 2 catalytic subunit
YP_003915439.1	major facilitator superfamily (MFS), drug:H+ antiporter-3 (12 spanner) (DHA3) family, tetracycline resistance determinant TetV (TC 2.A.1.21.3). Identified by similarity to protein SP:O31137 (Mycobacterium smegmatis). Probable drug antiporter which uses the proton motive force for the active efflux of tetracycline
YP_003915441.1	phosphotransferase system enzyme I (EI) Family (TC 8.A.7.y.z). Enzyme I of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane
YP_003915442.1	catalyzes the phosphorylation of fructose-1- phosphate to fructose-1,6-biphosphate. Involved in the catabolism of fructose
YP_003915443.1	DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway
YP_003915444.1	identified by match to protein family PF02517: CAAX amino terminal protease family. Members of this family are probably proteases (after a prenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein, the AAX tripeptide is removed by one of the CAAX prenyl proteases). The family contains the Q03530 CAAX prenyl protease. 8 transmembrane helices predicted by TMHMM2.0
YP_003915445.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915446.1	identified by match to PF00440: bacterial regulatory proteins, tetR family
YP_003915451.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915453.1	catalyses several reactions, including the formation of L-homocysteine from O-acetyl-L-homoserine and H2S, and the formation of L-methionine from O-acetyl-L- homoserine and methanethiol
YP_003915454.1	identified by match to protein domain PF00300
YP_003915455.1	match to protein family TIGR02937. Sigma-70 family
YP_003915456.1	involved in the repair of alkylated DNA
YP_003915457.1	haem-containing catalase-peroxidases are bifunctional antioxidant enzymes that exhibit both catalase and broad-spectrum peroxidase activities, depending on the steady-state concentration of hydrogen peroxide
YP_003915458.1	acts as a global negative controlling element, employing Fe(2+) as a cofactor to bind the operator of the repressed genes. Match to protein family PF01475
YP_003915459.1	betaine/carnitine/choline fransporter (BCCT) family (TC 2.A.15.y.z)
YP_003915460.1	catalyzes the formation of acetyl-CoA from acetate and CoA
YP_003915461.1	TCDB: ATP-binding cassette (ABC) superfamily, taurine uptake transporter (TauT) family (TC3.A.1.17). ABCISSE: ABC transporter, permease (IM), OTCN-family (osmoprotectants, taurine, cyanate and nitrate), aliphatic sulfonates import. Part of the ABC transporter complex ssuABC involved in aliphatic sulfonates import. Is also involved in taurine transport
YP_003915462.1	TCDB: ATP-binding cassette (ABC) superfamily, taurine uptake transporter (TauT) family (TC 3.A.1.17.z). ABCISSE: ABC transporter, permease (IM), OTCN-family (osmoprotectants, taurine, cyanate and nitrate), aliphatic sulfonates import. Part of the ABC transporter complex ssuABC involved in aliphatic sulfonates import
YP_003915463.1	TCDB: ATP-binding cassette (ABC) superfamily, taurine uptake transporter (TauT) family (TC 3.A.1.17.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OTCN- family (osmoprotectants, taurine, cyanate and nitrate), aliphatic sulfonates import. Part of the ABC transporter complex ssuABC involved in aliphatic sulfonates import
YP_003915464.1	possibly involved in the metabolism of lipids. Match to PF08028. Acyl-CoA dehydrogenases catalyze the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD
YP_003915465.1	possibly involved in the metabolism of lipids. Identified by match to PF00296. Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long- chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulfonate monooxygenase (SsuD), and coenzyme F420-dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds
YP_003915466.1	catalyzes the transfer of the gamma-glutamyl moiety of glutathione to an acceptor that may be an amino acid, a peptide or water (forming glutamate)
YP_003915468.1	TCDB: ATP-binding cassette (ABC) superfamily, methionine uptake transporter (MUT) family (TC 3.A.1.24.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), DLM-family. Part of the ABC transporter complex MetNIQ involved in methionine import. The complex is composed of two ATP-binding proteins (MetN), two transmembrane proteins (MetI) and a solute-binding protein (MetQ)
YP_003915469.1	TCDB: ATP-binding cassette (ABC) superfamily, methionine uptake transporter (MUT) family (TC 3.A.1.24.z). ABCISSE: ABC transporter, permease (IM), DLM- family. Part of the ABC transporter complex MetNIQ involved in methionine import. The complex is composed of two ATP-binding proteins (MetN), two transmembrane proteins (MetI) and a solute-binding protein (MetQ)
YP_003915470.1	TCDB: ATP-binding cassette (ABC) superfamily, methionine uptake transporter (MUT) family (TC 3.A.1.24.z). ABCISSE: ABC transporter, lipoprotein (LPP), DLM-family. Part of the ABC transporter complex metNIQ involved in methionine import. The complex is composed of two ATP-binding proteins (MetN), two transmembrane proteins (MetI) and a solute-binding protein (MetQ)
YP_003915471.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5). ABCISSE: ABC transporter, binding protein (BP), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003915472.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003915473.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003915474.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, fused ATP-binding protein (ABC2), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003915475.1	possibly involved in the metabolism of lipids. Match to PF08028. Acyl-CoA dehydrogenases catalyze the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD
YP_003915476.1	possibly involved in the metabolism of lipids. Identified by match to PF00296. Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long- chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulfonate monooxygenase (SsuD), and coenzyme F420-dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds
YP_003915477.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.987) with cleavage site probability 0.986 between position 61 and 62. 1 transmembrane helice predicted by TMHMM2.0 after the signal peptide
YP_003915478.1	identified by similarity to protein SP:O68212 (Actinomyces naeslundii). Fimbriae mediate bacterial adhesion. C-terminal Gram positive anchor (PF00746)
YP_003915479.1	identified by match to protein family PF04203. Sortase is a transpeptidase that attaches surface proteins by the threonine of an LPXTG motif to the cell wall. Possible role in synthesis of functional type 2 fimbriae
YP_003915484.1	5 -nucleotidases are enzymes that catalyze the hydrolysis of phosphate esterified at carbon 5 of the ribose and deoxyribose portions of nucleotide molecules
YP_003915485.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915486.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.992 between position 38 and 39
YP_003915488.1	3-oxoacyl-ACP reductase catalyses the following reaction: (3R)-3-hydroxyacyl-[acyl- carrier-protein] + NADP(+) <=> 3-oxoacyl-[acyl-carrier- protein] + NADPH. It is involved in fatty acid biosynthesis
YP_003915490.1	possibly involved in the intracellular release of iron from iron-siderophore complexes
YP_003915491.1	identified by match to protein family PF04954. Match to protein domain PF08021. Possibly involved in removal of iron from iron-siderophore complexes
YP_003915492.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003915493.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003915494.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, binding protein (BP), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003915495.1	identified by match to protein domain PF00165: bacterial regulatory helix-turn-helix proteins, AraC family
YP_003915497.1	identified by match to protein family PF04954. Match to protein domain PF08021. Possibly involved in removal of iron from iron-siderophore complexes
YP_003915498.1	identified by match to PF08274 and PF03831. This protein family includes an uncharacterised member designated PhnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon- phosphorus bond cleavage (alkylphosphonates utilization as phosphorus source)
YP_003915500.1	phosphoribosylformylglycinamidine synthase catalyzes the fourth step in the de novo biosynthesis of purines. In Bacillus subtilis it is formed from three proteins: PurS, PurQ and smPurL
YP_003915501.1	phosphoribosylformylglycinamidine synthase catalyzes the fourth step in the de novo biosynthesis of purines. In Bacillus subtilis it is formed from three proteins: PurS, PurQ and smPurL
YP_003915502.1	phosphoribosylformylglycinamidine synthase catalyzes the fourth step in the de novo biosynthesis of purines. In Bacillus subtilis it is formed from three proteins: PurS, PurQ and smPurL
YP_003915504.1	contains ankyrin repeats (PF0023). Such repeats occur in a large number of functionally diverse proteins mainly from eukaryotes. They have been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers
YP_003915505.1	catalyzes the formation of 5-methyl-uridine at position 747 (M-5-U747) in 23S rRNA
YP_003915506.1	CPA superfamily, monovalent cation:proton antiporter-1 (CPA1) family (TC 2.A.36.y.z). Na+/H+ antiporters are key transporters in maintaining the pH of actively metabolising cells
YP_003915507.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.735 between position 34 and 35
YP_003915510.1	identified by match to protein family PF01370: NAD dependent epimerase/dehydratase family. This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions
YP_003915511.1	catalyzes the last step in heme biosynthesis: the chelation of a ferrous ion to proto-porphyrin IX, to form protoheme: Protoheme + 2 H+ <=> protoporphyrin + Fe2+
YP_003915513.1	identified by similarity to protein SP:Q6M8T2 (Corynebacterium glutamicum). IT superfamily, citrate- Mg2+:H+ (CitM) citrate-Ca2+:H+ (CitH) symporter (CitMHS) family (TC 2.A.11.y.z)
YP_003915514.1	identified by similarity to protein SP:Q8NU70 (Corynebacterium glutamicum). CitAB controls citrate utilization in Corynebacterium glutamicum
YP_003915515.1	match to PF01636. This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation. This family also includes homoserine kinase
YP_003915516.1	catalyses the following reaction : a phosphate monoester + H(2)O <=> an alcohol + phosphate
YP_003915517.1	catalyzes the phosphorylation of aspartate. The product of this reaction can then be used in the biosynthesis of lysine or in the pathway leading to homoserine, which participates in the biosynthesis of threonine, isoleucine and methionine
YP_003915520.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003915521.1	major facilitator superfamily, drug:H+ antiporter-2 (14 spanner) (DHA2) family (TC 2.A.1.3.z). Identified by match to protein family TIGR00711
YP_003915522.1	may play a role in DNA repair. It seems to be involved in an recBC-independent recombinational process of DNA repair. It may act with recF and recO
YP_003915523.1	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII complex. PolIII associates with the gamma complex (composed of gamma, delta, delta, psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex
YP_003915525.1	identified by match to cd00085: HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins
YP_003915527.1	identified by match to PF03171. This family contains members of the 2-oxoglutarate (2OG) and Fe(II)- dependent oxygenase superfamily
YP_003915530.1	match to protein domain PF01323
YP_003915531.1	6 transmembrane helices predicted by TMHMM2.0
YP_003915532.1	amino acid-polyamine-organocation (APC) superfamily, amino acid transporter (AAT) family, histidine permease (TC 2.A.3.1.9). Identified by similarity to protein SP:Q9H86 (Pseudomonas aeruginosa)
YP_003915533.1	identified by match to protein domain PF00300
YP_003915534.1	match to PF00561: alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes
YP_003915535.1	catalyzes the aldol condensation of glyoxylate with acetyl-CoA to form malate, the second step of the glyoxylate bypass, an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants
YP_003915536.1	catalyzes the conversion of isocitrate to succinate and glyoxylate. This is the first step in the glyoxylate bypass, an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants
YP_003915538.1	identified by match to protein domain PF02223. dTMP kinase (thymidylate kinase) catalyzes the phosphorylation of thymidine 5-monophosphate (dTMP) to thymidine 5- diphosphate (dTDP) in the presence of ATP and magnesium
YP_003915540.1	match to protein domain PF01381: helix-turn-helix
YP_003915542.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.454 between position 41 and 42
YP_003915543.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003915545.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003915546.1	ATP-dependent Clp proteases act as chaperones to target the proteases to substrates
YP_003915547.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915549.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. 5 transmembrane helices predicted by TMHMM2.0
YP_003915552.1	catalyzes the following reaction: D-amino acid + H(2)O + acceptor <=> 2-oxo acid + NH(3) + reduced acceptor. Acts to some extent on all D-amino acids except D-aspartate and D-glutamate
YP_003915554.1	identified by match to protein family PF01370: NAD dependent epimerase/dehydratase family. This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions
YP_003915555.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003915556.1	in Escherichia coli umuD and umuC genes have been shown to encode E. coli s fifth DNA polymerase, pol V (consisting of a heterotrimer of UmuD (2)C). The main function of pol V appears to be the bypass of DNA lesions that would otherwise block replication by pols I-IV
YP_003915557.1	in Escherichia coli umuD and umuC genes have been shown to encode E. coli s fifth DNA polymerase, pol V (consisting of a heterotrimer of UmuD (2)C). The main function of pol V appears to be the bypass of DNA lesions that would otherwise block replication by pols I-IV
YP_003915558.1	identified by match to PF00933. Glycoside hydrolase family 3 comprises enzymes with a number of known activities; beta-glucosidase (EC:3.2.1.21); beta- xylosidase (EC:3.2.1.37); N-acetyl beta-glucosaminidase (EC:3.2.1.52); glucan beta-1,3-glucosidase (EC:3.2.1.58); cellodextrinase (EC:3.2.1.74); exo-1,3-1,4-glucanase (EC:3. 2.1)
YP_003915559.1	identified by match to PF00082. Subtilases are a family of serine proteases. The vast majority of the family are endopeptidases. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.964 between position 32 and 33
YP_003915562.1	EC 2.7.4.7 is involved in thiamin biosynthesis. It catalyzes the phosphorylation of HMP-P to HMP-PP
YP_003915564.1	identified by match to PF00440: bacterial regulatory proteins, tetR family
YP_003915565.1	6 transmembrane helices predicted by TMHMM2.0
YP_003915566.1	TCDB: ATP-binding cassette (ABC) superfamily (TC 3. A.1.y.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), DRI-family
YP_003915567.1	12 transmembrane helices predicted by TMHMM2.0
YP_003915568.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003915569.1	exchanges the guanine residue with 7-aminomethyl-7- deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, - Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2- cyclopenten-1-yl)amino)methyl)- 7-deazaguanosine)
YP_003915570.1	10 transmembrane helices predicted by TMHMM2.0
YP_003915572.1	major facilitator superfamily, drug:H+ antiporter-2 (14 spanner) (DHA2) family (TC 2.A.1.3.z). Identified by match to protein family TIGR00711
YP_003915573.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003915574.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915575.1	serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. This protein may be a resolvase (match to PF07508 and PF00239)
YP_003915577.1	identified by match to PF00436. The Escherichia coli single-strand binding protein binds tightly to single- stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids
YP_003915578.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915582.1	TCDB: ATP-binding cassette (ABC) superfamily, () drug resistance ATPase-1 (Drug RA1) family (TC 3.A.1.120.z). ABCISSE: fused ATP-binding protein (ABC2), ART-family. Duplicated ATPase domains (PF00005)
YP_003915583.1	identified by match to PF08240. Zn-dependent alcohol dehydrogenases catalyse the following reaction: an alcohol + NAD(+) <=> an aldehyde or ketone + NADH
YP_003915584.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915585.1	7 transmembrane helices predicted by TMHMM2.0
YP_003915586.1	match to PS00430: TonB-dependent receptor proteins signature. In Escherichia coli the TonB protein interacts with outer membrane receptor proteins that carry out high- affinity binding and energy-dependent uptake of specific substrates into the periplasmic space. 2 transmembrane helices predicted by TMHMM2.0
YP_003915587.1	identified by match to protein domain PF08241
YP_003915589.1	identified by match to protein family PF01551. Members of this family are zinc metallopeptidases with a range of specificities. Peptidase family M23 are also endopeptidases. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0. 740 between position 37 and 38
YP_003915590.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915591.1	match to protein family PF02195. Proteins containing this domain, appear to be related to the Escherichia coli plasmid protein ParB, which preferentially cleaves single-stranded DNA
YP_003915594.1	similar to  excisionases from Mycobacterium phages
YP_003915595.1	match to protein family PF09250
YP_003915597.1	identified by match to protein domain PF00165: bacterial regulatory helix-turn-helix proteins, AraC family
YP_003915598.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690
YP_003915599.1	TCDB: ATP-binding cassette (ABC) superfamily, siderophore-Fe3+ uptake transporter (SIUT) family (TC 3.A. 1.21.z). ABCISSE: ABC transporter, permease and ATP- binding protein (IM-ABC), DPL-family, SID-subfamily (siderophore uptake)
YP_003915600.1	TCDB: ATP-binding cassette (ABC) superfamily, siderophore-Fe3+ uptake transporter (SIUT) family (TC 3.A. 1.21.z). ABCISSE: ABC transporter, permease and ATP- binding protein (IM-ABC), DPL-family, SID-subfamily (siderophore uptake)
YP_003915601.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003915602.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003915603.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, binding protein (BP), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003915604.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, binding protein (BP), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003915605.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, binding protein (BP), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003915606.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690
YP_003915607.1	identified by match to protein family PF04954. Match to protein domain PF08021. Possibly involved in removal of iron from iron-siderophore complexes
YP_003915608.1	identified by match to protein domain PF00165: bacterial regulatory helix-turn-helix proteins, AraC family
YP_003915609.1	C-5 cytosine-specific DNA methylases are enzymes that specifically methylate the C-5 carbon of cytosines in DNA. They are found as a component of type II restriction- modification systems in prokaryotes and some bacteriophages
YP_003915610.1	match to PF08751: TrwC relaxase. Similar to proteins involved in the conjugal tranfer of plasmids
YP_003915611.1	the SMF family (DNA processing chain A, dprA) are a group of bacterial proteins. In Helicobacter pylori, dprA is required for natural chromosomal and plasmid transformation
YP_003915612.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915613.1	match to protein family PF00589. Possible phage integrase or tyrosine recombinase subunit
YP_003915614.1	match to protein family PF00589. Possible phage integrase or tyrosine recombinase subunit
YP_003915616.1	6 transmembrane helices predicted by TMHMM2.0
YP_003915617.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, ATP-binding protein (ABC), DRI-family, DRB-subfamily (drug resistance, ). Possible function in drug efflux
YP_003915618.1	5 transmembrane helices predicted by TMHMM2.0
YP_003915619.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. 6 transmembrane helices predicted by TMHMM2.0
YP_003915620.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915621.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915624.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915625.1	identified by match to protein family PF00849. Pseudouridylate synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5- ribosyluracil, psi)
YP_003915626.1	identified by match to protein family PF02567. PhzC/PhzF is involved in dimerisation of two 2, 3-dihydro-3- oxo-anthranilic acid molecules to create phenazine-1- carboxylic acid (PCA) by P. fluorescens. This family also contains a  thymidilate synthase from Mycobacterium tuberculosis. Many phenazine compounds are found in nature and are produced by bacteria such as Pseudomonas spp., Streptomyces spp., and Pantoea agglomerans. These compounds have been implicated in the virulence and competitive fitness of producing organisms. For example, the phenazine pyocyanin produced by Pseudomonas aeruginosa contributes to its ability to colonise the lungs of cystic fibrosis patients. Similarly, phenazine-1-carboxylic acid, produced by a number of Pseudomonas, increases survival in soil environments and has been shown to be essential for the biological control activity of certain strains
YP_003915627.1	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_003915628.1	may be involved in DNA repair
YP_003915629.1	match to protein domain IPR011991: winged helix repressor DNA-binding
YP_003915630.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915631.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915635.1	match to PF00149. The metallophosphoesterase motif is found in a large number of proteins invoved in phosphorylation. These include Ser/Thr phosphatases, DNA polymerase, exonucleases, and other phosphatases
YP_003915637.1	match to protein domain PF03061: thioesterase superfamily
YP_003915638.1	benzoate:H+ symporter (BenE) family, benzoate permease (TC 2.A.46.1.1). Identified by match to protein family PF03594
YP_003915639.1	catalyzes the first step in NAD biosynthesis from aspartate. Specifically catalyzes the NAD or NADP- dependent dehydrogenation of L-aspartate to iminoaspartate
YP_003915640.1	involved in protocatechuate catabolism
YP_003915641.1	3-oxoadipate enol-lactonase catalyses the formation of 3-oxoadipate from 3-oxoadipate enol-lactone. It is involved in aromatic acids catabolism
YP_003915642.1	catalyses the cyclization of 3-carboxy-cis,cis- muconate to 4-carboxy-muconolactone. Involved in aromatic acids catabolism
YP_003915643.1	catalyses the following reaction: 3,4- dihydroxybenzoate + O(2) <=> 3-carboxy-cis,cis-muconate
YP_003915644.1	catalyses the following reaction: 3,4- dihydroxybenzoate + O(2) <=> 3-carboxy-cis,cis-muconate
YP_003915645.1	catalyses the following reaction: 4-hydroxybenzoate + NADPH + O(2) <=> protocatechuate + NADP(+) + H(2)O
YP_003915646.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003915647.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.321 between position 26 and 27
YP_003915648.1	acetyl-CoA C-acyltransferase (also named 3-ketoacyl- CoA thiolase or thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation
YP_003915649.1	identified by similarity to protein SP:Q01103 (Pseudomonas putida). Catalyses the following reaction : succinyl-CoA + 3-oxoadipate = succinate + 3-oxoadipyl-CoA
YP_003915650.1	identified by similarity to protein SP: P0A102 (Pseudomonas putida). Catalyses the following reaction : succinyl-CoA + 3-oxoadipate = succinate + 3-oxoadipyl-CoA
YP_003915651.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003915652.1	match to protein domain IPR011588: glyoxalase/extradiol ring-cleavage dioxygenase domain
YP_003915653.1	triacylglycerol lipase hydrolyzes ester bonds in triacylglycerol giving diacylglycerol, monoacylglycerol, glycerol and free fatty acids. Signal peptide predicted by SignalP 3.0 HMM (probability: 1) with cleavage site probability 0.991 between position 34 and 35
YP_003915654.1	identified by match to protein family PF02230. This family consists of both phospholipases and carboxylesterases with broad substrate specificity
YP_003915656.1	7 transmembrane helices predicted by TMHMM2.0
YP_003915657.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003915659.1	involved in molybdoterin cofactor biosynthesis. Catalyses the following reaction: molybdopterin + ATP --> molybdopterin-AMP + diphosphate. The function of several enzymes, such as xanthine oxidase, sulfite oxidase, nitrate reductase, depends on the molybdopterin cofactor
YP_003915660.1	is involved, together with MoaA, in the conversion of a guanosine derivative (5 -GTP) into the molybdopterin precursor Z. The function of several enzymes, such as xanthine oxidase, sulfite oxidase, nitrate reductase, depends on the molybdopterin cofactor
YP_003915661.1	involved in the biosynthesis of a demolybdo- cofactor (molybdopterin), necessary for molybdo-enzymes such as xanthine oxidase, sulfite oxidase, nitrate reductase: molybdopterin-AMP + molybdate --> molybdenum cofactor + AMP + H2O
YP_003915662.1	molybdoterin synthase converts molybdopterin precursor Z into molybdopterin. This requires the incorporation of two sulfur atoms into precursor Z to generate a dithiolene group. Heterodimer of 2 MoaD subunits and 2 MoaE subunits
YP_003915663.1	involved in the biosynthesis of a demolybdo cofactor (molybdopterin), necessary for molybdoenzymes. Plays a role in the activation of the small subunit of the molybdopterin converting factor (MoaD)
YP_003915664.1	molybdoterin synthase converts molybdopterin precursor Z into molybdopterin. This requires the incorporation of two sulfur atoms into precursor Z to generate a dithiolene group. Heterodimer of 2 MoaD subunits and 2 MoaE subunits
YP_003915668.1	is involved, together with MoaC, in the conversion of a guanosine derivative (5 -GTP) into the molybdopterin precursor Z. The function of several enzymes, such as xanthine oxidase, sulfite oxidase, nitrate reductase, depends on the molybdopterin cofactor
YP_003915669.1	TCDB: ATP-binding cassette (ABC) superfamily, MolT- family (molybdate uptake transporter), molybdate porter (TC 3.A.1.8.1). ABCISSE: ABC transporter, binding protein (BP), MOI-family, molybdate import. Part of the ABC transporter complex ModABC involved in molybdate import
YP_003915670.1	TCDB: ATP-binding cassette (ABC) superfamily, MolT- family (molybdate uptake transporter), molybdate porter (TC 3.A.1.8.1). ABCISSE: ABC transporter, permease (IM), MOI-family, molybdate import. Part of the ABC transporter complex ModABC involved in molybdate import
YP_003915671.1	N-terminal section of the protein: ABC transporter, ATP-binding subunit ModC; TCDB: ATP-binding cassette (ABC) superfamily, MolT-family (molybdate uptake transporter), molybdate porter (TC 3.A.1.8.1). ABCISSE: ABC transporter, ATP-binding protein (ABC), MOI-family, molybdate import. Part of the ABC transporter complex ModABC involved in molybdate import. C-terminal section of the protein: molybdopterin biosynthesis protein MoeA; involved in the biosynthesis of a demolybdo-cofactor (molybdopterin), necessary for molybdo-enzymes such as xanthine oxidase, sulfite oxidase, nitrate reductase: molybdopterin-AMP + molybdate --> molybdenum cofactor + AMP + H2O
YP_003915672.1	links a guanosine 5 -phosphate to molydopterin, forming molybdopterin guanine dinucleotide: molybdenum cofactor + GTP = molybdopterin guanine dinucleotide + diphosphate + 2 H2O
YP_003915673.1	match to PF02683: Cytochrome C biogenesis protein transmembrane region
YP_003915674.1	match to protein domain PF01323
YP_003915676.1	identified by match to PF00126: bacterial regulatory helix-turn-helix protein, lysR family. Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini
YP_003915677.1	the respiratory nitrate reductase enzyme complex allows the bacteria to use nitrate as an electron acceptor during anaerobic growth. The gamma subunit is a b-type cytochrome that receives electrons from the quinone pool. It then transfers these via the iron-sulfur clusters of the beta subunit to the molybdenum cofactor found in the alpha subunit
YP_003915678.1	the respiratory nitrate reductase enzyme complex allows the bacteria to use nitrate as an electron acceptor during anaerobic growth. The delta subunit is not part of the nitrate reductase enzyme but is most likely needed for assembly of the multi-subunit enzyme complex
YP_003915679.1	the respiratory nitrate reductase enzyme complex allows the bacteria to use nitrate as an electron acceptor during anaerobic growth
YP_003915680.1	major facilitator superfamily, nitrate/nitrite porter family, 24 TMS, 2 domain, NarK1-NarK2 porter (TC 2. A.1.8.11). In Paracoccus pantotrophus, this transporter comprises 2 domains: NarK1, a NO3-/H+ symporter; and NarK2, a NO3-/NO2- antiporter
YP_003915681.1	identified by match to protein family PF07152. This family consists of several hypothetical bacterial proteins of around 180 residues in length, which are often known as YaeQ. YaeQ is homologous to RfaH, a specialised transcription elongation protein. YaeQ is known to compensate for loss of RfaH function in Escherichia coli and Salmonella typhimurium
YP_003915682.1	glycerophosphoryl diester phosphodiesterases display broad specificity for glycerophosphodiesters; glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol, and bis(glycerophosphoglycerol)
YP_003915684.1	catalyzes the hydrolysis of cytosine into uracil and ammonia
YP_003915685.1	catalyses the formation of UMP and diphosphate from uracil and 5-phospho-alpha-D-ribose 1-diphosphate
YP_003915686.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915687.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915688.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915689.1	COG2062; phosphohistidine phosphatase SixA from Escherichia coli exhibits phosphatase activity towards the HPT domain of the ArcB sensor involved in the multistep his-asp phosphorelay
YP_003915691.1	TC 3.A.1.117.z. ABCISSE: ABC transporter, permease and ATP-binding protein (IM-ABC), DPL-family, antibiotic resistance or production (ARP) subfamily. Possible function in antibiotic resistance or production (export)
YP_003915692.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003915693.1	TC 9.B.74.y.z. The phage infection protein (PIP) family is a  transport protein family. Identified by match to protein domains TIGR03061 and TIGR03062
YP_003915695.1	match to PF03372: Endonuclease/Exonuclease/phosphatase family. This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.974 between position 28 and 29
YP_003915696.1	identified by similarity to protein SP: Q9LAV7 (Thermobifida fusca). TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1.1.z). ABCISSE: ABC transporter, permease (IM), OSP-family (oligosaccharides or polyols), cellobiose import
YP_003915697.1	identified by similarity to protein SP: Q9LAV6 (Thermobifida fusca). TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1.1.z). ABCISSE: ABC transporter, binding protein (BP), OSP-family (oligosaccharides or polyols), cellobiose import
YP_003915698.1	identified by similarity to protein SP:Q9LAV5 (Thermobifida fusca). In Thermobifida fusca, bglC is most active against cellobiose
YP_003915699.1	identified by similarity to protein SP:O87590 (Thermobifida fusca). In Thermobifida fusca, CelR Binds to the 14-bp operator sequence 5-TGGGAGCGCTCCCA-3 in the upstream regions of cellulase genes; these operator sequences are modulated by cellobiose
YP_003915701.1	catalyzes the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate while hydrolyzing GTP
YP_003915702.1	identified by match to protein family PF03551
YP_003915703.1	match to PF00561: alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes
YP_003915704.1	flavohemoproteins from bacteria (e.g. Escherichia coli hmpA) and fungi consist of two distinct domains, an N- terminal globin domain and a C-terminal FAD-containing reductase domain
YP_003915705.1	identified by match to protein family PF02082
YP_003915707.1	catalyses the following reaction: alpha-D-mannose 1- phosphate <=> D-mannose 6-phosphate
YP_003915708.1	match to protein family TIGR00614: recQ family
YP_003915709.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915710.1	identified by match to PF00326 and PF02897. Prolyl oligopeptidase family consist of a number of evolutionary related peptidases whose catalytic activity seems to be provided by a charge relay system similar to that of the trypsin family of serine proteases, but which evolved by independent convergent evolution
YP_003915712.1	NADPH:quinone reductase catalyzes the following reaction: NADPH + quinone <=> NADP(+) + semiquinone. Quinone or similar compounds may act as acceptor
YP_003915715.1	catalyzes the reduction of 2,5-diketogluconic acid to 2-keto-L-gulonic acid, a key intermediate in the production of ascorbic acid. Can also reduce ethyl 2- methylacetoacetate stereoselectively to ethyl (2R)-methyl- (3S)-hydroxybutanoate and can also accept some other beta- keto esters. Identified by similarity to protein SP:Q46857 (Escherichia coli)
YP_003915716.1	match to protein family PF08386. This is a C- terminal domain associated with  hydrolases and bacterial peptidases that belong to MEROPS peptidase family S33 (clan SC). Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.604 between position 25 and 26
YP_003915717.1	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication once it is clamped onto DNA. DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII complex. PolIII associates with the gamma complex (composed of gamma, delta, delta prime, psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex
YP_003915718.1	catalyzes the phosphorylation of thymidine 5- monophosphate (dTMP) to thymidine 5-diphosphate (dTDP) in the presence of ATP and magnesium
YP_003915719.1	catalyzes the conversion of cysteine and succinyl- homoserine into cystathionine and succinate. Several other reactions may also be catalysed in some organisms
YP_003915720.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915721.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_003915723.1	probably involved in phosphate transport and/or metabolism. Identified by match to PF01895
YP_003915724.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915725.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915726.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.991) with cleavage site probability 0.479 between position 35 and 36
YP_003915727.1	CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes
YP_003915728.1	bifunctional enzyme catalyzing non-consecutive reactions in the 1-deoxy-D-xylulose 5-phosphate pathway of isoprenoid precursor biosynthesis
YP_003915729.1	activates cysteine and transfers it to tRNA(Cys) as the first step in protein biosynthesis
YP_003915730.1	identified by match to protein family PF00588: SpoU rRNA Methylase family. Possible role in rRNA modification
YP_003915732.1	identified by match to PF02913 and PF01565
YP_003915736.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915738.1	identified by similarity to protein SP:P96483 (Streptomyces reticuli). In Streptomyces reticuli, MsiK assists the cellobiose and maltose ABC transport systems. TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1.1.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OSP- family (oligosaccharides or polyols)
YP_003915739.1	synthesis of trehalose from trehalose-6-phosphate
YP_003915740.1	synthesis of trehalose 6-phosphate from UDP-glucose and glucose-6-phosphate
YP_003915741.1	match to protein domain PF01323
YP_003915742.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915743.1	match to PF02384. This domain is found in N-6 adenine-specific DNA methylase from type I and type IC restriction systems. These enzymes are responsible for the methylation of specific DNA sequences in order to prevent the host from digesting its own genome via its restriction enzymes. Match to PS00092 pattern: N-6 Adenine-specific DNA methylases signature
YP_003915745.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003915746.1	identified by match to PF00296. Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulfonate monooxygenase (SsuD), and coenzyme F420- dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds
YP_003915747.1	9 transmembrane helices predicted by TMHMM2.0
YP_003915748.1	DNA repair enzyme that 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_003915750.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915751.1	chaperonins are involved in productive folding of proteins. With the aid of cochaperonin GroES, GroEL encapsulates non-native substrate proteins inside the cavity of the GroEL-ES complex and promotes folding by using energy derived from ATP hydrolysis
YP_003915754.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915755.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915757.1	N-terminal section of the protein: match to PF00313 (cold-shock DNA-binding domain). The so-called cold shock proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organization of the prokaryotic nucleoid
YP_003915759.1	catalyzes the reversible interconversion of 3- phosphonooxypyruvate and glutamate to phosphoserine and 2- oxoglutarate to. It is required both in the major phosphorylated pathway of serine biosynthesis and in pyridoxine biosynthesis. Also catalyses the third step in the biosynthesis of the coenzyme pyridoxal 5-phosphate : (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + L-glutamate <=> 4-phosphonooxy-L-threonine + 2-oxoglutarate
YP_003915760.1	identified by similarity to protein SP:P0A672 (Mycobacterium tuberculosis). Iron-binding repressor of siderophore biosynthesis and iron uptake. Synonym: DtxR (Corynebacterium glutamicum)
YP_003915761.1	identified by match to protein family PF01551. Members of this family are zinc metallopeptidases with a range of specificities. Peptidase family M23 are also endopeptidases
YP_003915765.1	identified by match to PF00480: ROK family
YP_003915766.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915767.1	an ATP-dependent DNA helicase which facilitates the progress of replication forks. Non-essential in Escherchichia coli, PcrA is an essential DNA helicase in Bacillus subtilis, fulfilling functions both in repair and rolling-circle replication
YP_003915768.1	succinyl-CoA synthetase, which is composed of alpha and beta subunits, catalyzes the interconversion of succinyl-CoA and succinate. Involved in the TCA cycle
YP_003915769.1	succinyl-CoA synthetase, which is composed of alpha and beta subunits, catalyzes the interconversion of succinyl-CoA and succinate. Involved in the TCA cycle
YP_003915771.1	identified by similarity to protein SP:P0C0L7 (Escherichia coli). Proton symporter that senses osmotic shifts and responds by importing osmolytes such as proline, glycine betaine, stachydrine, pipecolic acid, ectoine and taurine. It is both an osmosensor and an osmoregulator which is available to participate early in the bacterial osmoregulatory response. Metabolite:H+ symporter (MHS) family, (Poline/glycine-betaine):(H+/Na+) symporter (also transports taurine, ectoine, pipecolate, proline-betaine, N,N-dimethylglycine, carnitine, and 1- carboxymethyl-pyridinium) (subject to osmotic activation) (TC 2.A.1.6.4)
YP_003915773.1	possible DNA or RNA helicase
YP_003915775.1	5 transmembrane helices predicted by TMHMM2.0
YP_003915778.1	match to protein domain PF01381: helix-turn-helix
YP_003915779.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915780.1	catalyses the following reaction: 4- guanidinobutanoate + H(2)O <=> 4-aminobutanoate + urea. The ortholog found in Arthrobacter sp. KUJ 8602 also acts on D-arginine, 3-guanidinopropionate and L-arginine
YP_003915781.1	domain present in thiamine pyrophosphate-requiring enzymes (acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase)
YP_003915783.1	catalyzes the following reaction: myo-inositol phosphate + H(2)O <=> myo-inositol + phosphate. Acts on five of the six isomers of myo-inositol phosphate, all except myo-inositol 2-phosphate, but does not act on myo- inositol bearing more than one phosphate group
YP_003915784.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003915785.1	major facilitator superfamily, drug:H+ antiporter-2 (14 spanner) (DHA2) family (TC 2.A.1.3.z)
YP_003915786.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003915787.1	CoA-transferases catalyse reversible transfer reactions of coenzyme A groups from CoA-thioesters to free acids
YP_003915788.1	possibly involved in the metabolism of lipids. Match to protein domains PF08028, PF02771 and PF02770. Acyl-CoA dehydrogenases catalyze the alpha,beta- dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD
YP_003915789.1	catalyses the following reaction: an aldehyde + NAD(+) + H(2)O <=> an acid + NADH
YP_003915790.1	identified by similarity to protein SP:P52041 (Clostridium acetobutylicum). Reduces 3-hydroxybutanoyl- CoA to acetoacetyl-CoA
YP_003915793.1	match to protein domain PF03061: thioesterase superfamily
YP_003915794.1	identified by match to protein family PF04954. Match to protein domain PF08021. Possibly involved in removal of iron from iron-siderophore complexes
YP_003915795.1	DNA repair enzyme that hydrolyzes the deoxyribose N- glycosidic bond to excise various alkylated bases from a damaged DNA polymer
YP_003915796.1	DNA repair enzyme that hydrolyzes the deoxyribose N- glycosidic bond to excise various alkylated bases from a damaged DNA polymer
YP_003915797.1	identified by match to PF01022: bacterial regulatory protein, ArsR family. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003915798.1	identified by similarity to protein SP:P13512 (Ralstonia metallidurans). Cation diffusion facilitator (CDF) family, Cd2+, Zn2+, Co2+ efflux permease (TC 2.A.4.1. 1). Also binds Cu2+ and Ni2+. Increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt (is considered to be an efflux pump that remove these ions from cells)
YP_003915799.1	TCDB: ATP-binding cassette (ABC) superfamily, lipoprotein translocase (LPT) family (TC 3.A.1.125.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), o228 family (members of this family might be involved in a more general lipoprotein releasing mechanism common to all prokaryotes)
YP_003915800.1	TCDB: ATP-binding cassette (ABC) superfamily, lipoprotein translocase (LPT) family (TC 3.A.1.125.z). ABCISSE: ABC transporter, permease (IM2: 2 IM domains fused into a single polypeptide chain), o228 family (members of this family might be involved in a more general lipoprotein releasing mechanism common to all prokaryotes)
YP_003915805.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.748 between position 22 and 23
YP_003915807.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915808.1	6 transmembrane helices predicted by TMHMM2.0
YP_003915809.1	PF03631 (ribonuclease_BN, ribonuclease BN-like family): this family contains integral membrane proteins with 5 to 6 predicted transmembrane spans. The family includes ribonuclease BN, which is involved in tRNA maturation
YP_003915810.1	identified by similarity to protein SP:O86308 (Micrococcus luteus). Bacterial growth factor or cytokine involved in resuscitation of dormant bacteria and stimulation of bacterial growth. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.996 between position 36 and 37
YP_003915811.1	CoA-transferases catalyse reversible transfer reactions of coenzyme A groups from CoA-thioesters to free acids
YP_003915812.1	match to PF08223: PaaX-like protein C-terminal domain. This family contains proteins that are similar to the product of the paaX gene of Escherichia coli. This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid
YP_003915813.1	catalyses the formation of N-formylkynurenine from L-tryptophan, the first step in the kynurenine pathway (major pathway of tryptophan metabolism)
YP_003915814.1	identified by match to PF03358. FMN reductase reductase catalyses the following reaction: NAD(P)H + FMN = NAD(P)(+) + FMNH(2)
YP_003915815.1	identified by similarity to protein SP:P42270 (Escherichia coli). Also named OHED hydratase. Involved in the homoprotocatechuic acid pathway. Catalyses the conversion of 2-oxohept-3-ene-1,7-dioc acid into 2,4- dihydroxyhept-2-ene-1,7-dioic acid
YP_003915816.1	identified by similarity to protein SP:Q47098 (Escherichia coli). Involved in the homoprotocatechuic acid pathway. Catalyses the conversion of 2,4- dihydroxyhept-2-ene-1,7-dioic acid into succinic semialdehyde and pyruvic acid
YP_003915817.1	8 transmembrane helices predicted by TMHMM2.0
YP_003915818.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.998) with cleavage site probability 0.256 between position 28 and 29
YP_003915820.1	catalyses the NADP-dependent decarboxylative reduction of 10-formyltetrahydrofolate into tetrahydrofolate. Involved in DNA synthesis and in de novo purine biosynthesis pathway
YP_003915821.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003915822.1	EC 3.2.1.24 hydrolyses terminal, non-reducing alpha- D-mannose residues in alpha-D-mannosides. Also hydrolyzes alpha-D-lyxosides and heptopyranosides with the same configuration at C-2, C-3 and C-4 as mannose
YP_003915823.1	identified by match to protein domain PF00300
YP_003915824.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003915825.1	major facilitator superfamily (MFS), aromatic acid:H+ symporter (AAHS) family (TC 2.A.1.15.z). Members of this family transport compounds such as benzoate, hydroxybenzoate, niacin...
YP_003915827.1	catalyses the last two steps in de novo purine biosynthesis. Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3) catalyses the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR (5-formylaminoimidazole-4-carboxamide ribonucleotide) and tetrahydrofolate. IMP cyclohydrolase (EC 3.5.4.10) catalyses the formation of IMP from FAICAR
YP_003915830.1	match to PF02687: this is a family of predicted permeases and hypothetical transmembrane proteins
YP_003915831.1	TCDB: ATP-binding cassette (ABC) superfamily, lipoprotein translocase (LPT) family (TC 3.A.1.125.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), o228 family (members of this family might be involved in a more general lipoprotein releasing mechanism common to all prokaryotes)
YP_003915832.1	identified by match to protein family PF03551
YP_003915833.1	metal ion (Mn2+-iron) transporter (Nramp) family protein (TC 2.A.55.y.z). The generalized transport reaction catalyzed by Nramp family proteins is: Me2+ (out) + H+ (out) -> Me2+ (in) + H+ (in)
YP_003915835.1	catalyzes the irreversible hydrolytic deamination of adenosine to ammonia and inosine, or of desoxyadenosine to ammonia and desoxyinosine
YP_003915836.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003915837.1	enzymes named acetyl-coenzyme A carboxylase (EC 6.4. 1.2), propionyl-coenzyme A carboxylase (EC 6.4.1.3) and acyl-coenzyme A carboxylase are constituted by several types of subunits. Alpha subunits contains the biotin carboxylase (BC, EC 6.3.4.14) and biotin carboxyl carrier protein (BCCP) domains, beta subunits contain the carboxyltransferase (CT) domain. An epsilon subunit is present in some microorganisms
YP_003915838.1	identified by match to PF02626 and PF02682. EC 3.5. 1.24 may be involved in the degradation of urea, together with EC 6.3.4.6, or in cyanuric acid metabolism
YP_003915839.1	identified by match to protein family PF03746. This family includes LamB. The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilisation of lactams such as 2-pyrrolidinone
YP_003915841.1	catalyses the following reaction: ATP + formate + tetrahydrofolate => ADP + phosphate + 10- formyltetrahydrofolate
YP_003915842.1	major facilitator superfamily, drug:H+ antiporter-2 (14 spanner) (DHA2) family (TC 2.A.1.3.z). Identified by match to protein family TIGR00711
YP_003915843.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003915844.1	involved in the TCA cycle. Catalyses the interconversion of isocitrate and 2-oxoglutarate. Oxalosuccinate can also be used as a substrate
YP_003915850.1	match to protein domain PF00075 (RNase H). This domain is often associated with reverse transcriptases (important enzyme in retroviral replication cycle)
YP_003915851.1	dGTPase catalyses the formation of deoxyguanosine from dGTP. It is involved in purine metabolism
YP_003915855.1	match to PF00196: bacterial regulatory proteins, luxR family. This domain is a DNA-binding, helix-turn- helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators
YP_003915856.1	identified by similarity to protein SP:Q9LBW5 (Mycobacterium gastri). Catalyzes the isomerization of the D-arabino-3-hexulose 6-phosphate into fructose 6-phosphate in microorganisms that can use formaldehyde as a carbon source (ribulose monophosphate pathway of formaldehyde fixation)
YP_003915857.1	identified by similarity to protein SP:Q9LBW4 (Mycobacterium gastri). Catalyzes the formation of D- arabino-3-hexulose-6-phosphate from D-ribulose 5-phosphate and formaldehyde in microorganisms that can use formaldehyde as a carbon source (ribulose monophosphate pathway of formaldehyde fixation)
YP_003915858.1	cd00038: effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription
YP_003915859.1	chaperone that serves for the intracellular sequestration and transport of Cu(+). Delivers Cu(+) to the copper-transporting ATPase CopA. Identified by similarity to protein SP:O32221 (Bacillus subtilis)
YP_003915860.1	involved in copper export. Forms an heterodimer with CopZ during the transfer of Cu(+). TCDB: P-type ATPase (P-ATPase) superfamily (TC 3.A.3.y.z). Identified by similarity to protein SP:O32220 (Bacillus subtilis)
YP_003915861.1	presence of one conserved barrel domain of the cupin superfamily (PF07883)
YP_003915862.1	PF02012: BNR/Asp-box repeats. These repeats are found in a variety of non-homologous proteins, including bacterial ribonucleases, sulphite oxidases, reelin, netrins, sialidases, neuraminidases, some lipoprotein receptors, and a variety of glycosyl hydrolases. Similar to protein SP:Q6SK52 (Arthrobacter aurescens plasmid)
YP_003915863.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.999) with cleavage site probability 0.520 between position 25 and 26. Similar to protein SP:A1RCQ1 (Arthrobacter aurescens plasmid)
YP_003915864.1	2 transmembrane helices predicted by TMHMM2.0. Similar to protein SP:A1RCQ0 (Arthrobacter aurescens plasmid)
YP_003915865.1	P-type ATPase (P-ATPase) superfamily (TC 3.A.3.y.z). Involved in export of cations
YP_003915866.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915867.1	TCDB: P-type ATPase (P-ATPase) superfamily (TC 3.A. 3.y.z). Possibly involved in export of cations
YP_003915868.1	identified by match to PF01022: bacterial regulatory protein, ArsR family. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003915870.1	identified by match to PF02661: Fic protein family. cAMP may be a regulation factor in cell division of some bacteria. The Fic (filamentation induced by cAMP) protein is involved in the synthesis of PAB or folate. It would appear that the Fic protein and cAMP are involved in a regulatory mechanism of cell division via folate metabolism and in these organisms cell division could be controlled by coordination of cAMP, Fic and Fts proteins
YP_003915871.1	match to PF00239 and PF02796. Possibly involved in site-specific recombination of DNA
YP_003915873.1	identified by match to protein family PF05713: bacterial mobilisation protein (MobC). This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis- active site of a mobilising plasmid, the origin of transfer (oriT) region
YP_003915874.1	identified by match to protein family PF03432: Relaxase/Mobilisation nuclease domain. Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation
YP_003915875.1	similar to Arthrobacter plasmidic proteins
YP_003915876.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.990 between position 30 and 31
YP_003915877.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915878.1	3 transmembrane helices predicted by TMHMM2.0
YP_003915882.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915883.1	IPR001478; PDZ domains are found in diverse signaling proteins in bacteria, yeasts, plants, insects and vertebrates
YP_003915884.1	identified by similarity to protein SP:Q6DKY2 (Bacillus stearothermophilus). Heat-stable reverse transcriptase. Possible group II intron associated protein
YP_003915888.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915889.1	identified by match to PF01613
YP_003915890.1	final step in methionine synthesis
YP_003915892.1	identified by match to PF00126: bacterial regulatory helix-turn-helix protein, lysR family. Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini
YP_003915893.1	catalyses several reactions, including the formation of L-homocysteine from O-acetyl-L-homoserine and H2S, and the formation of L-methionine from O-acetyl-L- homoserine and methanethiol
YP_003915894.1	catalyzes the conversion of cysteine and succinyl- homoserine into cystathionine and succinate. Several other reactions may also be catalysed in some organisms
YP_003915895.1	match to PF00132: Bacterial transferase hexapeptide repeat. A number of different transferase protein families contain this repeat, such as galactoside acetyltransferase- like proteins, the gamma-class of carbonic anhydrases, and tetrahydrodipicolinate-N-succinlytransferases
YP_003915896.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915897.1	catalyses the following reaction: 10- formyltetrahydrofolate + H(2)O <=> formate + tetrahydrofolate
YP_003915898.1	methylenetetrahydrofolate dehydrogenase (EC 1.5.1. 5) catalyses the following reaction: 5,10- methylenetetrahydrofolate + NADP(+) <=> 5,10- methenyltetrahydrofolate + NADPH. Methylenetetrahydrofolate cyclohydrolase (EC 3.5.4.9) catalyses the following reaction: 5,10- methenyltetrahydrofolate + H(2)O <=> 10- formyltetrahydrofolate methenyltetrahydrofolate cyclohydrolase
YP_003915899.1	major facilitator superfamily (MFS), metabolite:H+ symporter (MHS) family (TC 2.A.1.6.z)
YP_003915900.1	identified by match to PF00126: bacterial regulatory helix-turn-helix protein, lysR family. Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini
YP_003915902.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915903.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003915904.1	6 transmembrane helices predicted by TMHMM2.0
YP_003915905.1	2 transmembrane helices predicted by TMHMM2.0
YP_003915906.1	removes the damaged DNA at cytosines and guanines by cleaving on the 3 -side of the apurinic/apyrimidinic sites
YP_003915907.1	activates tryptophan and transfers it to tRNA(Trp) as the first step in protein biosynthesis
YP_003915908.1	match to PF02834. Corresponds to a number of known and predicted phosphoesterases, including bacterial and archaeal 2 ,5 RNA ligases. The physiological substrate(s) in prokaryotes may include small 2 ,5 -link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles
YP_003915909.1	decomposes hydrogen peroxide to molecular oxygen and water. Its main function is to protect cells from the toxic effects of hydrogen peroxide
YP_003915913.1	9 transmembrane helices predicted by TMHMM2.0
YP_003915914.1	the succinate dehydrogenase complex catalyses the interconversion of fumarate and succinate. It contains several subunits: a flavoprotein (SdhA), an iron-sulfur protein (SdhB), and membrane anchor proteins (SdhC and SdhD). Involved in the TCA cycle
YP_003915915.1	the succinate dehydrogenase complex catalyses the interconversion of fumarate and succinate. It contains several subunits: a flavoprotein (SdhA), an iron-sulfur protein (SdhB), and membrane anchor proteins (SdhC and SdhD). Involved in the TCA cycle
YP_003915916.1	the succinate dehydrogenase complex catalyses the interconversion of fumarate and succinate. It contains several subunits: a flavoprotein (SdhA), an iron-sulfur protein (SdhB), and membrane anchor proteins (SdhC and SdhD). Involved in the TCA cycle
YP_003915917.1	the succinate dehydrogenase complex catalyses the interconversion of fumarate and succinate. It contains several subunits: a flavoprotein (SdhA), an iron-sulfur protein (SdhB), and membrane anchor proteins (SdhC and SdhD). Involved in the TCA cycle
YP_003915918.1	catalyses the following reaction: GDP + alpha-D- mannose 1-phosphate <=> phosphate + GDP-mannose. Participates in fructose and mannose metabolism
YP_003915919.1	identified by similarity to protein SP:P0ABC9 (Escherichia coli). Betaine/carnitine/choline fransporter (BCCT) family, choline:H+ symporter (TC 2.A.15.3.1). Involved in the osmoregulatory choline-glycine betaine pathway (choline uptake)
YP_003915920.1	involved in the synthesis of the osmoprotectant betaine
YP_003915921.1	catalyzes the following reaction: choline + O2 <=> betaine aldehyde + H2O2. Involved in the synthesis of the osmoprotectant betaine
YP_003915923.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-2 (CUT2) family (TC 3.A.1. 2.z). ABCISSE: ABCISSE: ABC transporter, binding protein (BP), MOS-family (monosaccharides: pentoses and hexoses)
YP_003915924.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-2 (CUT2) family (TC 3.A.1. 2.z). ABCISSE: ABCISSE: ABC transporter, fused ATP- binding protein (ABC2), MOS-family (monosaccharides: pentoses and hexoses)
YP_003915925.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-2 (CUT2) family (TC 3.A.1. 2.z). ABCISSE: ABCISSE: ABC transporter, permease (IM), MOS-family (monosaccharides: pentoses and hexoses)
YP_003915926.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-2 (CUT2) family (TC 3.A.1. 2.z). ABCISSE: ABCISSE: ABC transporter, permease (IM), MOS-family (monosaccharides: pentoses and hexoses)
YP_003915927.1	catalyzes the hydrolysis of cytidine into uridine and ammonia
YP_003915928.1	catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism
YP_003915929.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915930.1	catalyzes the irreversible hydrolytic deamination of adenosine to ammonia and inosine, or of desoxyadenosine to ammonia and desoxyinosine
YP_003915931.1	identified by match to protein family PF00171
YP_003915932.1	match to protein domain PF03819. In Escherichia coli, MazG was characterized as a nucleoside triphosphate pyrophosphohydrolase which can hydrolyze all eight of the canonical ribo- and deoxynucleoside triphosphates to their respective monophosphates and PPi, with a preference for deoxynucleotides
YP_003915933.1	other names: 2-phosphoglycerate dehydratase, 2- phospho-D-glycerate hydro-lyase. Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate
YP_003915934.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915936.1	identified by match to protein family PF02541. Similar to exopolyphosphatase (Ppx, EC 3.6.1.11) and guanosine pentaphosphate phospho-hydrolase (GppA, EC 3.6.1. 40) proteins
YP_003915937.1	identified by match to PF00082. Subtilases are a family of serine proteases. The vast majority of the family are endopeptidases. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.974 between position 38 and 39. 1 transmembrane helice predicted by TMHMM2.0 after the signal peptide
YP_003915938.1	NADH dehydrogenase catalyzes the following reaction: NADH + acceptor <=> NAD(+) + reduced acceptor
YP_003915939.1	6 transmembrane helices predicted by TMHMM2.0
YP_003915940.1	amino acid-polyamine-organocation (APC) superfamily (TC 2.A.3.y.z)
YP_003915941.1	match to protein family PF01594
YP_003915942.1	catalyzes the conversion of threonine into 2- oxobutanoate. Involved in isoleucine biosynthesis. The enzyme from a number of sources also acts on L-serine
YP_003915943.1	necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites
YP_003915944.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915946.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915948.1	generates undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide
YP_003915949.1	identified by match to protein family PF02562: PhoH, PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation
YP_003915951.1	match to PF01478: Type IV leader peptidase family. This group of aspartic endopeptidases belong to MEROPS peptidase family A24 (type IV prepilin peptidase family, clan AD), subfamily A24A. Possibly involved in protein secretion
YP_003915952.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003915953.1	catalyzes the reversible hydration of fumarate to L- malate. Involved in the TCA cycle
YP_003915954.1	carbonate dehydratases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide. They are ubiquitous enzymes involved in fundamental processes like respiration, pH homeostasis and ion transport
YP_003915956.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915957.1	catalyzes the hydrolysis of fructose 1,6- bisphosphate to fructose 6-phosphate. Involved in gluconeogenesis
YP_003915958.1	catalyzes the interconversion of mannose-6- phosphate and fructose-6-phosphate. In prokaryotes, it is involved in a variety of pathways including capsular polysaccharide biosynthesis and D-mannose metabolism
YP_003915960.1	phosphoribosylaminoimidazole carboxylase catalyses the sixth step of de novo purine biosynthesis, the decarboxylation of 1-(5-phosphoribosyl)-5-amino-4- imidazole-carboxylate (AIR)
YP_003915961.1	phosphoribosylaminoimidazole carboxylase catalyses the sixth step of de novo purine biosynthesis, the decarboxylation of 1-(5-phosphoribosyl)-5-amino-4- imidazole-carboxylate (AIR)
YP_003915962.1	identified by match to protein family PF04138. Members of this family are predicted to be integral membrane proteins with three or four transmembrane spans. They are involved in the synthesis of cell surface polysaccharides
YP_003915964.1	identified by match to protein family PF02467. WhiB is a  transcription factor in Actinobacteria, required for differentiation and sporulation
YP_003915965.1	match to PF00535: glycosyl transferase family 2. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP- N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids
YP_003915966.1	1 transmembrane helice predicted by TMHMM2.0
YP_003915967.1	identified by match to protein family PF02628. One member of this family, CtaA, is required for cytochrome aa3 biosynthesis in Bacillus subtilis
YP_003915971.1	4 transmembrane helices predicted by TMHMM2.0
YP_003915972.1	activates fatty acids by binding to coenzyme A. Possibly involved in the synthesis of cellular lipids or their degradation via beta-oxidation
YP_003915973.1	identified by match to protein family PF02366. Transfers mannosyl residues to the hydroxy of serine or threonine residues, producing cell-wall mannoproteins
YP_003915975.1	succinate-semialdehyde dehydrogenase (NAD(P)(+)) reduces succinate semialdehyde into succinate. Involved in the degradation of gamma-aminobutyrate
YP_003915976.1	identified by match to protein domain PF01841: Transglutaminase-like superfamily. Most microbial homologues of the transglutaminases are probably proteases. 8 transmembrane helices predicted by TMHMM2.0
YP_003915978.1	identified by match to protein family PIRSF002849. AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes
YP_003915979.1	identified by match to protein family PF01026
YP_003915980.1	match to protein domains PF03990 (DUF348 domain of unknown function), PF07501 (G5 domain) and PF06737 (transglycosylase-like domain). The PF07501 domain is also found in proteins involved in metabolism of bacterial cell walls suggesting this domain may have an adhesive function
YP_003915981.1	specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3 prime-end of 16S rRNA in the 30S particle. Its inactivation leads to kasugamycin resistance
YP_003915982.1	forms part of the non-mevalonate pathway for terpenoid biosynthesis
YP_003915985.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003915987.1	TCDB: ATP-binding cassette (ABC) superfamily, () drug resistance ATPase-2 (Drug RA2) family (TC 3.A.1.121.z). ABCISSE: fused ATP-binding protein (ABC2), ART-family, ARE-subfamily (antibiotic resistance)
YP_003915988.1	glucosamine-1-phosphate N-acetyltransferase (EC 2.3. 1.157) and UDP-N-acetylglucosamine diphosphorylase (EC 2.7. 7.23) perform the last two steps in the synthesis of UDP-N-acetylglucosamine, which is an essential precursor in both the peptidoglycan and the lipopolysaccharide metabolic pathway
YP_003915989.1	catalyzes the formation of PRPP from ATP and ribose 5-phosphate. PRPP is then used in various biosynthetic pathways, as for example in the formation of purines, pyrimidines, histidine and tryptophan
YP_003915993.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.575 between position 36 and 37. 7 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003915994.1	TCDB: ATP-binding cassette (ABC) superfamily, lipoprotein translocase (LPT) family (TC 3.A.1.125.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), o228 family (members of this family might be involved in a more general lipoprotein releasing mechanism common to all prokaryotes)
YP_003916001.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1) with cleavage site probability 0.973 between position 26 and 27
YP_003916002.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1) with cleavage site probability 0.751 between position 32 and 33
YP_003916006.1	match to PF00239. Possibly involved in site- specific recombination of DNA
YP_003916008.1	part of the 50S ribosomal subunit. Contacts the 5S rRNA
YP_003916009.1	cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through abortion of translation and is essential for cell viability
YP_003916010.1	cysteine desulfurase catalyses the following reaction: L-cysteine + [enzyme]-cysteine <=> L-alanine + [enzyme]-S-sulfanylcysteine. It is involved in the biosynthesis of iron-sulfur clusters, thio-nucleosides in tRNA, thiamine, biotin, lipoate and pyranopterin (molybdopterin) and functions by mobilizing sulfur
YP_003916011.1	identified by match to protein family TIGR01994. The SUF system is an iron-sulfur cluster assembly system that operates under iron starvation and oxidative stress. SufU may act as a scaffold on which the Fe-S cluster is built and from which it is transferred
YP_003916012.1	NhaA Na+:H+antiporter (NhaA) family (TC 2.A.33.y.z). Na(+)/H(+) antiporter extrudes sodium in exchange for external protons. Active at alkaline pH. In E. coli, NhaA protein probably functions in the regulation of the internal pH when the external pH is alkaline. It also uses the H+ gradient to expel Na+ from the cell. Its activity is highly pH dependent
YP_003916014.1	necessary for strand-specific repair. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognized by TRCF which releases RNAP and the truncated transcript; the TCRF may replace RNAP at the lesion site and then recruit the uvrA/B/C repair system
YP_003916015.1	3 transmembrane helices predicted by TMHMM2.0
YP_003916017.1	TCDB: P-type ATPase (P-ATPase) superfamily (TC 3.A. 3.y.z). Involved in export of cations
YP_003916020.1	catalyzes a reversible aldol reaction between acetaldehyde and glyceraldehyde 3-phosphate to generate 2- deoxyribose 5-phosphate
YP_003916021.1	this family is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), hosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM). PGM (EC:5.4.2.2) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose. PGM/PMM (EC:5.4.2.2; EC:5.4.2.8) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate. Both PNGM (EC:5.4.2.3) and PAGM (EC:5.4.2.10) are involved in the biosynthesis of UDP-N-acetylglucosamine
YP_003916022.1	catalyzes the cleavage of guanosine, deoxyguanosine, inosine, deoxyinosine, adenosine or deoxyadenosine to respective bases and sugar-1-phosphate molecules
YP_003916023.1	E3 component of pyruvate dehydrogenase and 2- oxoglutarate dehydrogenase complexes
YP_003916025.1	major facilitator superfamily (MFS), metabolite:H+ symporter (MHS) family (TC 2.A.1.6.z)
YP_003916027.1	enzymes named acetyl-coenzyme A carboxylase (EC 6.4. 1.2), propionyl-coenzyme A carboxylase (EC 6.4.1.3) and acyl-coenzyme A carboxylase are constituted by several types of subunits. Alpha subunits contains the biotin carboxylase (BC, EC 6.3.4.14) and biotin carboxyl carrier protein (BCCP) domains, beta subunits contain the carboxyltransferase (CT) domain. An epsilon subunit is present in some microorganisms
YP_003916029.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.973) with cleavage site probability 0.445 between position 32 and 33
YP_003916032.1	match to PF02545. Maf is a  inhibitor of septum formation in eukaryotes, bacteria, and archaea
YP_003916033.1	Resistance-Nodulation-Cell Division (RND) superfamily (TC 2.A.6.y.z). C-terminal part of the protein: PS50156 domain (sterol-sensing domain). In bacteria, this domain is found in a number of drug resistance protein
YP_003916034.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003916037.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.890) with cleavage site probability 0.644 between position 24 and 25. 3 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003916039.1	3 transmembrane helices predicted by TMHMM2.0
YP_003916040.1	identified by match to PF00903: glyoxalase/bleomycin resistance protein/dioxygenase superfamily
YP_003916042.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916043.1	identified by match to protein family PIRSF002849. AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes
YP_003916044.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916045.1	match to PF06271. The molecular function of this region is unknown. However it be involved in transport of an as yet unknown set of ligands
YP_003916046.1	match to PF00481: protein phosphatase 2C
YP_003916047.1	match to PF00498. The forkhead-associated (FHA) domain is a phosphopeptide recognition domain found in many regulatory proteins
YP_003916048.1	identified by match to protein domain PD000001. Match to PS00108 pattern. Protein kinases are a group of enzymes that possess a catalytic subunit which transfers the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. They play a role in a mulititude of cellular processes, including division, proliferation, apoptosis, and differentiation
YP_003916050.1	identified by similarity to protein SP: P96886 (Mycobacterium tuberculosis). Enzymes named acetyl- coenzyme A carboxylase (EC 6.4.1.2), propionyl-coenzyme A carboxylase (EC 6.4.1.3) and acyl-coenzyme A carboxylase are constituted by several types of subunits. Alpha subunits contains the biotin carboxylase (BC, EC 6.3.4.14) and biotin carboxyl carrier protein (BCCP) domains, beta subunits contain the carboxyltransferase (CT) domain. An epsilon subunit is present in some microorganisms
YP_003916051.1	enzymes named acetyl-coenzyme A carboxylase (EC 6.4. 1.2), propionyl-coenzyme A carboxylase (EC 6.4.1.3) and acyl-coenzyme A carboxylase are constituted by several types of subunits. Alpha subunits contains the biotin carboxylase (BC, EC 6.3.4.14) and biotin carboxyl carrier protein (BCCP) domains, beta subunits contain the carboxyltransferase (CT) domain. An epsilon subunit is present in some microorganisms
YP_003916052.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003916053.1	acts both as a biotin-operon repressor and as the enzyme that synthesizes the corepressor, acetyl-CoA:carbon- dioxide ligase. This protein also activates biotin to form biotinyl-5-adenylate and transfers the biotin moiety to biotin-accepting proteins
YP_003916054.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916055.1	identified by similarity to protein SP:P27580 (Arthrobacter nicotianae). Plays essential roles in regulation of cellular metabolism by catalyzing the synthesis of a second messenger, cAMP
YP_003916056.1	match to PF00481: protein phosphatase 2C
YP_003916057.1	catalyzes the formation of phosphodiester linkages between 5 prime-phosphoryl and 3 prime-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA
YP_003916058.1	catalyzes the following reaction: myo-inositol phosphate + H(2)O <=> myo-inositol + phosphate. Acts on five of the six isomers of myo-inositol phosphate, all except myo-inositol 2-phosphate, but does not act on myo- inositol bearing more than one phosphate group
YP_003916059.1	5 transmembrane helices predicted by TMHMM2.0
YP_003916060.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.959 between position 37 and 38
YP_003916062.1	identified by match to PF00480: ROK family
YP_003916063.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916064.1	match to PF00905. The large number of penicillin binding proteins, which are represented in this group of sequences, are responsible for the final stages of peptidoglycan biosynthesis for cell wall formation. The proteins synthesise cross-linked peptidoglycan from lipid intermediates, and contain a penicillin-sensitive transpeptidase carboxy-terminal domain
YP_003916065.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916067.1	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
YP_003916068.1	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
YP_003916069.1	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
YP_003916071.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916073.1	identified by match to PF01636. This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides. It also includes homoserine kinase
YP_003916074.1	3 transmembrane helices predicted by TMHMM2.0
YP_003916075.1	identified by match to protein family TIGR01509: HAD-superfamily hydrolase, subfamily IA, variant 3; match to protein family PF00702: haloacid dehalogenase-like hydrolase
YP_003916076.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003916077.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003916078.1	catalyzes the reduction of 2,5-diketogluconic acid to 2-keto-L-gulonic acid, a key intermediate in the production of ascorbic acid. Can also reduce ethyl 2- methylacetoacetate stereoselectively to ethyl (2R)-methyl- (3S)-hydroxybutanoate and can also accept some other beta- keto esters. Identified by similarity to protein SP:Q46857 (Escherichia coli)
YP_003916082.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916083.1	match to PS00383 pattern (tyrosine specific protein phosphatases active site)
YP_003916084.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003916085.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916088.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916089.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916091.1	match to PF01636. This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation. This family also includes homoserine kinase
YP_003916092.1	identified by match to PF00126: bacterial regulatory helix-turn-helix protein, lysR family. Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini
YP_003916093.1	catalyses the conversion of L-threonine to L-2- amino-3-oxobutanoate
YP_003916094.1	catalyzes the addition of acetyl-CoA to glycine to form 2-amino-3-oxobutanoate: the second reaction step of the main metabolic degradation pathway for threonine
YP_003916095.1	match to protein domain PF00356. Numerous bacterial transcription regulatory proteins bind DNA via a helix- turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR. Within this family, the HTH motif is situated towards the N-terminus
YP_003916096.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1. 1.z). ABCISSE: ABC transporter, binding protein (BP), OSP-family (oligosaccharides or polyols)
YP_003916097.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1. 1.z). ABCISSE: ABC transporter, permease (IM), OSP- family (oligosaccharides or polyols)
YP_003916098.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1. 1.z). ABCISSE: ABC transporter, permease (IM), OSP- family (oligosaccharides or polyols)
YP_003916099.1	catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5- dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L- glutamate
YP_003916100.1	identified by match to protein domain PF08241
YP_003916101.1	in Escherichia coli, Tpx is an antioxidant protein with a thiol peroxidase activity
YP_003916102.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.999) with cleavage site probability 0.515 between position 29 and 30. Match to PS00383 pattern (aldehyde dehydrogenases glutamic acid active site)
YP_003916103.1	identified by match to PF01636. This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides. It also includes homoserine kinase
YP_003916104.1	identified by match to PF01636. This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides. It also includes homoserine kinase
YP_003916105.1	identified by match to protein family PF02517: CAAX amino terminal protease family. Members of this family are probably proteases (after a prenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein, the AAX tripeptide is removed by one of the CAAX prenyl proteases). The family contains the Q03530 CAAX prenyl protease. 6 transmembrane helices predicted by TMHMM2.0
YP_003916106.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916108.1	catalyses several reactions, including the formation of L-homocysteine from O-acetyl-L-homoserine and H2S, and the formation of L-methionine from O-acetyl-L- homoserine and methanethiol
YP_003916109.1	first reaction in L-methionine biosynthesis
YP_003916110.1	identified by match to protein family PF00657
YP_003916111.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916112.1	7 transmembrane helices predicted by TMHMM2.0
YP_003916114.1	identified by match to protein family PF02230. This family consists of both phospholipases and carboxylesterases with broad substrate specificity
YP_003916115.1	match to protein domain PF01479. The S4 domain was detected in proteins such as the bacterial ribosomal protein S4, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA
YP_003916116.1	activates glycine and transfers it to tRNA(Gly) as the first step in protein biosynthesis
YP_003916118.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.937) with cleavage site probability 0.418 between position 40 and 41. 9 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003916119.1	Chromate Ion Transporter (CHR) family (TC 2.A.51.y. z). match to PF02417: this region is found in known and predicted chromate transporters, these proteins reduce chromate accumulation and are essential for chromate resistance
YP_003916120.1	12 transmembrane helices predicted by TMHMM2.0
YP_003916121.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.867 between position 34 and 35
YP_003916122.1	identified by match to protein family PF01207. Members of this family catalyse the reduction of the 5,6- double bond of a uridine residue on tRNA. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA
YP_003916123.1	dGTPase catalyses the formation of deoxyguanosine from dGTP. It is involved in purine metabolism
YP_003916124.1	a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division
YP_003916125.1	8 transmembrane helices predicted by TMHMM2.0
YP_003916126.1	3 transmembrane helices predicted by TMHMM2.0
YP_003916128.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916129.1	11 transmembrane helices predicted by TMHMM2.0
YP_003916132.1	catalyzes the condensation of 5-amino-6-(1-D)- ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4- dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8- lumazine
YP_003916133.1	identified by match to PF00296. Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulfonate monooxygenase (SsuD), and coenzyme F420- dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds
YP_003916134.1	match to PF01381: helix-turn-helix. This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003916135.1	responsible for the removal of the amino-terminal (initiator) methionine from nascent eukaryotic cytosolic and cytoplasmic prokaryotic proteins if the penultimate amino acid is small and uncharged
YP_003916136.1	catalyses the following reaction: ATP + 7,8- diaminononanoate + CO(2) <=> ADP + phosphate + dethiobiotin
YP_003916138.1	catalyzes an intermediate step in the biosynthesis of biotin, the addition of 6-carboxy-hexanoyl-CoA (pimeloyl-coA) to alanine to form 8-amino-7-oxononanoate: 6-carboxyhexanoyl-CoA + L-alanine <=> 8-amino-7- oxononanoate + CoA + CO(2)
YP_003916139.1	catalyzes an intermediate step in the biosynthesis of biotin, the transamination of 7-keto-8-aminopelargonic acid (7-KAP) to form 7,8- diaminopelargonic acid (DAPA): S- adenosyl-L-methionine + 8-amino-7-oxononanoate <=> S- adenosyl-4-methylthio-2-oxobutanoate + 7,8- diaminononanoate
YP_003916140.1	catalyses the following reaction: dethiobiotin + sulfur + 2 S-adenosyl-L-methionine <=> biotin + 2 L- methionine + 2 5-deoxyadenosine
YP_003916141.1	match to PF03807: NADP oxidoreductase coenzyme F420- dependent
YP_003916143.1	may be involved in aerobactin-like siderophore biosynthesis
YP_003916144.1	L-lysine 6-monooxygenase (NADPH) catalyzes the conversion of lysine to its N6-hydroxy derivative, the initial event in the biosynthesis of aerobactin, a siderophore which functions as a virulence determinant in many septicemic organisms
YP_003916145.1	identified by match to protein family PF00282
YP_003916146.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003916147.1	match to PF00534: Glycosyl transferases group 1. Proteins containing this domain transfer UDP, ADP, GDP or CMP linked sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. The bacterial enzymes are involved in various biosynthetic processes that include exopolysaccharide biosynthesis, lipopolysaccharide core biosynthesis and the biosynthesis of the slime polysaccaride colanic acid
YP_003916148.1	3 transmembrane helices predicted by TMHMM2.0
YP_003916149.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.990) with cleavage site probability 0.909 between position 29 and 30. 7 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003916150.1	match to PF00534: Glycosyl transferases group 1. Proteins containing this domain transfer UDP, ADP, GDP or CMP linked sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. The bacterial enzymes are involved in various biosynthetic processes that include exopolysaccharide biosynthesis, lipopolysaccharide core biosynthesis and the biosynthesis of the slime polysaccaride colanic acid
YP_003916151.1	identified by match to protein family PF01551. Members of this family are zinc metallopeptidases with a range of specificities. Peptidase family M23 are also endopeptidases. Signal peptide predicted by SignalP 3.0 HMM (probability: 0.993) with cleavage site probability 0. 690 between position 27 and 28
YP_003916153.1	associates with the elongation factor-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome
YP_003916154.1	catalyses the reversible transfer of the gamma- phosphoryl group from an ATP donor to UMP, yielding UDP, which is the starting point for the synthesis of all other pyrimidine nucleotides
YP_003916155.1	responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another
YP_003916156.1	phosphatidate cytidylyltransferase catalyzes the synthesis of CDP-diacylglycerol from CTP and phosphatidate. It produces key intermediates in phospholipid biosynthesis
YP_003916158.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003916159.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003916160.1	Solute:Sodium Symporter (SSS) family (2.A.21.y.z). Members of the SSS family catalyze solute:Na+ symport. The solutes transported may be sugars, amino acids, organo cations such as choline, nucleosides, inositols, vitamins, urea or anions, depending on the system
YP_003916161.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916162.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916163.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. 1 transmembrane helice predicted by TMHMM2.0
YP_003916164.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916165.1	Solute:Sodium Symporter (SSS) family (2.A.21.y.z). Members of the SSS family catalyze solute:Na+ symport. The solutes transported may be sugars, amino acids, organo cations such as choline, nucleosides, inositols, vitamins, urea or anions, depending on the system
YP_003916166.1	identified by match to protein family PF01037
YP_003916167.1	the pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO2. It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3)
YP_003916168.1	the pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO2. It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3)
YP_003916169.1	the pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO2. It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3)
YP_003916170.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, binding protein (BP), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003916171.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003916172.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003916173.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, fused ATP-binding protein (ABC2), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003916174.1	identified by similarity to protein SP:Q6DKY2 (Bacillus stearothermophilus). Heat-stable reverse transcriptase. Possible group II intron associated protein
YP_003916175.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, binding protein (BP), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003916176.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003916177.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003916178.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, fused ATP-binding protein (ABC2), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003916179.1	match to protein domain PF01814: Hemerythrin HHE cation binding domain. Members of this family occur all across nature and are involved in a variety of processes. For instance, in Nereis diversicolor, protein P80255 binds cadmium so as to protect the organism from toxicity
YP_003916181.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916182.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003916183.1	possibly involved in the metabolism of lipids. Match to protein domains PF08028, PF02771 and PF02770. Acyl-CoA dehydrogenases catalyze the alpha,beta- dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD
YP_003916184.1	catalyses the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH. Forms part of a non-mevalonate pathway for terpenoid biosynthesis
YP_003916185.1	match to protein family PF02163: Peptidase family M50. Match to PS00142 pattern: neutral zinc metallopeptidases, zinc-binding region signature. 4 transmembrane helices predicted by TMHMM2.0
YP_003916186.1	identified by match to protein domain PF03795
YP_003916187.1	match to protein domain PF00472. This domain is found in peptide chain release factors, and a number of smaller proteins of unknown function
YP_003916188.1	identified by match to PF03358. FMN reductase reductase catalyses the following reaction: NAD(P)H + FMN = NAD(P)(+) + FMNH(2)
YP_003916189.1	part of the non-mevalonate pathway for terpenoid biosynthesis
YP_003916190.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916196.1	match to protein domains PF01590 and PF00486
YP_003916199.1	activates proline and transfers it to tRNA(Pro) as the first step in protein biosynthesis
YP_003916200.1	6 transmembrane helices predicted by TMHMM2.0
YP_003916203.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916205.1	participates in both the termination and antitermination of transcription. Interacts with RNA polymerase and binds RNA
YP_003916207.1	one of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex
YP_003916208.1	associates with free 30S ribosomal subunits. Essential for efficient processing of 16S rRNA
YP_003916210.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003916211.1	match to protein domain PF00174, which corresponds to the molybdopterin binding domain of oxidoreductases that require a molybdopterin cofactor
YP_003916212.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916213.1	match to protein family TIGR02937. Sigma-70 family
YP_003916214.1	match to protein domain PF02469: Fasciclin domain. This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria (for example in the bacterial immunogenic protein MPT70)
YP_003916215.1	responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs
YP_003916216.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916217.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916218.1	EC 2.7.1.26 catalyses the following reaction : ATP + riboflavin = ADP + FMN. EC 2.7.7.2 catalyses the following reaction : ATP + FMN = diphosphate + FAD
YP_003916219.1	identified by match to protein domain PF08241
YP_003916220.1	one of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA
YP_003916223.1	3 transmembrane helices predicted by TMHMM2.0
YP_003916224.1	match to PF01965: DJ-1/PfpI family. The family includes the protease PfpI Q51732. This domain is also found in transcriptional regulators such as Q9RJG8
YP_003916225.1	match to protein domain PF00266: aminotransferase class-V. This domain is found in aminotransferases, and other enzymes, including cysteine desulphurase
YP_003916227.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916228.1	identified by match to PF00582: universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general stress endurance activity
YP_003916229.1	Tripartite Tricarboxylate Transporter (TTT) Family, tricarboxylate transporter (TC 2.A.80.1.1). Identified by similarity to protein SP:Q6M234 (Corynebacterium glutamicum). Component of the TctCBA citrate uptake system
YP_003916230.1	possible TctB component of the TctCBA citrate uptake system (TC 2.A.1.1)
YP_003916231.1	Tripartite Tricarboxylate Transporter (TTT) Family, tricarboxylate transporter (TC 2.A.80.1.1). Identified by similarity to protein SP:Q8NLW1 (Corynebacterium glutamicum). Component of the TctCBA citrate uptake system
YP_003916232.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916233.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916234.1	identified by match to protein family PF00743. Flavin-containing monooxygenase is a broad spectrum monooxygenase that accepts substrates as diverse as hydrazines, phosphines, boron-containing compounds, sulfides, selenides, iodide, as well as primary, secondary and tertiary amines. Generally converts nucleophilic heteroatom-containing chemicals and drugs into harmless, readily excreted metabolites
YP_003916235.1	catalyzes the decarboxylation of prephenate into phenylpyruvate. Involved in phenylalanine biosynthesis
YP_003916236.1	identified by match to PF09339: IclR helix-turn- helix domain and PF01614. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003916237.1	also named branched-chain alpha-keto acid dehydrogenase E1 component alpha chain. The branched-chain alpha-keto dehydrogenase complex catalyzes the oxidative decarboxylation of 4-methyl-2-oxopentanoate, 3-methyl-2- oxopentanoate and 3-methyl-2-oxobutanoate (branched chain 2-oxo acids derived from the transamination of leucine, valine and isoleucine). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2; EC 2.3. 1.168) and lipoamide dehydrogenase (E3; EC1.8.1.4). The E1 component is composed of alpha and beta chains
YP_003916238.1	also named branched-chain alpha-keto acid dehydrogenase E1 component beta chain. The branched-chain alpha-keto dehydrogenase complex catalyzes the oxidative decarboxylation of 4-methyl-2-oxopentanoate, 3-methyl-2- oxopentanoate and 3-methyl-2-oxobutanoate (branched chain 2-oxo acids derived from the transamination of leucine, valine and isoleucine). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2; EC 2.3. 1.168) and lipoamide dehydrogenase (E3; EC1.8.1.4). The E1 component is composed of alpha and beta chains
YP_003916239.1	possible lipoamide acyltransferase or N-terminal section of lipoamide acyltransferase (lipoyl-binding site). The branched-chain alpha-keto dehydrogenase complex catalyzes the oxidative decarboxylation of 4-methyl-2- oxopentanoate, 3-methyl-2-oxopentanoate and 3-methyl-2- oxobutanoate (branched chain 2-oxo acids derived from the transamination of leucine, valine and isoleucine). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2; EC 2.3.1.168) and lipoamide dehydrogenase (E3; EC1.8.1.4). The E1 component is composed of alpha and beta chains
YP_003916240.1	possibly involved in the metabolism of lipids. Match to protein family PF01370: NAD dependent epimerase/dehydratase family. This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions
YP_003916241.1	match to protein family PF00501. This family of enzymes includes luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely- related synthetases
YP_003916242.1	catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids
YP_003916246.1	3 transmembrane helices predicted by TMHMM2.0
YP_003916247.1	catalyses the following reaction: an alcohol + NAD(+) <=> an aldehyde or ketone + NADH
YP_003916248.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916249.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.351 between position 44 and 45
YP_003916250.1	bifunctional enzyme, with a phosphorolytic 3 to 5 exoribonuclease activity and a 3 -terminal oligonucleotide polymerase activity. It is involved in mRNA processing and degradation
YP_003916251.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916253.1	takes part in the activated methyl cycle, by salvaging the homocysteine moiety from the cycle intermediate S-D-ribosyl-L-homocysteine. As a by-product of this reaction, 4,5-dihydroxy-2,3-pentanedione is formed, which is the precursor of the autoinducer AI-2, a signal molecule, which may be used by a variety of bacteria for communication among and between species
YP_003916254.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.977) with cleavage site probability 0.233 between position 29 and 30
YP_003916255.1	identified by match to PF05193 and PF00675. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They also include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity
YP_003916256.1	match to PF00561: alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes
YP_003916257.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.769 between position 35 and 36
YP_003916258.1	catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5- tetrahydrodipicolinate
YP_003916259.1	identified by match to PF07719. The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins. It mediates protein-protein interactions and the assembly of multiprotein complexes. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding
YP_003916260.1	10 transmembrane helices predicted by TMHMM2.0
YP_003916261.1	catalyses the condensation of aspartate semialdehyde and pyruvate, the first reaction specific to the biosynthesis of lysine and of diaminopimelate
YP_003916262.1	identified by match to PF00753 (metallo-beta- lactamase superfamily) and PF07521 (RNA-metabolising metallo-beta-lactamase motif)
YP_003916264.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OTCN-family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L-proline
YP_003916265.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, permease (IM), OTCN- family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L- proline
YP_003916266.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, permease (IM), OTCN- family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L- proline
YP_003916267.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, binding protein (BP), OTCN-family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L-proline
YP_003916268.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, binding protein (BP), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003916272.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003916273.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003916274.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003916275.1	E3 component of pyruvate dehydrogenase and 2- oxoglutarate dehydrogenase complexes
YP_003916276.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916277.1	DNA motor protein, which is both required to move DNA out of the region of the septum during cell division and for the septum formation. Tracks DNA in an ATP- dependent manner by generating positive supercoils in front of it and negative supercoils behind it
YP_003916278.1	involved in phospholipid biosynthesis
YP_003916279.1	match to protein family PF02464: competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon, and is thought to be specifically required at some stage in the process of transformation
YP_003916280.1	match to PF01381: helix-turn-helix. This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003916282.1	RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyses an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination
YP_003916283.1	RecX is a  bacterial regulatory protein. The gene encoding RecX is found downstream of recA, and is thought to interact with the RecA protein
YP_003916284.1	the MiaB enzyme is responsible for the modification of the isopentenylated adenine-37 base of most bacterial and eukaryotic tRNAs that read codons beginning with uracil. Adenine-37 is next to the anticodon on the 3 side in these tRNAs, and lack of modification at this site leads to an increased spontaneous mutation frequency
YP_003916286.1	catalyzes the isomerization of L,L- to D,L-meso- diaminopimelate in the biosynthetic pathway leading from aspartate to lysine
YP_003916291.1	match to protein domain PF05175. This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases
YP_003916292.1	identified by match to protein family PF01926
YP_003916293.1	possible DNA or RNA helicase
YP_003916295.1	LexA represses around 20 genes of the cellular SOS response to DNA damage in Escherichia coli. In the presence of single-stranded DNA, the recA protein interacts with lexA causing an autocatalytic cleavage which disrupts the DNA- binding part of lexA, leading to derepression of the SOS regulon and eventually DNA repair
YP_003916296.1	match to protein domain PF01476. This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation. It may have a general peptidoglycan binding function
YP_003916297.1	catalyzes the the transfer of an amino group from 3- (imidazol-4-yl)-2-oxopropyl phosphate to glutamic acid to form histidinol phosphate and 2-oxoglutarate. Involved in histidine biosynthesis
YP_003916298.1	catalyzes the following reaction: D-erythro-1- (imidazol-4-yl)glycerol 3-phosphate <=> 3-(imidazol-4-yl)- 2-oxopropyl phosphate + H(2)O. Involved in histidine biosynthesis
YP_003916299.1	imidazole glycerol phosphate synthase converts N1- (5-phosphoribulosyl)-formimino-5-aminoimidazole-4- carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). Involved in histidine biosynthesis
YP_003916301.1	catalyses the following reaction: 1-(5- phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide <=> 5-((5-phospho-1-deoxyribulos-1- ylamino)methylideneamino)- 1-(5-phosphoribosyl)imidazole-4- carboxamide. Involved in histidine biosynthesis
YP_003916303.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003916304.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916306.1	IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins
YP_003916307.1	L35 is a basic protein of 60 to 70 amino-acid residues from the large (50S) subunit
YP_003916308.1	binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit
YP_003916309.1	identified by match to protein family PF00588: SpoU rRNA Methylase family. Possible role in rRNA modification
YP_003916310.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003916311.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.878) with cleavage site probability 0.809 between position 28 and 29. 1 transmembrane helice predicted by TMHMM2.0 after the signal peptide
YP_003916312.1	activates phenylalanine and transfers it to tRNA(Phe) as the first step in protein biosynthesis
YP_003916313.1	activates phenylalanine and transfers it to tRNA(Phe) as the first step in protein biosynthesis
YP_003916315.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916317.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916318.1	match to protein domain PF00156. This family includes a range of diverse phosphoribosyl transferase enzymes
YP_003916319.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.971 between position 30 and 31. 1 transmembrane helice predicted by TMHMM2.0 after the signal peptide
YP_003916320.1	identified by match to PF01648: 4- phosphopantetheinyl transferase superfamily. Holo-[acyl- carrier-protein] synthase catalyses the following reaction: CoA-(4-phosphopantetheine) + apo-[acyl-carrier- protein] => adenosine 3,5-bisphosphate + holo-[acyl- carrier-protein]. All polyketide synthases, fatty-acid synthases and non-ribosomal peptide synthases require post- translational modification of their constituent acyl- carrier-protein (ACP) domains to become catalytically active. The inactive apo-proteins are converted into their active holo-forms by transfer of the 4-phosphopantetheinyl moiety of CoA to the sidechain hydroxy group of a conserved serine residue in each ACP domain
YP_003916321.1	identified by match to protein domain PF03976. This domain is about 230 amino acids in length and has polyphosphate kinase activity
YP_003916322.1	identified by match to protein family PF01433. This group of metallopeptidases belong to the MEROPS peptidase family M1 (clan MA(E)). Members of this family are aminopeptidases. The members differ widely in specificity, hydrolysing acidic, basic or neutral N-terminal residues. Match to PS00142 pattern: neutral zinc metallopeptidases, zinc-binding region signature
YP_003916323.1	match to protein domains TIGR02353 and TIGR01733. May be involved in enterobactin-like siderophore biosynthesis
YP_003916324.1	identified by match to protein family PF04909
YP_003916325.1	NADPH:quinone reductase catalyzes the following reaction: NADPH + quinone <=> NADP(+) + semiquinone. Quinone or similar compounds may act as acceptor
YP_003916326.1	catalyzes the third step in the biosynthesis of arginine from glutamate, the NADP-dependent reduction of N- acetyl-5-glutamyl phosphate into N-acetylglutamate 5- semialdehyde
YP_003916327.1	glutamate N-acetyltransferase (EC 2.3.1.35) catalyses the production of L-ornithine and N-acetyl-L- glutamate from N(2)-acetyl-L-ornithine and L-glutamate. Amino-acid N-acetyltransferase (EC 2.3.1.1) catalyses the formation of N-acetyl-L-glutamate from acetyl-CoA and L- glutamate. Involved in arginine biosynthesis
YP_003916328.1	catalyses the formation of N-acetyl-L-glutamate 5- phosphate from N-acetyl-L-glutamate. Involved in arginine biosynthesis
YP_003916329.1	catalyses the following reaction: N(2)-acetyl-L- ornithine + 2-oxoglutarate <=> N-acetyl-L-glutamate 5- semialdehyde + L-glutamate. Involved in arginine biosynthesis
YP_003916330.1	catalyzes the conversion of ornithine and carbamoyl phosphate to citrulline. It is involved in the biosynthesis of arginine and, in some bacteria, it is also involved in the degradation of arginine (the arginine deaminase pathway)
YP_003916331.1	regulates arginine biosynthesis when complexed with arginine by binding at site that overlap the promotors of the arginine biosynthesis genes
YP_003916332.1	identified by match to PF01844
YP_003916333.1	match to protein domain PF01661. This domain is an ADP-ribose binding module. It is found in a number of otherwise unrelated proteins
YP_003916334.1	catalyzes the formation of arginine and fumarate from argininosuccinate, the last step in the biosynthesis of arginine
YP_003916336.1	catalyses the formation of AMP and diphosphate from adenine and 5-phospho-alpha-D-ribose 1-diphosphate. Involved in purine salvage
YP_003916337.1	match to protein family PS51198: UvrD-like DNA helicase ATP-binding domain profile. UvrD-like DNA helicases belong to superfamily 1 (SF1)
YP_003916338.1	activates tyrosine and transfers it to tRNA(Tyr) as the first step in protein biosynthesis
YP_003916341.1	identified by match to PF00702. This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases
YP_003916343.1	identified by similarity to protein SP:Q50760 (Mycobacterium tuberculosis)
YP_003916344.1	catalyses the phosphorylation of NAD to NADP utilising ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus
YP_003916345.1	RecN is thought to be involved in recombinational repair of damaged DNA
YP_003916346.1	catalyzes the ATP-dependent formation of CTP from UTP and glutamine
YP_003916347.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003916348.1	site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids
YP_003916349.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003916350.1	match to PF01381: helix-turn-helix. This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003916351.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.981) with cleavage site probability 0.558 between position 27 and 28. 3 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003916352.1	2-methylcitrate synthase catalyses the conversion of oxaloacetate and propanoyl-CoA into (2R,3S)-2- hydroxybutane-1,2,3-tricarboxylate and coenzyme A. The enzyme acts on acetyl-CoA, propanoyl-CoA, butanoyl-CoA and pentanoyl-CoA. Involved in the metabolism of propionate
YP_003916353.1	catalyses the formation of pyruvate and succinate from (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate. Involved in the metabolism of propionate
YP_003916354.1	involved in the metabolism of propionate
YP_003916355.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003916356.1	catalyzes the synthesis of propionyl-CoA from propionate and CoA
YP_003916357.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916358.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916359.1	identified by similarity to protein SP:Q8NMH8 (Corynebacterium glutamicum). Dicarboxylate/Amino Acid:Cation (Na+ or H+) symporter (DAACS) family, C4- dicarboxylate transporter (substrates: fumarate, D- and L- malate, succinate, succinamide, orotate, iticonate, mesaconate) (TC 2.A.23.1.3)
YP_003916360.1	identified by match to protein family PF00657
YP_003916361.1	identified by match to PF00903: glyoxalase/bleomycin resistance protein/dioxygenase superfamily
YP_003916363.1	identified by match to protein family PF01656. chromosome partitioning protein
YP_003916364.1	identified by match to protein family PF02616. ScpA participates in chromosomal partition during cell division. Component of a cohesin-like complex composed of scpA, scpB and smc
YP_003916365.1	identified by match to protein family PIRSF019345. ScpB participates in chromosomal partition during cell division. Component of a cohesin-like complex composed of scpA, scpB and smc
YP_003916366.1	identified by match to protein family PF00849. Pseudouridylate synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5- ribosyluracil, psi)
YP_003916367.1	catalyses the following reaction: prephenate + NAD(+) <=> 4-hydroxyphenylpyruvate + CO(2) + NADH. Involved in tyrosine biosynthesis
YP_003916368.1	catalyzes the transfer of a phosphate group from ATP to either CMP or UMP to form CDP or UDP and ADP
YP_003916369.1	possible role in ribosome assembly and stability
YP_003916370.1	identified by match to protein family PF02567. PhzC/PhzF is involved in dimerisation of two 2, 3-dihydro-3- oxo-anthranilic acid molecules to create phenazine-1- carboxylic acid (PCA) by P. fluorescens. This family also contains a  thymidilate synthase from Mycobacterium tuberculosis. Many phenazine compounds are found in nature and are produced by bacteria such as Pseudomonas spp., Streptomyces spp., and Pantoea agglomerans. These compounds have been implicated in the virulence and competitive fitness of producing organisms. For example, the phenazine pyocyanin produced by Pseudomonas aeruginosa contributes to its ability to colonise the lungs of cystic fibrosis patients. Similarly, phenazine-1-carboxylic acid, produced by a number of Pseudomonas, increases survival in soil environments and has been shown to be essential for the biological control activity of certain strains
YP_003916371.1	TCDB: ATP-binding cassette (ABC) superfamily, () drug resistance ATPase-2 (Drug RA2) family (TC 3.A.1.121.z). ABCISSE: fused ATP-binding protein (ABC2), ART-family, ARE-subfamily (antibiotic resistance)
YP_003916372.1	phenol 2-monooxygenase catalyzes the following reaction: Phenol + NADPH + O(2) => catechol + NADP(+) + H(2)O. Also active with resorcinol and o-cresol
YP_003916374.1	match to PF00498. The forkhead-associated (FHA) domain is a phosphopeptide recognition domain found in many regulatory proteins
YP_003916375.1	identified by match to PF00376. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA
YP_003916377.1	members of the MerR-family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA
YP_003916378.1	identified by match to protein family PF01656. chromosome partitioning protein
YP_003916379.1	biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate
YP_003916381.1	activates fatty acids by binding to coenzyme A. Possibly involved in the degradation of lipids via beta- oxidation
YP_003916382.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916383.1	match to protein family PIRSF017388
YP_003916384.1	1-acylglycerol-3-phosphate O-acyltransferase catalyzes the following reaction: Acyl-CoA + 1-acyl-sn- glycerol 3-phosphate <=> CoA + 1,2-diacyl-sn-glycerol 3- phosphate. It is involved in phospholipid biosynthesis
YP_003916385.1	involved in phenylalanine, tyrosine and tryptophan biosynthesis
YP_003916386.1	identified by match to protein domain PD000001. Match to PS00108 pattern. Protein kinases are a group of enzymes that possess a catalytic subunit which transfers the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. They play a role in a mulititude of cellular processes, including division, proliferation, apoptosis, and differentiation
YP_003916387.1	identified by match to protein family PF02467. WhiB is a  transcription factor in Actinobacteria, required for differentiation and sporulation
YP_003916388.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916389.1	match to PF01580. This domain is found extensively in a wide variety of proteins from prokaryotes and plasmids
YP_003916390.1	identified by match to protein domain PF00437
YP_003916391.1	identified by match to protein domain PF00482
YP_003916392.1	identified by match to protein domain PF00482
YP_003916393.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916394.1	identified by match to protein family PF07811. The members of this family are similar to a region of the protein product of the bacterial tadE locus. In various bacterial species, the tad locus is closely linked to flp- like genes, which encode proteins required for the production of pili involved in adherence to surfaces. It is thought that the tad loci encode proteins that act to assemble or export an Flp pilus in various bacteria
YP_003916395.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916396.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.997) with cleavage site probability 0.440 between position 27 and 28
YP_003916397.1	directs the termination of translation in response to the peptide chain termination codons UGA and UAA
YP_003916398.1	TCDB: general secretory pathway (Sec) family, general secretory pathway (Sec-SRP) complex (TC 3.A.5.1.1). ABCISSE: ATP-binding protein (ABC), CDI- family. CDI family systems are found only in eubacteria and are comprised of two proteins: the FtsE ATP-binding protein and the FtsX permease. It is possible that CDI systems play a role in the proper membrane targeting or insertion of some proteins essential for septum formation
YP_003916399.1	ABCISSE: IM (permease), CDI-family. CDI family systems are found only in eubacteria and are comprised of two proteins: the FtsE ATP-binding protein and the FtsX permease. It is possible that CDI systems play a role in the proper membrane targeting or insertion of some proteins essential for septum formation
YP_003916400.1	identified by match to protein family PF01551. Members of this family are zinc metallopeptidases with a range of specificities. Peptidase family M23 are also endopeptidases. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 1. 000 between position 32 and 33
YP_003916401.1	in bacteria, SsrA RNA recognizes ribosomes stalled on defective messages and acts as a tRNA and mRNA to mediate the addition of a short peptide tag to the C- terminus of the partially synthesized nascent polypeptide chain. The SsrA-tagged protein is then degraded by C- terminal-specific proteases. SmpB binds specifically to the ssrA RNA and is required for stable association of ssrA with ribosomes
YP_003916402.1	match to protein family PF00589
YP_003916403.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.718 between position 29 and 30
YP_003916404.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916405.1	identified by match to protein family PF02537. CrcB is a  integral membrane protein possibly involved in chromosome condensation. Overexpression in E. coli also leads to camphor resistance
YP_003916406.1	identified by match to protein family PF02537. CrcB is a  integral membrane protein possibly involved in chromosome condensation. Overexpression in E. coli also leads to camphor resistance
YP_003916407.1	identified by match to PF00582: universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general stress endurance activity
YP_003916408.1	identified by match to PF01325 and PF02742. The diphtheria toxin repressor protein (DTXR) is a member of this group. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron- binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N- terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation
YP_003916409.1	catalyses the following reaction: L-histidinol phosphate + H(2)O <=> L-histidinol + phosphate. Involved in histidine biosynthesis
YP_003916410.1	identified by match to protein family PF03193
YP_003916411.1	sixth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids (phenylalanine, tyrosine and tryptophan), p-aminobenzoic acid, folate and ubiquinone
YP_003916412.1	the sigma factor RpoE is involved in heat shock and oxidative stress response; it is believed to control protein processing in the extracytoplasmic compartment
YP_003916413.1	may act on RpoE. Match to protein family TIGR02949. Anti-sigma factors bind to sigma factors and inhibit their transcriptional activity
YP_003916414.1	match to protein family SSF52266
YP_003916415.1	it is a component of the multienzyme 2-oxoglutarate dehydrogenase complex in which multiple copies of it are bound to a core of molecules of EC 2.3.1.61 (Dihydrolipoyllysine-residue succinyltransferase), which also binds multiple copies of EC 1.8.1.4 (Dihydrolipoyl dehydrogenase). Involved in the TCA cycle
YP_003916416.1	possible transporter. Match to PF00571 (CBS domain pair)
YP_003916417.1	match to PF00571 (CBS domain pair)
YP_003916418.1	TCDB: ATP-binding cassette (ABC) superfamily, Manganese/Zinc/Iron Chelate Uptake Transporter (MZT) Family (TC 3.A.1.15.z). ABCISSE: ABC transporter, ATP- binding protein (ABC), MET-family. This family is comprised of systems involved in the uptake of various metallic cations such as iron, manganese and zinc
YP_003916419.1	TCDB: ATP-binding cassette (ABC) superfamily, Manganese/Zinc/Iron Chelate Uptake Transporter (MZT) Family (TC 3.A.1.15.z). ABCISSE: ABC transporter, permease (IM), MET-family. This family is comprised of systems involved in the uptake of various metallic cations such as iron, manganese and zinc
YP_003916421.1	identified by match to SM00507
YP_003916422.1	match to protein family PF01475
YP_003916423.1	identified by match to PF00753: metallo-beta- lactamase superfamily. Apart from the beta-lactamases, a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl- glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake
YP_003916425.1	match to PF01230: histidine triad motif. The histidine triad motif (HIT) is related to the sequence H- phi-H-phi-H-phi-phi (where phi is a hydrophobic amino acid). Proteins containing HIT domains form a superfamily of nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides
YP_003916427.1	identified by similarity to protein SP:P43329 (Escherichia coli)
YP_003916428.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-2 (CUT2) family (TC 3.A.1. 2.z). ABCISSE: ABCISSE: ABC transporter, binding protein (BP), MOS-family (monosaccharides: pentoses and hexoses)
YP_003916429.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-2 (CUT2) family (TC 3.A.1. 2.z). ABCISSE: ABCISSE: ABC transporter, permease (IM), MOS-family (monosaccharides: pentoses and hexoses)
YP_003916430.1	TCDB: ATP-binding cassette (ABC) superfamily (TC 3. A.1.y.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), NO family (NO family systems represent few ABC proteins with unknown function and which are apparently unrelated to existent families)
YP_003916432.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003916433.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916435.1	5 transmembrane helices predicted by TMHMM2.0
YP_003916436.1	activates arginine and transfers it to tRNA(Arg) as the first step in protein biosynthesis
YP_003916437.1	catalyzes the conversion of diaminopimelic acid into lysine, the last step in the biosynthesis of lysine
YP_003916438.1	catalyzes NAD-dependent reduction of aspartate 4- semialdehyde into homoserine. This reaction is the third step in a pathway leading from aspartate to homoserine. The latter participates in the biosynthesis of threonine and then isoleucine as well as in that of methionine
YP_003916439.1	catalyzes the formation of threonine from homoserine-phosphate
YP_003916440.1	catalyses the formation of O-phospho-L-homoserine from homoserine. Involved in the biosynthesis of threonine
YP_003916441.1	facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho RNA-dependent ATPase activity, and release of the mRNA from the DNA template
YP_003916442.1	directs the termination of translation in response to the peptide chain termination codons UGA and UAA
YP_003916443.1	HemK methylates the translation termination release factors RF1 and RF2, which plays a pivotal role in the termination of translation
YP_003916445.1	match to protein family PF00953. Catalyzes the formation of undecaprenyl-pyrophosphoryl-N-acetylmuramoyl- pentapeptide from UDP-MurNAc-pentapeptide and undecaprenyl- phosphate. Involved in peptidoglycan biosynthesis
YP_003916446.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916447.1	H(+)-transporting two-sector ATPase (also named ATP synthase or ATPase) is composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane- embedded proton channel that is composed of at least 3 subunits (A-C). It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient
YP_003916448.1	H(+)-transporting two-sector ATPase (also named ATP synthase or ATPase) is composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane- embedded proton channel that is composed of at least 3 subunits (A-C). It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient
YP_003916449.1	H(+)-transporting two-sector ATPase (also named ATP synthase or ATPase) is composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane- embedded proton channel that is composed of at least 3 subunits (A-C). It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient
YP_003916450.1	H(+)-transporting two-sector ATPase (also named ATP synthase or ATPase) is composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane- embedded proton channel that is composed of at least 3 subunits (A-C). It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient
YP_003916451.1	H(+)-transporting two-sector ATPase (also named ATP synthase or ATPase) is composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane- embedded proton channel that is composed of at least 3 subunits (A-C). It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient
YP_003916452.1	H(+)-transporting two-sector ATPase (also named ATP synthase or ATPase) is composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane- embedded proton channel that is composed of at least 3 subunits (A-C). It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient
YP_003916453.1	H(+)-transporting two-sector ATPase (also named ATP synthase or ATPase) is composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane- embedded proton channel that is composed of at least 3 subunits (A-C). It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient
YP_003916454.1	H(+)-transporting two-sector ATPase (also named ATP synthase or ATPase) is composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane- embedded proton channel that is composed of at least 3 subunits (A-C). It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient
YP_003916455.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916456.1	identified by match to protein family PF01370: NAD dependent epimerase/dehydratase family. This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions
YP_003916457.1	catalyzes the hydrolysis of N-acetylglucosamine-6- phosphate to glucosamine-6-phosphate and acetate
YP_003916458.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916461.1	9 transmembrane helices predicted by TMHMM2.0
YP_003916462.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916464.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, ATP-binding protein (ABC), DRI-family, DRB-subfamily (drug resistance, ). Possible function in drug efflux
YP_003916465.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease (IM), DRI-family, DRB-subfamily (drug resistance, ). Possible function in drug efflux
YP_003916467.1	possible DNA or RNA helicase
YP_003916468.1	nicotinamidase converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD)
YP_003916469.1	nicotinate phosphoribosyltransferase catalyses the formation of nicotinate D-ribonucleotide and PPi from 5- phospho-alpha-D-ribose 1-diphosphate and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products
YP_003916470.1	involved in the modulation of the specificity of the clpAP-mediated ATP-dependent protein degradation
YP_003916472.1	converts L-glutamate to D-glutamate, a component of peptidoglycan
YP_003916474.1	removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates
YP_003916475.1	hydrolyzes non-standard nucleotides such as XTP and dITP/ITP. Might exclude non-standard purines from DNA precursor pool, preventing thus incorporation into DNA and avoiding chromosomal lesions
YP_003916477.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003916478.1	TCDB: ATP-binding cassette (ABC) superfamily (TC 3. A.1.y.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), NO family (NO family systems represent few ABC proteins with unknown function and which are apparently unrelated to existent families)
YP_003916479.1	TC 3.1.y.z. ABCISSE: ABC transporter, permease (IM)
YP_003916481.1	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication once it is clamped onto DNA. DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII complex. PolIII associates with the gamma complex (composed of gamma, delta, delta, psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex
YP_003916483.1	SbcCD cleaves DNA hairpin structures. These structures can inhibit DNA replication and are intermediates in certain DNA recombination reactions. The complex acts as a 3 ->5 double strand exonuclease that can open hairpins. It also has a 5 single-strand endonuclease activity
YP_003916484.1	SbcCD cleaves DNA hairpin structures. These structures can inhibit DNA replication and are intermediates in certain DNA recombination reactions. The complex acts as a 3 ->5 double strand exonuclease that can open hairpins. It also has a 5 single-strand endonuclease activity
YP_003916485.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003916486.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003916487.1	major facilitator superfamily (MFS), metabolite:H+ symporter (MHS) family (TC 2.A.1.6.z)
YP_003916490.1	match to protein domain PF00356. Numerous bacterial transcription regulatory proteins bind DNA via a helix- turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR. Within this family, the HTH motif is situated towards the N-terminus
YP_003916491.1	enzymes of this family comprise mostly alpha- amylases (EC 3.2.1.1); pullulanases (EC 3.2.1.41); cyclomaltodextrin glucanotransferase (EC 2.4.1.19); cyclomaltodextrinase (EC 3.2.1.54); trehalose-6-phosphate hydrolase (EC 3.2.1.93); malto-oligosyltrehalose trehalohydrolase (EC 3.2.1.141)
YP_003916492.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1. 1.z). ABCISSE: ABC transporter, binding protein (BP), OSP-family (oligosaccharides or polyols), maltooligosaccharides import
YP_003916493.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1. 1.z). ABCISSE: ABC transporter, permease (IM), OSP- family (oligosaccharides or polyols), maltooligosaccharides import
YP_003916494.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1. 1.z). ABCISSE: ABC transporter, permease (IM), OSP- family (oligosaccharides or polyols), maltooligosaccharides import
YP_003916495.1	8 transmembrane helices predicted by TMHMM2.0
YP_003916496.1	identified by match to protein domains PF02909 and PF00440
YP_003916497.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003916499.1	identified by match to PF00487. Fatty acid desaturases catalyze the insertion of a double bond at the delta position of fatty acids
YP_003916500.1	TCDB: ATP-binding cassette (ABC) superfamily, () drug resistance ATPase-1 (Drug RA1) family (TC 3.A.1.120.z). ABCISSE: fused ATP-binding protein (ABC2), ART-family. Duplicated ATPase domains (PF00005)
YP_003916501.1	identified by match to PF01022. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003916503.1	match to protein domain PF00156. This family includes a range of diverse phosphoribosyl transferase enzymes
YP_003916504.1	involved in the catabolism of tyrosine
YP_003916505.1	5-carboxymethyl-2-hydroxymuconic-semialdehyde dehydrogenase catalyzes the formation of 5-carboxymethyl-2- hydroxymuconate from 5-carboxymethyl-2-hydroxymuconate semialdehyde
YP_003916506.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003916507.1	involved in the homoprotocatechuic acid pathway. EC 5.3.3.10 (5-carboxymethyl-2-hydroxymuconate Delta- isomerase ) catalyses the conversion of 5-carboxymethyl- 2hydroxymuconate to 5-carboxy-2-oxohept-3-enedioate. The latter is converted to 2-hydroxyhepta-2,4-dienediotae by EC 4.1.1.68 (5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase)
YP_003916508.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease (IM)
YP_003916509.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, ATP-binding protein (ABC)
YP_003916514.1	match to protein family PF04464. Possibly involved in teichoic acid biosynthesis
YP_003916516.1	involved in the biosynthesis of isoleucine, leucine and valine. Catalyses the dehydratation of 2, 3-dihydroxy-3- methylpentanoate and 2, 3-dihydroxy-3-methylbutanoate into 3-methyl-2-oxopentanoate and 2-oxoisovalerate, respectively
YP_003916517.1	identified by match to SM00530: Helix-turn-helix XRE-family like proteins. This is a large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003916518.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.646 between position 58 and 59
YP_003916519.1	match to PS00120 pattern: lipases, serine active site
YP_003916521.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003916522.1	quinolinate synthetase A subunit. Quinolinate synthetase complex (A and B subunits) is involved in the de novo biosynthetic pathway of pyridine nucleotide formation. It catalyses the formation of quinolinic acid
YP_003916523.1	quinolinate synthetase B subunit. Quinolinate synthetase complex (A and B subunits) is involved in the de novo biosynthetic pathway of pyridine nucleotide formation. It catalyses the formation of quinolinic acid
YP_003916524.1	involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate in the presence of Mg2+ to produce nicotinic acid mononucleotide, pyrophosphate and carbon dioxide
YP_003916525.1	identified by match to protein family PIRSF005572: cysteine desulfurase, NifS type. Cysteine desulfurase catalyses the following reaction: L-cysteine + [enzyme]- cysteine <=> L-alanine + [enzyme]-S-sulfanylcysteine. It is involved in the biosynthesis of iron-sulfur clusters, thio-nucleosides in tRNA, thiamine, biotin, lipoate and pyranopterin (molybdopterin) and functions by mobilizing sulfur
YP_003916526.1	match to PF08239: bacterial SH3 domain. A homologue of the SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.938 between position 26 and 27
YP_003916527.1	match to PF08239: bacterial SH3 domain. A homologue of the SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins
YP_003916528.1	N-terminal section of the protein: match to protein family PF02557 (VanY, D-alanyl-D-alanine carboxypeptidase). C-terminal section of the protein: match to PF08239 (bacterial SH3 domain) protein family PF02557
YP_003916529.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916530.1	match to protein family PF08327
YP_003916531.1	match to protein domain PF01872. This domain is found in the C-terminus of the bifunctional deaminase- reductase in combination with PF00383 as well as in isolation in some archaebacterial proteins
YP_003916533.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003916534.1	identified by match to PF00296. Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulfonate monooxygenase (SsuD), and coenzyme F420- dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds
YP_003916535.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916536.1	5 transmembrane helices predicted by TMHMM2.0
YP_003916537.1	Resistance-Nodulation-Cell Division (RND) superfamily (TC 2.A.6.y.z). Match to protein family PF00873 (AcrB/AcrD/AcrF family). Some Members of this family are involved in drug resistance
YP_003916540.1	other name: malate:quinone oxidoreductase. Takes part in the citric acid cycle. It oxidises L-malate to oxaloacetate and donates electrons to ubiquinone-1 and other artificial acceptors or, via the electron transfer chain, to oxygen. NAD is not an acceptor and the natural direct acceptor for the enzyme is most likely a quinone
YP_003916541.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, binding protein (BP), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003916542.1	match to PF02826 (D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain)
YP_003916543.1	peroxiredoxin protects cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides. The Bcp protein shows substrate selectivity toward fatty acid hydroperoxides rather than hydrogen peroxide or alkyl hydroperoxides
YP_003916544.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003916545.1	identified by match to protein family PF01370: NAD dependent epimerase/dehydratase family. This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions
YP_003916546.1	8 transmembrane helices predicted by TMHMM2.0
YP_003916547.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003916548.1	identified by similarity to protein SP:Q9KK76 (Brevibacterium linens). A variety of isoprenoid compounds are synthesized by various organisms. In bacteria this pathway leads to the synthesis of isopentenyl tRNA, isoprenoid quinones, and sugar carrier lipids. Farnesyltranstransferase catalyzes the sequential addition of the three molecules of isopentenyl pyrophosphate onto dimethylallyl pyrophosphate to form geranylgeranyl pyrophosphate
YP_003916549.1	identified by similarity to protein SP:Q93QX6 (Corynebacterium glutamicum), match to protein family PF00494. Phytoene synthase catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP) into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. It is found in all organisms that synthesize carotenoids: plants and photosynthetic bacteria as well as some non- photosynthetic bacteria and fungi
YP_003916550.1	identified by similarity to protein SP:Q93QX5 (Corynebacterium glutamicum), match to protein family TIGR02734. Involved in carotenoid biosynthesis. Phytoene is converted to lycopene by desaturation at four (two symmetrical pairs of) sites. This is achieved by two enzymes (CrtP and CrtQ) in cyanobacteria (Gloeobacter being an exception) and plants, but by a single enzyme in most other bacteria and in fungi. This single enzyme is called the bacterial-type phytoene desaturase, or CrtI
YP_003916551.1	identified by similarity to protein SP:Q93QX4 (Corynebacterium glutamicum). In Corynebacterium glutamicum MJ233C, CrtYe and CrtYf encode the proteins of a C50 carotenoid epsilon cyclase, which is involved in C50 carotenoid biosynthesis. It catalyzes the formation of flavuxanthin from lycopene
YP_003916552.1	identified by similarity to protein SP:Q93QX3 (Corynebacterium glutamicum). In Corynebacterium glutamicum MJ233C, CrtYe and CrtYf encode the proteins of a C50 carotenoid epsilon cyclase, which is involved in C50 carotenoid biosynthesis. It catalyzes the formation of flavuxanthin from lycopene
YP_003916553.1	identified by similarity to protein SP:Q93QX2 (Corynebacterium glutamicum). In Corynebacterium glutamicum MJ233C, CrtEb converts lycopene into the acyclic C50 carotenoid flaxuxanthin by the addition of two C5 isoprenoid groups
YP_003916554.1	catalyses the interconversion of isopentenyl diphosphate and dimethylallyl diphosphate. Dimethylallyl phosphate is the initial substrate for the biosynthesis of carotenoids and other long chain isoprenoids
YP_003916557.1	acetolactate synthase catalyses the first common step in the biosynthesis of the 3 branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. The resulting products are 2-acetolactate and 2-aceto2-hydroxybutanoate
YP_003916558.1	acetolactate synthase catalyses the first common step in the biosynthesis of the 3 branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. The resulting products are 2-acetolactate and 2-aceto2-hydroxybutanoate
YP_003916559.1	catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the branched chain amino acids leucine, valine and isoleucine
YP_003916560.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.464 between position 43 and 44
YP_003916561.1	identified by match to protein domain PF08241
YP_003916562.1	match to PF00196: Bacterial regulatory proteins, luxR family
YP_003916563.1	match to PF00196: Bacterial regulatory proteins, luxR family
YP_003916568.1	match to PF02018
YP_003916570.1	match to PF00132: Bacterial transferase hexapeptide repeat. A number of different transferase protein families contain this repeat, such as galactoside acetyltransferase- like proteins, the gamma-class of carbonic anhydrases, and tetrahydrodipicolinate-N-succinlytransferases
YP_003916571.1	match to protein family PF02706. This family includes proteins involved in lipopolysaccharide (lps) biosynthesis
YP_003916572.1	match to PF00535: glycosyl transferase family 2. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP- N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids
YP_003916573.1	10 transmembrane helices predicted by TMHMM2.0
YP_003916575.1	14 transmembrane helices predicted by TMHMM2.0
YP_003916576.1	identified by match to PF00686. This family includes a range of sulphotransferase proteins including flavonyl 3-sulphotransferase, aryl sulphotransferase, alcohol sulphotransferase, estrogen sulphotransferase and phenol-sulphating phenol sulphotransferase. These enzymes are responsible for the transfer of sulphate groups to specific compounds
YP_003916578.1	match to protein domain PF00801
YP_003916579.1	divalent anion:Na+ symporter (DASS) family (TC 2.A. 47.y.z). Functionally characterized proteins of the DASS family transport (1) organic di- and tricarboxylates of the Krebs Cycle as well as dicarboxylate amino acid, (2) inorganic sulfate and (3) phosphate
YP_003916581.1	identified by match to PF01583. Ultimate step in biosynthesis of 3-phosphoadenosine 5-phosphosulfate (PAPS), the primary biological sulfuryl donor
YP_003916582.1	identified by similarity to protein SP:P65163 (Mycobacterium tuberculosis). This enzyme (PAPS 3- phosphatase) is considered as an important regulator of the sulfate assimilation pathway, by controlling the pools of PAP and PAPS
YP_003916583.1	catalyses the formation of diphosphate and adenylyl sulphate from ATP and sulphate. This enzyme participates in 3 metabolic pathways: purine metabolism, selenoamino acid metabolism, and sulfur metabolism
YP_003916584.1	catalyses the formation of diphosphate and adenylyl sulphate from ATP and sulphate. This enzyme participates in 3 metabolic pathways: purine metabolism, selenoamino acid metabolism, and sulfur metabolism
YP_003916585.1	match to protein family PF08660. Possibly involved in the biosynthesis of an exopolysaccharide
YP_003916586.1	match to PF04101: Glycosyltransferase family 28 C- terminal domain. This family family comprises enzymes with a number of known activities; 1,2-diacylglycerol 3-beta- galactosyltransferase (EC 2.4.1.46); 1,2-diacylglycerol 3- beta-glucosyltransferase (EC 2.4.1.157); beta-N- acetylglucosamine transferase (EC 2.4.1)
YP_003916587.1	catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent
YP_003916593.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916596.1	match to PF00535 and PF00534
YP_003916597.1	match to PF00535: glycosyl transferase family 2. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP- N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids
YP_003916598.1	match to PF00534: Glycosyl transferases group 1. Proteins containing this domain transfer UDP, ADP, GDP or CMP linked sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. The bacterial enzymes are involved in various biosynthetic processes that include exopolysaccharide biosynthesis, lipopolysaccharide core biosynthesis and the biosynthesis of the slime polysaccaride colanic acid
YP_003916599.1	match to PF00534: Glycosyl transferases group 1. Proteins containing this domain transfer UDP, ADP, GDP or CMP linked sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. The bacterial enzymes are involved in various biosynthetic processes that include exopolysaccharide biosynthesis, lipopolysaccharide core biosynthesis and the biosynthesis of the slime polysaccaride colanic acid
YP_003916600.1	catalyzes the oxidation of UDP-N-acetyl-D- mannosamine to UDP-N-acetyl-D-mannosaminuronic acid. In Escherichia coli, UDP-N-acetyl-D-glucosamine 2-epimerase and UDP-N-acetyl-D-mannosamine dehydrogenase are responsible for the formation of UDP-N-acetyl-D- mannosaminuronic acid from UDP-N-acetyl-D-glucosamine
YP_003916601.1	catalyses the formation of UDP-N-acetyl-D- mannosamine from UDP-N-acetyl-D-glucosamine. The enzyme also hydrolyses the product to UDP and N-acetyl-D- mannosamine. In Escherichia coli, UDP-N-acetyl-D- glucosamine 2-epimerase and UDP-N-acetyl-D-mannosamine dehydrogenase are responsible for the formation of UDP-N- acetyl-D-mannosaminuronic acid from UDP-N-acetyl-D- glucosamine
YP_003916603.1	activates methionine and transfers it to tRNA(Met) as the first step in protein biosynthesis
YP_003916604.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916605.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916606.1	involved in leucine biosynthesis. Catalyzes the oxidative decarboxylation of 3-isopropylmalate into 2-oxo- 4-methylvalerate
YP_003916607.1	last step in the biosynthesis of the branched-chain amino acids L-isoleucine, L-valine and L-leucine
YP_003916608.1	catalyses the formation of UDP-glucose from UDP- galactose. Involved in the catabolism of galactose
YP_003916615.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916616.1	identified by match to protein family PF01926
YP_003916617.1	catalyses the following reaction: ATP + thiamine phosphate <=> ADP + thiamine diphosphate
YP_003916618.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003916619.1	catalyzes the isomerization between (2R,3S)-3- isopropylmalate and (2S)-2-isopropylmalate, via the formation of (2S)-2-isopropylmaleate. Involved in leucine biosynthesis
YP_003916620.1	catalyzes the isomerization between (2R,3S)-3- isopropylmalate and (2S)-2-isopropylmalate, via the formation of (2S)-2-isopropylmaleate. Involved in leucine biosynthesis
YP_003916621.1	catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine = phosphate + UDP-N-acetyl-3-(1-carboxyvinyl)-D-glucosamine
YP_003916622.1	1-acylglycerol-3-phosphate O-acyltransferase catalyzes the following reaction: Acyl-CoA + 1-acyl-sn- glycerol 3-phosphate <=> CoA + 1,2-diacyl-sn-glycerol 3- phosphate. It is involved in phospholipid biosynthesis
YP_003916623.1	catalyzes the following reaction: sn-glycerol 3- phosphate + NAD(P)(+) <=> glycerone phosphate + NAD(P)H. Involved in glycerophospholipid metabolism
YP_003916624.1	participates in forming UDP-N-acetylmuramyl pentapeptide, the peptidoglycan precursor
YP_003916627.1	match to PF2734 (DAK2; predicted phosphatase domain of the dihydroxyacetone kinase family) domain
YP_003916628.1	RecG protein is a junction-specific DNA helicase that drives branch migration of Holliday intermediates in genetic recombination and DNA repair
YP_003916629.1	match to PS00092 pattern: N-6 Adenine-specific DNA methylases signature. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes
YP_003916631.1	identified by match to PF00155: aminotransferase class I and II
YP_003916632.1	reversibly transfers an adenylyl group from ATP to 4-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate: ATP + pantetheine 4-phosphate = diphosphate + 3-dephospho-CoA
YP_003916633.1	catalyses the formation of UDP-glucose from glucose- 1-phosphate
YP_003916635.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease (IM), CLS-family (capsular polysaccharide, lipopolysaccharide and teichoic acids). A typical system is made of a conserved permease (IM) and an ATP-binding subunit (ABC). In addition to these proteins, capsular polysaccharide exporter systems require two accessory proteins to perform their function: a periplasmic or a lipid-anchored outer membrane protein called OMA and a cytoplasmic membrane protein MPA2
YP_003916636.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, ATP-binding protein (ABC), CLS-family (capsular polysaccharide, lipopolysaccharide and teichoic acids). A typical system is made of a conserved permease (IM) and an ATP-binding subunit (ABC). In addition to these proteins, capsular polysaccharide exporter systems require two accessory proteins to perform their function: a periplasmic or a lipid-anchored outer membrane protein called OMA and a cytoplasmic membrane protein MPA2
YP_003916637.1	match to PF00535: glycosyl transferase family 2. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP- N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids
YP_003916638.1	match to protein family PF01066. Possibly involved in phospholipid biosynthesis
YP_003916639.1	match to PF00535: glycosyl transferase family 2. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP- N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids
YP_003916640.1	involved in teichoic acid biosynthesis
YP_003916652.1	ribosomal protein L32 is part of the 50S ribosomal subunit
YP_003916653.1	digests double-stranded RNA. Involved in the processing of ribosomal RNA precursors and of some mRNAs
YP_003916654.1	formamidopyrimidine-DNA glycosylases is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; EC:3.2.2.23) and cleaves both the 3- and 5- phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; EC:4.2.99. 18). It has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8- oxoguanine (8-oxoG). Its AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3- and 5-phosphates
YP_003916655.1	match to protein family PF00144: beta-lactamase
YP_003916656.1	identified by match to protein family TIGR02168. Smc participates in chromosomal partition during cell division. Component of a cohesin-like complex composed of scpA, scpB and smc
YP_003916657.1	drug:H+ antiporter-1 (12 Spanner) (DHA1) family transporter (TC 2.A.1.2.z). Match to PR01035 (Tetracycline resistance protein signature)
YP_003916658.1	identified by match to protein family TIGR00064. FtsY is a functional homolog of SRP receptor. Integral membrane proteins, are specifically recognized by a direct interaction between their noncleaved signal anchor sequences and the bacterial signal recognition particle (SRP) consisting of Ffh and 4.5S RNA. Recognition occurs during synthesis at the ribosome and leads to a cotranslational targeting to SecYE that is mediated by FtsY and the hydrolysis of GTP
YP_003916659.1	3-methyladenine DNA glycosylase is a base excision- repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3- methyladenine from damaged DNA
YP_003916660.1	involved in the uptake of ammonia. Ammonia channel transporter (Amt) family (TC 1.A.11.y.z). The generalized transport reactions catalyzed by members of the Amt family are suggested to be: NH4+ (out) <--> NH4+ (in)
YP_003916661.1	decomposes hydrogen peroxide to molecular oxygen and water. Its main function is to protect cells from the toxic effects of hydrogen peroxide
YP_003916662.1	identified by match to PF03631 (ribonuclease_BN, ribonuclease BN-like family): this family contains integral membrane proteins with 5 to 6 predicted transmembrane spans. The family includes ribonuclease BN, which is involved in tRNA maturation
YP_003916663.1	identified by match to PF01243: pyridoxamine 5- phosphate oxidase. This entry represents the FMN-binding domain present in pyridoxamine 5-phosphate oxidases, as well as in a number of proteins that have not been demonstrated to have enzymatic activity
YP_003916664.1	identified by match to protein family PF05532. CsbD is a bacterial general stress response protein. Its expression is mediated by sigma-B, an alternative sigma factor. The role of CsbD in stress response is unclear
YP_003916665.1	major facilitator superfamily, drug:H+ antiporter-2 (14 spanner) (DHA2) family (TC 2.A.1.3.z). Identified by match to protein family TIGR00711
YP_003916668.1	match to protein family PF02585 and PF05401. Possibly involved in polysaccharide synthesis
YP_003916669.1	match to PF00535: glycosyl transferase family 2. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP- N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids
YP_003916674.1	identified by match to protein family TIGR00959. Integral membrane proteins, are specifically recognized by a direct interaction between their noncleaved signal anchor sequences and the bacterial signal recognition particle (SRP) consisting of Ffh and 4.5S RNA. Recognition occurs during synthesis at the ribosome and leads to a cotranslational targeting to SecYE that is mediated by FtsY and the hydrolysis of GTP
YP_003916677.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003916679.1	match to the inorganic pyrophosphatase (PS00387) and Trp-Asp (WD) repeats (PS00678) signatures
YP_003916682.1	match to PF00534: Glycosyl transferases group 1. Proteins containing this domain transfer UDP, ADP, GDP or CMP linked sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. The bacterial enzymes are involved in various biosynthetic processes that include exopolysaccharide biosynthesis, lipopolysaccharide core biosynthesis and the biosynthesis of the slime polysaccaride colanic acid
YP_003916687.1	match to protein family PF00501. This family of enzymes includes luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely- related synthetases
YP_003916688.1	match to protein family PF00501. This family of enzymes includes luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely- related synthetases
YP_003916689.1	thermonuclease catalyzes the hydrolysis of both DNA and RNA at the 5-position of the phosphodiester
YP_003916690.1	thermonuclease catalyzes the hydrolysis of both DNA and RNA at the 5-position of the phosphodiester
YP_003916692.1	match to PF00132: Bacterial transferase hexapeptide repeat. A number of different transferase protein families contain this repeat, such as galactoside acetyltransferase- like proteins, the gamma-class of carbonic anhydrases, and tetrahydrodipicolinate-N-succinlytransferases
YP_003916693.1	match to PF00534: Glycosyl transferases group 1. Proteins containing this domain transfer UDP, ADP, GDP or CMP linked sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. The bacterial enzymes are involved in various biosynthetic processes that include exopolysaccharide biosynthesis, lipopolysaccharide core biosynthesis and the biosynthesis of the slime polysaccaride colanic acid
YP_003916695.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, binding protein (BP), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003916696.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003916697.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003916698.1	identified by match to PF01844
YP_003916699.1	resistance to homoSer/Thr (RhtB) family protein (TC 2.A.76.y.z). The family includes homoserine, threonine and leucine efflux proteins. The transport reaction presumably catalyzed by members of the RhtB family is: amino acid (in) + nH+ (out) <--> amino acid (out) + nH+ (in)
YP_003916702.1	essential for efficient processing of 16S rRNA. It is needed in a step prior to rbfA during the maturation of 16S rRNA
YP_003916703.1	specifically methylates guanosine-37 in various tRNAs
YP_003916704.1	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_003916705.1	signal peptidases remove the signal peptides from secretory proteins. In prokaryotes three types of signal peptidases are known: type I (gene lepB) which is responsible for the processing of the majority of exported pre-proteins; type II (gene lsp) which only process lipoproteins, and a third type involved in the processing of pili subunits
YP_003916707.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.703 between position 44 and 45
YP_003916708.1	non-secretory protein prediction by SignalP 3.0 HMM
YP_003916709.1	recognizes and cleaves the RNA strand of RNA-DNA heteroduplexes
YP_003916711.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, binding protein (BP), OTCN-family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L-proline
YP_003916712.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, permease (IM), OTCN- family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L- proline
YP_003916713.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OTCN-family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L-proline
YP_003916716.1	match to protein family TIGR00368
YP_003916717.1	the SMF family (DNA processing chain A, dprA) are a group of bacterial proteins. In Helicobacter pylori, dprA is required for natural chromosomal and plasmid transformation
YP_003916718.1	site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids
YP_003916720.1	match to PS00082 extradiol ring-cleavage dioxygenases signature
YP_003916721.1	match to protein domain PF01872. This domain is found in the C-terminus of the bifunctional deaminase- reductase in combination with PF00383 as well as in isolation in some archaebacterial proteins
YP_003916722.1	catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP
YP_003916723.1	also named fatty acid synthase ACP. Carrier of the growing fatty acid chain in fatty acid biosynthesis
YP_003916724.1	involved in the initiation of fatty-acid biosynthesis in bacteria
YP_003916726.1	the pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO2. It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3)
YP_003916728.1	thiol-specific antioxidant proteins confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF
YP_003916730.1	identified by match to protein domain PF08241
YP_003916731.1	5 transmembrane helices predicted by TMHMM2.0
YP_003916733.1	identified by match to protein family PF05532. CsbD is a bacterial general stress response protein. Its expression is mediated by sigma-B, an alternative sigma factor. The role of CsbD in stress response is unclear
YP_003916734.1	match to protein domain PF05175. This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases
YP_003916735.1	match to PF04101: Glycosyltransferase family 28 N- terminal domain. This family family comprises enzymes with a number of known activities; 1,2-diacylglycerol 3-beta- galactosyltransferase (EC 2.4.1.46); 1,2-diacylglycerol 3- beta-glucosyltransferase (EC 2.4.1.157); beta-N- acetylglucosamine transferase (EC 2.4.1)
YP_003916736.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003916737.1	removes the acetyl group from N-acetyl-ornithine. Involved in arginine biosynthesis
YP_003916738.1	major facilitator superfamily (MFS), metabolite:H+ symporter (MHS) family (TC 2.A.1.6.z)
YP_003916739.1	identified by match to protein family PF03006: HlyIII, Haemolysin-III related
YP_003916740.1	match to protein family PF06414. This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid
YP_003916741.1	3 transmembrane helices predicted by TMHMM2.0
YP_003916742.1	catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product, gluconate-6-phoshate, is an important precursor of gluconate metabolism
YP_003916743.1	Gluconate:H+ Symporter (GntP) Family (TC 2.A.8.y.z). Match to protein family PF02447
YP_003916745.1	match to PF00392: bacterial regulatory proteins, gntR family, and to PF07729: FCD domain
YP_003916746.1	involved in the pentose phosphate pathway. Catalyzes the oxidative decarboxylation of 6- phosphogluconate into ribulose 5-phosphate
YP_003916749.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916751.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916752.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916753.1	excinuclease ABC catalyses nucleotide excision repair in a multi-step process
YP_003916754.1	match to PS51257: prokaryotic membrane lipoprotein lipid attachment site profile
YP_003916755.1	Dicarboxylate/Amino Acid:Cation (Na+ or H+) symporter (DAACS) family (TC 2.A.23.y.z). The members of the DAACS family catalyze Na+ and/or H+ symport together with (a) a Krebs cycle dicarboxylate (malate, succinate, or fumarate), (b) a dicarboxylic amino acid (glutamate or aspartate), (c) a small, semipolar, neutral amino acid (Ala, Ser, Cys, Thr), (d) both neutral and acidic amino acids or (e) most zwitterionic and dibasic amino acids
YP_003916756.1	catalyses the first step of the synthesis of L- cysteine from L-serine
YP_003916757.1	responsible for the formation of cysteine from O- acetyl-serine and hydrogen sulfide with the concomitant release of acetic acid
YP_003916758.1	plays a role in preventing oxidative-stress damage caused by reactive oxygen species by reducing the oxidized form of methionine back to methionine and thereby reactivating peptides that had been damaged
YP_003916762.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.987 between position 31 and 32
YP_003916763.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.697 between position 29 and 30
YP_003916764.1	match to PF00149. The metallophosphoesterase motif is found in a large number of proteins invoved in phosphoryation. These include Ser/Thr phosphatases, DNA polymerase, exonucleases, and other phosphatases
YP_003916766.1	catalyses the reversible oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3- diphospho-glycerate
YP_003916767.1	involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
YP_003916768.1	possibly involved in the metabolism of lipids. Match to protein domains PF08028, PF02771 and PF02770. Acyl-CoA dehydrogenases catalyze the alpha,beta- dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD
YP_003916772.1	exoribonuclease specific for small oligoribonucleotides. Belongs to the oligoribonuclease family
YP_003916773.1	11 transmembrane helices predicted by TMHMM2.0
YP_003916774.1	12 transmembrane helices predicted by TMHMM2.0
YP_003916775.1	9 transmembrane helices predicted by TMHMM2.0
YP_003916776.1	similar to  excisionases from Mycobacterium phages
YP_003916777.1	match to PF04607. This region of unknown function is found in RelA and SpoT of Escherichia coli, and their homologues in plants and in other eubacteria
YP_003916778.1	TCDB: ATP-binding cassette (ABC) superfamily, () drug resistance ATPase-2 (Drug RA2) family (TC 3.A.1.121.z). ABCISSE: fused ATP-binding protein (ABC2), ART-family, ARE-subfamily (antibiotic resistance)
YP_003916780.1	2 transmembrane helices predicted by TMHMM2.0. Signal peptide predicted by SignalP 3.0 HMM (probability: 0.652) with cleavage site probability 0.343 between position 21 and 22
YP_003916782.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916783.1	catalyses the following reaction: (3R)-3- hydroxyacyl-ACP + NADP(+) <=> 3-oxoacyl- ACP + NADPH. Is involved in fatty acid biosynthesis
YP_003916784.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases. Possibly involved in the metabolism of lipid
YP_003916785.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.997) with cleavage site probability 0.464 between position 32 and 33
YP_003916786.1	match to PF04294: VanW, VanW like protein. Family members include vancomycin resistance protein W (VanW). Genes encoding members of this family have been found in vancomycin resistance gene clusters vanB and vanG. The function of VanW is unknown
YP_003916787.1	responsible for the third and final step of the L- serine biosynthetic pathway
YP_003916788.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, ATP-binding protein (ABC), YLU-family (unclassified systems)
YP_003916789.1	8 transmembrane helices predicted by TMHMM2.0
YP_003916790.1	identified by match to protein family PF00588: SpoU rRNA Methylase family. Possible role in rRNA modification
YP_003916791.1	part of the 50S ribosomal subunit
YP_003916792.1	catalyses the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes. Lipoylation is essential for the function of several key enzymes involved in oxidative metabolism, including pyruvate dehydrogenase (E(2) domain), 2-oxoglutarate dehydrogenase (E(2) domain), the branched-chain 2-oxoacid dehydrogenases and the glycine cleavage system (H protein)
YP_003916793.1	identified by match to PF00753: metallo-beta- lactamase superfamily. Apart from the beta-lactamases, a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl- glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake
YP_003916794.1	catalyzes the removal of single amino acids from the amino terminus of small peptides
YP_003916797.1	this family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o- hydroxybenzylidenepyruvate hydratase-aldolase, trans-2- carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3- deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase family
YP_003916798.1	match to protein family PF00903: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
YP_003916799.1	identified by similarity to potein SP:Q33DR0 (Arthrobacter ureafaciens). Catalyzes the oxidation of acyl-coenzyme A (acyl-CoA) thioester to the corresponding trans-2-enoyl-CoA thioester: acyl-CoA + O2 --> trans-2- enoyl-CoA + H2O2. Probably involved in beta-oxidation of fatty acids
YP_003916800.1	identified by match to PF00440: bacterial regulatory proteins, tetR family
YP_003916801.1	acetyl-CoA C-acyltransferase (also named 3-ketoacyl- CoA thiolase or thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation
YP_003916803.1	match to PF01575 (MaoC like domain). Enoyl-CoA hydratase is involved in fatty acid metabolism. It catalyzes the hydratation of 2-trans-enoyl-CoA into 3- hydroxyacyl-CoA
YP_003916804.1	match to PF00534: Glycosyl transferases group 1. Proteins containing this domain transfer UDP, ADP, GDP or CMP linked sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. The bacterial enzymes are involved in various biosynthetic processes that include exopolysaccharide biosynthesis, lipopolysaccharide core biosynthesis and the biosynthesis of the slime polysaccaride colanic acid
YP_003916805.1	prolyl aminopeptidase releases N-terminal proline from a peptide
YP_003916807.1	match to PF03807: NADP oxidoreductase coenzyme F420- dependent
YP_003916808.1	metal ion (Mn2+-iron) transporter (Nramp) family protein (TC 2.A.55.y.z). The generalized transport reaction catalyzed by Nramp family proteins is: Me2+ (out) + H+ (out) --> Me2+ (in) + H+ (in)
YP_003916809.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916810.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003916811.1	identified by match to protein family PF01546: peptidase family M20/M25/M40. This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification
YP_003916812.1	Acyl-CoA dehydrogenases catalyze the alpha,beta- dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD. They are involved in the metabolism of lipids
YP_003916815.1	catalyses the formation of undecaprenyl phosphate from undecaprenyl diphosphate. Involved in peptidoglycan biosynthesis
YP_003916816.1	activates cysteine and transfers it to tRNA(Cys) as the first step in protein biosynthesis
YP_003916818.1	identified by match to protein family TIGR01509: HAD-superfamily hydrolase, subfamily IA, variant 3; match to protein family PF00702: haloacid dehalogenase-like hydrolase
YP_003916819.1	match to protein family PF02163: Peptidase family M50. Match to PS00142 pattern: neutral zinc metallopeptidases, zinc-binding region signature. 6 transmembrane helices predicted by TMHMM2.0
YP_003916820.1	identified by match to protein family PF08704: GCD14, tRNA methyltransferase complex GCD14 subunit. tRNA (adenine-N(1)-)-methyltransferase catalyses the following reaction: S-adenosyl-L-methionine + tRNA <=> S-adenosyl-L- homocysteine + tRNA containing N(1)-methyladenine. The enzymes from different sources are specific for different adenine residues in tRNA
YP_003916821.1	COG1222: RPT1, ATP-dependent 26S proteasome regulatory subunit. Proteasomes are large protein complexes, which main function is to degrade unneeded or damaged proteins
YP_003916822.1	identified by match to protein family PF03136: DUF245,  proteasome component. Proteasomes are large protein complexes, which main function is to degrade unneeded or damaged proteins
YP_003916824.1	identified by match to protein family PF03136: DUF245,  proteasome component. Proteasomes are large protein complexes, which main function is to degrade unneeded or damaged proteins
YP_003916825.1	identified by match to protein family PF00254: FKBP- type peptidyl-prolyl cis-trans isomerase. Peptidylprolyl isomerase is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Signal peptide predicted by SignalP 3.0 HMM (probability: 1) with cleavage site probability 0.529 between position 27 and 28
YP_003916826.1	identified by match to protein family PF00254: FKBP- type peptidyl-prolyl cis-trans isomerase. Peptidylprolyl isomerase is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides
YP_003916828.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.673) with cleavage site probability 0.443 between position 23 and 24
YP_003916829.1	identified by match to protein family TIGR01411: twin-arginine translocation protein TatA/E. The twin- arginine translocation system is a Sec-independent exporter for folded proteins, often with a redox cofactor already bound, across the bacterial inner membrane
YP_003916830.1	identified by match to protein family PF00902: Sec- independent protein translocase protein (TatC). The twin- arginine translocation system is a Sec-independent exporter for folded proteins, often with a redox cofactor already bound, across the bacterial inner membrane
YP_003916831.1	DEAD box helicase. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression
YP_003916832.1	identified by match to protein family PF07969: amidohydrolase family
YP_003916833.1	match to PF00535: glycosyl transferase family 2. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP- N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids
YP_003916835.1	identified by match to protein family PF01145. The band 7 protein is an integral membrane protein which is thought to regulate cation conductance. A variety of proteins belong to this family
YP_003916836.1	3 transmembrane helices predicted by TMHMM2.0
YP_003916837.1	rRNA methyltransferase catalyzes the following reaction: S-adenosyl-L-methionine + rRNA => S-adenosyl-L- homocysteine + rRNA containing N(1)-methylguanine. It is required for translation and cell growth
YP_003916838.1	involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
YP_003916839.1	identified by match to protein family PF03969: AFG1_ATPase, AFG1-like ATPase
YP_003916840.1	identified by match to PF01022. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003916841.1	match to protein family PF03969: activator of Hsp90 ATPase homolog 1-like protein
YP_003916842.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916843.1	identified by match to protein family PF01758. Bile acid:Na+ symporter (BASS) family (TC 2.A.28.y.z): these symporters exhibit broad specificity, taking up a variety of non bile organic compounds as well as taurocholate and other bile salts
YP_003916844.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916845.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916847.1	identified by match to protein family PF01037: AsnC_trans_reg, AsnC family
YP_003916848.1	involved in tryptophane biosynthesis
YP_003916849.1	in Corynebacterium glutamicum, a cytochrome aa3 terminal oxidase (EC 1.9.3.1) receives electrons from a bc1 complex (EC 1.10.2.2). The bc1 complex is encoded by qcrA (Rieske iron-sulfur protein), qcrB (cytochrome B) and qcrC (cytochrome c1). Cytochrome aa3 is composed of subunits I (ctaD), II (ctaC), III (ctaE) and IV (ctaF). These subunits form the cytochrome bc1-aa3 supercomplex
YP_003916850.1	in Corynebacterium glutamicum, a cytochrome aa3 terminal oxidase (EC 1.9.3.1) receives electrons from a bc1 complex (EC 1.10.2.2). The bc1 complex is encoded by qcrA (Rieske iron-sulfur protein), qcrB (cytochrome B) and qcrC (cytochrome c1). Cytochrome aa3 is composed of subunits I (ctaD), II (ctaC), III (ctaE) and IV (ctaF). These subunits form the cytochrome bc1-aa3 supercomplex
YP_003916851.1	in Corynebacterium glutamicum, a cytochrome aa3 terminal oxidase (EC 1.9.3.1) receives electrons from a bc1 complex (EC 1.10.2.2). The bc1 complex is encoded by qcrA (Rieske iron-sulfur protein), qcrB (cytochrome B) and qcrC (cytochrome c1). Cytochrome aa3 is composed of subunits I (ctaD), II (ctaC), III (ctaE) and IV (ctaF). These subunits form the cytochrome bc1-aa3 supercomplex
YP_003916852.1	in Corynebacterium glutamicum, a cytochrome aa3 terminal oxidase (EC 1.9.3.1) receives electrons from a bc1 complex (EC 1.10.2.2). The bc1 complex is encoded by qcrA (Rieske iron-sulfur protein), qcrB (cytochrome B) and qcrC (cytochrome c1). Cytochrome aa3 is composed of subunits I (ctaD), II (ctaC), III (ctaE) and IV (ctaF). These subunits form the cytochrome bc1-aa3 supercomplex
YP_003916853.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003916854.1	in Corynebacterium glutamicum, a cytochrome aa3 terminal oxidase (EC 1.9.3.1) receives electrons from a bc1 complex (EC 1.10.2.2). The bc1 complex is encoded by qcrA (Rieske iron-sulfur protein), qcrB (cytochrome B) and qcrC (cytochrome c1). Cytochrome aa3 is composed of subunits I (ctaD), II (ctaC), III (ctaE) and IV (ctaF). These subunits form the cytochrome bc1-aa3 supercomplex
YP_003916855.1	in Corynebacterium glutamicum, a cytochrome aa3 terminal oxidase (EC 1.9.3.1) receives electrons from a bc1 complex (EC 1.10.2.2). The bc1 complex is encoded by qcrA (Rieske iron-sulfur protein), qcrB (cytochrome B) and qcrC (cytochrome c1). Cytochrome aa3 is composed of subunits I (ctaD), II (ctaC), III (ctaE) and IV (ctaF). These subunits form the cytochrome bc1-aa3 supercomplex
YP_003916856.1	in Corynebacterium glutamicum, a cytochrome aa3 terminal oxidase (EC 1.9.3.1) receives electrons from a bc1 complex (EC 1.10.2.2). The bc1 complex is encoded by qcrA (Rieske iron-sulfur protein), qcrB (cytochrome B) and qcrC (cytochrome c1). Cytochrome aa3 is composed of subunits I (ctaD), II (ctaC), III (ctaE) and IV (ctaF). These subunits form the cytochrome bc1-aa3 supercomplex
YP_003916857.1	identified by match to protein family TIGR00049
YP_003916858.1	identified by match to protein family PF01546: peptidase family M20/M25/M40. This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification
YP_003916859.1	2 transmembrane helices predicted by TMHMM2.0
YP_003916860.1	catalyzes the fourth step in the de novo biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate
YP_003916861.1	match to PF00561: alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes
YP_003916862.1	generates undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide
YP_003916863.1	involved in DNA repair and recF pathway recombination
YP_003916864.1	catalyzes the first step in the biosynthesis of leucine, the condensation of acetyl-CoA and 2- oxoisovalerate to form 2-isopropylmalate
YP_003916866.1	in Escherichia coli, the protein Era is involved in 16S rRNA maturation and ribosome assembly
YP_003916867.1	possible transporter. Match to PF00571 (CBS domain pair)
YP_003916869.1	identified by match to protein family PF02562: PhoH, PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation
YP_003916872.1	involved in protein folding and renaturation after stress
YP_003916873.1	match to protein family PF01628: HrcA protein C terminal domain. HrcA is found to negatively regulate the transcription of heat shock genes
YP_003916875.1	3 transmembrane helices predicted by TMHMM2.0
YP_003916876.1	catalyzes the oxidative decarboxylation of coproporphyrinogen III into protoporphyrinogen IX, a common step in the pathway for the biosynthesis of porphyrins such as heme, chlorophyll or cobalamin: coproporphyrinogen-III + O(2) + 2 H(+) <=> protoporphyrinogen-IX + 2 CO(2) + 2 H(2)O
YP_003916877.1	the extremely conserved LepA protein, present in all bacteria and mitochondria, is an elongation factor required for accurate and efficient protein synthesis
YP_003916879.1	Binds directly to 16S ribosomal RNA
YP_003916880.1	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication once it is clamped onto DNA. DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII complex. PolIII associates with the gamma complex (composed of gamma, delta, delta prime, psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex
YP_003916881.1	identified by match to protein family PF03772, some members of this family have been shown to be essential for bacterial competence in uptake of extracellular DNA. 10 transmembrane helices predicted by TMHMM2.0
YP_003916882.1	helix-hairpin-helix DNA-binding domain. The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins
YP_003916883.1	identified by match to protein family PF02645: uncharacterised protein, DegV family COG1307. The structure of this protein revealed a bound fatty-acid molecule in a pocket between the two protein domains. The structure indicates that this family has the molecular function of fatty-acid binding and may play a role in the cellular functions of fatty acid transport or metabolism
YP_003916885.1	match to HNH endonuclease signature (cd00085)
YP_003916886.1	catalyzes the Mg-ATP-dependent phosphorylation of glycerol to yield glycerol 3-phosphate. Key enzyme of glycerol metabolism in bacteria, phosphorylation of glycerol prevents diffusion through the membrane
YP_003916887.1	glycerol facilitators function as solute nonspecific channels, and may transport glycerol, dihydroxyacetone, propanediol, urea and other small neutral molecules in physiologically important processes. Belongs to the the Major Intrinsic Protein (MIP) family (TC 1.A.8.y.z)
YP_003916888.1	catalyzes the following reaction: sn-glycerol-3- phosphate + acceptor = glycerone phosphate + reduced acceptor. In bacteria, it is associated with the utilization of glycerol coupled to respiration
YP_003916890.1	match to PS00120 pattern: lipases, serine active site
YP_003916891.1	formation of the primosome proceeds with the subsequent actions of dnaB, dnaC, dnaT and primase. PriA then functions as a helicase within the primosome
YP_003916892.1	catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis
YP_003916893.1	catalyzes two steps in the biosynthesis of coenzyme A: EC 6.3.2.5 conjugues cysteine to 4-phosphopantothenate to form 4-phosphopantothenoylcysteine (CTP + (R)-4- phosphopantothenate + L-cysteine = CMP + PPi + N-((R)-4- phosphopantothenoyl)-L-cysteine), EC 4.1.1.36 decarboxylates 4-phosphopantothenoylcysteine to form 4- phosphopantotheine (N-((R)-4-phosphopantothenoyl)-L- cysteine = pantotheine 4-phosphate + CO2)
YP_003916894.1	DNA-directed RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
YP_003916895.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP)
YP_003916896.1	match to SM00278 (Helix-hairpin-helix DNA-binding motif, class 1)
YP_003916897.1	decarboxylates orotidine-5-phosphate to form uridine 5-phosphate (UMP). Involved in pyrimidine biosynthesis
YP_003916898.1	carbamoyl-phosphate synthase is involved in both arginine and pyrimidine biosynthesis and catalyzes the ATP- dependent formation of carbamoyl-phosphate from glutamine and carbon dioxide. In bacteria it is composed of two subunits: a large chain (gene carB) and a small chain (gene carA)
YP_003916899.1	carbamoyl-phosphate synthase is involved in both arginine and pyrimidine biosynthesis and catalyzes the ATP- dependent formation of carbamoyl-phosphate from glutamine and carbon dioxide. In bacteria it is composed of two subunits: a large chain (gene carB) and a small chain (gene carA)
YP_003916900.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916901.1	catalyzes the third step in the de novo biosynthesis of pyrimidine, the conversion of N-carbamoyl- L-aspartate into dihydroorotate
YP_003916902.1	catalyzes the conversion of aspartate and carbamoyl phosphate to carbamoylaspartate, the second step in the de novo biosynthesis of pyrimidine
YP_003916903.1	regulates pyrimidine biosynthesis by binding to the mRNA of the pyr genes. Has also a uracil phosphoribosyltransferase activity: formation of UMP and diphosphate from uracil and 5-phospho-alpha-D-ribose 1- diphosphate
YP_003916904.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.881) with cleavage site probability 0.567 between position 37 and 38
YP_003916906.1	regulates rRNA biosynthesis by transcriptional antitermination
YP_003916907.1	required for efficient translation
YP_003916909.1	involved in phenylalanine, tyrosine and tryptophan biosynthesis
YP_003916910.1	fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids (phenylalanine, tyrosine and tryptophan), p-aminobenzoic acid, folate and ubiquinone
YP_003916911.1	last enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids (phenylalanine, tyrosine and tryptophan), p-aminobenzoic acid, folate and ubiquinone
YP_003916912.1	fourth enzyme in the shikimate pathway, a seven- step biosynthetic pathway which converts erythrose-4- phosphate to chorismic acid. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids (phenylalanine, tyrosine and tryptophan), p-aminobenzoic acid, folate and ubiquinone
YP_003916913.1	aminodeoxychorismate lyase converts 4- aminodeoxychorismate to pyruvate and p-aminobenzoate, a precursor of folic acid in bacteria. Identified by match to protein family PF02618
YP_003916914.1	identified by match to protein family TIGR00250. Could be a nuclease that resolves Holliday junction intermediates in genetic recombination
YP_003916917.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.558) with cleavage site probability 0.558 between position 23 and 24
YP_003916918.1	One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit
YP_003916920.1	cell growth inhibition by several D-amino acids can be explained by an in vivo production of D-aminoacyl-tRNA molecules. D-tyrosyl-tRNA(Tyr) deacylase cleaves any D- amino acid (and glycine, which does not have distinct D/L forms) from charged tRNA
YP_003916921.1	identified by match to protein family PF03551
YP_003916922.1	6 transmembrane helices predicted by TMHMM2.0
YP_003916924.1	activates aspartate and transfers it to tRNA(Asp) as the first step in protein biosynthesis
YP_003916925.1	activates histidine and transfers it to tRNA(His) as the first step in protein biosynthesis
YP_003916928.1	GTP diphosphokinase (EC 2.7.6.5) produces pppGpp (or ppGpp) from ATP and GTP (or GDP). Guanosine-3,5- bis(diphosphate) 3-diphosphatase (EC 3.1.7.2) hydrolyzes ppGpp into GTP. In eubacteria ppGpp is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance
YP_003916929.1	identified by match to protein family PF02355. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF)
YP_003916930.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.509 between position 32 and 33. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF)
YP_003916931.1	match to bacterial YajC preprotein translocase signature PR02699. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF). Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA
YP_003916932.1	the RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair
YP_003916933.1	the RuvA protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair
YP_003916934.1	the RuvC protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair
YP_003916936.1	involved in pyridoxal biosynthesis. Hydrolyses glutamine to glutamate and ammonia. Channels an ammonia molecule to pdxS
YP_003916937.1	catalyzes the reduction of 2,5-diketogluconic acid to 2-keto-L-gulonic acid, a key intermediate in the production of ascorbic acid. Can also reduce ethyl 2- methylacetoacetate stereoselectively to ethyl (2R)-methyl- (3S)-hydroxybutanoate and can also accept some other beta- keto esters. Identified by similarity to protein SP:Q46857 (Escherichia coli)
YP_003916940.1	identified by match to PF09587. Poly-gamma- glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein
YP_003916941.1	hydrolyzes unblocked, C-terminal dipeptides from oligopeptides, with broad specificity
YP_003916942.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003916943.1	match to protein domain PF01872. This domain is found in the C-terminus of the bifunctional deaminase- reductase in combination with PF00383 as well as in isolation in some archaebacterial proteins
YP_003916945.1	combines ammonia with five- and three-carbon phosphosugars to form PLP (pyridoxal 5-phosphate) which is the biologically active form of vitamin B6. Forms a complex with pdxT
YP_003916946.1	match to PF01230: histidine triad motif. The histidine triad motif (HIT) is related to the sequence H- phi-H-phi-H-phi-phi (where phi is a hydrophobic amino acid). Proteins containing HIT domains form a superfamily of nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides
YP_003916947.1	activates threonine and transfers it to tRNA(Thr) as the first step in protein biosynthesis
YP_003916951.1	identified by match to PF00903: glyoxalase/bleomycin resistance protein/dioxygenase superfamily
YP_003916952.1	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication once it is clamped onto DNA. DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII complex. PolIII associates with the gamma complex (composed of gamma, delta, delta prime, psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex
YP_003916955.1	catalyses the following reaction: formaldehyde + mycothiol + NAD+ = S-formylmycothiol + NADH + H+. The S- formylmycothiol formed hydrolyses to mycothiol and formate
YP_003916956.1	identified by match to PF00753: metallo-beta- lactamase superfamily. Apart from the beta-lactamases, a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl- glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake
YP_003916957.1	4 transmembrane helices predicted by TMHMM2.0
YP_003916959.1	identified by match to protein family PF00462
YP_003916961.1	uridine kinase catalyzes the phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP
YP_003916963.1	match to PF01381: helix-turn-helix. This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003916964.1	match to PF07992: pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases
YP_003916965.1	match to PF00313: cold-shock DNA-binding domain. The so-called cold shock proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organization of the prokaryotic nucleoid
YP_003916969.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003916970.1	ribonucleotide reductase catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. It is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues)
YP_003916971.1	catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. It is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues)
YP_003916972.1	probably involved in ribonucleotide reductase function. ribonucleotide reductases are enzymes that provide the precursors of DNA synthesis
YP_003916973.1	electron transport system for the ribonucleotide reductase system nrdEF
YP_003916975.1	TPP-binding module. Catalyzes the formation of acetate from pyruvate (catalytic activity: pyruvate + ferricytochrome b1 + H2O = acetate + CO2 + ferrocytochrome b1)
YP_003916978.1	identified by match to PF00291: pyridoxal-phosphate dependent enzyme
YP_003916979.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.987) with cleavage site probability 0.704 between position 24 and 25. 7 transmembrane helices predicted by TMHMM2.0
YP_003916980.1	1 transmembrane helice predicted by TMHMM2.0
YP_003916981.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.976 between position 27 and 28. 1 transmembrane helice predicted by TMHMM2.0
YP_003916983.1	TCDB: ATP-binding cassette (ABC) superfamily, () drug resistance ATPase-2 (Drug RA2) family (TC 3.A.1.121.z). ABCISSE: fused ATP-binding protein (ABC2), ART-family, ARE-subfamily (antibiotic resistance)
YP_003916984.1	the succinate dehydrogenase complex catalyses the interconversion of fumarate and succinate. It contains several subunits: a flavoprotein (SdhA), an iron-sulfur protein (SdhB), and membrane anchor proteins (SdhC and SdhD). Involved in the TCA cycle
YP_003916988.1	identified by match to protein family PF01370: NAD dependent epimerase/dehydratase family. This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions
YP_003916990.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003916991.1	identified by match to protein family PF01037
YP_003916992.1	may catalyze the transamination reaction in phenylalanine biosynthesis
YP_003916993.1	amino acid-polyamine-organocation (APC) superfamily, amino acid transporter (AAT) family (TC 2.A.3.1.z)
YP_003916996.1	CorA metal ion transporter (MIT) family protein (TC 1.A.35.y.z). Functionally characterized proteins from this family includes the Mg2+-Co2+-Ni2+ CorA permeases of Salmonella typhimurium and E. coli. Match to protein family PF01544
YP_003916997.1	identified by match to cd00085: HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins
YP_003916998.1	identified by match to protein family TIGR00090: iojap homolog
YP_003916999.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917000.1	catalyses the following reaction: ATP + nicotinate ribonucleotide <=> diphosphate + deamido-NAD(+). Involved in the biosynthesis of NAD(+) and NADP(+)
YP_003917001.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917002.1	catalyzes the NADP-dependent reduction of L- glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. Involved in proline biosynthesis from glutamate
YP_003917003.1	catalyzes the ATP-dependent phosphorylation of L- glutamate into L-glutamate 5-phosphate. Involved in proline biosynthesis from glutamate
YP_003917004.1	Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis
YP_003917005.1	L27 is a protein from the large (50S) subunit
YP_003917006.1	part of the 50S ribosomal subunit. Binds to 23S rRNA in the presence of protein L20
YP_003917007.1	match to PF10150: ribonuclease E/G family. Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs. In E. coli, both RNase E and RNase G have been shown to play a role in the maturation of the 5 end of 16S RNA
YP_003917008.1	5 transmembrane helices predicted by TMHMM2.0. Match to IPR012932: vitamin K epoxide reductase
YP_003917009.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917010.1	8 transmembrane helices predicted by TMHMM2.0
YP_003917012.1	catalyses the following reaction: ATP + nucleoside diphosphate <=> ADP + nucleoside triphosphate. Required for the synthesis of nucleoside triphosphates other than ATP
YP_003917013.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.872) with cleavage site probability 0.380 between position 52 and 53. 2 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003917014.1	leds to conversion of folates to polyglutamate derivatives. It preferes 5,10-methylenetetrahydrofolate, rather than 10-formyltetrahydrofolate as folate substrate: ATP + tetrahydropteroyl-(gamma-Glu)(n) + L-glutamate <=> ADP + phosphate + tetrahydropteroyl-(gamma-Glu)(n+1)
YP_003917016.1	3 transmembrane helices predicted by TMHMM2.0
YP_003917017.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. 5 transmembrane helices predicted by TMHMM2.0
YP_003917018.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003917019.1	Resistance-Nodulation-Cell Division (RND) superfamily (TC 2.A.6.y.z). Match to PS50156: sterol- sensing domain. In bacteria, this domain is found in a number of drug resistance proteins
YP_003917020.1	4 transmembranes helice predicted by TMHMM2.0
YP_003917021.1	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication once it is clamped onto DNA. DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII complex. PolIII associates with the gamma complex (composed of gamma, delta, delta, psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex
YP_003917022.1	sulfite reductase catalyzes the reduction of sulfite to sulphide. Involved in the sulfate assimilation pathway
YP_003917023.1	catalyzes two sequential methylation reactions, the first forming precorrin-1 and the second leading to the formation of precorrin-2 (dihydrosirohydrochlorin): (1) S- adenosyl-L-methionine + uroporphyrinogen III <=> S- adenosyl-L-homocysteine + precorrin-1, (2) S-adenosyl-L- methionine + precorrin-1 <=> S-adenosyl-L-homocysteine + precorrin-2
YP_003917024.1	TCDB: ATP-binding cassette (ABC) superfamily, taurine uptake transporter (TauT) family (TC 3.A.1.17.z). ABCISSE: ABC transporter, permease (IM), OTCN-family (osmoprotectants, taurine, cyanate and nitrate), aliphatic sulfonates import. Part of an ABC transporter complex involved in aliphatic sulfonates import
YP_003917025.1	TCDB: ATP-binding cassette (ABC) superfamily, taurine uptake transporter (TauT) family (TC 3.A.1.17.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OTCN- family (osmoprotectants, taurine, cyanate and nitrate), aliphatic sulfonates import. Part of an ABC transporter complex involved in aliphatic sulfonates import
YP_003917026.1	TCDB: ATP-binding cassette (ABC) superfamily, taurine uptake transporter (TauT) family (TC 3.A.1.17.z). ABCISSE: ABC transporter, binding protein (BP), OTCN- family (osmoprotectants, taurine, cyanate and nitrate), aliphatic sulfonates import. Part of an ABC transporter complex involved in aliphatic sulfonates import
YP_003917027.1	catalyses the formation of diphosphate and adenylyl sulphate from ATP and sulphate. This enzyme participates in 3 metabolic pathways: purine metabolism, selenoamino acid metabolism, and sulfur metabolism
YP_003917028.1	catalyses the formation of diphosphate and adenylyl sulphate from ATP and sulphate. This enzyme participates in 3 metabolic pathways: purine metabolism, selenoamino acid metabolism, and sulfur metabolism
YP_003917029.1	identified by similarity to protein SP:P65668 (Mycobacterium tuberculosis). Involved in sulfate assimilation. Catalyzes the following reaction: adenylyl sulfate (APS) + reduced acceptor => AMP + sulfite + acceptor
YP_003917030.1	catalyzes the reduction of sulfite to sulphide. Involved in the sulfate assimilation pathway
YP_003917031.1	identified by match to protein family PF01903. The function of CbiX is uncertain, however it is found in cobalamin biosynthesis operons and so may have a related function. Some CbiX proteins contain a striking histidine- rich region at their C-terminus, which suggests that it might be involved in metal chelation
YP_003917032.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003917035.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 1.000 between position 39 and 40
YP_003917040.1	Clp displays ATP-dependent endopeptidase activity. It contains subunits of two types, ClpP, with peptidase activity, and ClpA or ClpX, with ATPase activity
YP_003917041.1	Clp displays ATP-dependent endopeptidase activity. It contains subunits of two types, ClpP, with peptidase activity, and ClpA or ClpX, with ATPase activity
YP_003917042.1	the trigger factor is found in several prokaryotes, and is involved in protein export. It is a ribosome- associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. It acts as a chaperone by maintaining the newly synthesised protein in an open conformation. The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity (EC 5.2.1. 8)
YP_003917043.1	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_003917044.1	catalyzes the interconversion of ribose 5-phosphate to ribulose 5-phosphate. Involved in the pentose phosphate pathway
YP_003917045.1	catalyzes the removal of single amino acids from the amino terminus of small peptides
YP_003917047.1	identified by match to protein family PF02566: OsmC, OsmC-like protein. Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. This family also contains an organic hydroperoxide detoxification protein that has a novel pattern of oxidative stress regulation
YP_003917048.1	identified by match to protein family PF01152: bacterial-like globin. Globins are heme-containing proteins involved in binding and/or transporting oxygen
YP_003917050.1	identified by similarity to protein SP:P0AGG2 (Escherichia coli). Can hydrolyze a broad range of acyl- CoA thioesters. Its physiological function is not known
YP_003917051.1	match to PF03473. The MOSC (MOCO sulfurase C- terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. The MOSC domain is predicted to be a sulfur- carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters
YP_003917052.1	identified by match to protein family TIGR01950. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species
YP_003917053.1	identified by match to PF01613
YP_003917054.1	TCDB: ATP-binding cassette (ABC) superfamily, () drug resistance ATPase-2 (Drug RA2) family (TC 3.A.1.121.z). ABCISSE: fused ATP-binding protein (ABC2), ART-family, ARE-subfamily (antibiotic resistance)
YP_003917055.1	this protein is essential for replication of the chromosome. It is also involved in DNA recombination and repair
YP_003917058.1	identified by match to PF00890. This family includes members that bind FAD such as the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase
YP_003917059.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690
YP_003917060.1	identified by match to protein family PF01037
YP_003917061.1	resistance to homoSer/Thr (RhtB) family protein (TC 2.A.76.y.z). The family includes homoserine, threonine and leucine efflux proteins. The transport reaction presumably catalyzed by members of the RhtB family is: amino acid (in) + nH+ (out) <--> amino acid (out) + nH+ (in)
YP_003917062.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, ATP-binding protein (ABC), CBY-family (Cobalt uptake, unknown), Y179- subfamily (CBU-like systems). The function of CBU-like systems is unknown
YP_003917063.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease (IM), CBY-family (Cobalt uptake, unknown), Y179-subfamily (CBU-like systems). The function of CBU-like systems is unknown
YP_003917064.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease (IM), CBY-family (Cobalt uptake, unknown), Y179-subfamily (CBU-like systems). The function of CBU-like systems is unknown
YP_003917065.1	match to protein family PF00501. This family of enzymes includes luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely- related synthetases
YP_003917066.1	acetyl-CoA C-acyltransferase (also named 3-ketoacyl- CoA thiolase or thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation
YP_003917068.1	the SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet
YP_003917069.1	the SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet
YP_003917070.1	the SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet
YP_003917072.1	TCDB: ATP-binding cassette (ABC) superfamily, drug exporter-1 (DrugE1) family (TC 3.A.1.105.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), DRA-family (Drug and Antibiotic resistance), DRR-subfamily (Polyketide drug resistance). The typical organization of DRR systems consists of 1 ABC transporter (ABC) and 1 or 2 permeases (IM). Possible function in drug efflux
YP_003917073.1	TCDB: ATP-binding cassette (ABC) superfamily, drug exporter-1 (DrugE1) family (TC 3.A.1.105.z). ABCISSE: ABC transporter, permease (IM), DRA-family (Drug and Antibiotic resistance), DRR-subfamily (Polyketide drug resistance). The typical organization of DRR systems consists of 1 ABC transporter (ABC) and 1 or 2 permeases (IM). Possible function in drug efflux
YP_003917074.1	identified by match to protein family PF02628. One member of this family, CtaA, is required for cytochrome aa3 biosynthesis in Bacillus subtilis
YP_003917075.1	6 transmembranes helices predicted by TMHMM2.0
YP_003917076.1	identified by match to protein family PF03551
YP_003917077.1	converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group
YP_003917078.1	catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to ribose 5- phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate. The second reaction catalyzed by transketolase involves the transfer of a 2-carbon fragment from D-xylulose 5-phosphate to the aldose D- erythrose-4-phosphate, affording fructose-6-phosphate and glyceraldehyde 3-phosphate
YP_003917079.1	catalyzes the reversible formation of D-erythrose 4- phosphate and D-fructose 6-phosphate from sedoheptulose 7- phosphate and D-glyceraldehyde 3-phosphate
YP_003917080.1	catalyzes the reversible isomerization of glucose-6- phosphate to fructose-6-phosphate. Also catalyzes the anomerization of D-glucose-6-phosphate
YP_003917081.1	catalyzes the first step in the pentose phosphate pathway, the reduction of glucose-6-phosphate to gluconolactone-6-phosphate
YP_003917082.1	subunit of glucose-6-phosphate 1- dehydrogenase
YP_003917083.1	involved in the pentose phosphate pathway. Catalyzes the hydrolysis of 6-phosphogluconolactone to 6- phosphogluconate
YP_003917084.1	catalyzes the oxidative deamination of D-amino acids to the corresponding keto acids, producing ammonia and hydrogen peroxide as by-products
YP_003917085.1	the members of this family catalyse the formation of glucose 1-phosphate from one of the following polyglucoses: glycogen, starch, glucan or maltodextrin
YP_003917086.1	catalyzes the formation of alpha-1,6 branch points in either glycogen or starch by cleavage of the alpha-1,4 glucosidic linkage, yielding a non-reducing end oligosaccharide chain and subsequent attachment to the alpha-1,6 position
YP_003917087.1	catalyzes an important step in the biosynthesis of alpha 1,4-glucans (glycogen or starch) in bacteria and plants: synthesis of the activated glucosyl donor, ADP- glucose, from glucose-1-phosphate and ATP
YP_003917088.1	involved in glycogen synthesis from ADP-glucose
YP_003917089.1	identified by match to protein family PF03840. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF)
YP_003917090.1	catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate
YP_003917091.1	catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3- phosphoglycerate
YP_003917092.1	catalyses the reversible oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3- diphospho-glycerate
YP_003917093.1	catalyses the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen
YP_003917095.1	match to PF1933: uncharacterised protein family UPF0052
YP_003917096.1	match to PF1933. This family contains an ATP- binding site and could be an ATPase
YP_003917097.1	excinuclease ABC catalyses nucleotide excision repair in a multi-step process
YP_003917098.1	1-acylglycerol-3-phosphate O-acyltransferase catalyzes the following reaction: Acyl-CoA + 1-acyl-sn- glycerol 3-phosphate <=> CoA + 1,2-diacyl-sn-glycerol 3- phosphate. It is involved in phospholipid biosynthesis
YP_003917099.1	identified by match to PF00702. This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases
YP_003917100.1	excinuclease ABC catalyses nucleotide excision repair in a multi-step process
YP_003917102.1	identified by match to PF00753: metallo-beta- lactamase superfamily. Apart from the beta-lactamases, a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl- glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake
YP_003917103.1	catalyzes the monomethyl esterification of trans- aconitate and related compounds. Possible role in detoxifying trans-aconitate
YP_003917104.1	possible DNA or RNA helicase
YP_003917105.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003917110.1	identified by match to PF04307: predicted membrane- bound metal-dependent hydrolase (DUF457)
YP_003917111.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917112.1	releases N-terminal proline from a peptide
YP_003917113.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003917114.1	match to PF0371: TerC, Integral membrane protein TerC family. 9 transmembranes helices predicted by TMHMM2. 0
YP_003917115.1	excinuclease ABC catalyses nucleotide excision repair in a multi-step process
YP_003917116.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917117.1	catalyzes the phosphorylation of the 3-hydroxyl group of dephosphocoenzyme A to form coenzyme A: ATP + dephospho-CoA = ADP + CoA
YP_003917118.1	match to PF01205: uncharacterized protein family UPF0029
YP_003917119.1	match to protein domain PF05175. This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases
YP_003917121.1	6 transmembranes helices predicted by TMHMM2.0
YP_003917122.1	binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence
YP_003917124.1	match to protein domain PF01522. This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB, which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast and endoxylanases which hydrolyses glucosidic bonds in xylan
YP_003917126.1	match to protein domain PF03061: thioesterase superfamily
YP_003917127.1	match to protein domain PF01872. This domain is found in the C-terminus of the bifunctional deaminase- reductase in combination with PF00383 as well as in isolation in some archaebacterial proteins
YP_003917128.1	2 transmembranes helices predicted by TMHMM2.0
YP_003917129.1	inorganic phosphate transporter (PiT) family (TC 2. A.20.y.z)
YP_003917130.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. Match to PF03861: ANTAR domain. ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins
YP_003917131.1	catalyses the conversion of phosphoenolpyruvate to pyruvate with the concomitant phosphorylation of ADP to ATP
YP_003917132.1	glutamate synthase participates in the ammonia assimilation process by catalyzing the formation of glutamate from glutamine and 2-oxoglutarate
YP_003917133.1	glutamate synthase participates in the ammonia assimilation process by catalyzing the formation of glutamate from glutamine and 2-oxoglutarate
YP_003917134.1	catalyzes the first step in lipoprotein biogenesis. It transfers the n-acyl diglyceride group on what will become the N-terminal cysteine of membrane lipoproteins
YP_003917135.1	tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan: the conversion of indoleglycerol phosphate and serine, to tryptophan and glyceraldehyde 3- phosphate. Also catalyzes the conversion of serine and indole into tryptophan and water, and of indoleglycerol phosphate into indole and glyceraldehyde phosphate
YP_003917136.1	tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan: the conversion of indoleglycerol phosphate and serine, to tryptophan and glyceraldehyde 3- phosphate. Also catalyzes the conversion of serine and indole into tryptophan and water, and of indoleglycerol phosphate into indole and glyceraldehyde phosphate
YP_003917137.1	catalyzes the fourth step in the biosynthesis of tryptophan: the ring closure of 1-(2-carboxy-phenylamino)- 1-deoxyribulose into indol-3-glycerol-phosphate
YP_003917138.1	2 transmembranes helices predicted by TMHMM2.0
YP_003917140.1	anthranilate synthase is the first enzyme in the branch pathway in tryptophane biosynthesis. It catalyzes the biosynthesis of anthranilate from chorismate and glutamine
YP_003917141.1	catalyses the following reaction: 1-(5- phosphoribosyl)-AMP + H(2)O <=> 1-(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide. Involved in Histidine biosynthesis
YP_003917143.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.654 between position 37 and 38
YP_003917147.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.727 between position 27 and 238
YP_003917148.1	match to protein domain PF00801
YP_003917149.1	imidazole glycerol phosphate synthase converts N1- (5-phosphoribulosyl)-formimino-5-aminoimidazole-4- carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). Involved in histidine biosynthesis
YP_003917150.1	catalyses the following reaction: 1-(5-phospho-D- ribosyl)-ATP + diphosphate <=> ATP + 5-phospho-alpha-D- ribose 1-diphosphate. Involved in histidine biosynthesis
YP_003917151.1	catalyses the following reaction: 1-(5- phosphoribosyl)-ATP + H(2)O <=> 1-(5-phosphoribosyl)-AMP + diphosphate. Involved in Histidine biosynthesis
YP_003917152.1	catalyzes the condensation of 5-amino-6-(1-D)- ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4- dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8- lumazine
YP_003917153.1	3,4-dihydroxy-2-butanone-4-phosphate synthase (4.1. 99.12) catalyses the following reaction: D-ribulose 5- phosphate <=> formate + L-3,4-dihydroxybutan-2-one 4- phosphate. GTP cyclohydrolase II (3.5.4.25) catalyses the following reaction:GTP + 3 H(2)O <=> formate + 2, 5-diamino- 6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + diphosphate
YP_003917154.1	catalyzes the biosynthesis of riboflavin (vitamin B2) by dismutation of 6,7-dimethyl-8-(1-D-ribityl)lumazine (Lum): 2 6,7-dimethyl-8-(1-D-ribityl)lumazine => riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6- dihydroxypyrimidine
YP_003917155.1	EC 3.5.4.26 catalyses the following reaction: 2,5- diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H2O = 5-amino-6-(5-phosphoribosylamino)uracil + NH3. EC 1. 1.1.193 catalyses the following reaction: 5-amino-6-(5- phosphoribitylamino)uracil + NADP+ = 5-amino-6-(5- phosphoribosylamino)uracil + NADPH
YP_003917156.1	Nicotinamide Ribonucleoside (NR) Uptake Permease (PnuC) family (TC 4.B.1.y.z). PnuC of Salmonella typhimurium and Haemophilus influenzae are believed to function cooperatively with NadR homologues, multifunctional proteins that together with PnuC, participate in Nicotinamide Ribonucleoside phosphorylation, transport and transcriptional regulation
YP_003917157.1	involved in the pentose phosphate pathway. Catalyzes the interconversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate
YP_003917159.1	catalyses the following reaction : 10- formyltetrahydrofolate + L-methionyl-tRNA(fMet) + H(2)O => tetrahydrofolate + N-formylmethionyl-tRNA(fMet). Involved in initiation of protein biosynthesis
YP_003917160.1	involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
YP_003917163.1	identified by match to PF03969
YP_003917165.1	identified by match to PF02657. This family consists of the SufE-related proteins. These have been implicated in Fe-S metabolism and export
YP_003917166.1	match to PF04073: YbaK / prolyl-tRNA synthetases associated domain. This domain of unknown function is found in numerous prokaryote organisms. The structure of YbaK shows a novel fold. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes. Thus, the domain is thought to be involved in oligo-nucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA
YP_003917168.1	match to PS00120 pattern: lipases, serine active site
YP_003917169.1	plays a role in preventing oxidative-stress damage caused by reactive oxygen species by reducing the oxidized form of methionine back to methionine and thereby reactivating peptides that had been damaged
YP_003917171.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003917172.1	catalyses the production of glycine and acetaldehyde from threonine
YP_003917174.1	ribonuclease D cleaves multimeric tRNA precursor at the spacer region. Contribute to the 3 prime maturation of several stable RNA
YP_003917175.1	also named acetyl-CoA C-acyltransferase. Catalyzes the final step of fatty acid oxidation in which acetyl-CoA is released and the CoA ester of a fatty acid two carbons shorter is formed. Involved in the aerobic and anaerobic degradation of long-chain fatty acids. Part of the FadAB fatty acid oxidation complex
YP_003917176.1	identified by similarity to protein SP: P21177 (Escherichia coli). Catalyzes the formation of an hydroxyacyl-CoA by addition of water on enoyl-CoA. Also exhibits 3-hydroxyacyl-CoA epimerase and 3-hydroxyacyl-CoA dehydrogenase activities. Involved in the aerobic and anaerobic degradation of long-chain fatty acids. Part of the FadAB fatty acid oxidation complex
YP_003917178.1	Solute:Sodium Symporter (SSS) family (2.A.21.y.z). Members of the SSS family catalyze solute:Na+ symport. The solutes transported may be sugars, amino acids, organo cations such as choline, nucleosides, inositols, vitamins, urea or anions, depending on the system
YP_003917179.1	match to protein domain PF00355
YP_003917180.1	identified by match to PF00248 family: Aldo/keto reductase family. This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity
YP_003917181.1	catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate
YP_003917186.1	catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1- deoxy-D-xylulose-5-phosphate, a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxal (vitamin B6)
YP_003917187.1	match to PF01636. This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation. This family also includes homoserine kinase
YP_003917188.1	identified by match to protein domain PF08241
YP_003917189.1	catalyzes the reversible isomerization of citrate and isocitrate. Cis-aconitate is formed as an intermediary product during the course of the reaction
YP_003917191.1	11 transmembrane helices predicted by TMHMM2.0
YP_003917192.1	voltage-gated K+ Channel beta-subunit family, TrkA regulatory subunit of TrkH and TrkG (TC 8.A.5.2.1). Part of a potassium transport system (regulatory subunit). TrkA domains can bind NAD+ and NADH, possibly allowing K+ transporters to be responsive to the redox state of the cell. Systems regulated by TrkA include TrkG/H (TC 2.A.38. 1.1)
YP_003917193.1	voltage-gated K+ Channel beta-subunit family, TrkA regulatory subunit of TrkH and TrkG (TC 8.A.5.2.1). Part of a potassium transport system (regulatory subunit). TrkA domains can bind NAD+ and NADH, possibly allowing K+ transporters to be responsive to the redox state of the cell. Systems regulated by TrkA include TrkG/H (TC 2.A.38. 1.1)
YP_003917194.1	6 transmembranes helices predicted by TMHMM2.0
YP_003917197.1	removes dUTP from the nucleotide triphosphate pool and therefore prevents the incorporation of uracil into the DNA
YP_003917198.1	2 transmembranes helices predicted by TMHMM2.0
YP_003917201.1	match to protein family PF01663. This family consists of phosphodiesterases. They catalyse the cleavage of phosphodiester and phosphosulfate bonds in NAD, deoxynucleotides and nucleotide sugars
YP_003917203.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917204.1	DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings. Made up of two chains. The A chain is responsible for DNA breakage and rejoining; the B chain catalyzes ATP hydrolysis
YP_003917205.1	TCDB: ATP-binding cassette (ABC) superfamily, CydDC cysteine exporter (CydDC-E) family (TC 3.A.1.129.z). ABCISSE: ABC transporter, permease and ATP-binding protein (IM-ABC)2, DPL-family, CYD-subfamily (Cytochrome bd biogenesis and cysteine export)
YP_003917206.1	the cytochrome bd oxidase is a widely distributed prokaryotic quinol oxidase, which performs a variety of physiological functions in vivo. It is involved in energy- transducing respiration in Escherichia coli and Bacillus species. It plays also a role in aerotolerant nitrogen fixation and protection against metal toxicity and oxidative stress in Azotobacter vinelandii
YP_003917207.1	the cytochrome bd oxidase is a widely distributed prokaryotic quinol oxidase, which performs a variety of physiological functions in vivo. It is involved in energy- transducing respiration in Escherichia coli and Bacillus species. It plays also a role in aerotolerant nitrogen fixation and protection against metal toxicity and oxidative stress in Azotobacter vinelandii
YP_003917208.1	identified by match to protein family PF03965: penicillinase repressor
YP_003917209.1	match to protein family PF05569. production of beta- Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription
YP_003917210.1	DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings. Made up of two chains. The A chain is responsible for DNA breakage and rejoining; the B chain catalyzes ATP hydrolysis
YP_003917212.1	RpoD is a primary sigma factor and directs the transcription of a wide variety of genes. Match to protein family TIGR02393
YP_003917214.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003917216.1	selectively releases N-terminal amino acid residues from polypeptides and proteins. It is in general involved in the processing, catabolism and degradation of intracellular proteins
YP_003917217.1	E3 component of pyruvate dehydrogenase and 2- oxoglutarate dehydrogenase complexes
YP_003917218.1	it is a component of the multienzyme 2-oxoglutarate dehydrogenase complex, which is involved in the TCA cycle
YP_003917219.1	4 transmembranes helices predicted by TMHMM2.0
YP_003917221.1	first committed step in the biosynthesis of lipoyl cofactor. The lipoyl cofactor is essential for the function of several key enzymes involved in oxidative metabolism
YP_003917222.1	catalyzes the final step in the de-novo biosynthesis of the lipoyl cofactor, with the other enzyme involved being EC 2.3.1.181
YP_003917223.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917224.1	match to PF06271
YP_003917225.1	plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. The activity of class I glutamate--ammonia ligase is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive
YP_003917226.1	match to protein family PF00589
YP_003917227.1	match to PF01381. This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003917240.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.536 between position 40 and 41
YP_003917241.1	similar to protein Gp28 (SP:Q855T5; Mycobacterium phage Che9d)
YP_003917243.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.991) with cleavage site probability 0.664 between position 32 and 33
YP_003917244.1	similar to protein Gp28 (SP:Q855T5; Mycobacterium phage Che9d)
YP_003917248.1	regulates the activity of glutamate--ammonia ligase by attachment of the adenylyl moiety of ATP
YP_003917249.1	plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. The activity of class I glutamate--ammonia ligase is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive
YP_003917250.1	catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate: 5,10-methylenetetrahydrofolate + 3-methyl-2- oxobutanoate + H2O = tetrahydrofolate + 2-dehydropantoate
YP_003917252.1	responsible for the removal of the amino-terminal (initiator) methionine from nascent eukaryotic cytosolic and cytoplasmic prokaryotic proteins if the penultimate amino acid is small and uncharged
YP_003917254.1	catalyzes the terminal step in the biosynthesis of histidine, the four-electron oxidation of L-histidinol to histidine
YP_003917255.1	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication once it is clamped onto DNA. DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII complex. PolIII associates with the gamma complex (composed of gamma, delta, delta prime, psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex
YP_003917256.1	identified by match to protein family PF00849. Pseudouridylate synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5- ribosyluracil, psi)
YP_003917257.1	releases signal peptides from bacterial membrane prolipoproteins
YP_003917258.1	match to PF05103
YP_003917259.1	3 transmembrane helices predicted by TMHMM2.0
YP_003917262.1	FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. It is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. It forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells
YP_003917263.1	match to PF08478: POTRA domain, FtsQ-type. The POTRA domain (for polypeptide-transport-associated domain) is found in different types of proteins, usually associated with a transmembrane beta-barrel
YP_003917264.1	involved in peptidoglycan biosynthesis
YP_003917265.1	catalyzes the following reaction: UDP-N- acetylglucosamine + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D- Ala-D-Ala)- diphosphoundecaprenol <=> UDP + GlcNAc-(1->4)- Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D- Ala)- diphosphoundecaprenol. Involved in peptidoglycan biosynthesis
YP_003917266.1	plays a role in the stabilization of the FtsZ ring during cell division
YP_003917267.1	involved in peptidoglycan biosynthesis
YP_003917268.1	catalyzes the formation of undecaprenyl- pyrophosphoryl-N-acetylmuramoyl-pentapeptide from UDP- MurNAc-pentapeptide and undecaprenyl-phosphate. Involved in peptidoglycan biosynthesis
YP_003917269.1	involved in peptidoglycan biosynthesis: ATP + UDP-N- acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D- alanyl-D-alanine => ADP + phosphate + UDP-N-acetylmuramoyl- L-alanyl-gamma-D-glutamyl-L-lysyl-D- alanyl-D-alanine. Also catalyzes the reaction when the C-terminal residue of the tripeptide is meso-2, 4-diaminoheptanedioate (acylated at its L-center)
YP_003917270.1	catalyzes the addition of an amino acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D- glutamate (UMAG) in the biosynthesis of bacterial cell- wall peptidoglycan. Corresponds probably to EC 6.3.2.7 rather than 6.3.2.13, as the cell-wall peptidoglycan type of Arthrobacter arilaitensis is Lys-Glu (variation A4alpha)
YP_003917271.1	match to PF00905. The large number of penicillin binding proteins, which are represented in this group of sequences, are responsible for the final stages of peptidoglycan biosynthesis for cell wall formation. The proteins synthesise cross-linked peptidoglycan from lipid intermediates, and contain a penicillin-sensitive transpeptidase carboxy-terminal domain
YP_003917272.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917274.1	this protein often is found with other genes of the dcw (division cell wall) gene cluster, including mraW, ftsI, murE, murF, ftsW, murG, etc.
YP_003917275.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917276.1	DNA polymerase IV is involved in DNA repair
YP_003917277.1	identified by similarity to protein SP:Q9KK76 (Brevibacterium linens). A variety of isoprenoid compounds are synthesized by various organisms. In bacteria this pathway leads to the synthesis of isopentenyl tRNA, isoprenoid quinones, and sugar carrier lipids. Farnesyltranstransferase catalyzes the sequential addition of the three molecules of isopentenyl pyrophosphate onto dimethylallyl pyrophosphate to form geranylgeranyl pyrophosphate
YP_003917279.1	match to protein domain PF01476. This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation. It may have a general peptidoglycan binding function
YP_003917280.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003917281.1	catalyzes the NAD-dependent reversible oxidative deamination of glutamate to 2-oxoglutarate and ammonia
YP_003917283.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917285.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917287.1	the translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF)
YP_003917289.1	match to protein family PF02482
YP_003917290.1	match to protein domain PF00156. This family includes a range of diverse phosphoribosyl transferase enzymes
YP_003917291.1	possible role in the MtrAB signal transduction pathway
YP_003917292.1	member of the two-component regulatory system mtrA/mtrB. Seems to function as a membrane-associated protein kinase that phosphorylates MtrA in response to environmental signals
YP_003917293.1	member of the two-component regulatory system mtrA/mtrB
YP_003917295.1	catalyzes the Claisen rearrangement of chorismate to prephenate, which can subsequently be converted to precursors of either phenylalanine or tyrosine
YP_003917296.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, fused ATP-binding protein (ABC2), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003917297.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003917298.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003917299.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, binding protein (BP), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003917301.1	13 transmembrane helices predicted by TMHMM2.0. Match to protein domain PF07732: multicopper oxidase
YP_003917302.1	10 transmembrane helices predicted by TMHMM2.0
YP_003917305.1	catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34
YP_003917306.1	identified by match to protein family PIRSF005572: cysteine desulfurase, NifS type. Cysteine desulfurase catalyses the following reaction: L-cysteine + [enzyme]- cysteine <=> L-alanine + [enzyme]-S-sulfanylcysteine. It is involved in the biosynthesis of iron-sulfur clusters, thio-nucleosides in tRNA, thiamine, biotin, lipoate and pyranopterin (molybdopterin) and functions by mobilizing sulfur
YP_003917307.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.912) with cleavage site probability 0.909 between position 28 and 29
YP_003917308.1	catalyzes the condensation of 6-hydroxymethyl-7,8- dihydropteridine pyrophosphate to para-aminobenzoic acid to form 7,8-dihydropteroate. This is the second step in the three steps pathway leading from 6-hydroxymethyl-7,8- dihydropterin to 7,8-dihydrofolate. It is the target of sulfonamides which are substrates analog that compete with para-aminobenzoic acid
YP_003917309.1	match to protein domain PF01872. This domain is found in the C-terminus of the bifunctional deaminase- reductase in combination with PF00383 as well as in isolation in some archaebacterial proteins
YP_003917310.1	match to protein domain PF00781
YP_003917311.1	match to protein domain PF0026
YP_003917312.1	identified by match to protein family PF00588: SpoU rRNA Methylase family. Possible role in rRNA modification
YP_003917313.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917315.1	identified by match to PIRSF000089. Electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, (housekeeping) ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II). They consist of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit
YP_003917316.1	electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, (housekeeping) ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II). They consist of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit
YP_003917317.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917318.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.994 between position 28 and 29. Presence of transmembrane helices
YP_003917319.1	identified by match to protein family PF04012. This family includes PspA, which is a protein that suppresses sigma54-dependent transcription
YP_003917320.1	identified by match to PF03699: Uncharacterised protein family (UPF0182). This family contains uncharacterised integral membrane proteins
YP_003917321.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917324.1	match to protein family PS51198: UvrD-like DNA helicase ATP-binding domain profile and PS51217: DNA helicase, UvrD-like, C terminal. UvrD-like DNA helicases belong to superfamily 1 (SF1)
YP_003917325.1	NAD(+) diphosphatase catalyses the following reaction: NAD(+) + H(2)O <=> AMP + NMN
YP_003917326.1	identified by match to PF01636. This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides. It also includes homoserine kinase
YP_003917327.1	match to protein family PS51198: UvrD-like DNA helicase ATP-binding domain profile and PS51217: DNA helicase, UvrD-like, C terminal. UvrD-like DNA helicases belong to superfamily 1 (SF1)
YP_003917328.1	match to protein family PS51198: UvrD-like DNA helicase ATP-binding domain profile and PS51217: DNA helicase, UvrD-like, C terminal. UvrD-like DNA helicases belong to superfamily 1 (SF1)
YP_003917329.1	involved in the repair of alkylated DNA
YP_003917330.1	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The beta chain is required for initiation of replication once it is clamped onto DNA. DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the POLIII complex. PolIII associates with the gamma complex (composed of gamma, delta, delta, psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex
YP_003917331.1	TCDB: ATP-binding cassette (ABC) superfamily, methionine uptake transporter (MUT) family (TC3.A.1.24). ABCISSE: ABC transporter, ATP-binding protein (ABC), DLM- family. Part of the ABC transporter complex MetNIQ involved in methionine import. The complex is composed of two ATP-binding proteins (MetN), two transmembrane proteins (MetI) and a solute-binding protein (MetQ)
YP_003917332.1	TCDB: ATP-binding cassette (ABC) superfamily, methionine uptake transporter (MUT) family (TC3.A.1.24). ABCISSE: ABC transporter, permease (IM), DLM-family. Part of the ABC transporter complex MetNIQ involved in methionine import. The complex is composed of two ATP- binding proteins (MetN), two transmembrane proteins (MetI) and a solute-binding protein (MetQ)
YP_003917333.1	TCDB: ATP-binding cassette (ABC) superfamily, methionine uptake transporter (MUT) family (TC3.A.1.24). ABCISSE: ABC transporter, lipoprotein (LPP), DLM-family. Part of the ABC transporter complex metNIQ involved in methionine import. The complex is composed of two ATP- binding proteins (MetN), two transmembrane proteins (MetI) and a solute-binding protein (MetQ)
YP_003917334.1	involved in the second step of porphyrin biosynthesis, via the C5 pathway by transfering the amino group on carbon 2 of glutamate-1- semialdehyde to the neighbouring carbon, to give delta-aminolevulinic acid
YP_003917335.1	catalyzes the second step in the biosynthesis of heme, the condensation of two molecules of 5- aminolevulinate to form porphobilinogen: 2 5- aminolevulinate <=> porphobilinogen + 2 H(2)O
YP_003917336.1	uroporphyrinogen-III synthase catalyses the following reaction: hydroxymethylbilane <=> uroporphyrinogen III + H(2)O
YP_003917337.1	involved in the biosynthesis of porphyrins and related macrocycles, catalyzes the assembly of four porphobilinogen (PBG) units in a head to tail fashion to form hydroxymethylbilane: 4 porphobilinogen + H2O <=> hydroxymethylbilane + 4 NH3
YP_003917338.1	catalyzes the last step in heme biosynthesis: the chelation of a ferrous ion to proto-porphyrin IX, to form protoheme: Protoheme + 2 H+ <=> protoporphyrin + Fe2+
YP_003917340.1	catalyzes the 6-electron oxidation of protoporphyrinogen IX to form protoporphyrin IX: protoporphyrinogen-IX + 1.5 O(2) <=> protoporphyrin-IX + 3 H(2)O. Also oxidizes the pathway intermediate coproporphyrinogen III: coproporphyrinogen-III + O2 <=> coproporphyrin-III + H2O
YP_003917341.1	fifth enzyme of the heme biosynthetic pathway, catalyzes the sequential decarboxylation of the four acetyl side chains of uroporphyrinogen to yield coproporphyrinogen: Uroporphyrinogen III <=> coproporphyrinogen + 4 CO(2) and uroporphyrinogen I <=> coproporphyrinogen I + CO2
YP_003917342.1	catalyzes the NADPH-dependent reduction of glutamyl- tRNA(Glu) to glutamate 1-semialdehyde (GSA): L-glutamate 1- semialdehyde + NADP+ + tRNA(Glu) <=>L-glutamyl-tRNA(Glu) + NADPH
YP_003917343.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003917345.1	exoribonuclease II catalyses the exonucleolytic cleavage in the 3- to 5-direction to yield nucleoside 5- phosphates. It is involved in mRNA degradation and tRNA precursor end processing
YP_003917346.1	DEAD box helicase. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression
YP_003917347.1	match to PF01555. This domain is found in DNA methylases. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. This family contains both N-4 cytosine-specific DNA methylases (EC 2.1.1.113) and N-6 Adenine-specific DNA methylases (2.1.1.72)
YP_003917348.1	match to PF02811. The PHP (Polymerase and Histidinol Phosphatase) domain is a  phosphoesterase domain
YP_003917349.1	responsible for the release of any N-terminal amino acid adjacent to a proline residue
YP_003917350.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917351.1	match to PF00571 (CBS domain pair)
YP_003917352.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917354.1	the twin-arginine translocation system is a Sec- independent exporter for folded proteins, often with a redox cofactor already bound, across the bacterial inner membrane
YP_003917355.1	match to protein family TIGR02937. Sigma-70 family
YP_003917356.1	match to PF01596. This family includes catechol o- methyltransferase, caffeoyl-CoA O-methyltransferase and a family of bacterial O-methyltransferases that may be involved in antibiotic production
YP_003917358.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.848) with cleavage site probability 0.238 between position 22 and 23
YP_003917359.1	match to protein family PF03641: Possible lysine decarboxylase. The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes proteins annotated as lysine decarboxylases, although the evidence for this is not clear
YP_003917360.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family, glutamate porter (TC 3.A.1.3.9). ABCISSE: ABC transporter, ATP- binding protein (ABC), PAO-family (polar amino acid and opines). Part of the ABC transporter complex gluABCD involved in glutamate import
YP_003917361.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family, glutamate porter (TC 3.A.1.3.9). ABCISSE: ABC transporter, binding protein (BP), PAO-family (polar amino acid and opines). Part of the ABC transporter complex gluABCD involved in glutamate import
YP_003917362.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family, glutamate porter (TC 3.A.1.3.9). ABCISSE: ABC transporter, permease (IM), PAO-family (polar amino acid and opines). Part of the ABC transporter complex gluABCD involved in glutamate import
YP_003917363.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family, glutamate porter (TC 3.A.1.3.9). ABCISSE: ABC transporter, permease (IM), PAO-family (polar amino acid and opines). Part of the ABC transporter complex gluABCD involved in glutamate import
YP_003917364.1	catalyzes the fifth step in the biosynthesis of lysine from aspartate semialdehyde: the hydrolysis of succinyl-diaminopimelate to diaminopimelate and succinate
YP_003917365.1	involved in the biosynthesis of diaminopimelate and lysine from aspartate semialdehyde (EC 2.3.1.117)
YP_003917367.1	catalyzes the synthesis of citrate from oxaloacetate and acetyl-CoA. Involved in TCA cycle
YP_003917368.1	catalyzes the formation of N-succinyl-LL-2,6- diaminopimelate from N-succinyl-L-2-amino-6-oxopimelate in lysine biosynthesis
YP_003917369.1	match to protein domain PF00037: 4Fe-4S binding domain. Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases
YP_003917371.1	identified by match to PF01022. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003917372.1	4 transmembrane helices predicted by TMHMM2.0
YP_003917373.1	match to protein family TIGR01394. This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP- binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown
YP_003917374.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917375.1	catalyzes the adenylation by ATP of the carboxyl- terminal glycine of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1)
YP_003917376.1	involved in the formation of the thiazole moiety of thiamin pyrophosphate: catalyzes the formation of thiazole from 1-deoxy-D-xylulose 5-phosphate (DXP) and dehydroglycine, with the help of the sulfur carrier protein ThiS
YP_003917377.1	sulfur carrier protein involved in thiamin biosynthesis : carries the sulfur needed for thiazole assembly on its carboxy terminus (ThiS-COSH)
YP_003917378.1	required for the biosynthesis of the thiazole moiety of thiamine diphosphate
YP_003917379.1	N-terminal section of the protein:  RNaseH. C-terminal section of the protein:  GNAT-family acetyltransferase
YP_003917380.1	9 transmembrane helices predicted by TMHMM2.0
YP_003917381.1	identified by match to protein family PF02566: OsmC, OsmC-like protein. Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. This family also contains an organic hydroperoxide detoxification protein that has a novel pattern of oxidative stress regulation
YP_003917382.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917383.1	match to PF00561: alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes
YP_003917384.1	6 transmembrane helices predicted by TMHMM2.0. Match to PF07947. The members of this family are similar to the hypothetical protein yhhN expressed by E. coli. Many of the members of this family are annotated as being possible transmembrane proteins, and in fact they all have a high proportion of hydrophobic residues
YP_003917385.1	match to protein family PF00903: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
YP_003917388.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917390.1	8 transmembrane helices predicted by TMHMM2.0
YP_003917391.1	4 transmembrane helices predicted by TMHMM2.0
YP_003917396.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917397.1	match to protein family PF00903: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
YP_003917398.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917400.1	involved in phospholipid biosynthesis
YP_003917401.1	match to PF02834. Corresponds to a number of known and predicted phosphoesterases, including bacterial and archaeal 2 ,5 RNA ligases. The physiological substrate(s) in prokaryotes may include small 2 ,5 -link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles
YP_003917402.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917403.1	identified by match to protein domain PF08241
YP_003917404.1	acetyl-CoA C-acyltransferase (also named 3-ketoacyl- CoA thiolase or thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation
YP_003917405.1	long-chain-fatty-acid--CoA ligase activates long- chain fatty acids for both the synthesis of cellular lipids and their degradation via beta-oxidation
YP_003917406.1	possibly involved in the metabolism of lipids. Match to protein domains PF08028, PF02771 and PF02770. Acyl-CoA dehydrogenases catalyze the alpha,beta- dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD
YP_003917408.1	identified by match to PF00753: metallo-beta- lactamase superfamily. Apart from the beta-lactamases, a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl- glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake
YP_003917409.1	identified by match to protein family PF00849. Pseudouridylate synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5- ribosyluracil, psi)
YP_003917410.1	5 transmembrane helices predicted by TMHMM2.0
YP_003917413.1	identified by match to protein domain PF00300
YP_003917415.1	match to protein family PF00454. This domain is present in a wide range of protein kinases, involved in diverse cellular functions
YP_003917416.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917417.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003917418.1	match to PF00561: alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes
YP_003917421.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917422.1	match to protein domain PF02861: Clp amino terminal domain. This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates
YP_003917423.1	possible DNA-binding protein. Match to protein domain IPR009057: homeodomain-like
YP_003917425.1	catalyses the conversion of D-lactate to pyruvate. Probable quinone-dependent lactate dehydrogenase, functionning when lactate is used as a carbon and energy source
YP_003917426.1	match to PF01555. This domain is found in DNA methylases. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. Match to PS00092 pattern: N-6 Adenine- specific DNA methylases signature
YP_003917430.1	identified by match to protein family TIGR00092: GTP-binding protein YchF
YP_003917431.1	forms part of the non-mevalonate pathway for terpenoid biosynthesis
YP_003917432.1	exodeoxyribonuclease VII catalyses the exonucleolytic cleavage in either 5 - to 3 - or 3 - to 5 - direction to yield nucleoside 5-phosphates. In E. coli, ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis
YP_003917433.1	exodeoxyribonuclease VII catalyses the exonucleolytic cleavage in either 5 - to 3 - or 3 - to 5 - direction to yield nucleoside 5-phosphates. In E. coli, ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis
YP_003917434.1	identified by match to protein domain PF03976. This domain is about 230 amino acids in length and has polyphosphate kinase activity
YP_003917436.1	catalyses the following reaction: L-alanine + 2- oxoglutarate <=> pyruvate + L-glutamate
YP_003917437.1	match to PS51257: prokaryotic membrane lipoprotein lipid attachment site profile
YP_003917438.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003917439.1	identified by match to protein family PF01037
YP_003917441.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917442.1	catalyses the following reaction: ATP + 5- formyltetrahydrofolate => ADP + phosphate + 5,10- methenyltetrahydrofolate
YP_003917447.1	catalyzes the ATP-dependent formation of GMP from xanthosine 5-phosphate and glutamine
YP_003917448.1	3 transmembrane helices predicted by TMHMM2.0
YP_003917449.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.976) with cleavage site probability 0.602 between position 37 and 38
YP_003917450.1	catalyzes the NAD-dependent oxidation of IMP to XMP. Involved in the de novo synthesis of the guanine nucleotides
YP_003917452.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.7762 between position 29 and 30
YP_003917453.1	catalyzes the NAD-dependent oxidation of IMP to XMP. Involved in the de novo synthesis of the guanine nucleotides
YP_003917454.1	match to protein domain PF01757. This family includes a range of acyltransferase enzymes. 11 transmembrane helices predicted by TMHMM2.0
YP_003917456.1	chaperonins are involved in productive folding of proteins. With the aid of cochaperonin GroES, GroEL encapsulates non-native substrate proteins inside the cavity of the GroEL-ES complex and promotes folding by using energy derived from ATP hydrolysis
YP_003917457.1	cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts
YP_003917458.1	amino acid-polyamine-organocation (APC) superfamily, amino acid transporter (AAT) family, lysine:H+ symporter (TC 2.A.3.1.2). Identified by similarity to protein SP:P25737 (Escherichia coli)
YP_003917460.1	possible glutamate--cysteine ligase (6.3.2.2). Match to protein family PF04107: glutamate-cysteine ligase family 2(GCS2)
YP_003917464.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003917465.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003917475.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003917476.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits: subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003917477.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits: subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003917478.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917480.1	glycoside hydrolase family 32 comprises enzymes with several known activities: invertase (EC 3.2.1.26); inulinase (EC 3.2.1.7); levanase (EC 3.2.1.65); exo- inulinase (EC 3.2.1.80); sucrose:sucrose 1- fructosyltransferase (EC 2.4.1.99); fructan:fructan 1- fructosyltransferase (EC 2.4.1.100)
YP_003917481.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003917482.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003917483.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003917484.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003917485.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, binding protein (BP), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003917486.1	match to protein domain PF00356. Numerous bacterial transcription regulatory proteins bind DNA via a helix- turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR. Within this family, the HTH motif is situated towards the N-terminus
YP_003917487.1	match to protein domain PF00356. Numerous bacterial transcription regulatory proteins bind DNA via a helix- turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR. Within this family, the HTH motif is situated towards the N-terminus
YP_003917488.1	glycoside hydrolase family 32 comprises enzymes with several known activities: invertase (EC 3.2.1.26); inulinase (EC 3.2.1.7); levanase (EC 3.2.1.65); exo- inulinase (EC 3.2.1.80); sucrose:sucrose 1- fructosyltransferase (EC 2.4.1.99); fructan:fructan 1- fructosyltransferase (EC 2.4.1.100)
YP_003917489.1	fructokinase catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into glucose-6-phosphate
YP_003917490.1	major facilitator superfamily, Oligosaccharide:H+ Symporter (OHS) Family (TC 2.A.1.5.z). Members of this family transport saccharides such as lactose, sucrose, raffinose and meliobiose
YP_003917493.1	hydrolyses O-sialoglycoproteins. Does not cleave unglycosylated proteins, desialylated glycoproteins or glycoproteins that are only N-glycosylated
YP_003917494.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917495.1	match to protein domain PF00814: glycoprotease family
YP_003917496.1	match to protein domain PF02367: uncharacterised P- loop hydrolase UPF0079. These proteins are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting a role in cell wall biosynthesis
YP_003917497.1	catalyzes the pyridoxal-dependent conversion of L- alanine into D-alanine, a key building block of bacterial peptidoglycan
YP_003917498.1	Large Conductance Mechanosensitive Ion Channel (MscL) Family (TC 1.A.22.1.z). This type of protein forms a nonselective ion channel
YP_003917499.1	catalyzes the phosphorylation of pantothenic acid to form 4-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway
YP_003917500.1	catalyses the formation of D-glucosamine 6- phosphate from D-fructose 6-phosphate. It is involved in the pathway for bacterial cell-wall peptidoglycan and lipopolysaccharide biosyntheses, being a step in the pathway for UDP-N-acetylglucosamine biosynthesis
YP_003917501.1	catalyses the following reaction: CoA-(4- phosphopantetheine) + apo-ACP => adenosine 3,5-bisphosphate + holo-ACP. All polyketide synthases, fatty-acid synthases and non- ribosomal peptide synthases require post-translational modification of their constituent ACP (ACP) domains to become catalytically active. The inactive apo-proteins are converted into their active holo-forms by transfer of the 4-phosphopantetheinyl moiety of CoA to the sidechain hydroxy group of a conserved serine residue in each ACP domain
YP_003917502.1	match to protein domain PF01256: carbohydrate kinase
YP_003917503.1	catalyses the formation of UDP-glucuronate from UDP- glucose
YP_003917504.1	catalyses the formation of D-glucosamine 1- phosphate from D-glucosamine 6-phosphate. It is involved in the pathway for bacterial cell-wall peptidoglycan and lipopolysaccharide biosyntheses, being an essential step in the pathway for UDP-N-acetylglucosamine biosynthesis
YP_003917505.1	ribosomal protein S9 is one of the proteins from the small ribosomal subunit
YP_003917506.1	this protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly
YP_003917507.1	formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs
YP_003917508.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.999) with cleavage site probability 0.720 between position 29 and 30
YP_003917509.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.999) with cleavage site probability 0.431 between position 29 and 30
YP_003917511.1	part of the 50S ribosomal subunit. Contacts protein L32
YP_003917512.1	DNA-directed RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
YP_003917513.1	located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA
YP_003917514.1	part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome
YP_003917515.1	ribosomal protein L36 is the smallest protein from the large subunit of the prokaryotic ribosome
YP_003917517.1	responsible for the removal of the amino-terminal (initiator) methionine from nascent eukaryotic cytosolic and cytoplasmic prokaryotic proteins if the penultimate amino acid is small and uncharged
YP_003917518.1	catalyses the following reaction: ATP + AMP <=> 2 ADP
YP_003917519.1	identified by match to protein family PF00344. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF)
YP_003917520.1	binds to the 23S rRNA. Part of the 50S ribosomal subunit
YP_003917521.1	part of the 50S ribosomal subunit
YP_003917522.1	located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
YP_003917523.1	part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S and 23S rRNAs
YP_003917524.1	this protein binds to the 23S rRNA, and is important in its secondary structure. Part of the 50S ribosomal subunit
YP_003917525.1	one of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_003917526.1	part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA
YP_003917527.1	part of the 50S ribosomal subunit. One of two assembly inititator proteins, it binds directly to the 5 prime-end of the 23S rRNA, where it nucleates assembly of the 50S subunit
YP_003917528.1	part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19
YP_003917530.1	match to PF03372: Endonuclease/Exonuclease/phosphatase family. This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. Signal peptide predicted by SignalP 3.0 HMM (probability: 0.899) with cleavage site probability 0.551 between position 43 and 44
YP_003917531.1	identified by match to PF00903: glyoxalase/bleomycin resistance protein/dioxygenase superfamily
YP_003917532.1	identified by match to protein domain PF00165: bacterial regulatory helix-turn-helix proteins, AraC family
YP_003917533.1	one of the primary rRNA binding proteins, it binds specifically to the 5 prime-end of 16S ribosomal RNA
YP_003917534.1	ribosomal protein L29 is one of the proteins from the large ribosomal subunit
YP_003917535.1	part of the 50S ribosomal subunit. Cross-links to the A and P site tRNAs
YP_003917536.1	part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14
YP_003917537.1	this protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g., L4, L17, and L20
YP_003917538.1	forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_003917539.1	part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome
YP_003917540.1	part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome
YP_003917541.1	one of the primary rRNA binding proteins. It is important during the early stages of 50S assembly
YP_003917542.1	part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19
YP_003917543.1	involved in the binding of tRNA to the ribosomes
YP_003917544.1	37 transmembrane helices predicted by TMHMM2.0
YP_003917545.1	responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome
YP_003917546.1	responsible for the translocation of the peptidyl- tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind
YP_003917547.1	part of the 30S ribosomal subunit. Contacts proteins S9 and S11
YP_003917548.1	part of the 30S ribosomal subunit. Contacts proteins S8 and S17
YP_003917549.1	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
YP_003917550.1	DNA-directed RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
YP_003917551.1	match to PF04073: YbaK / prolyl-tRNA synthetases associated domain. This domain of unknown function is found in numerous prokaryote organisms. The structure of YbaK shows a novel fold. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes. Thus, the domain is thought to be involved in oligo-nucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA
YP_003917552.1	match to protein domain PF01757. This family includes a range of acyltransferase enzymes. 10 transmembrane helices predicted by TMHMM2.0
YP_003917553.1	seems to be the binding site for several of the factors involved in protein synthesis and appears to be essential for accurate translation
YP_003917555.1	part of the 50S ribosomal subunit. Binds directly to 23S rRNA. Is involved in E site tRNA release and is also a translational repressor protein: it controls the translation of the L11 operon by binding to its mRNA
YP_003917556.1	this protein binds directly to 23S ribosomal RNA
YP_003917557.1	influences transcription termination and antitermination. Acts as a component of the transcription complex, and interacts with the termination factor rho and RNA polymerase
YP_003917558.1	identified by match to protein family PF00584. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF)
YP_003917559.1	catalyses the following reaction: L-aspartate + 2- oxoglutarate <=> oxaloacetate + L-glutamate
YP_003917560.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003917561.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003917562.1	identified by match to protein domain PF04024. This domain is found in Phage shock protein C (PspC) that is thought to be a transcriptional regulator
YP_003917564.1	identified by match to protein domain PF04024. This domain is found in Phage shock protein C (PspC) that is thought to be a transcriptional regulator
YP_003917565.1	catalyzes the phosphorylation of fructose-6- phosphate to fructose-1,6-biphosphate
YP_003917567.1	match to PF08768: domain of unknown function (DUF1794)
YP_003917569.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.998) with cleavage site probability 0.386 between position 19 and 20. 8 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003917570.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003917571.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917572.1	catalyzes the following reaction: ATP + (phosphate)(n) <=> ADP + (phosphate)(n+1). involved in phosphate metabolism of bacteria
YP_003917573.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003917574.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917575.1	catalyzes the reductive methylation of dUMP to dTMP with concomitant conversion of 5,10- methylenetetrahydrofolate to dihydrofolate
YP_003917576.1	catalyzes the NADPH-linked reduction of 7,8- dihydrofolate to 5,6,7,8-tetrahydrofolate, but also the NADPH-linked reduction of folate to 7,8-dihydrofolate
YP_003917577.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917578.1	catalyzes the NADP-dependent reductive dephosphorylation of L-aspartyl phosphate to L-aspartate- semialdehyde. Second step in the common biosynthetic pathway leading from aspartate to diaminopimelate and lysine, to methionine, and to threonine
YP_003917579.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917580.1	catalyses the formation of UDP-N-acetylmuramate from UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine. Involved in the biosynthesis of peptidoglycan
YP_003917581.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690
YP_003917582.1	match to PF01575. Several bacterial proteins that are composed solely of this domain have (R)-specific enoyl- CoA hydratase activity
YP_003917583.1	match to PF01575. Several bacterial proteins that are composed solely of this domain have (R)-specific enoyl- CoA hydratase activity
YP_003917584.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917586.1	match to PF04607. This region of unknown function is found in RelA and SpoT of Escherichia coli, and their homologues in plants and in other eubacteria
YP_003917587.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.976) with cleavage site probability 0.739 between position 24 and 25
YP_003917588.1	required for the synthesis of the hydromethylpyrimidine (HMP) moiety of thiamine (4-amino-2- methyl-5-hydroxymethylpyrimidine)
YP_003917589.1	DEAD box helicase. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression
YP_003917590.1	3 transmembrane helices predicted by TMHMM2.0
YP_003917591.1	catalyzes the conversion of cysteine and succinyl- homoserine into cystathionine and succinate. Several other reactions may also be catalysed in some organisms
YP_003917592.1	catalyses the synthesis of L-cystathionine from L- serine and L-homocysteine
YP_003917594.1	serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of 2 cysteine thiol groups to a disulphide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulphide and a dithiol
YP_003917596.1	match to protein family PF04461: protein of unknown function (DUF520)
YP_003917597.1	4 transmembrane helices predicted by TMHMM2.0
YP_003917598.1	in Escherichia coli, HtpX is a  membrane- bound zinc metalloprotease that has been suggested to participate in the proteolytic quality control of membrane proteins in conjunction with FtsH, a membrane-bound and ATP-dependent protease. 6 transmembrane helices predicted by TMHMM2.0. Match to protein family PF01435
YP_003917599.1	drug/metabolite transporter (DMT) superfamily, chloramphenicol-sensitivity protein (RarD) family (TC 2.A. 7.7.z). No member of the RarD family is functionally characterized. Identified by match to TIGR00688
YP_003917600.1	catalyzes the transfer of an amino group from GABA to alpha-ketoglutarate, yielding succinate semialdehyde and glutamic acid
YP_003917602.1	Neurotransmitter:Sodium Symporter (NSS) Family (Tc 2.A.22.y.z). Members of the NSS family catalyze uptake of a variety of neurotransmitters, amino acids, osmolytes and related nitrogenous substances by a solute:Na+ symport mechanism. Sometimes Cl- is cotransported, and some exhibit a K+ dependency. Might be involved in the transport of gamma-aminobutyric acid
YP_003917603.1	match to PF07905: purine catabolism regulatory protein-like family. The bacterial proteins found in this family are similar to the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, O32138). PucR is thought to be a transcriptional activator involved in the induction of the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression. The other members of this family are also annotated as being  regulatory proteins
YP_003917605.1	match to protein family IPR001310: histidine triad (HIT) protein. The histidine triad motif (HIT) is related to the sequence H-phi-H-phi-H-phi-phi (where phi is a hydrophobic amino acid). Proteins containing HIT domains form a superfamily of nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides
YP_003917606.1	produces prenyl diphosphates which act as the priming substrates for other groups of prenyl transferases. Is implicated in the biosynthesis of ubiquinone
YP_003917607.1	catalyses the conversion of chorismate to isochorismate, the first step in the biosynthesis of both the respiratory chain component menaquinone (MK, vitamin K2) and phylloquinone (vitamin K1): Chorismate <=> isochorismate
YP_003917608.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family (TC 3.A.1.3.z). ABCISSE: ABC transporter, binding protein (BP), PAO-family (polar amino acid and opines). The PAO family includes transport systems for amino acids that have polar or charged side chains: lysine, histidine, ornithine, arginine, glutamine, glutamate, cystine and diaminopimelic acid
YP_003917609.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family (TC 3.A.1.3.z). ABCISSE: ABC transporter, permease (IM), PAO- family (polar amino acid and opines). The PAO family includes transport systems for amino acids that have polar or charged side chains: lysine, histidine, ornithine, arginine, glutamine, glutamate, cystine and diaminopimelic acid
YP_003917610.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family (TC 3.A.1.3.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), PAO-family (polar amino acid and opines). The PAO family includes transport systems for amino acids that have polar or charged side chains: lysine, histidine, ornithine, arginine, glutamine, glutamate, cystine and diaminopimelic acid
YP_003917611.1	EC 2.2.1.9 plays a key role in the menaquinone biosynthetic pathway, converting isochorismate and 2- oxoglutarate to SHCHC (2-succinyl-6-hydroxyl-2,4- cyclohexadiene-1-carboxylic acid), pyruvate and carbon dioxide
YP_003917612.1	match to PS00583 pattern: PTS HPR domain serine phosphorylation site
YP_003917613.1	catalyzes the conversion of 2-succinyl-6-hydroxy- 2, 4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2- carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway
YP_003917615.1	6 transmembrane helices predicted by TMHMM2.0
YP_003917616.1	possible component of pyruvate dehydrogenase (EC 2. 3.1.12), branched-chain alpha-ketoacid dehydrogenase (EC 2. 3.1.168) or 2-oxoglutarate dehydrogenase (EC 2.3.1.61) complexes
YP_003917617.1	possible component of pyruvate dehydrogenase (EC 2. 3.1.12), branched-chain alpha-ketoacid dehydrogenase (EC 2. 3.1.168) or 2-oxoglutarate dehydrogenase (EC 2.3.1.61) complexes
YP_003917618.1	possible component of pyruvate dehydrogenase (EC 2. 3.1.12), branched-chain alpha-ketoacid dehydrogenase (EC 2. 3.1.168) or 2-oxoglutarate dehydrogenase (EC 2.3.1.61) complexes
YP_003917619.1	identified by match to protein family PF01037
YP_003917620.1	involved in aromatic ring opening step of the phenylacetic acid catabolic pathway
YP_003917621.1	phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA as the second catabolic step in phenylacetic acid degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA
YP_003917622.1	phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA as the second catabolic step in phenylacetic acid degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA
YP_003917623.1	phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA as the second catabolic step in phenylacetic acid degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA
YP_003917624.1	phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA as the second catabolic step in phenylacetic acid degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA
YP_003917625.1	phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA as the second catabolic step in phenylacetic acid degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA
YP_003917626.1	4 transmembrane helices predicted by TMHMM2.0
YP_003917627.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family (TC 3.A.1.3.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), PAO-family (polar amino acid and opines). The PAO family includes transport systems for amino acids that have polar or charged side chains: lysine, histidine, ornithine, arginine, glutamine, glutamate, cystine and diaminopimelic acid
YP_003917628.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family (TC 3.A.1.3.z). ABCISSE: ABC transporter, permease and binding protein (BP-IM), PAO-family (polar amino acid and opines). The PAO family includes transport systems for amino acids that have polar or charged side chains: lysine, histidine, ornithine, arginine, glutamine, glutamate, cystine and diaminopimelic acid
YP_003917629.1	oligopeptidase B cleaves peptide bonds on the C- terminal side of lysyl and argininyl residues. Prolyl oligopeptidase family protein (match to PF00326 and PF02897)
YP_003917630.1	match to PF00583: acetyltransferase (GNAT) family. Match to PF042229: Uncharacterised protein family (UPF0157)
YP_003917631.1	PaaD protein is nearly always found adjacent to other genes of the phenylacetic acid degradation pathway. Its function is currently unknown, but a role as thioesterases is suggested
YP_003917632.1	catalyses the formation of phenylacetyl-CoA from phenylacetate. Involved in the catabolism of phenylacetic acid
YP_003917633.1	identified by match to PF00440: bacterial regulatory proteins, tetR family
YP_003917634.1	7 transmembrane helices predicted by TMHMM2.0
YP_003917635.1	enzymes of this family comprise mostly alpha- amylases (EC 3.2.1.1); pullulanases (EC 3.2.1.41); cyclomaltodextrin glucanotransferase (EC 2.4.1.19); cyclomaltodextrinase (EC 3.2.1.54); trehalose-6-phosphate hydrolase (EC 3.2.1.93); malto-oligosyltrehalose trehalohydrolase (EC 3.2.1.141)
YP_003917636.1	involved in aromatic ring opening step of the phenylacetic acid catabolic pathway
YP_003917637.1	match to PS00383 pattern (tyrosine specific protein phosphatases active site) and PS50056 (tyrosine specific protein phosphatases family profile)
YP_003917638.1	identified by match to protein family PF01163. Protein kinases are a group of enzymes that possess a catalytic subunit which transfers the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. They play a role in a mulititude of cellular processes, including division, proliferation, apoptosis, and differentiation
YP_003917639.1	3-hydroxyacyl-CoA dehydrogenase is an enzyme involved in fatty acid metabolism. It catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA
YP_003917640.1	enoyl-CoA hydratase is involved in fatty acid metabolism. It catalyzes the hydratation of 2-trans-enoyl- CoA into 3-hydroxyacyl-CoA
YP_003917641.1	acetyl-CoA C-acyltransferase (also named 3-ketoacyl- CoA thiolase or thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation
YP_003917642.1	identified by similarity to protein SP:P0C0L7 (Escherichia coli). Proton symporter that senses osmotic shifts and responds by importing osmolytes such as proline, glycine betaine, stachydrine, pipecolic acid, ectoine and taurine. It is both an osmosensor and an osmoregulator which is available to participate early in the bacterial osmoregulatory response. Metabolite:H+ symporter (MHS) family, (Poline/glycine-betaine):(H+/Na+) symporter (also transports taurine, ectoine, pipecolate, proline-betaine, N,N-dimethylglycine, carnitine, and 1- carboxymethyl-pyridinium) (subject to osmotic activation) (TC 2.A.1.6.4)
YP_003917643.1	amino acid-polyamine-organocation (APC) superfamily, amino acid transporter (AAT) family, asparagine permease (AnsP) (TC 2.A.3.1.8)
YP_003917644.1	converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4- dihydroxy-2-naphthoic acid (DHNA): o-succinylbenzoyl-CoA <=> CoA + 1,4-dihydroxy-2-naphthoate
YP_003917645.1	converts 2-succinylbenzoate (OSB) to 2- succinylbenzoyl-CoA (OSB-CoA) : ATP + 2-succinylbenzoate + CoA = AMP + diphosphate + 2-succinylbenzoyl-CoA
YP_003917646.1	converts 1,4-dihydroxy-2-naphthoate (DHNA) to dimethylmenaquinone (DMK)
YP_003917647.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917648.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.947) with cleavage site probability 0.685 between position 26 and 27
YP_003917649.1	identified by match to protein family PF01578
YP_003917650.1	identified by match to protein family PF05140
YP_003917651.1	identified by match to PF02683: Cytochrome C biogenesis protein transmembrane region
YP_003917652.1	identified by match to protein family PF08534. This family of redoxins includes peroxiredoxin, thioredoxin and glutaredoxin proteins
YP_003917653.1	identified by match to protein domain PF00300
YP_003917654.1	4 transmembrane helices predicted by TMHMM2.0
YP_003917655.1	modulates transcription in response to the NADH/NAD(+) redox state
YP_003917656.1	identified by match to PF05768: glutaredoxin-like domain (DUF836). This family contains several viral glutaredoxins, and many related bacterial and eukaryotic proteins of unknown function. Glutaredoxins are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase
YP_003917657.1	identified by match to PF00702. This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases
YP_003917659.1	catalyses the conversion of 2-oxoglutarate to glutamate
YP_003917660.1	identified by match to PF01022: bacterial regulatory protein, ArsR family. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003917661.1	AcuC may be involved in growth of some bacteria on butanediol and acetoin
YP_003917662.1	K+ transporter (Trk) family (TC 2.A.38.y.z). Membrane component of a Trk-type K+ transport system. Match to protein family PF02386
YP_003917663.1	voltage-gated K+ Channel beta-subunit family, TrkA regulatory subunit of TrkH and TrkG (TC 8.A.5.2.1). Part of a potassium transport system (regulatory subunit). TrkA domains can bind NAD+ and NADH, possibly allowing K+ transporters to be responsive to the redox state of the cell. Systems regulated by TrkA include TrkG/H (TC 2.A.38. 1.1)
YP_003917664.1	catalyses the terminal step in the biosynthesis of proline from glutamate, the NAD(P) dependent oxidation of 1-pyrroline-5-carboxylate into proline
YP_003917665.1	match to protein domain PF01261: xylose isomerase- like TIM barrel . This TIM alpha/beta barrel structure is found in xylose isomerase and in endonuclease IV (EC.1.21. 2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins
YP_003917666.1	identified by match to protein family PF02541. Similar to exopolyphosphatase (Ppx, EC 3.6.1.11) and guanosine pentaphosphate phospho-hydrolase (GppA, EC 3.6.1. 40) proteins
YP_003917667.1	catalytic activity: ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
YP_003917668.1	identified by match to PF01022. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003917669.1	match to protein domain PF05175. This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases
YP_003917670.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917671.1	predicted sulfurtransferase
YP_003917672.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917673.1	possible DNA or RNA helicase
YP_003917674.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.710 between position 48 and 49
YP_003917675.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917678.1	3 transmembrane helices predicted by TMHMM2.0
YP_003917679.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.984 between position 32 and 33
YP_003917682.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.691) with cleavage site probability 0.462 between position 29 and 30. 1 transmembrane helice predicted by TMHMM2.0 after the signal peptide
YP_003917683.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.998) with cleavage site probability 0.533 between position 21 and 22. 2 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003917684.1	identified by match to protein domain PF00437
YP_003917687.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003917688.1	also named endonuclease III. It is a DNA repair enzyme that acts both as a DNA N-glycosylase, removing oxidized pyrimidines from DNA, and as an apurinic/apyrimidinic endonuclease, introducing a single- strand nick at the site from which the damaged base was removed
YP_003917689.1	catalyzes the formation of acetyl-CoA from acetate and CoA
YP_003917690.1	third enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids (phenylalanine, tyrosine and tryptophan), p-aminobenzoic acid, folate and ubiquinone
YP_003917691.1	match to PF00089. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S)) and to peptidase family S6 (Hap serine peptidases). 4 transmembrane helices predicted by TMHMM2.0
YP_003917692.1	cd00038: effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription
YP_003917693.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003917694.1	identified by match to protein domain PF01042: endoribonuclease L-PSP; endoribonuclease active on single- stranded mRNA. Inhibits protein synthesis by cleavage of mRNA. Previously thought to inhibit protein synthesis initiation. This protein may also be involved in the regulation of purine biosynthesis
YP_003917696.1	match to PF00912 and PF00905. Transglycosylase and transpeptidase in the N- and C-terminus respectively. The transglycosylase domain catalyses the polymerisation of murein glycan chains. Possibly involved in peptidoglycan biosynthesis
YP_003917697.1	match to protein domain PF00149. The metallophosphoesterase motif is found in a large number of proteins invoved in phosphoryation. These include Ser/Thr phosphatases, DNA polymerase, exonucleases, and other phosphatases
YP_003917698.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease and ATP-binding protein (IM-ABC), DPL-family, LLP- subfamily (LIP-like exporters). The function of LIP-like exporters is presently unknown
YP_003917699.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease and ATP-binding protein (IM-ABC), DPL-family, LLP- subfamily (LIP-like exporters). The function of LIP-like exporters is presently unknown
YP_003917700.1	catalyzes the seventh step of the de novo biosynthesis of purine nucleotides, the conversion of carboximideaminoimidazole ribonucleotide (CAIR) into succinoaminoimidazolecarboximide ribonucleotide (SAICAR)
YP_003917701.1	catalyzes the second step in the de novo biosynthesis of purine, the ATP-dependent addition of 5- phosphoribosylamine to glycine to form 5- phosphoribosylglycinamide
YP_003917703.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917704.1	catalyzes the first step in purine biosynthesis, the transfer of the ammonia group of glutamine to PRPP to form 5-phosphoribosylamine
YP_003917705.1	catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis
YP_003917706.1	identified by match to PF02146: Sir2 family. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. Function: modulate the activities of several enzymes which are inactive in their acetylated form. Catalytic activity: NAD+ + an acetylprotein = nicotinamide + O-acetyl-ADP-ribose + a protein
YP_003917708.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917709.1	part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with dnaK, dnaJ and grpE. Acts before dnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of clpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by dnaK
YP_003917711.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917712.1	identified by match to protein family PF03741. This family contains a number of integral membrane proteins that also contains the TerC protein. TerC has been implicated in resistance to tellurium. This protein may be involved in efflux of tellurium ions
YP_003917714.1	4 transmembrane helices predicted by TMHMM2.0
YP_003917715.1	catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA
YP_003917716.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003917717.1	heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
YP_003917718.1	match to protein domain PF00226. DnaJ domains (J- domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system
YP_003917719.1	identified by match to protein family PF01025. Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK (Hsp70) is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes the grpE protein is the co- chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate- bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle
YP_003917720.1	identified by match to protein family TIGR02350. Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK (Hsp70) is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes, the grpE protein is a co- chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate- bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle
YP_003917721.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917722.1	DEAD box helicase. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression
YP_003917723.1	Resistance-Nodulation-Cell Division (RND) superfamily (TC 2.A.6.y.z)
YP_003917724.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003917725.1	resistance to homoSer/Thr (RhtB) family protein (TC 2.A.76.y.z). The family includes homoserine, threonine and leucine efflux proteins. The transport reaction presumably catalyzed by members of the RhtB family is: amino acid (in) + nH+ (out) <--> amino acid (out) + nH+ (in)
YP_003917726.1	identified by match to protein family PF01451. Protein tyrosine (pTyr) phosphorylation is a common post- translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; EC:3.1.3.48) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation. Low molecular weight (LMW) protein-tyrosine phosphatases (or acid phosphatase) act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates
YP_003917727.1	aminodeoxychorismate synthase catalyzes the biosynthesis of 4-amino-4-deoxychorismate from chorismate and glutamine. It is involved in folate biosynthesis
YP_003917728.1	cardiolipin synthase catalyzes the transfer of a phosphatidyl group to phosphodidylglycerol to form cardiolipin (diphosphatidylglycerol)
YP_003917729.1	aminodeoxychorismate lyase converts 4- aminodeoxychorismate to pyruvate and p-aminobenzoate, a precursor of folic acid in bacteria
YP_003917730.1	TC 3.A.1.y.z. ABCISSE for N-terminal section of the protein: ABC transporter, fused ATP-binding protein (ABC2), CBY-family (Cobalt uptake, unknown), Y179- subfamily (CBU-like systems); C-terminal section of the protein: permease (IM), CBY-family, Y179-subfamily. The function of CBU-like systems is unknown
YP_003917731.1	6 transmembrane helices predicted by TMHMM2.0
YP_003917732.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917733.1	identified by match to protein family PF03334. Na(+)/H(+) antiporters has several roles in bacterial cells: (i) establishment of an electrochemical potential of Na(+) across the cytoplasmic membrane, which is the driving force for Na(+)-coupled processes such as Na(+)/solute symport and Na(+)-driven flagellar rotation; (ii) extrusion of Na(+) and Li(+), which are toxic if accumulated at high concentrations in cells; (iii) intracellular pH regulation under alkaline conditions; and (iv) cell volume regulation
YP_003917734.1	Na(+)/H(+) antiporters has several roles in bacterial cells: (i) establishment of an electrochemical potential of Na(+) across the cytoplasmic membrane, which is the driving force for Na(+)-coupled processes such as Na(+)/solute symport and Na(+)-driven flagellar rotation; (ii) extrusion of Na(+) and Li(+), which are toxic if accumulated at high concentrations in cells; (iii) intracellular pH regulation under alkaline conditions; and (iv) cell volume regulation
YP_003917735.1	identified by match to protein family PF01899. Na(+)/H(+) antiporters has several roles in bacterial cells: (i) establishment of an electrochemical potential of Na(+) across the cytoplasmic membrane, which is the driving force for Na(+)-coupled processes such as Na(+)/solute symport and Na(+)-driven flagellar rotation; (ii) extrusion of Na(+) and Li(+), which are toxic if accumulated at high concentrations in cells; (iii) intracellular pH regulation under alkaline conditions; and (iv) cell volume regulation
YP_003917736.1	Na(+)/H(+) antiporters has several roles in bacterial cells: (i) establishment of an electrochemical potential of Na(+) across the cytoplasmic membrane, which is the driving force for Na(+)-coupled processes such as Na(+)/solute symport and Na(+)-driven flagellar rotation; (ii) extrusion of Na(+) and Li(+), which are toxic if accumulated at high concentrations in cells; (iii) intracellular pH regulation under alkaline conditions; and (iv) cell volume regulation
YP_003917737.1	Na(+)/H(+) antiporters has several roles in bacterial cells: (i) establishment of an electrochemical potential of Na(+) across the cytoplasmic membrane, which is the driving force for Na(+)-coupled processes such as Na(+)/solute symport and Na(+)-driven flagellar rotation; (ii) extrusion of Na(+) and Li(+), which are toxic if accumulated at high concentrations in cells; (iii) intracellular pH regulation under alkaline conditions; and (iv) cell volume regulation
YP_003917738.1	Na(+)/H(+) antiporters has several roles in bacterial cells: (i) establishment of an electrochemical potential of Na(+) across the cytoplasmic membrane, which is the driving force for Na(+)-coupled processes such as Na(+)/solute symport and Na(+)-driven flagellar rotation; (ii) extrusion of Na(+) and Li(+), which are toxic if accumulated at high concentrations in cells; (iii) intracellular pH regulation under alkaline conditions; and (iv) cell volume regulation
YP_003917739.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003917740.1	catalyses the formation of dUMP from dCTP
YP_003917741.1	identified by match to protein family PF02557
YP_003917742.1	3 transmembrane helices predicted by TMHMM2.0
YP_003917743.1	catalyzes the reversible hydration of fumarate to L- malate. Involved in the TCA cycle
YP_003917745.1	Auxin Efflux Carrier (AEC) Family (TC 2.A.69.y.z). Homologues of the AEC family are found in bacteria as well as in archaea. The K. pneumoniae homologues has been implicated in malonate uptake, the O. oeni homologue is a malate permease
YP_003917746.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family, glutamate porter (TC 3.A.1.3.14). ABCISSE: ABC transporter, binding protein (BP), PAO-family (polar amino acid and opines), L- cystine impot. Part of the ABC transporter complex TcyABC involved in L-cystine import. Identified by similarity to protein SP:P94402 (Bacillus subtilis)
YP_003917747.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family, glutamate porter (TC 3.A.1.3.14). ABCISSE: ABC transporter, permease (IM), PAO-family (polar amino acid and opines), L-cystine impot. Part of the ABC transporter complex TcyABC involved in L-cystine import. Identified by similarity to protein SP:P42200 (Bacillus subtilis)
YP_003917748.1	TCDB: ATP-binding cassette (ABC) superfamily, polar amino acid uptake transporter (PAAT) family, glutamate porter (TC 3.A.1.3.14). ABCISSE: ABC transporter, ATP- binding protein (ABC), PAO-family (polar amino acid and opines), L-cystine impot. Part of the ABC transporter complex TcyABC involved in L-cystine import. Identified by similarity to protein SP:P39456 (Bacillus subtilis)
YP_003917750.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917752.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003917753.1	match to PF01436: NHL repeat
YP_003917754.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.999) with cleavage site probability 0.474 between position 26 and 27
YP_003917755.1	identified by match to protein family PF05425. Copper sequestering activity displayed by some bacteria is determined by copper-binding protein products of the copper resistance operon (cop). CopD, together with CopC, perform copper uptake into the cytoplasm
YP_003917756.1	identified by match to protein family PF04261. This family of dye-decolourising peroxidases lack a typical heme-binding region
YP_003917757.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.391 between position 26 and 27
YP_003917758.1	identified by match to protein family PF04234. CopC is a bacterial blue copper protein that binds 1 atom of copper per protein molecule. Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm
YP_003917759.1	3 transmembrane helices predicted by TMHMM2.0
YP_003917760.1	histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions. Identified by match to protein family PF00216
YP_003917761.1	histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions. Identified by match to protein family PF00216
YP_003917762.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003917764.1	part of the 30S ribosomal subunit. Contacts proteins S3 and S10
YP_003917765.1	part of the 50S ribosomal subunit. Cross-links to the P and E site tRNAs
YP_003917767.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003917768.1	TCDB: ATP-binding cassette (ABC) superfamily, Polyamine/Opine/Phosphonate Uptake Transporter (POPT) Family (TC 3.A.1.11.z). ABCISSE: ABC transporter, permease (IM), MOI-family, polyamine import. Part of an ABC transporter complex involved in import of polyamine (such as spermidine or putrescine)
YP_003917769.1	TCDB: ATP-binding cassette (ABC) superfamily, Polyamine/Opine/Phosphonate Uptake Transporter (POPT) Family (TC 3.A.1.11.z). ABCISSE: ABC transporter, permease (IM), MOI-family, polyamine import. Part of an ABC transporter complex involved in import of polyamine (such as spermidine or putrescine)
YP_003917770.1	TCDB: ATP-binding cassette (ABC) superfamily, Polyamine/Opine/Phosphonate Uptake Transporter (POPT) Family (TC 3.A.1.11.z). ABCISSE: ABC transporter, ATP- binding protein (ABC), MOI-family, polyamine import. Part of an ABC transporter complex involved in import of polyamine (such as spermidine or putrescine)
YP_003917771.1	TCDB: ATP-binding cassette (ABC) superfamily, Polyamine/Opine/Phosphonate Uptake Transporter (POPT) Family (TC 3.A.1.11.z). ABCISSE: ABC transporter, binding protein (BP), MOI-family, polyamine import. Part of an ABC transporter complex involved in import of polyamine (such as spermidine or putrescine)
YP_003917772.1	TCDB: ATP-binding cassette (ABC) superfamily, Polyamine/Opine/Phosphonate Uptake Transporter (POPT) Family (TC 3.A.1.11.z). ABCISSE: ABC transporter, binding protein (BP), MOI-family, polyamine import. Part of an ABC transporter complex involved in import of polyamine (such as spermidine or putrescine)
YP_003917773.1	identified by match to protein family PF01037: AsnC_trans_reg, AsnC family
YP_003917774.1	identified by match to protein family PF00202: aminotransferase class-III
YP_003917775.1	match to PS00142 pattern: neutral zinc metallopeptidases, zinc-binding region signature
YP_003917776.1	identified by match to cd00085: HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins
YP_003917777.1	match to protein family PF07905: purine catabolism regulatory protein-like family. The bacterial proteins found in this family are similar to the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, O32138). PucR is thought to be a transcriptional activator involved in the induction of the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression. The other members of this family are also annotated as being  regulatory proteins
YP_003917778.1	methylmalonate-semialdehyde dehydrogenase catalyses the following reaction: 2-methyl-3-oxopropanoate + CoA + H(2)O + NAD(+) <=> propanoyl-CoA + HCO(3)(-) + NADH. Involved in the catabolism of valine
YP_003917779.1	identified by match to protein family PF00202: aminotransferase class-III
YP_003917780.1	identified by match to PF02913 and PF01565
YP_003917781.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917784.1	shikimate dehydrogenase is the fourth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids (phenylalanine, tyrosine and tryptophan), p- aminobenzoic acid, folate and ubiquinone
YP_003917785.1	similar to Mycobacterium smegmatis rifampin ADP- ribosyl transferase (AF001493). Inactivates rifampin by ribosylation
YP_003917787.1	amino acid-polyamine-organocation (APC) Superfamily (TC 2.A.3.y.z)
YP_003917788.1	identified by match to protein domain PF00165: bacterial regulatory helix-turn-helix proteins, AraC family
YP_003917789.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003917790.1	catalyses the oxidative deamination of primary amines (such as biogenic amines) to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. Identified by similarity to protein SP:P46881 (Arthrobacter globiformis)
YP_003917791.1	4 transmembrane helices predicted by TMHMM2.0
YP_003917794.1	identified by match to protein family PF00171
YP_003917795.1	match to protein family PF04464. Possibly involved in teichoic acid biosynthesis
YP_003917796.1	TCDB: ATP-binding cassette (ABC) superfamily, Manganese/Zinc/Iron Chelate Uptake Transporter (MZT) Family (TC 3.A.1.15.z). ABCISSE: ABC transporter, binding protein (BP), MET-family. This family is comprised of systems involved in the uptake of various metallic cations such as iron, manganese and zinc
YP_003917797.1	identified by match to protein family PF07907. The sequences featured in this family are similar to two proteins expressed by Lactococcus lactis, YibE and YibF. Most of the members of this family are annotated as being membrane proteins, and in fact the sequences contain a high proportion of hydrophobic residues
YP_003917798.1	8 transmembrane helices predicted by TMHMM2.0
YP_003917800.1	match to protein family PF00724: NADH:flavin oxidoreductase / NADH oxidase family
YP_003917801.1	TCDB: Mg2+ Transporter-E (MgtE) Family (TC 9.A.19.y. z). Proteins from this family are capable of transporting Mg2+ and Co2+ but not Ni2+
YP_003917802.1	catalyzes the dehydratation of L-serine into ammonia and pyruvate
YP_003917803.1	catalyzes the transfer of the hydroxymethyl group of serine to tetrahydrofolate to form 5,10- methylenetetrahydrofolate and glycine. Also catalyzes the reaction of glycine with acetaldehyde to form L-threonine
YP_003917805.1	a component, with EC 1.4.4.2, EC 1.8.1.4 and the lipoyl-bearing H protein, of the glycine cleavage system, which catalyzes the oxidative cleavage of glycine to form NH3, C02, and 5,10-methylenetetrahydrofolate
YP_003917806.1	a component, with EC 2.1.2.10 and EC 1.8.1.4, of the glycine cleavage system
YP_003917807.1	identified by match to protein family PF00657
YP_003917808.1	identified by similarity to protein SP:Q44050 (Arthrobacter globiformis)
YP_003917809.1	amino acid-polyamine-organocation (APC) Superfamily (TC 2.A.3.y.z)
YP_003917810.1	ribonuclease H recognizes and cleaves the RNA strand of RNA-DNA heteroduplexes
YP_003917811.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.703) with cleavage site probability 0.284 between position 33 and 34
YP_003917812.1	glutathione transferase is involved in cellular detoxification by catalyzing the conjugation of glutathione with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress
YP_003917814.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003917815.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease and ATP-binding protein (IM-ABC), DPL-family, prokaryote drug export (PED) subfamily. Possible function in in antibiotic peptide or drug resistance or production (export)
YP_003917816.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003917817.1	N-terminal part of the protein: iron-siderophore ABC transporter, ATP-binding subunit. TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), ISVH-family (iron siderophores, vitamin B12 and hemin). C-terminal part of the protein:  siderophore-interacting protein. Possibly involved in removal of iron from iron-siderophore complexes
YP_003917818.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003917819.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003917820.1	identified by match to PF00753: metallo-beta- lactamase superfamily. Apart from the beta-lactamases, a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl- glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake
YP_003917821.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, binding protein (BP), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003917822.1	match to PF02687: this is a family of predicted permeases and hypothetical transmembrane proteins
YP_003917823.1	TCDB: ATP-binding cassette (ABC) superfamily (TC 3. A.1.y.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), o228 family (members of this family might be involved in a more general lipoprotein releasing mechanism common to all prokaryotes)
YP_003917826.1	identified by match to PF00924: mechanosensitive ion channel. Mechanosensitive channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. Two members of this protein family: Q57634 and Q58543 of M. jannaschii have been functionally characterised. Both proteins form mechanosensitive ion channels upon reconstitution into liposomes and functional examination by the patch-clamp technique. Therefore this family are likely to also be MS channel proteins. . TC 1.A.23.y.z (Small Conductance Mechanosensitive Ion Channel (MscS) Family)
YP_003917827.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.468 between position 31 and 32
YP_003917828.1	identified by match to protein family PF02567. PhzC/PhzF is involved in dimerisation of two 2, 3-dihydro-3- oxo-anthranilic acid molecules to create phenazine-1- carboxylic acid (PCA) by P. fluorescens. This family also contains a  thymidilate synthase from Mycobacterium tuberculosis. Many phenazine compounds are found in nature and are produced by bacteria such as Pseudomonas spp., Streptomyces spp., and Pantoea agglomerans. These compounds have been implicated in the virulence and competitive fitness of producing organisms. For example, the phenazine pyocyanin produced by Pseudomonas aeruginosa contributes to its ability to colonise the lungs of cystic fibrosis patients. Similarly, phenazine-1-carboxylic acid, produced by a number of Pseudomonas, increases survival in soil environments and has been shown to be essential for the biological control activity of certain strains
YP_003917829.1	major facilitator superfamily, drug:H+ antiporter-2 (14 spanner) (DHA2) family (TC 2.A.1.3.z). Identified by match to protein family TIGR00711
YP_003917832.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003917833.1	possibly involved in the metabolism of lipids. Match to protein domains PF08028, PF02771 and PF02770. Acyl-CoA dehydrogenases catalyze the alpha,beta- dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD
YP_003917834.1	match to protein family TIGR01970: ATP-dependent helicase HrpB
YP_003917835.1	match to PF00561: alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes
YP_003917837.1	identified by match to PF00248 family: Aldo/keto reductase family. This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity
YP_003917838.1	succinate-semialdehyde dehydrogenase (NAD(P)(+)) reduces succinate semialdehyde into succinate. Involved in the degradation of gamma-aminobutyrate
YP_003917839.1	5 transmembrane helices predicted by TMHMM2.0
YP_003917841.1	match to protein domain PF00746: Gram positive anchor. Surface proteins from Gram-positive cocci are covalently linked to the bacterial cell wall by sortase, a membrane-anchored transpeptidase that cleaves proteins between the threonine and the glycine of a conserved LPxTG motif, with the formation of a thioester between the conserved cysteine of sortase and the threonine carboxyl group. The newly liberated C-terminus of the threonine is transferred via an amide bond exchange to the amino group of the pentaglycine wall crossbridge, thereby tethering the C-terminus end of the surface protein to the bacterial peptidoglycan.The proteins that contain the conserved hexapeptide and hydrophobic anchor are diverse: they include M proteins, IgA and IgG binding proteins, fibronectin-binding proteins, wall-associated proteins, trypsin-resistant surface T protein, protein H precursor, etc. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.981 between position 35 and 36
YP_003917842.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003917843.1	match to PF08239: bacterial SH3 domain. A homologue of the SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins
YP_003917844.1	identified by match to PF00210. Ferritin is one of the major non-haem iron storage proteins in animals, plants, and microorganisms. It consists of a mineral core of hydrated ferric oxide, and a multi-subunit protein shell that encloses the former and assures its solubility in an aqueous environment
YP_003917845.1	match to protein family PTHR10724: Tex protein- related transcription accessory protein
YP_003917846.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.877 between position 34 and 35
YP_003917847.1	match to protein domain PF01479. The S4 domain was detected in proteins such as the bacterial ribosomal protein S4, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA
YP_003917848.1	identified by match to protein family PF00326. Prolyl oligopeptidase family consist of a number of evolutionary related peptidases whose catalytic activity seems to be provided by a charge relay system similar to that of the trypsin family of serine proteases, but which evolved by independent convergent evolutionidentified by match to protein family PF00326. Prolyl oligopeptidase family consist of a number of evolutionary related peptidases whose catalytic activity seems to be provided by a charge relay system similar to that of the trypsin family of serine proteases, but which evolved by independent convergent evolution
YP_003917850.1	4 transmembrane helices predicted by TMHMM2.0
YP_003917851.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003917852.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003917853.1	major facilitator superfamily, drug:H+ antiporter-2 (14 spanner) (DHA2) family (TC 2.A.1.3.z). Identified by match to protein family TIGR00711
YP_003917854.1	match to PF00313: cold-shock DNA-binding domain. The so-called cold shock proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organization of the prokaryotic nucleoid
YP_003917855.1	identified by match to PF00296. Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulfonate monooxygenase (SsuD), and coenzyme F420- dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds
YP_003917856.1	4 transmembrane helices predicted by TMHMM2.0
YP_003917857.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003917858.1	identified by match to protein family PF01037
YP_003917860.1	identified by match to PF00126: bacterial regulatory helix-turn-helix protein, lysR family. Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini
YP_003917861.1	enoyl-CoA hydratase catalyzes the hydratation of 2- trans-enoyl-CoA into 3-hydroxyacyl-CoA
YP_003917863.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease and ATP-binding protein (IM-ABC), DPL-family
YP_003917864.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease and ATP-binding protein (IM-ABC), DPL-family
YP_003917865.1	match to protein domain PF03061: thioesterase superfamily
YP_003917866.1	catalyzes the following reaction: N-(5-phospho- beta-D-ribosyl)anthranilate <=> 1-(2-carboxyphenylamino)-1- deoxy-D-ribulose 5-phosphate. Involved in tryptophane biosynthesis
YP_003917867.1	match to protein domain PF03061: thioesterase superfamily
YP_003917868.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. 4 transmembrane helices predicted by TMHMM2.0
YP_003917869.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003917870.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, ATP-binding protein (ABC), DRI-family, DRB-subfamily (drug resistance, ). Possible function in drug efflux
YP_003917871.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease (IM), DRI-family, DRB-subfamily (drug resistance, ). Possible function in drug efflux
YP_003917872.1	6 transmembrane helices predicted by TMHMM2.0
YP_003917873.1	proline dehydrogenase (EC 1.5.99.8) catalyses the following reaction: L-proline + acceptor + H(2)O <=> (S)-1- pyrroline-5-carboxylate + reduced acceptor. Pyrroline-5- carboxylate dehydrogenase (EC 1.5.1.12) catalyses the following reaction: 1-pyrroline-5-carboxylate + NAD(+) + H(2)O <=> L-glutamate + NADH
YP_003917874.1	identified by match to PF00126: bacterial regulatory helix-turn-helix protein, lysR family. Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini
YP_003917875.1	Solute:Sodium Symporter (SSS) family, Na+/proline symporter (TC 2.A.21.2.1)
YP_003917876.1	identified by match to protein family PF01370: NAD dependent epimerase/dehydratase family. This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions
YP_003917878.1	match to protein family HMM PF00144: beta- lactamase
YP_003917879.1	identified by match to PF01276: Orn/Lys/Arg decarboxylase, major domain
YP_003917881.1	7 transmembrane helices predicted by TMHMM2.0
YP_003917882.1	6 transmembrane helices predicted by TMHMM2.0
YP_003917884.1	match to protein family PF08282: haloacid dehalogenase-like hydrolase. The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P- type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification
YP_003917885.1	catalyzes the following reaction: (phosphate)(n) + D-glucose <=> (phosphate)(n-1) + D-glucose 6-phosphate. The polyphosphate-glucose phosphotransferase isolated from the Gram-positive bacterium Arthrobacter sp. strain KM, is a monomer that phosphorylates glucose and mannose with preference for glucose through the use of poly(P) and ATP
YP_003917887.1	catalyses the following reaction: an alcohol + NAD(+) <=> an aldehyde or ketone + NADH
YP_003917888.1	catalyzes the NAD-dependent, reversible oxidation of 3-hydroxbutyrate to methylmalonate. Involved in the catabolism of valine
YP_003917889.1	identified by match to PF00126: bacterial regulatory helix-turn-helix protein, lysR family. Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini
YP_003917890.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.574) with cleavage site probability 0.495 between position 29 and 30
YP_003917891.1	major facilitator superfamily (MFS), metabolite:H+ symporter (MHS) family (TC 2.A.1.6.z)
YP_003917892.1	match to PF05495: CHY zinc finger. This family of domains are likely to bind to zinc ions
YP_003917893.1	identified by match to PF00582: universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general stress endurance activity
YP_003917894.1	match to PF07992: pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases
YP_003917895.1	identified by similarity to protein SP:P54417 (Bacillus subtilis). betaine/carnitine/choline transporter (BCCT) family, glycine betaine:H+ symporter (TC 2.A.15.1. 1). High-affinity uptake of glycine betaine
YP_003917896.1	identified by match to PF00082. Subtilases are a family of serine proteases. The vast majority of the family are endopeptidases
YP_003917898.1	catalyses the following reaction: 10- formyltetrahydrofolate + H(2)O <=> formate + tetrahydrofolate
YP_003917899.1	sarcosine oxidase catalyzes the oxidative demethylation of sarcosine and forms equimolar amounts of formaldehyde, glycine and hydrogen peroxide
YP_003917900.1	sarcosine oxidase catalyzes the oxidative demethylation of sarcosine and forms equimolar amounts of formaldehyde, glycine and hydrogen peroxide
YP_003917901.1	sarcosine oxidase catalyzes the oxidative demethylation of sarcosine and forms equimolar amounts of formaldehyde, glycine and hydrogen peroxide
YP_003917902.1	sarcosine oxidase catalyzes the oxidative demethylation of sarcosine and forms equimolar amounts of formaldehyde, glycine and hydrogen peroxide
YP_003917903.1	catalyzes the transfer of the hydroxymethyl group of serine to tetrahydrofolate to form 5,10- methylenetetrahydrofolate and glycine. Also catalyzes the reaction of glycine with acetaldehyde to form L-threonine
YP_003917904.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003917905.1	creatininase catalyses the formation of creatine from creatinine
YP_003917906.1	identified by similarity to protein SP:P54417 (Bacillus subtilis). betaine/carnitine/choline transporter (BCCT) family, glycine betaine:H+ symporter (TC 2.A.15.1. 1). High-affinity uptake of glycine betaine
YP_003917907.1	hydrolyzes creatine to sarcosine and urea
YP_003917908.1	identified by similarity to protein SP:P0C0L7 (Escherichia coli). Proton symporter that senses osmotic shifts and responds by importing osmolytes such as proline, glycine betaine, stachydrine, pipecolic acid, ectoine and taurine. It is both an osmosensor and an osmoregulator which is available to participate early in the bacterial osmoregulatory response. Metabolite:H+ symporter (MHS) family, (Poline/glycine-betaine):(H+/Na+) symporter (also transports taurine, ectoine, pipecolate, proline-betaine, N,N-dimethylglycine, carnitine, and 1- carboxymethyl-pyridinium) (subject to osmotic activation) (TC 2.A.1.6.4)
YP_003917909.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003917910.1	presence of one conserved barrel domain of the cupin superfamily (PF07883)
YP_003917911.1	identified by match to PF03358. FMN reductase reductase catalyses the following reaction: NAD(P)H + FMN = NAD(P)(+) + FMNH(2)
YP_003917912.1	match to PF04434: SWIM zinc finger. SWIM is thought to be a versatile domain that can interact with DNA or proteins in different contexts
YP_003917913.1	possible DNA or RNA helicase
YP_003917914.1	identified by match to PF00903: glyoxalase/bleomycin resistance protein/dioxygenase superfamily
YP_003917915.1	drug:H+ antiporter-1 (12 Spanner) (DHA1) family transporter (TC 2.A.1.2.z). Match to PR01035 (Tetracycline resistance protein signature)
YP_003917916.1	3 transmembrane helices predicted by TMHMM2.0
YP_003917917.1	identified by match to PF03171. This family contains members of the 2-oxoglutarate (2OG) and Fe(II)- dependent oxygenase superfamily
YP_003917918.1	catalyzes two sequential methylation reactions, the first forming precorrin-1 and the second leading to the formation of precorrin-2 (dihydrosirohydrochlorin): (1) S- adenosyl-L-methionine + uroporphyrinogen III <=> S- adenosyl-L-homocysteine + precorrin-1, (2) S-adenosyl-L- methionine + precorrin-1 <=> S-adenosyl-L-homocysteine + precorrin-2
YP_003917919.1	uroporphyrinogen-III synthase catalyses the following reaction: hydroxymethylbilane <=> uroporphyrinogen III + H(2)O. Possible fusion with a response regulator domain protein
YP_003917920.1	fructokinase catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into glucose-6-phosphate
YP_003917921.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003917922.1	match to protein domain PF01261: xylose isomerase- like TIM barrel . This TIM alpha/beta barrel structure is found in xylose isomerase and in endonuclease IV (EC.1.21. 2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins
YP_003917923.1	identified by match to PF01408 (oxidoreductase family, NAD-binding Rossmann fold) and PF02894 (oxidoreductase family, C-terminal alpha/beta domain)
YP_003917924.1	identified by match to PF01408 (oxidoreductase family, NAD-binding Rossmann fold)
YP_003917925.1	match to protein domain PF01261: xylose isomerase- like TIM barrel. This TIM alpha/beta barrel structure is found in xylose isomerase and in endonuclease IV (EC.1.21. 2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins
YP_003917926.1	identified by match to PF00480: ROK family
YP_003917927.1	catalyzes the second step in the degradation of histidine, the hydration of urocanate into imidazolonepropionate
YP_003917928.1	DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation
YP_003917930.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.991) with cleavage site probability 0.786 between position 45 and 46
YP_003917931.1	catalyzes the first step in histidine degradation, the removal of an ammonia group from histidine to produce urocanic acid
YP_003917932.1	step in the major route of beta-alanine production for pantothenate biosynthesis in bacteria
YP_003917933.1	excinuclease ABC catalyses nucleotide excision repair in a multi-step process
YP_003917935.1	4 transmembrane helices predicted by TMHMM2.0
YP_003917937.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-2 (CUT2) family (TC 3.A.1. 2.z). ABCISSE: ABCISSE: ABC transporter, permease (IM), MOS-family (monosaccharides: pentoses and hexoses), ribose import
YP_003917938.1	catalyses the phosphorylation of ribose to ribose-5- phosphate. 2-deoxy-D-ribose can also act as acceptor
YP_003917939.1	match to protein domain PF00356. Numerous bacterial transcription regulatory proteins bind DNA via a helix- turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR. Within this family, the HTH motif is situated towards the N-terminus
YP_003917940.1	identified by match to PF01325, PF02742 and PF04023. The diphtheria toxin repressor protein (DTXR) is a member of this group. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N-terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation
YP_003917941.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.312 between position 36 and 37
YP_003917942.1	TCDB: ATP-binding cassette (ABC) superfamily, Manganese/Zinc/Iron Chelate Uptake Transporter (MZT) Family (TC 3.A.1.15.z). ABCISSE: ABC transporter, permease (IM), MET-family, manganese uptake. Identified by similarity to protein SP:Q55282 (Synechocystis sp.)
YP_003917943.1	TCDB: ATP-binding cassette (ABC) superfamily, Manganese/Zinc/Iron Chelate Uptake Transporter (MZT) Family (TC 3.A.1.15.z). ABCISSE: ABC transporter, ATP- binding protein (ABC), MET-family, manganese uptake. Identified by similarity to protein SP:Q55281 (Synechocystis sp.)
YP_003917944.1	TCDB: ATP-binding cassette (ABC) superfamily, Manganese/Zinc/Iron Chelate Uptake Transporter (MZT) Family (TC 3.A.1.15.z). ABCISSE: ABC transporter, binding protein (BP), MET-family, manganese uptake. Identified by similarity to protein SP:Q55280 (Synechocystis sp.)
YP_003917945.1	hydrolyzes N-formimino-glutamate into glutamate and formamide
YP_003917948.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003917949.1	8 transmembrane helices predicted by TMHMM2.0
YP_003917950.1	identified by match to PF00376 and PF09278. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA
YP_003917951.1	match to PF00376: MerR family regulatory protein
YP_003917952.1	identified by match to protein family PF01037
YP_003917953.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003917954.1	identified by match to protein family PF01451. Protein tyrosine (pTyr) phosphorylation is a common post- translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; EC:3.1.3.48) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation. Low molecular weight (LMW) protein-tyrosine phosphatases (or acid phosphatase) act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates
YP_003917955.1	amino acid-polyamine-organocation (APC) superfamily (TC 2.A.3.y.z)
YP_003917956.1	identified by match to PF00582: universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general stress endurance activity
YP_003917957.1	catalyses the following reaction: putrescine + O(2) + H(2)O <=> 4-aminobutanal + NH(3) + H(2)O(2)
YP_003917958.1	identified by match to PF00440: bacterial regulatory proteins, tetR family
YP_003917959.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917961.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917962.1	1 transmembrane helice predicted by TMHMM2.0
YP_003917963.1	identified by match to protein family PF01037
YP_003917964.1	3 transmembrane helices predicted by TMHMM2.0
YP_003917965.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003917966.1	3-phenylpropionate dioxygenase converts 3- phenylpropionic acid (PP) into cis-3-(3-carboxyethyl)-3,5- cyclohexadiene-1,2-diol (PP-dihydrodiol). Involved in the catabolism of 3-phenylpropionic acid
YP_003917967.1	identified by similarity to SP:P0ABW0. Part of multicomponent 3-phenylpropionate dioxygenase, that converts 3-phenylpropionic acid (PP) into cis-3-(3- carboxyethyl)-3,5-cyclohexadiene-1,2-diol (PP- dihydrodiol). Involved in the catabolism of 3- phenylpropionic acid
YP_003917968.1	match to PF01869: BadF/BadG/BcrA/BcrD ATPase family. This family includes the BadF and BadG proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase
YP_003917969.1	identified by match to PF00082. Subtilases are a family of serine proteases. The vast majority of the family are endopeptidases. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.991 between position 34 and 35
YP_003917970.1	match to protein family PF02652. Lactate Permease (LctP) Family (TC 2.A.14.y.z). Members of this family are involved in the uptake of L-lactate, D-lactate and glycolate
YP_003917971.1	identified by match to protein family PF02900. Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds
YP_003917972.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003917973.1	possible DNA or RNA helicase
YP_003917974.1	identified by match to protein family PF02566: OsmC, OsmC-like protein. Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. This family also contains an organic hydroperoxide detoxification protein that has a novel pattern of oxidative stress regulation
YP_003917975.1	L-idonate 5-dehydrogenase catalyzes the NADH/NADPH- dependent oxidation of L-idonate to 5-ketogluconate. It is involved in L-idonic acid degradation
YP_003917976.1	catalyzes a reversible reduction of 5-ketoglutanate to form D-gluconate
YP_003917977.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003917978.1	match to protein family PF02652. Lactate Permease (LctP) Family (TC 2.A.14.y.z). Members of this family are involved in the uptake of L-lactate, D-lactate and glycolate
YP_003917979.1	identified by match to PF02754. This domain is usually found in two copies per protein. It contains up to four conserved cysteines. The group includes proteins characterised as: heterodisulphide reductase, subunit B (HrdB); succinate dehydrogenase, subunit C (SdhC ); Fe-S oxidoreductase; glycerol-3-phosphate dehydrogenase subunit C (Anaerobic GlpC, ); and glycolate oxidase iron-sulfur subunit (GlcF)
YP_003917980.1	identified by match to protein family TIGR00273
YP_003917982.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003917983.1	2 transmembrane helices predicted by TMHMM2.0
YP_003917984.1	identified by match to protein family PF04264. This entry represents the lipid-binding protein YceI from Escherichia coli and the polyisoprenoid-binding protein TTHA0802 from Thermus thermophilus. The crystal structures of Yce1 and TTHA0802 suggest that this family of proteins plays an important role in isoprenoid quinone metabolism and/or transport and/or storage
YP_003917986.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, binding protein (BP), OTCN-family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L-proline
YP_003917987.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, permease (IM), OTCN- family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L- proline
YP_003917988.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OTCN-family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L-proline
YP_003917989.1	TCDB: ATP-binding cassette (ABC) superfamily, quaternary amine uptake transporter (QAT) family (TC 3.A.1. 12.z). ABCISSE: ABC transporter, permease (IM), OTCN- family (osmoprotectants, taurine, cyanate and nitrate). Part of an uptake system of osmoprotrectants such as glycine betaine, carnitine, choline, proline betaine and L- proline
YP_003917991.1	match to PF07683: Cobalamin synthesis protein cobW C-terminal domain
YP_003917992.1	Alanine or Glycine:Cation Symporter (AGCS) Family (TC 2.A.25.y.z). Members of the AGCS family transport alanine and/or glycine in symport with Na+ and or H+
YP_003917993.1	citrate lyase catalyses the formation of acetate and oxaloacetate from citrate
YP_003917994.1	amino acid-polyamine-organocation (APC) superfamily, amino acid transporter (AAT) family, D- Serine/D-alanine/glycine:H+ symporter (TC 2.A.3.1.7). Identified by similarity to protein SP:P0AAE0 (Escherichia coli)
YP_003917997.1	catalyzes the oxidative decarboxylation of malate into pyruvate. Uses preferentially NAD and has the ability to decarboxylate oxaloacetate
YP_003917998.1	match to PF00376: MerR family regulatory protein
YP_003917999.1	3 transmembrane helices predicted by TMHMM2.0
YP_003918000.1	identified by match to PF00155: aminotransferase class I and II
YP_003918001.1	identified by match to PF00126: bacterial regulatory helix-turn-helix protein, lysR family. Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini
YP_003918002.1	8 transmembrane helices predicted by TMHMM2.0
YP_003918003.1	3-hydroxybutyrate dehydrogenase catalyzes the following reaction: (R)-3-hydroxybutanoate + NAD+ = acetoacetate + NADH. It may be involved in the catabolism of the intracellular carbon storage compound poly-3- hydroxybutyrate
YP_003918004.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003918005.1	possibly involved in the metabolism of lipids. Match to protein domains PF08028, PF02771 and PF02770. Acyl-CoA dehydrogenases catalyze the alpha,beta- dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD
YP_003918006.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003918007.1	identified by match to PF01638: HxlR-like helix- turn-helix
YP_003918009.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, binding protein (BP), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003918010.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003918011.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003918012.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, fused ATP-binding protein (ABC2), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003918013.1	TCDB: ATP-binding cassette (ABC) superfamily (TC 3. A.1.y.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OTCN-family (osmoprotectants, taurine, cyanate and nitrate)
YP_003918014.1	activates fatty acids by binding to coenzyme A. Possibly involved in the synthesis of cellular lipids or their degradation via beta-oxidation
YP_003918016.1	match to PF01168: Alanine racemase, N-terminal domain
YP_003918017.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003918019.1	oxoacid CoA-transferase catalyses the following reaction: succinyl-CoA + a 3-oxo acid <=> succinate + a 3- oxoacyl-CoA. Acetoacetate or, more slowly, 3- oxopropanoate, 3-oxopentanoate, 3-oxo-4-methylpentanoate or 3-oxohexanoate can act as acceptor
YP_003918020.1	3-oxoacid CoA-transferase catalyses the following reaction: succinyl-CoA + a 3-oxo acid <=> succinate + a 3- oxoacyl-CoA. Acetoacetate or, more slowly, 3- oxopropanoate, 3-oxopentanoate, 3-oxo-4-methylpentanoate or 3-oxohexanoate can act as acceptor
YP_003918021.1	catalyses the following reaction: 2 acetyl-CoA <=> CoA + acetoacetyl-CoA
YP_003918022.1	11 transmembrane helices predicted by TMHMM2.0
YP_003918023.1	identified by match to protein domain PF00300
YP_003918024.1	identified by match to PF00149. The metallo- phosphoesterase motif is found in a large number of proteins invoved in phosphorylation. These include Ser/Thr phosphatases, DNA polymerase, exonucleases, and other phosphatases
YP_003918025.1	catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids
YP_003918028.1	catalyses the hydrolysis of L-asparagine to L- aspartate and ammonium
YP_003918029.1	catalyzes the reversible conversion of aspartate to fumarate and ammonia
YP_003918030.1	match to PS51257: prokaryotic membrane lipoprotein lipid attachment site profile
YP_003918031.1	identified by match to protein family PF00326. Prolyl oligopeptidase family consist of a number of evolutionary related peptidases whose catalytic activity seems to be provided by a charge relay system similar to that of the trypsin family of serine proteases, but which evolved by independent convergent evolution
YP_003918032.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.485 between position 41 and 42. 3 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003918033.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.702 between position 38 and 39. 1 transmembrane helice predicted by TMHMM2.0 after the signal peptide
YP_003918034.1	match to protein family TIGR02937. Sigma-70 family
YP_003918036.1	possible component of pyruvate dehydrogenase (EC 2. 3.1.12), branched-chain alpha-ketoacid dehydrogenase (EC 2. 3.1.168) or 2-oxoglutarate dehydrogenase (EC 2.3.1.61) complexes
YP_003918037.1	possible component of pyruvate dehydrogenase (EC 2. 3.1.12), branched-chain alpha-ketoacid dehydrogenase (EC 2. 3.1.168) or 2-oxoglutarate dehydrogenase (EC 2.3.1.61) complexes
YP_003918038.1	possible component of pyruvate dehydrogenase (EC 2. 3.1.12), branched-chain alpha-ketoacid dehydrogenase (EC 2. 3.1.168) or 2-oxoglutarate dehydrogenase (EC 2.3.1.61) complexes
YP_003918039.1	may catalyze the transamination reaction in phenylalanine biosynthesis
YP_003918040.1	4 transmembrane helices predicted by TMHMM2.0
YP_003918043.1	catalyzes the eight step in the de novo biosynthesis of purines, the formation of 5-phosphoribosyl- 5-amino-4-imidazolecarboxamide and fumarate from 1-(5- phosphoribosyl)-4-(N-succino-carboxamide). Also catalyzes the formation of fumarate and AMP from adenylosuccinate
YP_003918044.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918045.1	identified by match to PF02625. XdhC is believed to be involved in the attachment of molybdenum to Xanthine Dehydrogenase
YP_003918046.1	xanthine dehydrogenase catalyses the formation of xanthine from hypoxanthine and of urate from xanthine. It is involved in purine degradation
YP_003918047.1	xanthine dehydrogenase catalyses the formation of xanthine from hypoxanthine and of urate from xanthine. It is involved in purine degradation
YP_003918049.1	AzgA family purine transporter (TC 2.A.1.40.z). Possibly involved in transport of compounds such as hypoxanthine, adenine, guanine, guanosine and urate
YP_003918050.1	Nitrate/Nitrite Porter (NNP) family (TC 2.A.1.8.z)
YP_003918051.1	possible flavoprotein that may act as electron donnor in the assimilatory nitrite reductase. EC 1.7.1.4 catalyses the following reaction: ammonium hydroxide + 3 NAD(P)(+) + H(2)O <=> nitrite + 3 NAD(P)H
YP_003918052.1	the assimilatory nitrite reductase catalyses the following reaction: ammonium hydroxide + 3 NAD(P)(+) + H(2)O <=> nitrite + 3 NAD(P)H
YP_003918055.1	the assimilatory nitrite reductase catalyses the following reaction: ammonium hydroxide + 3 NAD(P)(+) + H(2)O <=> nitrite + 3 NAD(P)H. NirD contains a single Rieske [2Fe-2S] cluster binding domain involved in electron transfer
YP_003918056.1	the assimilatory nitrite reductase catalyses the following reaction: ammonium hydroxide + 3 NAD(P)(+) + H(2)O <=> nitrite + 3 NAD(P)H
YP_003918057.1	identified by match to PF00248 family: Aldo/keto reductase family. This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity
YP_003918058.1	identified by match to protein family PF01145. The band 7 protein is an integral membrane protein which is thought to regulate cation conductance. A variety of proteins belong to this family
YP_003918059.1	formate dehydrogenase catalyses the formation of CO(2) and NADH from formate and NAD(+)
YP_003918060.1	necessary for nitrate inducible formate dehydrogenase activity
YP_003918061.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003918062.1	identified by match to PF00903: glyoxalase/bleomycin resistance protein/dioxygenase superfamily
YP_003918063.1	activates fatty acids by binding to coenzyme A. Possibly involved in the synthesis of cellular lipids or their degradation via beta-oxidation
YP_003918064.1	match to protein family PF00378. This family contains a diverse set of enzymes including: Enoyl-CoA hydratase, Napthoate synthase, Carnitate racemase, 3- hydoxybutyryl-CoA dehydratase, Dodecanoyl-CoA delta- isomerase
YP_003918065.1	4 transmembrane helices predicted by TMHMM2.0
YP_003918066.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003918067.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. 5 transmembrane helices predicted by TMHMM2.0
YP_003918068.1	TCDB: ATP-binding cassette (ABC) superfamily, drug exporter-1 (DrugE1) family (TC 3.A.1.105.z). ABCISSE: ABC transporter, permease (IM), DRA-family (Drug and Antibiotic resistance), DRR-subfamily (Polyketide drug resistance). The typical organization of DRR systems consists of 1 ABC transporter (ABC) and 1 or 2 permeases (IM). Possible function in drug efflux
YP_003918069.1	TCDB: ATP-binding cassette (ABC) superfamily, drug exporter-1 (DrugE1) family (TC 3.A.1.105.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), DRA-family (Drug and Antibiotic resistance), DRR-subfamily (Polyketide drug resistance). The typical organization of DRR systems consists of 1 ABC transporter (ABC) and 1 or 2 permeases (IM). Possible function in drug efflux
YP_003918070.1	5 transmembrane helices predicted by TMHMM2.0
YP_003918072.1	match to PF00196: Bacterial regulatory proteins, luxR family
YP_003918074.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.999) with cleavage site probability 0.712 between position 26 and 27
YP_003918075.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918076.1	match to protein domain TIGR00746: LPXTG-motif cell wall anchor. Surface proteins from Gram-positive cocci are covalently linked to the bacterial cell wall by sortase, a membrane-anchored transpeptidase that cleaves proteins between the threonine and the glycine of a conserved LPxTG motif, with the formation of a thioester between the conserved cysteine of sortase and the threonine carboxyl group. The newly liberated C-terminus of the threonine is transferred via an amide bond exchange to the amino group of the pentaglycine wall crossbridge, thereby tethering the C-terminus end of the surface protein to the bacterial peptidoglycan.The proteins that contain the conserved hexapeptide and hydrophobic anchor are diverse: they include M proteins, IgA and IgG binding proteins, fibronectin-binding proteins, wall-associated proteins, trypsin-resistant surface T protein, protein H precursor, etc. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.628 between position 24 and 25
YP_003918078.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918079.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.487 between position 34 and 35
YP_003918081.1	catalyses the following reaction: L-aspartate + 2- oxoglutarate <=> oxaloacetate + L-glutamate
YP_003918082.1	identified by match to PF00149. The metallo- phosphoesterase motif is found in a large number of proteins invoved in phosphorylation. These include Ser/Thr phosphatases, DNA polymerase, exonucleases, and other phosphatases
YP_003918083.1	10 transmembrane helices predicted by TMHMM2.0
YP_003918085.1	identified by match to PF00702. This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases
YP_003918086.1	identified by match to PF00702. This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases
YP_003918087.1	match to PTHR11638: ATP-dependent CLP protease
YP_003918089.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.999) with cleavage site probability 0.726 between position 24 and 25. 2 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003918090.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003918094.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918095.1	lysophospholipase catalyses the release of fatty acids from lysophospholipids
YP_003918096.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits: subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003918097.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits: subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003918098.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918099.1	identified by match to PF07719. The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins. It mediates protein-protein interactions and the assembly of multiprotein complexes. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding
YP_003918102.1	TCDB: P-type ATPase (P-ATPase) superfamily (TC 3.A. 3.y.z). Involved in export of cations
YP_003918103.1	identified by match to PF01022: bacterial regulatory protein, ArsR family. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003918105.1	4 transmembrane helices predicted by TMHMM2.0
YP_003918106.1	identified by match to protein family PF03551
YP_003918110.1	first part of the IS
YP_003918116.1	identified by match to protein family PF02534. The TraG family are bacterial conjugation proteins. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome although the exact mechanism of action is unknown
YP_003918119.1	identified by match to SM00530: Helix-turn-helix XRE-family like proteins. This is a large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003918121.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918123.1	serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. This protein may be a resolvase (match to PF07508 and PF00239)
YP_003918124.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918125.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.992) with cleavage site probability 0.849 between position 33 and 34
YP_003918126.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918134.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.807) with cleavage site probability 0.454 between position 19 and 20
YP_003918136.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918143.1	match to PF00239 and PF02796. Possibly involved in site-specific recombination of DNA
YP_003918145.1	3 transmembrane helices predicted by TMHMM2.0
YP_003918147.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.854 between position 36 and 37
YP_003918149.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.999) with cleavage site probability 0.750 between position 34 and 35
YP_003918151.1	7 transmembrane helices predicted by TMHMM2.0
YP_003918158.1	match to PF00239 and PF02796. Possibly involved in site-specific recombination of DNA
YP_003918160.1	TCDB: ATP-binding cassette (ABC) superfamily, Manganese/Zinc/Iron Chelate Uptake Transporter (MZT) Family (TC 3.A.1.15.z). ABCISSE: ABC transporter, binding protein (BP), MET-family. This family is comprised of systems involved in the uptake of various metallic cations such as iron, manganese and zinc
YP_003918162.1	identified by match to protein family PF0775: Abi- like protein. This family, found in various bacterial species, contains sequences that are similar to the Abi group of proteins, which are involved in bacteriophage resistance mediated by abortive infection in Lactococcus species. The proteins are thought to have helix-turn-helix motifs, found in many DNA-binding proteins, allowing them to perform their function
YP_003918163.1	identified by match to PF03358. FMN reductase reductase catalyses the following reaction: NAD(P)H + FMN = NAD(P)(+) + FMNH(2)
YP_003918164.1	ribonucleotide reductase catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. It is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues)
YP_003918165.1	catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. It is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues)
YP_003918166.1	identified by match to PF03358. FMN reductase reductase catalyses the following reaction: NAD(P)H + FMN = NAD(P)(+) + FMNH(2)
YP_003918169.1	identified by match to protein family PF05713: bacterial mobilisation protein (MobC). This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis- active site of a mobilising plasmid, the origin of transfer (oriT) region
YP_003918170.1	identified by match to protein family PF03432: Relaxase/Mobilisation nuclease domain. Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation
YP_003918173.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918175.1	identified by match to protein family PF02534. The TraG family are bacterial conjugation proteins. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome
YP_003918177.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918178.1	7 transmembrane helices predicted by TMHMM2.0
YP_003918179.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918180.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918183.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918184.1	identified by match to protein family PF01551. Members of this family are zinc metallopeptidases with a range of specificities. Peptidase family M23 are also endopeptidases
YP_003918185.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.338 between position 48 and 49
YP_003918189.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003918190.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003918191.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, binding protein (BP), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003918200.1	3 transmembrane helices predicted by TMHMM2.0
YP_003918201.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918203.1	match to protein family PF01656.  chromosome partitioning protein. Similar to uncharacterized plasmidic proteins
YP_003918207.1	electron transport system for the ribonucleotide reductase system nrdEF
YP_003918212.1	match to PR00507. Site-specific DNA- methyltransferases specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the bacterial restriction-modification systems. Match to PS00092 pattern: N-6 Adenine-specific DNA methylases signature
YP_003918214.1	6 transmembrane helices predicted by TMHMM2.0
YP_003918215.1	identified by match to protein family PF04261. This family of dye-decolourising peroxidases lack a typical heme-binding region
YP_003918216.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.655 between position 38 and 39
YP_003918217.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.997) with cleavage site probability 0.878 between position 33 and 34. 4 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003918219.1	TCDB: ATP-binding cassette (ABC) superfamily, Manganese/Zinc/Iron Chelate Uptake Transporter (MZT) Family (TC 3.A.1.15.z). ABCISSE: ABC transporter, binding protein (BP), MET-family. This family is comprised of systems involved in the uptake of various metallic cations such as iron, manganese and zinc
YP_003918220.1	TCDB: ATP-binding cassette (ABC) superfamily, Manganese/Zinc/Iron Chelate Uptake Transporter (MZT) Family (TC 3.A.1.15.z). ABCISSE: ABC transporter, ATP- binding protein (ABC), MET-family. This family is comprised of systems involved in the uptake of various metallic cations such as iron, manganese and zinc
YP_003918221.1	TCDB: ATP-binding cassette (ABC) superfamily, Manganese/Zinc/Iron Chelate Uptake Transporter (MZT) Family (TC 3.A.1.15.z). ABCISSE: ABC transporter, permease (IM), MET-family. This family is comprised of systems involved in the uptake of various metallic cations such as iron, manganese and zinc
YP_003918224.1	match to PF00239. Possibly involved in site- specific recombination of DNA
YP_003918229.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918234.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.999 between position 30 and 31
YP_003918237.1	identified by match to PF04055. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation
YP_003918238.1	match to PR00420: Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
YP_003918239.1	identified by match to protein domain PF08241
YP_003918240.1	identified by match to PIRSF000451. Type III polyketide synthases catalyse formation of structurally diverse polyketides
YP_003918241.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003918243.1	10 transmembrane helices predicted by TMHMM2.0
YP_003918244.1	7 transmembrane helices predicted by TMHMM2.0
YP_003918245.1	sarcosine oxidase catalyzes the oxidative demethylation of sarcosine and forms equimolar amounts of formaldehyde, glycine and hydrogen peroxide
YP_003918246.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.999) with cleavage site probability 0.472 between position 34 and 35
YP_003918247.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918248.1	match to protein domain PF00746: Gram positive anchor. Surface proteins from Gram-positive cocci are covalently linked to the bacterial cell wall by sortase, a membrane-anchored transpeptidase that cleaves proteins between the threonine and the glycine of a conserved LPxTG motif, with the formation of a thioester between the conserved cysteine of sortase and the threonine carboxyl group. The newly liberated C-terminus of the threonine is transferred via an amide bond exchange to the amino group of the pentaglycine wall crossbridge, thereby tethering the C-terminus end of the surface protein to the bacterial peptidoglycan.The proteins that contain the conserved hexapeptide and hydrophobic anchor are diverse: they include M proteins, IgA and IgG binding proteins, fibronectin-binding proteins, wall-associated proteins, trypsin-resistant surface T protein, protein H precursor, etc.
YP_003918249.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.431 between position 38 and 39
YP_003918250.1	catalyzes the hydrolysis of glutamine to a glutamate and ammonia
YP_003918251.1	catalyzes the hydrolysis of the thioester bond in acyl-CoA thioesters
YP_003918252.1	lactoylglutathione lyase catalyzes the first step of the glyoxal pathway, the transformation of methylglyoxal and glutathione into S-lactoylglutathione which is then converted by glyoxalase II to lactic acid
YP_003918253.1	identified by match to protein family PF00657
YP_003918254.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. 4 transmembrane helices predicted by TMHMM2.0
YP_003918255.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003918256.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918257.1	identified by match to protein family PF04012. This family includes PspA, which is a protein that suppresses sigma54-dependent transcription
YP_003918258.1	TCDB: ATP-binding cassette (ABC) superfamily (TC 3. A.1.y.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), NO family (NO family systems represent few ABC proteins with unknown function and which are apparently unrelated to existent families)
YP_003918259.1	match to PR00420: Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
YP_003918260.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003918263.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690 (Major Facilitator Superfamily)
YP_003918264.1	match to protein domain PF09424. This domain is found in GatB and proteins related to bacterial Yqey. GatB transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain, but Yqey and its relatives may have a role in tRNA metabolism
YP_003918265.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.593) with cleavage site probability 0.268 between position 39 and 40
YP_003918266.1	possible ATP-grasp enzyme
YP_003918267.1	identified by match to protein family PF02388. The femAB operon codes for two nearly identical approximately 50-kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan. These proteins are also considered as a factor influencing the level of methicillin resistance
YP_003918269.1	match to PF00403: Heavy-metal-associated domain. This domain has been found in a number of heavy metal transport or detoxification proteins
YP_003918270.1	P-type ATPase (P-ATPase) superfamily (TC 3.A.3.y.z). Match to protein domain PF00403. Probably involved in export of cations such as Cu+ and Ag+
YP_003918271.1	amino acid-polyamine-organocation (APC) superfamily, amino acid transporter (AAT) family, D- Serine/D-alanine/glycine:H+ symporter (TC 2.A.3.1.7). Identified by similarity to protein SP:P0AAE0 (Escherichia coli)
YP_003918273.1	9 transmembrane helices predicted by TMHMM2.0
YP_003918276.1	identified by match to protein family TIGR01935: ribonuclease E inhibitor RraA.The Escherichia coli member of this family has been characterised as a regulator of RNase E, and its crystal structure has been analysed. It acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing. RNase E forms the core of a large RNA- catalysis machine termed the degradosomes. RraA (and RraB) causes remodelling of degradosome composition, which is associated with alterations in RNA decay and global transcript abundance and as such is a bacterial mechanism for the regulation of RNA cleavage
YP_003918277.1	amino acid-polyamine-organocation (APC) superfamily (TC 2.A.3.y.z)
YP_003918278.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918279.1	6 transmembrane helices predicted by TMHMM2.0
YP_003918280.1	catalyses the conversion of L-lactate to pyruvate. Probable quinone-dependent lactate dehydrogenase, functionning when lactate is used as a carbon and energy source
YP_003918281.1	major facilitator superfamily (MFS), metabolite:H+ symporter (MHS) family (TC 2.A.1.6.z)
YP_003918282.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003918283.1	Multi Antimicrobial Extrusion (MATE) Family protein (TC 2.A.66.1.z). Characterised members of the MATE family function as drug/sodium antiporters. These proteins mediate resistance to a wide range of cationic dyes, fluroquinolones, aminoglycosides and other structurally diverse antibodies and drugs
YP_003918285.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690
YP_003918286.1	identified by match to protein family PF02517: CAAX amino terminal protease family. Members of this family are probably proteases (after a prenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein, the AAX tripeptide is removed by one of the CAAX prenyl proteases). The family contains the Q03530 CAAX prenyl protease. 7 transmembrane helices predicted by TMHMM2.0
YP_003918287.1	match to PF08239: bacterial SH3 domain. A homologue of the SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins. Signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.812 between position 33 and 34
YP_003918288.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease and ATP-binding protein (IM-ABC), DPL-family, LLP- subfamily (LIP-like exporters). The function of LIP-like exporters is presently unknown
YP_003918289.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease and ATP-binding protein (IM-ABC), DPL-family, LLP- subfamily (LIP-like exporters). The function of LIP-like exporters is presently unknown
YP_003918290.1	match to protein family PF01329: pterin 4 alpha carbinolamine dehydratase
YP_003918292.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918294.1	identified by match to protein family PF00857. This is a family of hydrolase enzymes. Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate
YP_003918296.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918299.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003918300.1	3 transmembrane helices predicted by TMHMM2.0
YP_003918302.1	identified by match to PF08240 and PF00107. Zn- dependent alcohol dehydrogenasescatalyse the following reaction: an alcohol + NAD(+) <=> an aldehyde or ketone + NADH
YP_003918303.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918304.1	peroxiredoxin protects cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides. The Bcp protein shows substrate selectivity toward fatty acid hydroperoxides rather than hydrogen peroxide or alkyl hydroperoxides
YP_003918305.1	succinate-semialdehyde dehydrogenase (NAD(P)(+)) reduces succinate semialdehyde into succinate. Involved in the degradation of gamma-aminobutyrate
YP_003918306.1	identified by match to PF03441 and PF00875. DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light
YP_003918307.1	3 transmembrane helices predicted by TMHMM2.0
YP_003918308.1	5 transmembrane helices predicted by TMHMM2.0
YP_003918309.1	synonym: acetoin reductase. Catalyzes the production of 2,3-butanediol from acetoin. Identified by similarity to protein SP:O34788 (Bacillus subtilis)
YP_003918310.1	very short patch repair endonucleases recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5 prime side of the thymine
YP_003918311.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690
YP_003918312.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, binding protein (BP), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003918313.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003918314.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel), oligopeptides import
YP_003918315.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, fused ATP-binding protein (ABC2), OPN-family (oligopeptides and nickel), oligopeptides import
YP_003918316.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918317.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003918318.1	dihydroorotate oxidase catalyzes the fourth step in the de novo biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. In some organisms such as Bacillus subtilis, dihydroorotate oxidase is composed of two subunits: PyrDI and PyrDII
YP_003918319.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690
YP_003918322.1	allantoate deiminase catalyses the conversion of allantoate in ammonia, carbon dioxide andureidoglycolate. Involved in purine degradation
YP_003918323.1	dihydroorotate oxidase catalyzes the fourth step in the de novo biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. In some organisms such as Bacillus subtilis, dihydroorotate oxidase is composed of two subunits: PyrDI and PyrDII
YP_003918324.1	catalyzes the third step in the de novo biosynthesis of pyrimidine, the conversion of N-carbamoyl- L-aspartate into dihydroorotate
YP_003918325.1	catalyzes the reversible conversion of aspartate to fumarate and ammonia
YP_003918326.1	identified by similarity to protein SP:Q01269 (Pseudomonas aeruginosa). Forms an alternative pathway for phenylalanine biosynthesis. Can catalyze two reactions: prephenate dehydratase (EC 4.2.1.51: Prephenate = phenylpyruvate + H2O + CO2) and arogenate dehydratase (EC 4.2.1.91: L-arogenate = L-phenylalanine + H2O + CO2)
YP_003918327.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003918328.1	major facilitator superfamily (MFS), metabolite:H+ symporter (MHS) family (TC 2.A.1.6.z)
YP_003918329.1	identified by match to PF00456: transketolase, thiamine diphosphate binding domain
YP_003918330.1	identified by match to PF02779 (transketolase, pyrimidine binding domain) and PF02780 (transketolase, C- terminal domain)
YP_003918331.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003918332.1	match to PF01381: helix-turn-helix. This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003918333.1	identified by match to PF07804 (HipA-like C- terminal domain) and PF07805 (HipA-like N-terminal domain). The HipA protein is known to be involved in high- frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis. When expressed alone, it is toxic to bacterial cells but it is usually tightly associated with HipB and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products
YP_003918334.1	match to protein family PF00724: NADH:flavin oxidoreductase / NADH oxidase family
YP_003918335.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003918336.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, fused ATP- binding protein (ABC2), CBY-family (Cobalt uptake, unknown), Y179-subfamily (CBU-like systems). The function of CBU-like systems is unknown
YP_003918337.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease (IM), CBY-family (Cobalt uptake, unknown), Y179-subfamily (CBU-like systems). The function of CBU-like systems is unknown
YP_003918338.1	6 transmembrane helices predicted by TMHMM2.0
YP_003918339.1	catalyzes the hydrolysis of all of the commonly occuring purine and pyrimidine nucleosides into ribose and the associated base, but has a preference for inosine and uridine as substrates
YP_003918340.1	possible DNA or RNA helicase
YP_003918341.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003918342.1	major facilitator superfamily (MFS), Anion:Cation Symporter (ACS) Family, galactonate uptake (TC 2.A.1.14.7)
YP_003918343.1	catalyzes the first reaction in the D-galactonate catabolic pathway
YP_003918344.1	catalyzes the third reaction in the D-galactonate catabolic pathway
YP_003918345.1	catalyzes the second reaction in the D-galactonate catabolic pathway
YP_003918346.1	identified by match to PF09339: IclR helix-turn- helix domain. This family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003918347.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OPN-family (oligopeptides and nickel)
YP_003918348.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), OPN-family (oligopeptides and nickel)
YP_003918349.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, binding protein (BP), OPN-family (oligopeptides and nickel)
YP_003918350.1	TCDB: ATP-binding cassette (ABC) superfamily, peptide/opine/nickel uptake transporter (PepT) family (TC 3.A.1.5.z). ABCISSE: ABC transporter, permease (IM), OPN- family (oligopeptides and nickel)
YP_003918351.1	possible glutamate--cysteine ligase (6.3.2.2). Match to protein family PF04107: glutamate-cysteine ligase family 2(GCS2)
YP_003918353.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918355.1	identified by match to SM00705: CDGSH-type zinc finger domain. Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, however they are now recognised to bind DNA, RNA, protein and/or lipid substrates. The CDGSH-type zinc finger contains a CDGSH sequence motif (although the Ser residue can also be an Ala or Thr), and is found in proteins from a wide range of organisms with the exception of fungi. Proteins carrying this domain include ferredoxin-dependent glutamate synthase. CDGSH-type domains are also found in the iron-containing outer membrane protein mitoNEET. MitoNEET contains the conserved sequence C-X-C-X2-(S/T)-X3- P-X-C-D-G-(S/A/T)-H, a defining feature of CDGSH domains, and is likely involved in iron binding rather than zinc binding
YP_003918357.1	match to protein family TIGR01382. A role in the degradation of small peptides has been suggested
YP_003918360.1	NhaA Na+:H+antiporter (NhaA) family (TC 2.A.33.y.z). Na(+)/H(+) antiporter extrudes sodium in exchange for external protons. Active at alkaline pH. In E. coli, NhaA protein probably functions in the regulation of the internal pH when the external pH is alkaline. It also uses the H+ gradient to expel Na+ from the cell. Its activity is highly pH dependent
YP_003918361.1	TCDB: ATP-binding cassette (ABC) superfamily, phosphate uptake transporter (PhoT) family, phosphate transporter (TC 3.A.1.7.2). ABCISSE: ABC transporter, binding protein (BP), MOI-family, phosphate import. Part of an ABC transporter complex involved in phosphate import
YP_003918362.1	3 transmembrane helices predicted by TMHMM2.0
YP_003918364.1	possible glutamate--cysteine ligase (6.3.2.2). Match to protein family PF04107: glutamate-cysteine ligase family 2(GCS2)
YP_003918365.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.502) with cleavage site probability 0.387 between position 20 and 21
YP_003918366.1	ArsC reduces arsenate [As(V)] to arsenite [As(III)] and dephosphorylates tyrosine phosphorylated proteins, low- MW aryl phosphates and natural and synthetic acyl phosphates. Could switch between different functions in different circumstances
YP_003918367.1	Arsenical Resistance-3 (ACR3) Family, ArsB arsenite/antimonite exporter (TC 2.A.59.1.2). Identified by similarity to protein SP: P45946 (Bacillus subtilis). Confers resistance to arsenite by allowing cells to extrude this compound
YP_003918368.1	identified by match to PF01022: bacterial regulatory protein, ArsR family. ArsR-family transcriptional regulators include several proteins that appear to dissociate from DNA in the presence of metal ions
YP_003918369.1	identified by match to SM00705: CDGSH-type zinc finger domain. Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, however they are now recognised to bind DNA, RNA, protein and/or lipid substrates. The CDGSH-type zinc finger contains a CDGSH sequence motif (although the Ser residue can also be an Ala or Thr), and is found in proteins from a wide range of organisms with the exception of fungi. Proteins carrying this domain include ferredoxin-dependent glutamate synthase. CDGSH-type domains are also found in the iron-containing outer membrane protein mitoNEET. MitoNEET contains the conserved sequence C-X-C-X2-(S/T)-X3- P-X-C-D-G-(S/A/T)-H, a defining feature of CDGSH domains, and is likely involved in iron binding rather than zinc binding
YP_003918373.1	4 transmembrane helices predicted by TMHMM2.0
YP_003918377.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690
YP_003918378.1	possible transporter. Match to PF00571 (CBS domain pair)
YP_003918379.1	possible transporter. Match to PF00571 (CBS domain pair)
YP_003918380.1	glutaminase catalyzes the hydrolysis of glutamine to a glutamate and ammonia
YP_003918381.1	N-terminal section of the protein: COG4781 (membrane domain of membrane-anchored glycerophosphoryl diester phosphodiesterase); 7 transmembrane helices predicted by TMHMM2.0. C-terminal section of the protein: match to PF03009 (glycerophosphoryl diester phosphodiesterase family). Escherichia coli has two sequence related isozymes of glycerophosphoryl diester phosphodiesterase (GDPD) - periplasmic and cytosolic. glycerophosphoryl diester phosphodiesterases display broad specificity for glycerophosphodiesters; glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol, and bis(glycerophosphoglycerol)
YP_003918382.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.992) with cleavage site probability 0.758 between position 37 and 38
YP_003918383.1	identified by match to PF00296. Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulfonate monooxygenase (SsuD), and coenzyme F420- dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds
YP_003918386.1	identified by match to protein family PF00246: zinc carboxypeptidase
YP_003918388.1	Solute:Sodium Symporter (SSS) family (2.A.21.y.z). Members of the SSS family catalyze solute:Na+ symport. The solutes transported may be sugars, amino acids, organo cations such as choline, nucleosides, inositols, vitamins, urea or anions, depending on the system
YP_003918389.1	identified by match to PF07905: purine catabolism regulatory protein-like family. The bacterial proteins found in this family are similar to the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, O32138). PucR is thought to be a transcriptional activator involved in the induction of the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression. The other members of this family are also annotated as being  regulatory proteins
YP_003918390.1	catalyses the following reaction: 10- formyltetrahydrofolate + H(2)O <=> formate + tetrahydrofolate
YP_003918391.1	identified by match to protein family PF00392. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector- binding/oligomerisation domain. The GntR-like proteins can be divided into six sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships
YP_003918394.1	C-terminal part of the protein: Sigma 70 regions 2 and 4 (PF04542, PF08281). Presence of numerous PT repeats (XPTX) at the C-terminal part of the protein
YP_003918395.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918396.1	match to PF00535: glycosyl transferase family 2. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP- N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids
YP_003918400.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918401.1	match to PF00196: bacterial regulatory proteins, luxR family. This domain is a DNA-binding, helix-turn- helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators
YP_003918403.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918404.1	hydrolyzes allantoin into allantoate. Involved in purine degradation
YP_003918405.1	catalyses the following reaction: 2 glyoxylate <=> tartronate semialdehyde + CO(2)
YP_003918407.1	catalyses the following reaction: (R)-glycerate + NAD(P)(+) <=> 2-hydroxy-3-oxopropanoate + NAD(P)H
YP_003918408.1	catalyses the following reaction: hydroxypyruvate <=> 2-hydroxy-3-oxopropanoate
YP_003918409.1	Nucleobase:Cation Symporter-1 (NCS1) Family (TC 2.A. 39.y.z)
YP_003918410.1	identified by similarity to protein SP:Q00924 (Pseudomonas sp. strain NS671). Match to protein family PF01177: Asp/Glu/Hydantoin racemase. Hydantoin racemase is responsible for racemization of the D-5-substituted hydantoins to their corresponding L-amino acids
YP_003918416.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, binding protein (BP), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003918417.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003918418.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003918419.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, ATP-binding protein (ABC), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003918421.1	match to protein family PF07690: Major Facilitator Superfamily
YP_003918422.1	carbonate dehydratases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide. They are ubiquitous enzymes involved in fundamental processes like respiration, pH homeostasis and ion transport. Signal peptide predicted by SignalP 3.0 HMM (probability: 0.975) with cleavage site probability 0.621 between position 42 and 43
YP_003918423.1	identified by match to PF00440: bacterial regulatory proteins, tetR family
YP_003918424.1	enzymes named acetyl-coenzyme A carboxylase (EC 6.4. 1.2), propionyl-coenzyme A carboxylase (EC 6.4.1.3) and acyl-coenzyme A carboxylase are constituted by several types of subunits. Alpha subunits contains the biotin carboxylase (BC, EC 6.3.4.14) and biotin carboxyl carrier protein (BCCP) domains, beta subunits contain the carboxyltransferase (CT) domain. An epsilon subunit is present in some microorganisms
YP_003918425.1	enzymes named acetyl-coenzyme A carboxylase (EC 6.4. 1.2), propionyl-coenzyme A carboxylase (EC 6.4.1.3) and acyl-coenzyme A carboxylase are constituted by several types of subunits. Alpha subunits contains the biotin carboxylase (BC, EC 6.3.4.14) and biotin carboxyl carrier protein (BCCP) domains, beta subunits contain the carboxyltransferase (CT) domain. An epsilon subunit is present in some microorganisms
YP_003918426.1	match to PF01575. Several bacterial proteins that are composed solely of this domain have (R)-specific enoyl- CoA hydratase activity
YP_003918427.1	citrate lyase catalyses the formation of acetate and oxaloacetate from citrate
YP_003918428.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918430.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918431.1	major facilitator superfamily (TC 2.A.1.y.z). Identified by match to protein family PF07690
YP_003918432.1	4 transmembrane helices predicted by TMHMM2.0
YP_003918435.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918437.1	4 transmembrane helices predicted by TMHMM2.0
YP_003918438.1	3 transmembrane helices predicted by TMHMM2.0
YP_003918439.1	3 transmembrane helices predicted by TMHMM2.0
YP_003918440.1	identified by match to PF00753: metallo-beta- lactamase superfamily. Apart from the beta-lactamases, a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl- glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake
YP_003918441.1	identified by match to PF00126: bacterial regulatory helix-turn-helix protein, lysR family. Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini
YP_003918443.1	possibly involved in the metabolism of lipids. Match to PF08028. Acyl-CoA dehydrogenases catalyze the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD
YP_003918444.1	possibly involved in the metabolism of lipids. Match to PF08028, PF02770 and PF02771. Acyl-CoA dehydrogenases catalyze the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD
YP_003918445.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003918446.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, permease (IM), ISVH-family (iron siderophores, vitamin B12 and hemin)
YP_003918447.1	identified by match to protein family PF04954. Match to protein domain PF08021. Possibly involved in removal of iron from iron-siderophore complexes
YP_003918448.1	TCDB: ATP-binding cassette (ABC) superfamily, iron chelate uptake transporter (FeCT) family (TC 3.A.1.14.z). ABCISSE: ABC transporter, binding protein (BP), ISVH- family (iron siderophores, vitamin B12 and hemin)
YP_003918449.1	identified by match to PF01648: 4- phosphopantetheinyl transferase superfamily. Holo-[acyl- carrier-protein] synthase catalyses the following reaction: CoA-(4-phosphopantetheine) + apo-[acyl-carrier- protein] => adenosine 3,5-bisphosphate + holo-[acyl- carrier-protein]. All polyketide synthases, fatty-acid synthases and non-ribosomal peptide synthases require post- translational modification of their constituent acyl- carrier-protein (ACP) domains to become catalytically active. The inactive apo-proteins are converted into their active holo-forms by transfer of the 4-phosphopantetheinyl moiety of CoA to the sidechain hydroxy group of a conserved serine residue in each ACP domain
YP_003918450.1	Major Facilitator Superfamily (MFS), Enterobactin (Siderophore) Exporter (EntS) Family (TC 2.A.1.38.z)
YP_003918451.1	identified by match to protein domain PF03621. This domain is found in the MbtH protein O05821 (probably involved in mycobactin synthesis) as well as at the N terminus of the antibiotic synthesis protein NIKP1. Many of the members of this family are found in known antibiotic synthesis gene clusters. Possible involvement in the synthesis of siderophore group non-ribosomal peptides
YP_003918457.1	L-ornithine 5-monooxygenase catalyzes the conversion of L-ornithine into N5-hydroxy-L-ornithine, which is later incorporated in the siderophore pyoverdin, produced by Pseudomonas aeruginosa
YP_003918458.1	similar to enterobactin synthase subunit E, which includes (2,3-dihydroxybenzoyl)adenylate synthase activity (EC 2.7.7.58)
YP_003918459.1	plays a role in the siderophore biosynthesis and in the bacillibactin biosynthesis
YP_003918460.1	involved in the third stage of enterobactin (siderophore peptide) biosynthesis, the conversion of 2,3- dihydro-2,3-dihydroxybenzoate into 2,3-dihydroxybenzoate
YP_003918461.1	involved in the second stage of enterobactin (siderophore peptide) biosynthesis, the conversion of isochorismate into 2,3-dihydroxy-2,3-dihydrobenzoate
YP_003918462.1	signal peptide predicted by SignalP 3.0 HMM (probability: 1.000) with cleavage site probability 0.995 between position 30 and 31
YP_003918463.1	identified by similarity to protein SP:O31168 (Streptomyces aureofaciens). Catalyzes the following reaction: 2 RH + 2 Cl(-) + H(2)O(2) <=> 2 RCl + 2 H(2)O. Brings about the chlorination of a range of organic molecules, forming stable C-Cl bonds
YP_003918465.1	Gluconate:H+ Symporter (GntP) Family (TC 2.A.8.y.z). Match to protein family PF02447
YP_003918466.1	match to protein domain PF05651:  sugar diacid recognition
YP_003918468.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.994) with cleavage site probability 0.846 between position 30 and 31
YP_003918469.1	catalyses the following reaction: ATP + (R)- glycerate <=> ADP + 3-phospho-(R)-glycerate
YP_003918471.1	Sulfate Permease (SulP) Family, sulfate permease (TC 2.A.53.3.1)
YP_003918473.1	activates fatty acids by binding to coenzyme A. Possibly involved in the synthesis of cellular lipids or their degradation via beta-oxidation
YP_003918474.1	possibly involved in the regulation of the catechol catabolism.Match to PF00126: bacterial regulatory helix- turn-helix protein, lysR family
YP_003918475.1	identified by similarity to protein SP:Q76CC6 (Arthrobacter sp.). Involved in the degradation of aromatic compounds by converting cis,cis-muconate, the product of catechol ring cleavage to (4S)-muconolactone
YP_003918476.1	catalyses the third step in the catabolism of catechol to succinyl-CoA and acetyl-CoA in the beta- ketoadipate pathway
YP_003918477.1	catalyses the third step in the catabolism of catechol to succinyl-CoA and acetyl-CoA in the beta- ketoadipate pathway: the intradiol cleavage reaction of catechol to form cis,cis-muconate
YP_003918478.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.966) with cleavage site probability 0.717 between position 31 and 32. 3 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003918479.1	identified by match to cd00085: HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins
YP_003918480.1	major facilitator superfamily (MFS), drug:H+ antiporter-3 (12 spanner) (DHA3) family, multidrug (erythromycin, tetracycline, puromycin, bleomycin) resistance protein Cmr (TC 2.A.1.21.2). Identified by similarity to protein SP:Q79VC7 (Corynebacterium glutamicum). Probable drug antiporter which uses the proton motive force for the active efflux drugs
YP_003918481.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.976) with cleavage site probability 0.942 between position 24 and 25. 3 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003918483.1	electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, (housekeeping) ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II). They consist of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit
YP_003918484.1	electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, (housekeeping) ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II). They consist of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit
YP_003918485.1	6 transmembrane helices predicted by TMHMM2.0
YP_003918486.1	identified by match to protein domain PF08241
YP_003918490.1	match to PF02492 (CobW/HypB/UreG, nucleotide- binding domain) and PF07683 (Cobalamin synthesis protein cobW C-terminal domain). In Pseudomonas denitrificans, the cobW gene product may be involved in cobalamin biosynthesis
YP_003918491.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918494.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits: subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003918495.1	identified by match to PF02661: Fic protein family. cAMP may be a regulation factor in cell division of some bacteria. The Fic (filamentation induced by cAMP) protein is involved in the synthesis of PAB or folate. It would appear that the Fic protein and cAMP are involved in a regulatory mechanism of cell division via folate metabolism and in these organisms cell division could be controlled by coordination of cAMP, Fic and Fts proteins
YP_003918496.1	identified by match to PF04471. Mrr is involved in the acceptance of foreign DNA which is modified. Restricts both adenine- and cytosine-methylated DNA
YP_003918497.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits: subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003918498.1	type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. They have three different subunits: subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC:3.1.21.3), methylase (EC:2.1.1.72) and ATPase activities. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence
YP_003918503.1	presence of 2 conserved barrel domains of the cupin superfamily (PF07883)
YP_003918505.1	catalyzes the aldol condensation of glyoxylate with acetyl-CoA to form malate, the second step of the glyoxylate bypass, an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants
YP_003918506.1	catalyzes the oxidative decarboxylation of malate into pyruvate. Uses preferentially NAD and has the ability to decarboxylate oxaloacetate
YP_003918507.1	this family of bacterial transcriptional regulators groups several proteins, including gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces, and iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium
YP_003918508.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease and ATP-binding protein (IM-ABC), DPL-family, prokaryote drug export (PED) subfamily. Possible function in in antibiotic peptide or drug resistance or production (export)
YP_003918509.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003918510.1	identified by match to PF00248 family: Aldo/keto reductase family. This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity
YP_003918511.1	identified by match to protein family PF00795. This family contains nitrilases that break carbon-nitrogen bonds and appear to be involved in the reduction of organic nitrogen compounds and ammonia production. They all have distinct substrate specificity and include cyanide hydratases, aliphatic amidases, beta-alanine synthase, and a few other proteins with unknown molecular function
YP_003918512.1	identified by match to PF01408 (oxidoreductase family, NAD-binding Rossmann fold)
YP_003918513.1	catalyses the formation of UDP-glucose from UDP- galactose. Involved in the catabolism of galactose
YP_003918514.1	catalyzes the conversion of galactose to galactose 1-phosphate, first step of the Leloir pathway
YP_003918515.1	involved in conversion of galactose into alpha-D- glucose 1-phosphate, second step of the Leloir pathway
YP_003918516.1	DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway
YP_003918517.1	match to PF00440: bacterial regulatory proteins, tetR family
YP_003918518.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1. 1.z). ABCISSE: ABC transporter, binding protein (BP), OSP-family (oligosaccharides or polyols)
YP_003918519.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1. 1.z). ABCISSE: ABC transporter, permease (IM), OSP- family (oligosaccharides or polyols)
YP_003918520.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-1 (CUT1) family (TC 3.A.1. 1.z). ABCISSE: ABC transporter, permease (IM), OSP- family (oligosaccharides or polyols)
YP_003918521.1	hydrolysis of terminal non-reducing beta-D- galactose residues in beta-D-galactosides. Some enzymes in this group hydrolyze alpha-L-arabinosides
YP_003918522.1	identified by match to protein family PF1263. Aldose 1-epimerase (mutarotase) is the enzyme responsible for the anomeric interconversion of D-glucose and other aldoses (L-arabinose, D-xylose, D-galactose, maltose and lactose) between their alpha- and beta-forms
YP_003918523.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-2 (CUT2) family (TC 3.A.1. 2.z). ABCISSE: ABCISSE: ABC transporter, permease (IM), MOS-family (monosaccharides: pentoses and hexoses). Possibly involved in the uptake of multiple sugars such as arabinose, xylose, galactose, glucose, fucose
YP_003918524.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-2 (CUT2) family (TC 3.A.1. 2.z). ABCISSE: ABCISSE: ABC transporter, fused ATP- binding protein (ABC2), MOS-family (monosaccharides: pentoses and hexoses). Possibly involved in the uptake of multiple sugars such as arabinose, xylose, galactose, glucose, fucose
YP_003918525.1	TCDB: ATP-binding cassette (ABC) superfamily, carbohydrate uptake transporter-2 (CUT2) family (TC 3.A.1. 2.z). ABCISSE: ABCISSE: ABC transporter, binding protein (BP), MOS-family (monosaccharides: pentoses and hexoses). Possibly involved in the uptake of multiple sugars such as arabinose, xylose, galactose, glucose, fucose
YP_003918526.1	catalyzes the isomerization of L-arabinose to L- ribulose, the first reaction in its conversion into D- xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source
YP_003918527.1	catalyses the following reaction: L-ribulose 5- phosphate <=> D-xylulose 5-phosphate. Involved in the metabolism of L-arabinose
YP_003918528.1	catalyzes the formation of L-ribulose 5-phosphate from L-ribulose. Involved in the catabolism of L- arabinose. Match to protein domain PF00370: FGGY family of carbohydrate kinases, N-terminal domain
YP_003918529.1	match to protein domain PF00356. Numerous bacterial transcription regulatory proteins bind DNA via a helix- turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR. Within this family, the HTH motif is situated towards the N-terminus
YP_003918530.1	nucleobase:cation symporter-2 (NCS2) Family (TC 2.A. 40.y.z). Match to protein family PF00860
YP_003918531.1	catalyses the formation of 5-hydroxyisourate from urate. The latter decomposes spontaneously to form allantoin
YP_003918532.1	identified by match to PF00576: HIUase/Transthyretin family. This family includes transthyretin that is a thyroid hormone-binding protein that transports thyroxine from the bloodstream to the brain. However, most of the sequences listed in this family do not bind thyroid hormones. They are actually enzymes of the purine catabolism that catalyse the conversion of 5-hydroxyisourate (HIU) to 5-hydroxy-2-oxo-4- ureido-2,5-dihydro-1H-imidazole-5- carboxylate (OHCU). HIU hydrolysis is the original function of the family and is conserved from bacteria to mammals; transthyretins arose by gene duplications in the vertebrate lineage
YP_003918537.1	Auxin Efflux Carrier (AEC) Family (TC 2.A.69.y.z). Homologues of the AEC family are found in bacteria as well as in archaea. The K. pneumoniae homologues has been implicated in malonate uptake, the O. oeni homologue is a malate permease
YP_003918538.1	identified by match to PF00106. The short-chain dehydrogenases/reductases family (SDR) is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases
YP_003918541.1	identified by match to protein family PF01047. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds
YP_003918542.1	identified by match to PF02678. Pirin was identified to be a metal-binding protein, and it was found that the metal-binding residues of Pirins are highly conserved across mammals, plants, fungi, and prokaryotic organisms
YP_003918543.1	identified by match to PF00583: acetyltransferase (GNAT) family
YP_003918544.1	major facilitator superfamily, drug:H+ antiporter-2 (14 spanner) (DHA2) family (TC 2.A.1.3.z). Match to PR01036: Tetracycline resistance protein TetB signature
YP_003918545.1	match to protein family PF00929. This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III
YP_003918546.1	signal peptide predicted by SignalP 3.0 HMM (probability: 0.832) with cleavage site probability 0.394 between position 23 and 24. 7 transmembrane helices predicted by TMHMM2.0 after the signal peptide
YP_003918547.1	a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. DnaB is a DNA helicase which exhibits DNA-dependent ATPase activity
YP_003918548.1	identified by match to PF01613
YP_003918549.1	match to protein family PF00501. This family of enzymes includes luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely- related synthetases
YP_003918550.1	match to protein domain PF03061: thioesterase superfamily
YP_003918551.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918552.1	3 transmembrane helices predicted by TMHMM2.0
YP_003918553.1	match to protein domain PF01872. This domain is found in the C-terminus of the bifunctional deaminase- reductase in combination with PF00383 as well as in isolation in some archaebacterial proteins
YP_003918554.1	identified by match to PF07995. Proteins containing this domain are thought to be glucose/sorbosone dehydrogenases. Quinoprotein glucose dehydrogenase catalyses the following reaction: D-glucose + ubiquinone => D-glucono-1,5-lactone + ubiquinol. It is a PQQ- containing quinoprotein that catalyzes a direct oxidation of D-glucose to D-gluconate in the periplasm of some bacteria and concomitantly transfers electrons to ubiquinol oxidase through ubiquinone in the respiratory chain. Signal peptide predicted by SignalP 3.0 HMM (probability: 0.982) with cleavage site probability 0.254 between position 48 and 49
YP_003918555.1	identified by similarity to protein SP:P38946 (Clostridium kluyveri). Succinyl-CoA:coenzyme A transferase forms succinyl-CoA from succinate and acetyl- CoA and is believed to be involved in anaerobic succinate degradation
YP_003918556.1	match to PF01381: helix-turn-helix. This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003918557.1	binds to the 23S rRNA
YP_003918558.1	part of the 30S ribosomal subunit. Forms a tight heterodimer with protein S6
YP_003918559.1	this protein is essential for replication of the chromosome. It is also involved in DNA recombination and repair
YP_003918560.1	binds together with S18 to 16S ribosomal RNA
YP_003918561.1	match to protein domain PF01757. This family includes a range of acyltransferase enzymes. 9 transmembrane helices predicted by TMHMM2.0
YP_003918562.1	match to PF01381: helix-turn-helix. This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)
YP_003918564.1	match to protein family PF02127. This group of metallopeptidases belong to the MEROPS peptidase family M18, (clan MH). The catalysed reaction involves the release of an N-terminal aminoacid, usually neutral or hydrophobic, from a polypeptide
YP_003918565.1	2 transmembrane helices predicted by TMHMM2.0
YP_003918566.1	response regulators are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions
YP_003918567.1	protein-histidine kinases are key elements in two- component signal transduction systems, which enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. 5 transmembrane helices predicted by TMHMM2.0
YP_003918568.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, permease (IM), DRI-family, DRB-subfamily (drug resistance, ). Possible function in drug efflux
YP_003918569.1	TC 3.A.1.y.z. ABCISSE: ABC transporter, ATP-binding protein (ABC), DRI-family, DRB-subfamily (drug resistance, ). Possible function in drug efflux
YP_003918570.1	6 transmembrane helices predicted by TMHMM2.0
YP_003918572.1	8 transmembrane helices predicted by TMHMM2.0
YP_003918573.1	match to protein family PF02348. EC 2.7.7.43 catalyzes the reaction of CTP and NeuAc to form CMP-NeuAc, which is the nucleotide sugar donor used by sialyltransferases. The outer membrane lipooligosaccharides of some microorganisms contain terminal sialic acid attached to N-acetyllactosamine
YP_003918574.1	match to protein family PF03102. EC 2.5.1.57 catalyses the direct formation of Neu5Ac (the most common sialic acid) by condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc)
YP_003918575.1	match to PF00535: glycosyl transferase family 2. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP- N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids
YP_003918579.1	inositol-3-phosphate synthase is also named myo- inositol-1-phosphate synthase. It catalyses the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated to inositol. Inositol phosphates play an important role in signal transduction
YP_003918581.1	identified by match to protein family TIGR02692. Can add or repair the required CCA triplet at the 3 -end of tRNA molecules
YP_003918582.1	identified by match to PF00293. Members of the Nudix hydrolase superfamily catalyze the hydrolysis of nucleoside diphosphates linked to other moieties. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and house- cleaning enzymes
YP_003918583.1	identified by match to protein family PF03023. Deletion of the mviN virulence gene in Salmonella enterica serovar. Typhimurium greatly reduces virulence in a mouse model of typhoid-like disease. Open reading frames encoding homologues of MviN have since been identified in a variety of bacteria including pathogens and non- pathogens and plant-symbionts. In the nitrogen-fixing symbiont Rhizobium tropici, mviN is required for motility. The MviM protein is predicted to be membrane-associated
YP_003918584.1	1 transmembrane helice predicted by TMHMM2.0
YP_003918585.1	catalyses the following reaction: thioredoxin + NADP(+) <=> thioredoxin disulfide + NADPH. It supplies reducing equivalents for a wide variety of reactions, for example for pyrimidine synthesis
YP_003918586.1	serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of 2 cysteine thiol groups to a disulphide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulphide and a dithiol
YP_003918589.1	identified by match to TIGR00180. This HMM represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction
YP_003918590.1	ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single- stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis
YP_003918591.1	GidB (glucose-inhibited division protein B) appears to be present and in a single copy in all complete eubacterial genomes so far. Its mode of action is unknown, but a methytransferase fold is reported from the crystal structure. It may be a family of bacterial glucose inhibited division proteins that are involved in the regulation of cell division
YP_003918592.1	identified by match to protein domain PF01424. The function of the domain is predicted to be binding ssDNA
YP_003918593.1	The preprotein translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF). Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA
YP_003918595.1	identified by match to protein family PF00825. Ribonuclease P (EC 3.1.26.5) is a site specific endonuclease that generates mature tRNAs by cleaving-off the leader sequences at their 5 ends. In bacteria RNase P is known to be composed of two components: a large (about 400 base pairs) RNA (gene rnpB) and a small protein (119 to 133 amino acids) (gene rnpA)
YP_003918596.1	one of the proteins from the large subunit of the prokaryotic ribosome