-- dump date   	20140619_042245
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_001708795.1	binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself.
YP_001708796.1	binds the polymerase to DNA and acts as a sliding clamp
YP_001708797.1	Nu
YP_001708798.1	similar to full-length Gnd, these proteins seems to have a truncated C-terminal 6PGD domainin; in Methylobacillus flagellatus this gene is essential for NAD+-dependent oxidation of 6-phosphogluconate
YP_001708799.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_001708801.1	negatively supercoils closed circular double-stranded DNA
YP_001708802.1	negatively supercoils closed circular double-stranded DNA
YP_001708818.1	P
YP_001708822.1	smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group do not have the motif
YP_001708824.1	May have alternative downstream translational start site.
YP_001708825.1	PS00134 Serine proteases, trypsin family, histidine active site.
YP_001708826.1	Contains N- and C-terminal hydrophobic regions, 9x YD repeat and  sortase recognition site.
YP_001708830.1	N/R/C?
YP_001708841.1	PS00017 ATP/GTP-binding site motif A (P-loop)
YP_001708844.1	alpha-N-arabinofuranosidase (arabinosidase)
YP_001708845.1	Nu/R
YP_001708855.1	contains an N terminal GntR region and a C terminal FAD-dependent oxidoreductase
YP_001708874.1	N/R/C Appears to be associated with the deletion of the central portion of an EPS cluster and the insertion of a sugar hydrolase with the same Pfam match as Cmm tomatinase
YP_001708896.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_001708897.1	class II; LysRS2; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri, LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1
YP_001708903.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_001708904.1	present in two forms; L12 is normal, while L7 is aminoacylated at the N-terminal serine; the only multicopy ribosomal protein; 4:1 ratio of L7/L12 per ribosome; two L12 dimers bind L10; critically important for translation efficiency and fidelity; stimulates GTPase activity of translation factors
YP_001708913.1	Appears to have an N-terminal extension relative to homologues.
YP_001708916.1	catalyzes the formation of cystathionine from L-cysteine and O-succinyl-L-homoserine
YP_001708919.1	catalyzes the phosphorylation of ribulose to ribulose 5-phosphate
YP_001708920.1	catalyzes the formation of D-xylulose 5-phosphate from L-ribulose 5-phosphate
YP_001708921.1	catalyzes the formation of L-ribulose from L-arabinose in L-arabinose catabolism
YP_001708928.1	N/C
YP_001708929.1	catalyzes the interconversion of D-xylose to D-xylulose
YP_001708941.1	catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate
YP_001708942.1	AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation; utilizes magnesium and ATP; also involved in conversion of acetate to aceyl-CoA
YP_001708946.1	catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA
YP_001708947.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_001708948.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.
YP_001708949.1	catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde
YP_001708950.1	malate dehydrogenase; catalyzes the oxidation of malate to oxaloacetate
YP_001708952.1	catalyzes the formation of thymidine 5'-phosphate from thymidine
YP_001708958.1	May confer antibiotic resistance
YP_001708975.1	catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA
YP_001708986.1	Overlap with downstream CDS possibly due to mutation leading to late stop.
YP_001708988.1	Has hydrophobis regions but no predicted membrane spans.
YP_001708997.1	N/R
YP_001709005.1	Nu
YP_001709019.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate; uridine 5'-monophosphate synthase
YP_001709028.1	Contains possible coiled-coil region.
YP_001709031.1	Includes proline-rich N-terminal region which may not be real
YP_001709035.1	C-terminal region similar to sugar synthases eg. UniProt:SUSY_BETVU (EMBL:BVSSMRNA) Beta vulgaris (Sugar beet) Sucrose synthase
YP_001709049.1	Nu/R
YP_001709051.1	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme
YP_001709052.1	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Subunit beta' binds to sigma factor allowing it to bind to the -10 region of the promoter
YP_001709059.1	interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance
YP_001709060.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_001709061.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_001709062.1	EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu
YP_001709064.1	NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex
YP_001709065.1	binds directly near the 3' end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene confer resistance to tiamulin
YP_001709066.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_001709067.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_001709068.1	one of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation
YP_001709069.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_001709070.1	binds specifically to 23S rRNA during the early stages of 50S assembly; makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome; mutations in this gene result in erythromycin resistance; located near peptidyl-transferase center
YP_001709071.1	forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation
YP_001709072.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_001709074.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_001709075.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_001709076.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_001709077.1	part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13
YP_001709079.1	ribosomal protein L6 appears to have arisen as a result of an ancient gene duplication as based on structural comparison of the Bacillus stearothermophilus protein; RNA-binding appears to be in the C-terminal domain; mutations in the L6 gene confer resistance to aminoglycoside antibiotics such as gentamicin and these occur in truncations of the C-terminal domain; it has been localized to a region between the base of the L7/L12 stalk and the central protuberance
YP_001709080.1	binds 5S rRNA along with protein L5 and L25
YP_001709081.1	located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance
YP_001709082.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_001709083.1	late assembly protein
YP_001709084.1	forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase
YP_001709085.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_001709094.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_001709095.1	smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group have the motif
YP_001709096.1	located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA; makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5; contacts P-site tRNA
YP_001709097.1	located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome; interacts with S7 and S18 and IF-3
YP_001709098.1	catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Dimerization of the alpha subunit is the first step in the sequential assembly of subunits to form the holoenzyme
YP_001709099.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_001709101.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_001709102.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_001709103.1	forms a direct contact with the tRNA during translation
YP_001709104.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_001709105.1	N/R
YP_001709106.1	Nu/R
YP_001709118.1	part of the FhuBCD ATP-dependent iron (III) hydroxamate transporter involved in the high-affinity transport of Fe(3+)-ferrichrome
YP_001709130.1	Suspiciously late stop codon
YP_001709161.1	May be a gene remnant
YP_001709162.1	Homolog in Aeromonas hydrophila only identified in subtractive hybridisation between virulent and avirulent strains. Lies in low GC region.
YP_001709163.1	Homolog in Aeromonas hydrophila only identified in subtractive hybridisation between virulent and avirulent strains. Lies in low GC region.
YP_001709166.1	Possible gene remnant
YP_001709171.1	N/R/C?
YP_001709178.1	Possibly sortase sorted
YP_001709198.1	Nu/R
YP_001709203.1	catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate
YP_001709206.1	catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_001709210.1	Nu
YP_001709216.1	Frameplot suggests that this CDS does not have a legitimate translational stop
YP_001709222.1	Nu
YP_001709225.1	Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5)
YP_001709228.1	N/R/C
YP_001709237.1	catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions
YP_001709252.1	Frameplot suggests that the coding sequence may extend downstream
YP_001709255.1	P/R/C Part of NRPS disruption. The apparent cargo may have arrived after the recombination
YP_001709262.1	Similar to downstream CDS
YP_001709263.1	Similar to upstream CDS
YP_001709287.1	N/R/C
YP_001709288.1	catalyzes the formation of (R)-4'-phosphopantothenate in coenzyme A biosynthesis
YP_001709289.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_001709290.1	Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids
YP_001709292.1	Appears to be a fusion of an alanine racemase with an ATP-binding domain of unknown function
YP_001709294.1	C-terminal region similar to known O-sialoglycoprotein endopeptidase UniProt:GCP_PASHA (EMBL:A38108), N-terminal contains PF00583, GCN5-related N-acetyltransferase domain.
YP_001709297.1	10 kDa chaperonin; Cpn10; GroES; forms homoheptameric ring; binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it; folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES; release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring
YP_001709306.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_001709309.1	Hydrophobicity profile typical of sortase-sorted surface proteins but no LPXTG motif or similar.
YP_001709311.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_001709313.1	P/R
YP_001709315.1	Matches (only) two proteins from secondary metabolism gene clusters.
YP_001709324.1	catalyzes the conversion of l-glutamate to a-N-acetyl-l-glutamate in arginine biosynthesis
YP_001709328.1	Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents
YP_001709329.1	Nu/R
YP_001709332.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_001709334.1	Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; in M. bovis this protein has been shown to be involved in expression of antigenic proteins
YP_001709339.1	Contains Pfam match to PF01551;Peptidase
YP_001709345.1	Nu/C
YP_001709352.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_001709353.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_001709357.1	GC Frameplot suggests that an earlier stop codon has been lost.
YP_001709364.1	Tandem duplication indicated by similarity to upstream CDS.
YP_001709365.1	Tandem duplication indicated by similarity to downstream CDS.
YP_001709366.1	Converts isocitrate to alpha ketoglutarate
YP_001709368.1	N/R
YP_001709374.1	catalyzes the formation of a purine and ribose phosphate from a purine nucleoside; in E. coli this enzyme functions in xanthosine degradation
YP_001709375.1	catalyzes the reduction of nonspecific electron acceptors such as 2,6-dimethyl-1,4-benzoquinone and 5-hydroxy-1,4-naphthaquinone; does not have lipoamide dehydrogenase activity
YP_001709381.1	P
YP_001709385.1	ligase
YP_001709388.1	With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway
YP_001709409.1	Tandem duplication suggested by similarity to upstream CDS.
YP_001709410.1	Tandem duplication suggested by similarity to downstream CDS.
YP_001709414.1	Nu
YP_001709420.1	converts mannose-6-phosphate to mannose-1-phosphate; the resulting product is then converted to GDP-mannose by ManC which is then used in the synthesis of mannose-containing glycoconjugates that are important for mediating entry into host cells
YP_001709424.1	catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine
YP_001709439.1	functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins
YP_001709448.1	Contains an N-terminal domain in common with CarD from Myxococcus xanthus Q50887 but does not include the C-terminal DNA-binding domain so is unlikely to carry out the equivalent regulation role.
YP_001709457.1	N/R
YP_001709463.1	Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_001709466.1	with DhaL and DhaM forms dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone; DhaK is the dihydroxyacetone binding subunit of the dihydroxyacetone kinase
YP_001709474.1	catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr)
YP_001709476.1	with PdxT forms pyridoxal 5'-phosphate from glutamine, either ribose 5-phosphate or ribulose 5-phosphate, and either glyceraldehyde 3-phosphate or dihydroxyacetone phosphate
YP_001709477.1	with PdxST is involved in the biosynthesis of pyridoxal 5'-phosphate; PdxT catalyzes the hydrolysis of glutamine to glutamate and ammonia; PdxS utilizes the ammonia to synthesize pyridoxal 5'-phosphate
YP_001709479.1	endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity
YP_001709480.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_001709481.1	promotes strand exchange during homologous recombination; RuvAB complex promotes branch migration; RuvABC complex scans the DNA during branch migration and resolves Holliday junctions at consensus sequences; forms hexameric rings around opposite DNA arms; requires ATP for branch migration and orientation of RuvAB complex determines direction of migration
YP_001709483.1	part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane
YP_001709484.1	forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF
YP_001709490.1	primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination
YP_001709492.1	Catalyzes a two-step reaction, first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_001709493.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_001709496.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_001709498.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_001709500.1	N/R
YP_001709506.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_001709508.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_001709509.1	cytoplasmic enzyme involved in processing rRNA and some mRNAs; substrates typically have dsRNA regions; forms a homodimer; have N-terminal nuclease and C-terminal RNA-binding domains; requires magnesium as preferred ion for activity
YP_001709510.1	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_001709518.1	binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity
YP_001709520.1	Essential for efficient processing of 16S rRNA
YP_001709521.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_001709524.1	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_001709526.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_001709534.1	one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit
YP_001709535.1	EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP resulting in regeneration of the active form of EF-Tu
YP_001709536.1	Catalyzes the phosphorylation of UMP to UDP
YP_001709537.1	Rrf; Frr; ribosome-recycling factor; release factor 4; RF4; recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G; A GTPase-dependent process results in release of 50S from 70S; inhibited by release factor RF-1; essential for viability; structurally similar to tRNAs
YP_001709545.1	Contains extensive coiled-coil regions
YP_001709548.1	catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain
YP_001709549.1	May have later translational start site but not one which aligns with homologs.
YP_001709550.1	Nu/R/C
YP_001709569.1	short-chain oxidoreductase
YP_001709579.1	No obvious LPXTG motif
YP_001709659.1	Nu
YP_001709680.1	N/R
YP_001709683.1	Nu
YP_001709691.1	Contains domains (PF02987, Late embryogenesis abundant protein) common to plant proteins.
YP_001709705.1	Similarity to downstream CDS suggests tandem duplication.
YP_001709708.1	C-terminal region matches No N-terminal matches. Non-heme chloroperoxidase from Pseudomonas fluorescens UniProt:PRXC_PSEFL (EMBL:AF031153).
YP_001709711.1	UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin
YP_001709714.1	Contains TITITITITITITITITIT repeat at N-terminus.
YP_001709725.1	possible secreted protein; Similarity with downstream CDS suggests tandem duplication.
YP_001709728.1	Nu
YP_001709729.1	N
YP_001709743.1	Possibly sortase sorted though no clear LPXTG motif
YP_001709744.1	threonine/alanine-rich
YP_001709762.1	N/R
YP_001709766.1	Weak match to PF01047 MarR family
YP_001709770.1	catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase
YP_001709771.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_001709774.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_001709775.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_001709785.1	Similarity to CMS1046 suggest local inverted duplication
YP_001709786.1	Nu/R
YP_001709789.1	Similarity to CMS1042 suggest local inverted duplication
YP_001709791.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_001709792.1	this protein catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction; essential for DNA replication and repair of damaged DNA; similar to ligase LigB
YP_001709795.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA
YP_001709796.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA
YP_001709800.1	Nu
YP_001709801.1	activates fatty acids by binding to coenzyme A
YP_001709803.1	Seems to lack the appropriate stop codon.
YP_001709822.1	activates fatty acids by binding to coenzyme A
YP_001709826.1	Nu/R
YP_001709830.1	catalyzes the formation of acetate from pyruvate
YP_001709836.1	C-terminus duplicated downstream.
YP_001709839.1	N/I
YP_001709846.1	catalyzes the formation of thiamine monophosphate from 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate
YP_001709893.1	catalyzes the formation of fumarate from aspartate
YP_001709894.1	Includes hydrophobic N-terminal region. Contains repetative region, repeat length approx 23 residues.
YP_001709898.1	Nu/C
YP_001709916.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_001709923.1	primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence
YP_001709932.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_001709935.1	flavin dependent thymidylate synthase; ThyX; thymidylate synthase complementing protein; catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate; the enzyme from Mycobacterium tuberculosis forms homotetramers; uses FAD as a cofactor
YP_001709945.1	catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs
YP_001709947.1	catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A)
YP_001709948.1	IPP transferase; isopentenyltransferase; involved in tRNA modification; in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity
YP_001709949.1	involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate
YP_001709952.1	Represses a number of genes involved in the response to DNA damage
YP_001709954.1	catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis
YP_001709955.1	with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide
YP_001709956.1	catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide and the formation of 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate from N-(5-phospho-beta-D-ribosyl)anthranilate; involved in histidine and tryptophan biosynthesis
YP_001709961.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_001709967.1	catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily
YP_001709968.1	catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a tetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily
YP_001709969.1	catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate
YP_001709970.1	bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate
YP_001709971.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate
YP_001709972.1	catalyzes the formation of N-acetyl-l-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine
YP_001709973.1	catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation
YP_001709974.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_001709975.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_001709977.1	responsible for recognizing base lesions in the genome and initiating base excision DNA repair
YP_001709982.1	HMMPfam:PF00702;Haloacid dehalogenase-like hydrolase
YP_001709984.1	low similarity to PF01728;Ribosomal RNA methyltransferase RrmJ/FtsJ, none to hemolysin
YP_001709985.1	catalyzes the phosphorylation of NAD to NADP
YP_001709987.1	CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer
YP_001709989.1	site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; XerD specifically exchanges the bottom strands; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs
YP_001709994.1	catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate
YP_001709996.1	synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains
YP_001709997.1	N/C pat1
YP_001709998.1	possible serine protease with a serine active site
YP_001710000.1	possible serine protease, contains both a serine and a histidine active site, probably secreted
YP_001710051.1	Homologs often associated with surface polysaccharide biosynthesis
YP_001710055.1	N
YP_001710056.1	Possible downstream translational start sites.
YP_001710058.1	Contains hydrophilic region.
YP_001710060.1	Contains leucine-rich repeat
YP_001710061.1	Stop position appears to have been extended by IS insertion.
YP_001710062.1	N
YP_001710078.1	biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate
YP_001710085.1	N
YP_001710091.1	MraZ; UPF0040; crystal structure shows similarity to AbrB
YP_001710097.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_001710098.1	UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation
YP_001710100.1	UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis
YP_001710103.1	GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function
YP_001710109.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_001710111.1	catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer
YP_001710113.1	catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; uses a flavin nucleotide as an essential cofactor; class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus, which plays a role in the membrane association of the enzyme and provides the binding site for the respiratory quinones that serve as physiological electron acceptors
YP_001710121.1	N/R
YP_001710122.1	May form pseudogene with upstream CDS
YP_001710123.1	May form pseudogene with downstream CDS
YP_001710134.1	subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_001710136.1	subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone
YP_001710137.1	subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport
YP_001710140.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_001710141.1	acetolactate synthase large subunit; catalyzes the formation of 2-acetolactate from pyruvate
YP_001710142.1	with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit
YP_001710143.1	catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis
YP_001710147.1	catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate
YP_001710151.1	catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis
YP_001710152.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_001710155.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_001710166.1	Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine
YP_001710167.1	Lacks the appropriate stop codon so may be non-functional.
YP_001710173.1	Possible degradation of extracellular 5'-nucleotides for nutritional needs. May be sortase-sorted.
YP_001710179.1	possibly secreted
YP_001710181.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_001710186.1	N-terminal truncation relative to homologs may indicate pseudogene.
YP_001710189.1	Contains a PASTA domain which suggest an interaction with peptidoglycan
YP_001710201.1	catalyzes a two-step reaction, first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class-I aminoacyl-tRNA synthetase
YP_001710204.1	catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine
YP_001710205.1	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_001710206.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_001710207.1	Nu
YP_001710208.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_001710209.1	recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1; this protein is similar to release factor 2
YP_001710215.1	N/R
YP_001710220.1	catalyzes the interconversion of ribose 5-phosphate to ribulose 5-phosphate; enzyme from E. coli shows allose 6-phosphate isomerase activity
YP_001710224.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_001710225.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_001710226.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_001710228.1	binds and unfolds substrates as part of the ClpXP protease
YP_001710233.1	valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain
YP_001710234.1	catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using GTP
YP_001710242.1	N/R
YP_001710249.1	N-terminal truncation relative to homologue
YP_001710253.1	Possible C-terminal membrane association
YP_001710260.1	3'-5' exoribonuclease specific for small oligoribonuclotides
YP_001710263.1	catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers
YP_001710270.1	ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence
YP_001710274.1	N/R/C heme-binding?
YP_001710280.1	dGTPase family type 2 subfamily; presumably hydrolyzes dGTP to deoxyguanosine and triphosphate
YP_001710281.1	synthesizes RNA primers at the replication forks
YP_001710293.1	Similar to downstream CDS, some similarity to C-terminal portion of other hypotheticals
YP_001710294.1	Similar to upstream CDS, some similarity to C-terminal portion of other hypotheticals
YP_001710299.1	N/I
YP_001710311.1	Homologues in surface polysaccharide gene clusters.
YP_001710314.1	responsible for linkage of the initial sugar to the lipid carrier in surface polysaccharide biosynthesis
YP_001710323.1	carries the fatty acid chain in fatty acid biosynthesis
YP_001710324.1	FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs
YP_001710327.1	E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC
YP_001710330.1	Has high confidence N-terminal extension relative to homologues
YP_001710339.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_001710341.1	catalyzes the ATP-dependent addition of AMP to a subunit of glutamine synthetase; also catalyzes the reverse reaction - deadenylation; adenylation/deadenylation of glutamine synthetase subunits is important for the regulation of this enzyme
YP_001710346.1	Has weak matches to  protein kinases
YP_001710348.1	E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_001710349.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_001710355.1	Homologues in Mycobacteriophage
YP_001710356.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_001710357.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_001710361.1	N
YP_001710366.1	Catalyzes the conversion of citrate to isocitrate
YP_001710367.1	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_001710370.1	N-terminal extension relative to homologues predicted by Frameplot
YP_001710379.1	Nu/R/C?
YP_001710389.1	phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell
YP_001710390.1	catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA
YP_001710421.1	tandem duplication with upstream CDS
YP_001710422.1	tandem duplication with downstream CDS
YP_001710425.1	Appear to be a duplication of the C-terminal portion of the upstream CDS
YP_001710428.1	N/R
YP_001710430.1	Catalyzes a two-step reaction, first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_001710440.1	Era; Escherichia coli Ras-like protein; Bex; Bacillus Era-complementing segment; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds the cell membrane through apparent C-terminal domain; mutants are arrested during the cell cycle; Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome
YP_001710445.2	in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase
YP_001710449.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_001710452.1	one of 4 tandemly repeated diveregnt CDSs
YP_001710453.1	one of 4 tandemly repeated diveregnt CDSs
YP_001710454.1	one of 4 tandemly repeated diveregnt CDSs
YP_001710455.1	one of 4 tandemly repeated diveregnt CDSs
YP_001710456.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_001710462.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_001710466.1	leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase
YP_001710471.1	Nu
YP_001710493.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_001710498.1	N
YP_001710502.1	catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis
YP_001710517.1	transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria
YP_001710519.1	Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway
YP_001710520.1	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_001710521.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_001710522.1	involved in the peptidyltransferase reaction during translation
YP_001710530.1	IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 2 subfamily; some organisms carry two different copies of this enzyme; in some organisms, the type 2 subfamily is associated with resistance to the antibiotic pseudomonic acid (mupirocin)
YP_001710531.1	Nu/R
YP_001710544.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_001710548.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_001710549.1	Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex
YP_001710550.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_001710551.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_001710554.1	FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs
YP_001710555.1	catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis
YP_001710559.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_001710561.1	Nu/R
YP_001710583.1	lipoyl/octanoyltransferase; catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein
YP_001710584.1	catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group
YP_001710599.1	N
YP_001710610.1	N
YP_001710613.1	catalyzes the formation of succinate and diaminoheptanedioate from succinyldiaminoheptanedioate
YP_001710621.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex
YP_001710622.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_001710623.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_001710624.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_001710625.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex
YP_001710626.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_001710628.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0
YP_001710629.1	Nu/R
YP_001710640.1	N/R
YP_001710652.1	3'-5' exonuclease of DNA polymerase III
YP_001710653.1	RpmE2; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome
YP_001710656.1	catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate
YP_001710670.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_001710671.1	catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase
YP_001710672.1	catalyzes the reversible formation of D-erythrose 4-phosphate and D-fructose 6-phosphate from sedoheptulose 7-phosphate and D-glyceraldehyde 3-phosphate
YP_001710674.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_001710679.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_001710680.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_001710685.1	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision
YP_001710686.1	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate
YP_001710687.1	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion
YP_001710689.1	in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins
YP_001710692.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_001710694.1	N
YP_001710695.1	N
YP_001710698.1	glutamate synthase is composed of subunits alpha and beta; beta subunit is a flavin adenine dinucleotide-NADPH dependent oxidoreductase; provides electrons to the alpha subunit, which binds L-glutamine and 2-oxoglutarate and forms L-glutamate
YP_001710700.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_001710701.1	catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis
YP_001710702.1	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_001710703.1	involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water
YP_001710706.1	with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine
YP_001710707.1	PR-AMP cyclohydrolase; functions in histidine biosynthesis from PRPP; converts 1-(5-phosphoribosyl)-AMP to 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]imidazole-4- carboxyamide during the histidine biosynthesis pathway; binds zinc and magnesium; forms homodimers
YP_001710708.1	catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase
YP_001710709.1	long form of enzyme; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms active dimers and inactive hexamers which is dependent on concentration of substrates and inhibitors
YP_001710710.1	catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis
YP_001710711.1	catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate
YP_001710714.1	binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity
YP_001710715.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_001710716.1	catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine
YP_001710717.1	Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits
YP_001710718.1	N-terminal extension relative to homologues
YP_001710721.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_001710723.1	catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis
YP_001710724.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_001710725.1	regulates pyrimidine biosynthesis by binding to the mRNA of the pyr genes, also has been shown to have uracil phosphoribosyltransferase activity
YP_001710732.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_001710733.1	catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis
YP_001710734.1	Nu/R
YP_001710739.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_001710741.1	adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active
YP_001710742.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D
YP_001710743.1	dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate
YP_001710748.1	catalyzes the formation of L-methionine and acetate from O-acetyl-L-homoserine and methanethiol
YP_001710749.1	Catalyzes the conversion of acetyl-CoA and L-homoserine to CoA and O-acetyl-L-homoserine
YP_001710753.1	Nu
YP_001710762.1	kgd; produces succinic semialdehyde; part of alternative pathway from alpha-ketoglutarate to succinate; essential for normal growth
YP_001710766.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_001710771.1	binds to ssrA RNA (tmRNA) and is required for its successful binding to ribosomes; also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site; SmpB protects the tmRNA from RNase R degradation in Caulobacter crescentus; both the tmRNA and SmpB are regulated in cell cycle-dependent manner; functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation
YP_001710783.1	catalyzes the formation of pyruvate from D-cysteine
YP_001710787.1	RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs
YP_001710788.1	converts L-glutamate to D-glutamate, a component of peptidoglycan
YP_001710790.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate
YP_001710793.1	Match is to the C terminal portion. N-terminal half has no significant database matches.
YP_001710800.1	probably involved in polysaccharide biosynthesis
YP_001710817.1	N/R
YP_001710828.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_001710844.1	N/R
YP_001710845.1	Repetetive N-terminal region may not be encoded
YP_001710849.1	Nu/R
YP_001710871.1	N/R
YP_001710872.1	N/R
YP_001710881.1	type II enzyme; in Escherichia coli this enzyme forms a trimer of dimers which is allosterically inhibited by NADH and competitively inhibited by alpha-ketoglutarate; allosteric inhibition is lost when Cys206 is chemically modified which also affects hexamer formation; forms oxaloacetate and acetyl-CoA and water from citrate and coenzyme A; functions in TCA cycle, glyoxylate cycle and respiration; enzyme from Helicobacter pylori is not inhibited by NADH
YP_001710882.1	catalyzes the formation of N-succinyl-LL-2,6-diaminopimelate from N-succinyl-L-2-amino-6-oxopimelate in lysine biosynthesis
YP_001710890.1	Similar to CMS2218
YP_001710898.1	acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine
YP_001710899.1	part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor
YP_001710903.1	N/R
YP_001710905.1	contains 3x internal repeat
YP_001710924.1	Late stop compared to homologues
YP_001710925.1	catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis
YP_001710926.1	catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis
YP_001710958.1	Nu/R
YP_001710959.1	C-terminal extension relative to homologues
YP_001710971.1	N/R/C
YP_001710973.1	catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis
YP_001710974.1	catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases A1518 and A1519 in 16S rRNA; mutations in ksgA causes resistance to the translation initiation inhibitor kasugamycin
YP_001710976.1	methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content
YP_001710980.1	catalyzes the formation of citrate from acetyl-CoA and oxaloacetate
YP_001710995.1	N
YP_001710998.1	N-terminal extension relative to homologues
YP_001711006.1	Contains extra C-terminal CoA-binding domain fusion relative to homologues
YP_001711007.1	N
YP_001711013.1	N
YP_001711021.1	catalyzes the formation of 2,5-dioxopentanoate from 5-dehydro-4-deoxy-D-glucarate
YP_001711022.1	N
YP_001711030.1	catalyzes the hydrolysis of allophanate
YP_001711034.1	B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE
YP_001711035.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_001711041.1	N/R
YP_001711045.1	in some organisms the DhaK and DhaL subunits are encoded by separate genes; in others they are fused; functions along with DhaM to phosphorylate dihydroxyacetone
YP_001711049.1	Nu/R
YP_001711062.1	Nu/R
YP_001711069.1	translation-associated GTPase; the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure (PDB: 1NI3); fluorescence spectroscopy revealed nucleic acid binding; the yeast protein YBR025c interacts with the translation elongation factor eEF1
YP_001711072.1	catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate
YP_001711074.1	catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway
YP_001711075.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_001711076.1	catalyzes the bidirectional exonucleolytic cleavage of DNA
YP_001711079.1	class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle
YP_001711090.1	catalyzes the formation of 2-oxobutanoate from L-threonine
YP_001711099.1	Multi-domain protein with no full length matches
YP_001711113.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_001711114.1	catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG
YP_001711116.1	functions in degradation of stringent response intracellular messenger ppGpp; in Escherichia coli this gene is co-transcribed with the toxin/antitoxin genes mazEF; activity of MazG is inhibited by MazEF in vitro; ppGpp inhibits mazEF expression; MazG thus works in limiting the toxic activity of the MazF toxin induced during starvation; MazG also interacts with the GTPase protein Era
YP_001711118.1	Unusually low GC content
YP_001711120.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_001711121.1	the Ctc family of proteins consists of two types, one that contains the N-terminal ribosomal protein L25 domain only which in Escherichia coli binds the 5S rRNA while a subset of proteins contain a C-terminal extension that is involved in the stress response
YP_001711123.1	catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate
YP_001711126.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_001711127.1	forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis
YP_001711183.1	together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z
YP_001711192.1	GC Frameplot suggests recent fusion of 2 CDSs
YP_001711200.1	N/R/C
YP_001711203.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_001711218.1	Recent fusion suggested by GC Frameplot
YP_001711237.1	catalyzes the dehydration of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid to form O-succinylbenzoate
YP_001711238.1	catalyzes the formation of 1,4-dihydroxy-2-naphthoate from O-succinylbenzoyl-CoA
YP_001711242.1	N/R
YP_001711245.1	extra N-terminal integral membrane region ALL other homologues
YP_001711246.1	involved in de novo purine biosynthesis
YP_001711247.1	glycinamide ribonucleotide transformylase; GAR Tfase; catalyzes the synthesis of 5'-phosphoribosylformylglycinamide from 5'-phosphoribosylglycinamide and 10-formyltetrahydrofolate; PurN requires formyl folate for the reaction unlike PurT which uses formate
YP_001711249.1	Catalyzes the only substrate-level phosphorylation in the TCA cycle
YP_001711250.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_001711253.1	Nu/R
YP_001711256.1	UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin
YP_001711261.1	catalyzes the rearrangement of isopentenyl diphosphate to dimethylallyl phosphate
YP_001711262.1	N/R
YP_001711269.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_001711270.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_001711271.1	forms a complex with SecY and SecG; SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force
YP_001711273.1	binds directly to 23S ribosomal RNA
YP_001711274.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_001711277.1	P/R
YP_001711297.1	C-terminal extension relative to homologues
YP_001711341.1	C-terminal domain similar to upstream CDS
YP_001711342.1	C-terminal domain similar to downstream CDS
YP_001711360.1	type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese
YP_001711362.1	Nu/R
YP_001711367.1	catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate
YP_001711377.1	2,3-bisphosphoglycerate-dependent; catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate
YP_001711384.1	catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA
YP_001711394.1	60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is essential for growth
YP_001711402.1	Hydrophilic Asp-repeat in C-terminus
YP_001711403.1	catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate
YP_001711430.1	Nu/R
YP_001711440.1	heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE; multiple copies in some bacteria
YP_001711445.1	P/R part of the NRPS disruption
YP_001711470.1	good secretion signal
YP_001711471.1	Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway
YP_001711472.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_001711474.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_001711475.1	protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic
YP_001711476.1	Weak but full length match to Q6AB01_PROAC
YP_001711480.1	no signal sequence detected by Prosite
YP_001711482.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III
YP_001711483.1	catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins
YP_001711487.1	N/R
YP_001711488.1	catalyzes the formation of inosine from adenosine
YP_001711490.1	Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate
YP_001711491.1	Reclaims exogenous and endogenous cytidine and 2'-deoxycytidine molecules for UMP synthesis
YP_001711501.1	part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol
YP_001711502.1	part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase
YP_001711506.1	catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_001711510.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_001711512.1	RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not
YP_001711518.1	N/R
YP_001711521.1	N/C
YP_001711537.1	Nu
YP_001711549.1	N/I/C ISLxx5
YP_001711557.1	N/R
YP_001711588.1	Appears to be a fusion relative to S. coelicolor and others.
YP_001711603.1	converts homocysteine and S-adenosyl-methionine to methionine and S-adenosyl-homocysteine or S-methyl-methionine and homocysteine to two methionines
YP_001711610.1	in mycobacterium a dominant t-cell antigen and stimulates lymphoproliferation (by similarity).
YP_001711617.1	in an low GC region
YP_001711619.1	in a generally atypical region, low GC
YP_001711625.1	Nu/R
YP_001711626.1	N/R
YP_001711647.1	catalyzes the formation of dimethylmenaquinone from 1,4-dihydroxy-2-naphthoate and octaprenyl diphosphate
YP_001711651.1	Nu/R
YP_001711655.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_001711661.1	N/I/C associated with genes for sugar transport which could be another remnant of the Cmm patho island
YP_001711676.1	catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate
YP_001711677.1	catalyzes the removal of amino acids from the N termini of peptides
YP_001711692.1	located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif
YP_001711693.1	in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif
YP_001711694.1	required for 70S ribosome assembly
YP_001711707.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_001711718.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_001711719.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_001711720.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_001711721.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_001711731.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_001711734.1	functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria
YP_001711737.1	in Escherichia coli transcription of this gene is enhanced by polyamines