-- dump date   	20111121_011207
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_001654092.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_001654093.1	uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm
YP_001654095.1	contains N-terminal domain of unknown function fused to transcription elongation factor; GreA is necessary for efficient RNA polymerization through arresting sites; cleaves the nascent transcript and allows resumption of transcription elongation
YP_001654096.1	catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate
YP_001654097.1	in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall
YP_001654102.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_001654108.1	Similar to many proposed 5-formyltetrahydrofolate cyclo-ligase
YP_001654109.1	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_001654115.1	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_001654120.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_001654121.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_001654122.1	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_001654137.1	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_001654138.1	Catalyzes the phosphorylation of UMP to UDP
YP_001654139.1	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_001654140.1	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_001654144.1	with SufCD activates cysteine desulfurase SufS
YP_001654153.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_001654158.1	in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine, which is found in the wobble position of some tRNAs and affects ribosomal frameshifting; shows potassium-dependent dimerization and GTP hydrolysis; also involved in regulation of glutamate-dependent acid resistance and activation of gadE
YP_001654159.1	catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine
YP_001654160.1	note the PF07719 Tetratricopeptide repeat motif
YP_001654161.1	functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; in some organisms, there are paralogous proteins that have been found to be nonessential but do function in secretion of a subset of exported proteins
YP_001654163.1	EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains
YP_001654165.1	binds and unfolds substrates as part of the ClpXP protease
YP_001654166.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_001654167.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_001654170.1	catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using GTP
YP_001654174.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_001654177.1	involved in type III protein export
YP_001654180.1	note the NifU-like protein domains: PF01592;NifU-like N terminal domain and PF01106, NifU-like domain
YP_001654182.1	catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate
YP_001654185.1	catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon
YP_001654189.1	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_001654191.1	bifunctional enzyme DHBP synthase/GTP cyclohydrolase II; functions in riboflavin synthesis; converts GTP to 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine; converts ribulose 5-phopshate to 3,4-dihydroxy-2-butanone 4-phosphate
YP_001654192.1	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_001654196.1	Note the PF01161;Phosphatidylethanolamine-binding motif
YP_001654200.1	uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm
YP_001654201.1	member of preprotein translocase; forms a heterotrimer with SecD and SecF; links the SecD/SecF/YajC/YidC complex with the SecY/SecE/SecG complex
YP_001654205.1	catalyzes the formation of protoporphyrin IX from protoporphyrinogen IX
YP_001654206.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_001654207.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III
YP_001654209.1	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_001654210.1	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_001654211.1	Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile
YP_001654212.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_001654214.1	Note the PF00149;Calcineurin-like phosphoesterase motif
YP_001654217.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_001654218.1	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_001654221.1	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_001654222.1	catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine and catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis
YP_001654226.1	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_001654227.1	Note the PF04055;Radical SAM superfamily motif
YP_001654229.1	Note the Pfam PF02410;Domain of unknown function associated with iojap superfamily proteins
YP_001654230.1	FabF, beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP.
YP_001654231.1	Note the Pfam PF00293;NUDIX domain
YP_001654232.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_001654236.1	Synthesizes thioester adducts of fatty acids enzymatically to the phosphopantetheine group of acyl carrier protein
YP_001654237.1	catalyzes the formation of 8-amino-7-oxononanoate from 6-carboxyhexanoyl-CoA and L-alanine
YP_001654238.1	binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity
YP_001654241.1	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_001654242.1	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_001654244.1	protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus; this enzyme also cleaves other RNA substrates
YP_001654245.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_001654246.1	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_001654247.1	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_001654251.1	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_001654252.1	This protein performs the mismatch recognition step during the DNA repair process
YP_001654253.1	synthesizes RNA primers at the replication forks
YP_001654258.1	catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose
YP_001654259.1	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_001654260.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_001654261.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_001654262.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_001654263.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_001654264.1	catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis
YP_001654271.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_001654272.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_001654274.1	carries characteristic twin membrane spanning domains
YP_001654277.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_001654278.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_001654283.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_001654284.1	Catalyzes the only substrate-level phosphorylation in the TCA cycle
YP_001654289.1	catalyzes the rate-limiting step in dNTP synthesis
YP_001654290.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_001654291.1	tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine
YP_001654293.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_001654294.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_001654295.1	IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits
YP_001654297.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_001654298.1	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_001654305.1	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_001654314.1	catalyzes the removal of N-terminal amino acids from peptides and arylamides
YP_001654323.1	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_001654324.1	note that the product of this CDS has been proposed to be a putative type III secretion system translocator
YP_001654328.1	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_001654330.1	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_001654341.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain
YP_001654342.1	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_001654343.1	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_001654347.1	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_001654349.1	Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA
YP_001654358.1	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_001654361.1	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_001654362.1	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_001654363.1	HemK; PrmC; transfers a methyl group from S-adenosyl-methionine to amide nitrogen of specific glutamine residues in protein chain release factors PrfA and PrfB possibly stimulating release of completed polypeptide chains
YP_001654365.1	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_001654366.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA; Chlamydial proteins show a C-terminal extension of unknown function
YP_001654367.1	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_001654368.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_001654369.1	Essential for recycling GMP and indirectly, cGMP
YP_001654371.1	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_001654377.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_001654379.1	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_001654383.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_001654384.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_001654391.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_001654393.1	SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide
YP_001654394.1	component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA
YP_001654396.1	catalyzes the conversion of 2C-methyl-D-erythritol 2,4-clclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis; these proteins appear to consist of duplicate domains as compared to Escherichia coli IspG
YP_001654400.1	expressed in response to temperature increase; may be involved in expression of genes involved in the developmental cycle of Chlamydia
YP_001654401.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_001654402.1	catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate
YP_001654403.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_001654410.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_001654413.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_001654414.1	binds the polymerase to DNA and acts as a sliding clamp
YP_001654415.1	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_001654417.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_001654425.1	required for 70S ribosome assembly
YP_001654426.1	amylomaltase; acts to release glucose from maltodextrins
YP_001654431.1	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_001654432.1	catalyzes the formation of FMN from riboflavin and the formation of FAD from FMN; in Bacillus the ribC gene has both flavokinase and FAD synthetase activities
YP_001654433.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_001654434.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_001654435.1	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_001654436.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_001654437.1	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_001654439.1	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_001654442.1	Note the Pfam PF08282;haloacid dehalogenase-like hydrolase motif
YP_001654443.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_001654447.1	Note the Pfam PF01784, NIF3 (NGG1p interacting factor 3)
YP_001654449.1	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_001654450.1	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_001654460.1	catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate
YP_001654461.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_001654462.1	composes the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase complex, the enzyme that catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, which in turn controls the rate of fatty acid metabolism
YP_001654463.1	an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism
YP_001654464.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_001654465.1	forms a direct contact with the tRNA during translation
YP_001654467.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_001654471.1	Note the Pfam PF03631;Ribonuclease BN-like family
YP_001654475.1	members of this family of proteins have a broad spectrum of activity
YP_001654476.1	note the PFAM motif to yrdC domain PF01300
YP_001654485.1	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_001654489.1	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_001654496.1	Note the motifs for calcium binding and calmodulin-binding domain.
YP_001654498.1	When complexed with L-tryptophan it binds the operator region of the trp operon and prevents the initiation of transcription
YP_001654499.1	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_001654505.1	Note the alternate possible translational start site at codon 27.
YP_001654510.1	CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS
YP_001654511.1	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_001654512.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_001654513.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_001654515.1	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_001654516.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_001654517.1	negatively supercoils closed circular double-stranded DNA
YP_001654518.1	negatively supercoils closed circular double-stranded DNA
YP_001654520.1	carries characteristic twin membrane spanning domains
YP_001654521.1	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_001654524.1	carries characteristic twin membrane spanning domains
YP_001654525.1	in most organisms, only the N-terminal domain is present in a single polypeptide; in some archaea this domain is fused to a kinase domain; this gene is essential for growth in Escherichia coli and Bacillus subtilis; the secreted glycoprotease from Pasteurella haemolytica showed specificity for O-sialoglycosylated proteins; the Pyrococcus structure shows DNA-binding properties, iron-binding, ATP-binding, and AP endonuclease activity
YP_001654533.1	catalyzes the formation of fructose 1,6-bisphosphate from fructose 6-phosphate and diphosphate
YP_001654535.1	catalyzes the formation of fructose 1,6-bisphosphate from fructose 6-phosphate and diphosphate
YP_001654536.1	catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A
YP_001654537.1	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_001654538.1	catalyzes the formation of 5-aminolevulinate from (S)-4-amino-5-oxopentanoate
YP_001654541.1	Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_001654542.1	carries characteristic twin membrane spanning domains
YP_001654543.1	catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate
YP_001654546.1	catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate
YP_001654547.1	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_001654551.1	carries characteristic twin membrane spanning domains
YP_001654552.1	carries characteristic twin membrane spanning domains
YP_001654553.1	carries characteristic twin membrane spanning domains
YP_001654554.1	carries characteristic twin membrane spanning domains
YP_001654555.1	carries characteristic twin membrane spanning domains
YP_001654556.1	carries characteristic twin membrane spanning domains
YP_001654557.1	carries characteristic twin membrane spanning domains
YP_001654558.1	carries characteristic twin membrane spanning domains
YP_001654565.1	carries the fatty acid chain in fatty acid biosynthesis
YP_001654566.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_001654568.1	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_001654569.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_001654572.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_001654579.1	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_001654580.1	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_001654581.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_001654590.1	3'-5' exonuclease of DNA polymerase III
YP_001654594.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein
YP_001654598.1	involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate
YP_001654604.1	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_001654607.1	uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm
YP_001654608.1	uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm
YP_001654609.1	Part of the NQR complex which catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm
YP_001654611.1	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_001654616.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_001654617.1	carries characteristic twin membrane spanning domains
YP_001654621.1	catalyzes the formation of dUMP from dUTP
YP_001654622.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits
YP_001654626.1	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_001654627.1	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_001654628.1	transformation of prophobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_001654629.1	PknD; responsible for phosphorylation of proteins on serine and threonine residues; similar to eukaryotic Ser/Thr kinases; in Chlamydia trachomatis itseems to interact with Pkn1, another serine/threonine-protein kinase
YP_001654630.1	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_001654632.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the K subunit is a nonenzymatic component which binds the dimeric form by interacting with the G and E subunits
YP_001654633.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit I is part of the membrane proton channel.
YP_001654634.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the D subunit is part of the catalytic core of the ATP synthase complex
YP_001654635.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the B subunit is part of the catalytic core of the ATP synthase complex
YP_001654636.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the A subunit is part of the catalytic core of the ATP synthase complex
YP_001654638.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the E subunit is part of the catalytic core of the ATP synthase complex
YP_001654642.1	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_001654643.1	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_001654644.1	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_001654645.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_001654646.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_001654647.1	binds directly to 23S ribosomal RNA
YP_001654648.1	Modulates Rho-dependent transcription termination
YP_001654649.1	forms a complex with SecY and SecG; SecYEG forms a putative protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force
YP_001654650.1	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_001654651.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_001654655.1	catalyzes the formation of 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate from N-(5-phospho-beta-D-ribosyl)-anthranilate in tryptophan biosynthesis
YP_001654656.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_001654657.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_001654658.1	catalyzes the bidirectional exonucleolytic cleavage of DNA
YP_001654660.1	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_001654661.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_001654662.1	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_001654663.1	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_001654671.1	chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion
YP_001654672.1	a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA
YP_001654676.1	member of metallo-beta-lactamase family; the purified enzyme from Escherichia coli forms dimeric zinc phosphodiesterase; in Bacillus subtilis this protein is a 3'-tRNA processing endoribonuclease and is essential while in Escherichia coli it is not; associates with two zinc ions
YP_001654677.1	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; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs
YP_001654679.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_001654683.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_001654684.1	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_001654687.1	carries characteristic twin membrane spanning domains
YP_001654690.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_001654691.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP
YP_001654692.1	catalyzes the formation of aspartate semialdehyde from aspartyl phosphate
YP_001654693.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_001654695.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_001654696.1	catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis
YP_001654697.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_001654698.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_001654699.1	AroDE; bifunctional enzyme; can convert 3-dehydroquinate to 3-dehydroshkimate and then to shikimate; involved in the synthesis of aromatic amino acids and other metabolites; type I 3-DHQase
YP_001654704.1	catalyzes the oxidation of malate to oxaloacetate
YP_001654706.1	functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family
YP_001654710.1	catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate
YP_001654719.1	catalyzes the interconversion of tetrahydrodipicolinate and L,L-diaminopimelate in lysine biosynthesis
YP_001654722.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_001654723.1	Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons
YP_001654725.1	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_001654731.1	transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate
YP_001654734.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_001654737.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_001654740.1	catalyzes the formation of lipid A disaccharide from UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate; lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM
YP_001654747.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_001654748.1	involved in the peptidyltransferase reaction during translation
YP_001654759.1	Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone
YP_001654761.1	involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate
YP_001654762.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_001654763.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_001654764.1	catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane; functions in tetrapyrrole and heme biosynthesis
YP_001654765.1	catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate
YP_001654767.1	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_001654768.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_001654769.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_001654770.1	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_001654777.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_001654780.1	part of the preprotein secretory system; forms a complex with protein 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; in these organisms there is an unknown N-terminal domain
YP_001654782.1	catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate
YP_001654784.1	Catalyzes the formation of (d)CDP from ATP and (d)CMP
YP_001654786.1	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_001654787.1	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_001654791.1	recognizes the termination signals UGA 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 RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1
YP_001654792.1	Note the Pfam PF02201;SWIB-MDM2 domain.
YP_001654794.1	4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MEP cytidylyltransferase; MCT; catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; forms homodimers
YP_001654795.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_001654802.1	involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA
YP_001654807.1	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_001654817.1	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_001654823.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_001654824.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_001654825.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_001654830.1	unwinds double stranded DNA
YP_001654831.1	GidA; glucose-inhibited cell division protein A; involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs
YP_001654833.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_001654834.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_001654835.1	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_001654839.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_001654840.1	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_001654841.1	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_001654842.1	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_001654843.1	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_001654844.1	late assembly protein
YP_001654845.1	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_001654846.1	binds 5S rRNA along with protein L5 and L25
YP_001654847.1	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_001654848.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_001654849.1	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_001654850.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_001654851.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_001654852.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_001654853.1	one of the stabilizing components for the large ribosomal subunit
YP_001654854.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_001654855.1	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_001654856.1	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_001654857.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_001654858.1	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_001654859.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_001654860.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_001654861.1	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_001654863.1	modifies the free amino group of the aminoacyl moiety of methionyl-tRNA(fMet) which is important in translation initiation; inactivation of this gene in Escherichia coli severely impairs growth
YP_001654864.1	catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis
YP_001654865.1	in Pseudomonas aeruginosa this enzyme is a trimer of dimers; essential for membrane formation; performs third step of type II fatty acid biosynthesis; catalyzes dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP
YP_001654866.1	zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis
YP_001654867.1	Transfers the fatty acyl group on membrane lipoproteins
YP_001654869.1	3'-5' exonuclease of DNA polymerase III
YP_001654875.1	catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes
YP_001654876.1	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_001654878.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_001654880.1	note the tetratricopeptide repeat motifs
YP_001654884.1	pseudo in SeroD intact in Sero A
YP_001654890.1	E3 component of 2-oxoglutarate dehydrogenase complex; catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_001654891.1	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_001654908.1	This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. Promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex
YP_001654914.1	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_001654918.1	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_001654919.1	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_001654920.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_001654924.1	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_001654925.1	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_001654931.1	forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA
YP_001654938.1	HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine
YP_001654940.1	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_001654942.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma 54 factor is responsible for the expression of enzymes involved in nitrogen assimilation and metabolism; the rhizobia often have 2 copies of this sigma factor; in Rhizobium etli RpoN1 shown to be involved in the assimilation of several nitrogen and carbon sources during free-living aerobic growth and RpoN2 is involved in symbiotic nitrogen fixation; in Bradyrhizobium both RpoN1 and N2 are functional in free-living and symbiotic conditions, rpoN1 gene was regulated in response to oxygen
YP_001654948.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
YP_001654950.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_001654955.1	member of the CHLPN 76 kD protein family of proteins
YP_001654956.1	member of the CHLPN 76 kD protein family of proteins
YP_001654958.1	Assists in DNA repair by cleaving phosphodiester bonds at apurinic or apyrimidinic sties to produce new 5' ends that are base-free deoxyribose 5-phosphate residues
YP_001654959.1	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