-- dump date   	20140619_021704
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_980060.1	identified by match to protein family HMM PF04335
YP_980061.1	identified by match to protein family HMM PF03524
YP_980062.1	identified by match to protein family HMM PF03743
YP_980064.1	identified by match to protein family HMM PF00437
YP_980066.1	identified by match to protein family HMM PF02534
YP_980071.1	identified by match to protein family HMM PF01131; match to protein family HMM PF01751
YP_980073.1	identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621
YP_980084.1	identified by match to protein family HMM PF01656
YP_980086.1	identified by match to protein family HMM PF01051
YP_980089.1	identified by match to protein family HMM PF07424
YP_980112.1	identified by match to protein family HMM PF03135
YP_999720.1	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_999721.1	binds the polymerase to DNA and acts as a sliding clamp
YP_999722.1	negatively supercoils closed circular double-stranded DNA
YP_999724.1	identified by match to protein family HMM PF00174; match to protein family HMM PF03404
YP_999725.1	identified by match to protein family HMM PF03553; match to protein family HMM PF03600; match to protein family HMM PF06808
YP_999726.1	identified by match to protein family HMM PF00310; match to protein family HMM PF01493; match to protein family HMM PF01645; match to protein family HMM PF04898
YP_999727.1	identified by match to protein family HMM PF03235; match to protein family HMM PF07510
YP_999728.1	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_999729.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_999730.1	identified by match to protein family HMM PF00633; match to protein family HMM TIGR00426
YP_999731.1	identified by match to protein family HMM PF00301; match to protein family HMM PF02915
YP_999732.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_999736.1	identified by match to protein family HMM PF02568; match to protein family HMM PF06508; match to protein family HMM TIGR00364
YP_999737.1	identified by match to protein family HMM PF02600
YP_999739.1	identified by match to protein family HMM PF00015; match to protein family HMM PF00672
YP_999740.1	identified by match to protein family HMM PF03150
YP_999741.1	identified by match to protein family HMM PF01557
YP_999742.1	identified by match to protein family HMM PF00849
YP_999743.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_999744.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_999745.1	identified by match to protein family HMM PF00375
YP_999746.1	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_999747.1	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_999748.1	identified by match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644
YP_999749.1	identified by match to protein family HMM PF00710; match to protein family HMM TIGR00520
YP_999754.1	identified by match to protein family HMM PF01578
YP_999755.1	identified by match to protein family HMM PF01019; match to protein family HMM TIGR00066
YP_999758.1	identified by match to protein family HMM PF00912
YP_999760.1	identified by match to protein family HMM PF04402
YP_999761.1	identified by match to protein family HMM PF07690; match to protein family HMM TIGR00710
YP_999763.1	identified by match to protein family HMM PF00034
YP_999765.1	identified by match to protein family HMM PF00009; match to protein family HMM PF00679; match to protein family HMM PF03144; match to protein family HMM TIGR00231; match to protein family HMM TIGR01394
YP_999768.1	acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod
YP_999769.1	identified by match to protein family HMM PF00460; match to protein family HMM PF06429; match to protein family HMM PF07559
YP_999771.1	identified by match to protein family HMM PF01814; match to protein family HMM TIGR02481
YP_999778.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_999779.1	identified by match to protein family HMM PF03641
YP_999784.1	identified by match to protein family HMM PF03412
YP_999785.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_999786.1	with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation
YP_999787.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor directs late flagellar biosynthesis genes
YP_999789.1	identified by match to protein family HMM PF01656
YP_999790.1	positive regulator of class III flagellar genes
YP_999791.1	identified by match to protein family HMM PF01288; match to protein family HMM TIGR01498
YP_999792.1	catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis
YP_999793.1	Catalyzes the hydrolytic cleavage of a carbon-halogen bond in N-ethylammeline
YP_999794.1	identified by match to protein family HMM PF01343; match to protein family HMM TIGR00706
YP_999799.1	identified by match to protein family HMM PF02589
YP_999800.1	identified by match to protein family HMM PF00037; match to protein family HMM TIGR00273
YP_999801.1	identified by match to protein family HMM PF02754
YP_999802.1	identified by match to protein family HMM PF02652; match to protein family HMM TIGR00795
YP_999803.1	identified by match to protein family HMM PF03498
YP_999804.1	identified by match to protein family HMM PF03372
YP_999805.1	identified by match to protein family HMM PF03498
YP_999807.1	identified by match to protein family HMM PF01654
YP_999808.1	identified by match to protein family HMM PF02322; match to protein family HMM TIGR00203
YP_999809.1	identified by match to protein family HMM PF01177; match to protein family HMM TIGR00035
YP_999810.1	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_999811.1	catalyzes the formation of fumarate from aspartate
YP_999812.1	functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to dcuB
YP_999815.1	identified by match to protein family HMM TIGR02722
YP_999818.1	identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061
YP_999819.1	involved in the peptidyltransferase reaction during translation
YP_999820.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_999821.1	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_999822.1	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_999823.1	catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon
YP_999824.1	identified by match to protein family HMM PF01656
YP_999825.1	identified by match to protein family HMM PF02195; match to protein family HMM TIGR00180
YP_999826.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B' is part of the membrane proton channel.
YP_999827.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_999828.1	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_999829.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_999830.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_999831.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_999832.1	part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane
YP_999833.1	identified by match to protein family HMM PF01618
YP_999834.1	identified by match to protein family HMM PF02472; match to protein family HMM TIGR02801
YP_999836.1	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_999837.1	identified by match to protein family HMM PF00691; match to protein family HMM TIGR02802
YP_999840.1	identified by match to protein family HMM TIGR00128
YP_999841.1	enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine
YP_999842.1	identified by match to protein family HMM PF01171
YP_999845.1	identified by match to protein family HMM PF02130; match to protein family HMM TIGR00043
YP_999847.1	identified by match to protein family HMM PF01207
YP_999849.1	identified by match to protein family HMM PF01258
YP_999850.1	identified by match to protein family HMM PF02590
YP_999851.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits
YP_999852.1	identified by match to protein family HMM PF00459
YP_999853.1	identified by match to protein family HMM PF01103; match to protein family HMM PF07244
YP_999854.1	catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate
YP_999855.1	identified by match to protein family HMM PF01551
YP_999856.1	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_999858.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_999859.1	identified by match to protein family HMM PF04296
YP_999860.1	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_999861.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_999862.1	identified by match to protein family HMM PF02576
YP_999863.1	identified by match to protein family HMM PF07728
YP_999866.1	identified by match to protein family HMM PF00950; match to protein family HMM PF01032
YP_999867.1	identified by match to protein family HMM PF00005
YP_999868.1	identified by match to protein family HMM PF01297
YP_999869.1	identified by match to protein family HMM PF00015
YP_999870.1	identified by match to protein family HMM PF05787; match to protein family HMM TIGR01409
YP_999871.1	identified by match to protein family HMM PF00070; match to protein family HMM PF07992; match to protein family HMM TIGR01292
YP_999872.1	identified by match to protein family HMM PF00085; match to protein family HMM TIGR01068
YP_999873.1	identified by match to protein family HMM PF02021
YP_999874.1	catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine
YP_999875.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_999878.1	identified by match to protein family HMM PF00588; match to protein family HMM PF08032
YP_999879.1	identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096
YP_999880.1	RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome
YP_999881.1	in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase
YP_999885.1	identified by match to protein family HMM PF04055
YP_999886.1	together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z
YP_999889.1	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_999890.1	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_999891.1	identified by match to protein family HMM PF02659
YP_999893.1	identified by match to protein family HMM PF00081; match to protein family HMM PF02777
YP_999896.1	identified by match to protein family HMM PF03435
YP_999897.1	identified by match to protein family HMM PF00005
YP_999898.1	identified by match to protein family HMM PF00528
YP_999899.1	identified by match to protein family HMM PF01547
YP_999901.1	in Escherichia coli SbmA is involved in uptake of microcin J25; functions along with FhuA, TonB, and ExbB/D in this capacity; in Sinorhizobium meliloti, BacA is essential and required for symbiosis; defects appear to affect the cell envelope
YP_999902.1	identified by match to protein family HMM PF00571; match to protein family HMM PF01595; match to protein family HMM PF03471
YP_999903.1	identified by match to protein family HMM PF00149
YP_999904.1	identified by match to protein family HMM PF03831
YP_999905.1	identified by match to protein family HMM PF03741
YP_999906.1	identified by match to protein family HMM PF00551; match to protein family HMM TIGR00639
YP_999907.1	identified by match to protein family HMM PF01256; match to protein family HMM PF03853; match to protein family HMM TIGR00196; match to protein family HMM TIGR00197
YP_999908.1	identified by match to protein family HMM PF01936
YP_999909.1	identified by match to protein family HMM PF01078; match to protein family HMM PF07728; match to protein family HMM TIGR00368
YP_999910.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_999911.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_999912.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_999913.1	involved in the first step of tetrahydrofolate biosynthesis; catalyzes the formation of formate and 2-amino-4-hydroxy-6-(erythro-1,2, 3-trihydroxypropyl)dihydropteridine triphosphate from GTP and water; forms a homopolymer
YP_999914.1	involved in type III protein export during flagellum assembly
YP_999915.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_999916.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_999917.1	identified by match to protein family HMM PF00004
YP_999923.1	identified by match to protein family HMM PF03600; match to protein family HMM PF06808
YP_999924.1	identified by match to protein family HMM PF03169; match to protein family HMM TIGR00728; match to protein family HMM TIGR00733
YP_999925.1	identified by match to protein family HMM PF02673; match to protein family HMM TIGR00753
YP_999926.1	catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); 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
YP_999927.1	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_999928.1	identified by match to protein family HMM PF02086
YP_999937.1	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_999938.1	identified by match to protein family HMM PF00583
YP_999939.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate
YP_999940.1	identified by match to protein family HMM PF00202; match to protein family HMM TIGR00707
YP_999941.1	catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins
YP_999942.1	identified by match to protein family HMM PF00132
YP_999943.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate
YP_999944.1	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_999945.1	identified by match to protein family HMM PF06271
YP_999946.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_999947.1	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_999948.1	identified by match to protein family HMM PF03840; match to protein family HMM TIGR00810
YP_999949.1	identified by match to protein family HMM PF01027
YP_999950.1	identified by match to protein family HMM PF00484
YP_999951.1	identified by match to protein family HMM PF00924
YP_999952.1	identified by match to protein family HMM PF01106; match to protein family HMM PF01592; match to protein family HMM PF04324
YP_999953.1	identified by match to protein family HMM PF00266
YP_999954.1	identified by match to protein family HMM PF01814; match to protein family HMM TIGR02481
YP_999957.1	identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001
YP_999958.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_999965.1	identified by match to protein family HMM PF00083; match to protein family HMM PF07690
YP_999967.1	MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis
YP_999970.1	identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633
YP_999971.1	identified by match to protein family HMM PF00884; match to protein family HMM PF08019
YP_999972.1	identified by match to protein family HMM PF01219
YP_999974.1	catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis
YP_999977.1	identified by match to protein family HMM PF00015; match to protein family HMM PF00672; match to protein family HMM PF02743; match to protein family HMM PF05581
YP_999978.1	identified by match to protein family HMM PF02535
YP_999979.1	identified by match to protein family HMM PF00384; match to protein family HMM PF01568
YP_999983.1	identified by match to protein family HMM PF01145
YP_999984.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_999985.1	identified by match to protein family HMM PF01361; match to protein family HMM TIGR00013
YP_999986.1	identified by match to protein family HMM PF00578
YP_999987.1	identified by match to protein family HMM PF02677
YP_999988.1	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_999989.1	catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis
YP_999990.1	binds and unfolds substrates as part of the ClpXP protease
YP_999991.1	functions in MreBCD complex in some organisms
YP_999992.1	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_999993.1	four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity
YP_999995.1	Important for the balance of metabolites in the pentose-phosphate pathway
YP_999996.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR00338; match to protein family HMM TIGR01488
YP_999997.1	identified by match to protein family HMM PF01584
YP_999998.1	identified by match to protein family HMM PF00072; match to protein family HMM PF01584; match to protein family HMM PF01627; match to protein family HMM PF02518; match to protein family HMM PF02895
YP_999999.1	identified by match to protein family HMM PF00072; match to protein family HMM PF01584
YP_001000001.1	necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus
YP_001000002.1	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_001000005.1	catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate
YP_001000006.1	identified by match to protein family HMM PF00899
YP_001000007.1	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_001000008.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_001000009.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_001000010.1	identified by match to protein family HMM PF00005
YP_001000011.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR02141
YP_001000012.1	identified by match to protein family HMM PF03459
YP_001000013.1	identified by match to protein family HMM PF01547; match to protein family HMM TIGR01256
YP_001000014.1	identified by match to protein family HMM TIGR02072
YP_001000015.1	identified by match to protein family HMM PF04301
YP_001000016.1	identified by match to protein family HMM PF00155
YP_001000017.1	catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate
YP_001000018.1	identified by match to protein family HMM TIGR00347
YP_001000019.1	identified by match to protein family HMM PF00893
YP_001000020.1	identified by match to protein family HMM PF00893
YP_001000021.1	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_001000022.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_001000023.1	identified by match to protein family HMM PF03739
YP_001000024.1	identified by match to protein family HMM PF00278; match to protein family HMM PF02784; match to protein family HMM TIGR01048
YP_001000025.1	identified by match to protein family HMM TIGR01460
YP_001000026.1	identified by match to protein family HMM PF00800; match to protein family HMM PF01817; match to protein family HMM TIGR01807
YP_001000027.1	catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis
YP_001000028.1	the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod
YP_001000029.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_001000030.1	binds to and inhibits the function of flagella specific ATPase FliI
YP_001000031.1	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_001000032.1	identified by match to protein family HMM PF01475
YP_001000034.1	Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone
YP_001000035.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_001000036.1	catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine
YP_001000037.1	identified by match to protein family HMM PF01042
YP_001000038.1	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_001000039.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_001000040.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_001000042.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_001000043.1	identified by match to protein family HMM PF00037
YP_001000044.1	identified by match to protein family HMM PF00578
YP_001000045.1	membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export
YP_001000046.1	with MotA forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine
YP_001000047.1	With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine
YP_001000048.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_001000052.1	identified by match to protein family HMM PF01156
YP_001000054.1	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_001000055.1	identified by match to protein family HMM PF01925
YP_001000057.1	identified by match to protein family HMM PF00425
YP_001000058.1	identified by match to protein family HMM PF00117; match to protein family HMM PF00591; match to protein family HMM TIGR00566; match to protein family HMM TIGR01245
YP_001000059.1	identified by match to protein family HMM PF00697
YP_001000060.1	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_001000061.1	catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis
YP_001000063.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_001000065.1	identified by match to protein family HMM PF02541
YP_001000066.1	identified by match to protein family HMM PF00037
YP_001000067.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_001000068.1	identified by match to protein family HMM PF02152
YP_001000069.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX
YP_001000070.1	identified by match to protein family HMM PF03150
YP_001000071.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_001000072.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_001000073.1	identified by match to protein family HMM PF03653; match to protein family HMM TIGR00701
YP_001000074.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_001000076.1	identified by match to protein family HMM PF02321; match to protein family HMM TIGR01845
YP_001000077.1	identified by match to protein family HMM PF00873; match to protein family HMM TIGR00915
YP_001000078.1	identified by match to protein family HMM PF00529; match to protein family HMM TIGR01730
YP_001000079.1	identified by match to protein family HMM PF00440
YP_001000080.1	identified by match to protein family HMM PF00037; match to protein family HMM TIGR02745
YP_001000081.1	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_001000084.1	identified by match to protein family HMM PF03738
YP_001000085.1	Involved in the metabolism of aromatic amino acids
YP_001000086.1	putative nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ; the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription
YP_001000089.1	identified by match to protein family HMM PF00004
YP_001000090.1	identified by match to protein family HMM PF01794
YP_001000091.1	in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase; sulfite oxidase activity not demonstrated; requires inner membrane anchor protein YedZ
YP_001000092.1	type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase
YP_001000093.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_001000094.1	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_001000095.1	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_001000096.1	identified by match to protein family HMM PF00892
YP_001000097.1	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_001000098.1	catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis
YP_001000099.1	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_001000100.1	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_001000101.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_001000103.1	identified by match to protein family HMM PF00224; match to protein family HMM PF02887; match to protein family HMM TIGR01064
YP_001000104.1	identified by match to protein family HMM PF01266; match to protein family HMM PF06039
YP_001000105.1	type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP
YP_001000109.1	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_001000110.1	identified by match to protein family HMM PF02674
YP_001000111.1	identified by match to protein family HMM PF01475
YP_001000112.1	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_001000113.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_001000115.1	identified by match to protein family HMM PF05036
YP_001000116.1	AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate
YP_001000118.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_001000119.1	part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdC is the cytochrome b-556 subunit
YP_001000120.1	part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdC is the cytochrome b-556 subunit; the catalytic subunits are similar to succinate dehydrogenase SdhAB
YP_001000121.1	part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdC is the cytochrome b-556 subunit; the catalytic subunits are similar to succinate dehydrogenase SdhAB
YP_001000122.1	identified by match to protein family HMM PF00350; match to protein family HMM PF01926
YP_001000123.1	identified by match to protein family HMM PF00350; match to protein family HMM PF01926
YP_001000126.1	identified by match to protein family HMM PF00732
YP_001000130.1	identified by match to protein family HMM PF04264
YP_001000133.1	identified by match to protein family HMM PF00005
YP_001000136.1	identified by match to protein family HMM PF01205
YP_001000140.1	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_001000141.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_001000142.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_001000143.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_001000144.1	identified by match to protein family HMM PF01243
YP_001000145.1	identified by match to protein family HMM PF00890; match to protein family HMM PF01266; match to protein family HMM PF02910; match to protein family HMM PF07992; match to protein family HMM TIGR01409
YP_001000146.1	identified by match to protein family HMM PF00111; match to protein family HMM TIGR00384
YP_001000147.1	identified by match to protein family HMM PF02754
YP_001000148.1	identified by match to protein family HMM PF03070
YP_001000150.1	carries the fatty acid chain in fatty acid biosynthesis
YP_001000151.1	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_001000152.1	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_001000153.1	identified by match to protein family HMM PF00593; match to protein family HMM PF07715
YP_001000154.1	identified by match to protein family HMM PF00293; match to protein family HMM TIGR00052
YP_001000155.1	identified by match to protein family HMM PF00015
YP_001000156.1	identified by match to protein family HMM PF04325
YP_001000157.1	required for 70S ribosome assembly
YP_001000158.1	catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate
YP_001000159.1	3'-5' exonuclease of DNA polymerase III
YP_001000160.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_001000164.1	identified by match to protein family HMM PF04028
YP_001000165.1	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_001000167.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_001000168.1	identified by match to protein family HMM PF04332; match to protein family HMM PF07690
YP_001000169.1	identified by match to protein family HMM PF04055; match to protein family HMM TIGR00423
YP_001000170.1	identified by match to protein family HMM PF05193
YP_001000171.1	catalyzes branch migration in Holliday junction intermediates
YP_001000173.1	identified by match to protein family HMM PF00027
YP_001000174.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_001000175.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_001000176.1	identified by match to protein family HMM PF00005
YP_001000177.1	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_001000178.1	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_001000179.1	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_001000180.1	Modulates Rho-dependent transcription termination
YP_001000181.1	binds directly to 23S ribosomal RNA
YP_001000182.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_001000183.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_001000184.1	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_001000185.1	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_001000186.1	identified by match to protein family HMM PF00623; match to protein family HMM PF04983; match to protein family HMM PF04997; match to protein family HMM PF04998; match to protein family HMM PF05000; match to protein family HMM TIGR02386
YP_001000187.1	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_001000188.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_001000189.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_001000191.1	identified by match to protein family HMM PF05175
YP_001000192.1	identified by match to protein family HMM PF03692
YP_001000194.1	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_001000195.1	identified by match to protein family HMM PF01230
YP_001000196.1	catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA
YP_001000204.1	identified by match to protein family HMM PF05860; match to protein family HMM TIGR01901
YP_001000205.1	identified by match to protein family HMM PF01103
YP_001000206.1	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_001000207.1	identified by match to protein family HMM PF01408
YP_001000208.1	identified by match to protein family HMM PF00155; match to protein family HMM PF00266; match to protein family HMM PF01041; match to protein family HMM PF01053; match to protein family HMM PF01212
YP_001000209.1	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_001000210.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_001000211.1	identified by match to protein family HMM PF00905; match to protein family HMM PF00912; match to protein family HMM TIGR02074
YP_001000212.1	identified by match to protein family HMM PF00004; match to protein family HMM PF02861; match to protein family HMM PF07724; match to protein family HMM PF07728
YP_001000213.1	identified by match to protein family HMM PF02583
YP_001000214.1	identified by match to protein family HMM PF00595; match to protein family HMM PF03572; match to protein family HMM TIGR00225
YP_001000215.1	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_001000216.1	identified by match to protein family HMM PF02700; match to protein family HMM TIGR00302
YP_001000217.1	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_001000219.1	identified by match to protein family HMM PF01553
YP_001000220.1	identified by match to protein family HMM PF02537; match to protein family HMM TIGR00494
YP_001000221.1	molecular chaperone
YP_001000224.1	identified by match to protein family HMM PF02690
YP_001000225.1	identified by match to protein family HMM PF00905; match to protein family HMM PF03717
YP_001000226.1	forms a junction between the M-ring and FlgB during flagella biosynthesis
YP_001000227.1	with FlgF and B makes up the proximal portion of the flagellar basal body rod
YP_001000228.1	with FlgF and C makes up the proximal portion of the flagellar basal body rod; Vibrio parahaemolyticus protein is associated with the polar flagella
YP_001000229.1	identified by match to protein family HMM PF02618
YP_001000231.1	identified by match to protein family HMM PF03971; match to protein family HMM TIGR00178
YP_001000232.1	identified by match to protein family HMM PF00056; match to protein family HMM PF02866
YP_001000233.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_001000234.1	identified by match to protein family HMM PF00549; match to protein family HMM PF02629; match to protein family HMM TIGR01019
YP_001000235.1	identified by match to protein family HMM PF00037
YP_001000236.1	identified by match to protein family HMM PF01855
YP_001000237.1	identified by match to protein family HMM PF02775
YP_001000238.1	identified by match to protein family HMM PF01558
YP_001000241.1	identified by match to protein family HMM PF00348
YP_001000242.1	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_001000243.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_001000245.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_001000246.1	identified by match to protein family HMM PF01977; match to protein family HMM TIGR00148
YP_001000247.1	possibly involved in flagella export
YP_001000248.1	Also called hook-associated protein 2; involved in flagellin assembly
YP_001000249.1	flagellin specific chaperone
YP_001000251.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_001000252.1	identified by match to protein family HMM PF06149
YP_001000253.1	identified by match to protein family HMM PF06166
YP_001000255.1	identified by match to protein family HMM PF03600; match to protein family HMM PF07158
YP_001000256.1	identified by match to protein family HMM PF04909
YP_001000258.1	Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway
YP_001000259.1	identified by match to protein family HMM PF00070; match to protein family HMM PF03486; match to protein family HMM PF07992
YP_001000260.1	identified by match to protein family HMM PF01554; match to protein family HMM TIGR00797
YP_001000262.1	unwinds double stranded DNA
YP_001000273.1	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_001000274.1	identified by match to protein family HMM PF02637
YP_001000275.1	catalyzes the formation of 2-acetolactate from pyruvate, leucine resistant; also known as acetolactate synthase 3 large subunit
YP_001000276.1	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_001000277.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_001000278.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_001000279.1	identified by match to protein family HMM PF00902; match to protein family HMM TIGR00945
YP_001000280.1	mediates the export of protein precursors bearing twin-arginine signal peptides
YP_001000281.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_001000282.1	hydrolyzes diadenosine polyphosphate
YP_001000283.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.
YP_001000285.1	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_001000286.1	identified by match to protein family HMM PF00809; match to protein family HMM TIGR01496
YP_001000287.1	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_001000289.1	identified by match to protein family HMM PF01479; match to protein family HMM PF01728
YP_001000290.1	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_001000291.1	identified by match to protein family HMM TIGR00740
YP_001000294.1	identified by match to protein family HMM PF03458
YP_001000295.1	identified by match to protein family HMM PF01223
YP_001000296.1	identified by match to protein family HMM PF00730; match to protein family HMM TIGR01083
YP_001000297.1	identified by match to protein family HMM PF00639
YP_001000298.1	catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate
YP_001000300.1	identified by match to protein family HMM PF00691
YP_001000302.1	identified by match to protein family HMM PF00209
YP_001000303.1	identified by match to protein family HMM PF03473; match to protein family HMM PF03475
YP_001000304.1	identified by match to protein family HMM PF00085; match to protein family HMM PF02683
YP_001000305.1	identified by match to protein family HMM PF03976
YP_001000306.1	identified by match to protein family HMM PF03976
YP_001000307.1	identified by match to protein family HMM PF01546; match to protein family HMM PF07687; match to protein family HMM TIGR01891
YP_001000308.1	identified by match to protein family HMM PF00529; match to protein family HMM TIGR01730
YP_001000309.1	identified by match to protein family HMM PF00005; match to protein family HMM PF02687
YP_001000310.1	identified by match to protein family HMM PF02321
YP_001000312.1	identified by match to protein family HMM PF04311
YP_001000313.1	identified by match to protein family HMM PF03062
YP_001000314.1	identified by match to protein family HMM PF00210
YP_001000316.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR02138
YP_001000317.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR00974
YP_001000318.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_001000321.1	identified by match to protein family HMM PF01554; match to protein family HMM TIGR00797
YP_001000322.1	identified by match to protein family HMM PF01863
YP_001000324.1	identified by match to protein family HMM PF00708; match to protein family HMM PF01300; match to protein family HMM PF07503; match to protein family HMM TIGR00143
YP_001000325.1	identified by match to protein family HMM PF02492; match to protein family HMM TIGR00073
YP_001000326.1	identified by match to protein family HMM PF01455; match to protein family HMM TIGR00074
YP_001000327.1	identified by match to protein family HMM PF01924; match to protein family HMM TIGR00075
YP_001000328.1	identified by match to protein family HMM PF00586; match to protein family HMM PF02769; match to protein family HMM TIGR02124
YP_001000329.1	identified by match to protein family HMM PF01155; match to protein family HMM TIGR00100
YP_001000330.1	identified by match to protein family HMM PF04313
YP_001000331.1	required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA
YP_001000332.1	identified by match to protein family HMM PF00773; match to protein family HMM PF08206
YP_001000333.1	catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis
YP_001000334.1	identified by match to protein family HMM PF04748
YP_001000335.1	identified by match to protein family HMM PF02481
YP_001000336.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_001000337.1	identified by match to protein family HMM PF01189
YP_001000338.1	this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress
YP_001000339.1	identified by match to protein family HMM PF00719
YP_001000340.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_001000341.1	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_001000342.1	catalyzes the phosphorylation of NAD to NADP
YP_001000343.1	identified by match to protein family HMM PF02463
YP_001000344.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00990; match to protein family HMM TIGR00254
YP_001000345.1	identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010
YP_001000346.1	identified by match to protein family HMM PF01464; match to protein family HMM PF01476
YP_001000347.1	identified by match to protein family HMM PF03330; match to protein family HMM PF05036; match to protein family HMM TIGR00413
YP_001000348.1	identified by match to protein family HMM TIGR01662; match to protein family HMM TIGR01670
YP_001000349.1	identified by match to protein family HMM PF06835
YP_001000350.1	identified by match to protein family HMM PF03968
YP_001000351.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_001000353.1	identified by match to protein family HMM PF00905; match to protein family HMM PF03717
YP_001000354.1	identified by match to protein family HMM PF00557
YP_001000355.1	identified by match to protein family HMM PF00854
YP_001000361.1	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_001000362.1	heat shock protein involved in degradation of misfolded proteins
YP_001000363.1	heat shock protein involved in degradation of misfolded proteins
YP_001000364.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_001000365.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_001000366.1	identified by match to protein family HMM PF01479
YP_001000367.1	identified by match to protein family HMM PF02367; match to protein family HMM TIGR00150
YP_001000368.1	identified by match to protein family HMM PF00005
YP_001000369.1	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_001000370.1	functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to DcuA; DcuA and DcuB function as independent and mutually redundant C4-dicarboxylate (aspartate, malate, fumarate and succinate) transporters
YP_001000372.1	identified by match to protein family HMM PF03814; match to protein family HMM TIGR00680
YP_001000373.1	One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions
YP_001000374.1	identified by match to protein family HMM PF02669
YP_001000375.1	identified by match to protein family HMM PF02702
YP_001000376.1	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_001000380.1	binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity
YP_001000382.1	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_001000383.1	part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod
YP_001000384.1	identified by match to protein family HMM PF01515; match to protein family HMM TIGR00651
YP_001000385.1	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_001000386.1	identified by match to protein family HMM PF04313
YP_001000389.1	identified by match to protein family HMM PF01795; match to protein family HMM TIGR00006
YP_001000391.1	identified by match to protein family HMM PF02491; match to protein family HMM TIGR01174
YP_001000392.1	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_001000393.1	identified by match to protein family HMM PF00460; match to protein family HMM PF06429
YP_001000394.1	makes up the distal portion of the flagellar basal body rod
YP_001000395.1	identified by match to protein family HMM PF00120; match to protein family HMM PF03951; match to protein family HMM TIGR00653
YP_001000397.1	identified by match to protein family HMM PF01136
YP_001000398.1	identified by match to protein family HMM PF00731; match to protein family HMM TIGR01162
YP_001000400.1	glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA
YP_001000401.1	identified by match to protein family HMM PF01784; match to protein family HMM TIGR00486
YP_001000402.1	identified by match to protein family HMM PF02591
YP_001000403.1	catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A
YP_001000404.1	identified by match to protein family HMM PF00849
YP_001000405.1	identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM PF02978; match to protein family HMM TIGR00959
YP_001000406.1	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_001000408.1	identified by match to protein family HMM PF01782; match to protein family HMM PF05239; match to protein family HMM TIGR02273
YP_001000409.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_001000410.1	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_001000411.1	identified by match to protein family HMM PF00576; match to protein family HMM TIGR02962
YP_001000412.1	identified by match to protein family HMM PF01474; match to protein family HMM TIGR01358
YP_001000413.1	identified by match to protein family HMM PF03960
YP_001000414.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_001000415.1	identified by match to protein family HMM TIGR00044
YP_001000416.1	identified by match to protein family HMM PF00669
YP_001000418.1	identified by match to protein family HMM PF05175; match to protein family HMM TIGR00536
YP_001000419.1	identified by match to protein family HMM PF01435
YP_001000421.1	forms a trimer; related to eukaryotic protein gephyrin; functions during molybdenum cofactor biosynthesis
YP_001000422.1	identified by match to protein family HMM PF01544; match to protein family HMM TIGR00383
YP_001000426.1	identified by match to protein family HMM PF00528
YP_001000427.1	identified by match to protein family HMM PF00528
YP_001000428.1	identified by match to protein family HMM PF00005
YP_001000429.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01488; match to protein family HMM TIGR01490
YP_001000430.1	identified by match to protein family HMM PF00497
YP_001000433.1	identified by match to protein family HMM PF05860; match to protein family HMM TIGR01901
YP_001000441.1	Acts as a negative regulator of the grpE-dnaK-dnaJ and groELS class I heat shock operons by preventing heat-shock induction
YP_001000442.1	with DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins; may act as a thermosensor
YP_001000443.1	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_001000444.1	identified by match to protein family HMM PF02384
YP_001000445.1	identified by match to protein family HMM PF01420
YP_001000448.1	identified by match to protein family HMM PF04313; match to protein family HMM PF04851
YP_001000451.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_001000452.1	identified by match to protein family HMM PF00132; match to protein family HMM TIGR01172
YP_001000453.1	catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis
YP_001000454.1	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_001000455.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_001000456.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_001000457.1	catalyzes the formation of 2-octaprenylphenol from 3-octaprenyl-4-hydroxybenzoate
YP_001000458.1	required for the assembly of the flagellar basal body P-ring
YP_001000459.1	identified by match to protein family HMM PF03180
YP_001000460.1	identified by match to protein family HMM PF03180
YP_001000461.1	identified by match to protein family HMM PF03180
YP_001000462.1	identified by match to protein family HMM PF00528
YP_001000463.1	identified by match to protein family HMM PF00005
YP_001000464.1	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_001000466.1	identified by match to protein family HMM PF00580
YP_001000468.1	identified by match to protein family HMM PF00578
YP_001000469.1	periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC
YP_001000470.1	part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; secreted by twin arginine translocation pathway
YP_001000471.1	part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA
YP_001000472.1	identified by match to protein family HMM PF03892
YP_001000478.1	identified by match to protein family HMM PF01743
YP_001000479.1	produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine
YP_001000480.1	identified by match to protein family HMM PF00266
YP_001000481.1	identified by match to protein family HMM PF03008
YP_001000482.1	identified by match to protein family HMM PF00512; match to protein family HMM PF02518
YP_001000485.1	identified by match to protein family HMM PF00561
YP_001000486.1	identified by match to protein family HMM TIGR01552
YP_001000487.1	D-alanine--D-alanine ligase; DdlA; DdlB; cytoplasmic; catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis; there are two forms of this enzyme in Escherichia coli
YP_001000488.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_001000490.1	identified by match to protein family HMM PF03023; match to protein family HMM TIGR01695
YP_001000491.1	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_001000492.1	identified by match to protein family HMM PF00005; match to protein family HMM PF00664
YP_001000493.1	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_001000494.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_001000495.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_001000496.1	Acts on the hydroxyl group at position 7 of the steroid frame
YP_001000498.1	identified by match to protein family HMM PF00753
YP_001000499.1	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_001000500.1	transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate
YP_001000501.1	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_001000502.1	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_001000504.1	identified by match to protein family HMM PF00497
YP_001000505.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_001000506.1	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_001000507.1	catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine
YP_001000509.1	identified by match to protein family HMM PF01255; match to protein family HMM TIGR00055
YP_001000510.1	identified by match to protein family HMM PF01478; match to protein family HMM PF06750
YP_001000511.1	identified by match to protein family HMM PF03739
YP_001000512.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_001000513.1	catalyzes the formation of 2-oxobutanoate from L-threonine
YP_001000514.1	identified by match to protein family HMM PF02629
YP_001000515.1	identified by match to protein family HMM PF04323
YP_001000516.1	catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs
YP_001000517.1	identified by match to protein family HMM PF03553
YP_001000518.1	identified by match to protein family HMM PF00106; match to protein family HMM PF01370
YP_001000519.1	identified by match to protein family HMM PF00023
YP_001000520.1	catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate
YP_001000521.1	identified by match to protein family HMM PF01035; match to protein family HMM TIGR00589
YP_001000523.1	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_001000525.1	catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate
YP_001000526.1	identified by match to protein family HMM PF03205; match to protein family HMM TIGR00176
YP_001000527.1	identified by match to protein family HMM PF01464
YP_001000528.1	identified by match to protein family HMM PF02325
YP_001000529.1	charges one glutamine molecule and pairs it with tRNA(Gln)
YP_001000530.1	identified by match to protein family HMM PF00149
YP_001000531.1	catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine
YP_001000532.1	identified by match to protein family HMM TIGR00789
YP_001000534.1	identified by match to protein family HMM PF07690
YP_001000537.1	Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway
YP_001000539.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_001000540.1	identified by match to protein family HMM PF00717; match to protein family HMM TIGR02227
YP_001000541.1	identified by match to protein family HMM PF00994; match to protein family HMM PF03453; match to protein family HMM PF03454; match to protein family HMM TIGR00177
YP_001000542.1	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_001000544.1	identified by match to protein family HMM PF00892
YP_001000545.1	identified by match to protein family HMM PF00117; match to protein family HMM TIGR00566
YP_001000546.1	identified by match to protein family HMM PF00425
YP_001000547.1	identified by match to protein family HMM PF00589
YP_001000550.1	identified by match to protein family HMM PF05935
YP_001000551.1	identified by match to protein family HMM PF01323
YP_001000558.1	membrane protein involved in the flagellar export apparatus
YP_001000559.1	identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738
YP_001000560.1	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_001000561.1	identified by match to protein family HMM PF01580
YP_001000562.1	with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook
YP_001000563.1	identified by match to protein family HMM PF00005
YP_001000564.1	identified by match to protein family HMM PF00512; match to protein family HMM PF02518
YP_001000565.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_001000566.1	catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate
YP_001000568.1	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_001000569.1	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_001000570.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_001000571.1	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_001000572.1	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_001000573.1	identified by match to protein family HMM PF01230
YP_001000574.1	identified by match to protein family HMM PF01965; match to protein family HMM TIGR01383
YP_001000576.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_001000577.1	identified by match to protein family HMM PF00005
YP_001000578.1	identified by match to protein family HMM PF01235; match to protein family HMM TIGR00835
YP_001000579.1	identified by match to protein family HMM PF00588
YP_001000580.1	converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer
YP_001000583.1	identified by match to protein family HMM PF04314
YP_001000585.1	identified by match to protein family HMM PF02630
YP_001000586.1	identified by match to protein family HMM PF00291; match to protein family HMM TIGR01136; match to protein family HMM TIGR01139
YP_001000587.1	identified by match to protein family HMM PF00216
YP_001000589.1	identified by match to protein family HMM PF03061
YP_001000590.1	identified by match to protein family HMM PF04328
YP_001000591.1	identified by match to protein family HMM PF02554
YP_001000592.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_001000593.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_001000594.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_001000595.1	PEB1
YP_001000596.1	identified by match to protein family HMM PF00005
YP_001000597.1	identified by match to protein family HMM PF01739; match to protein family HMM PF03705
YP_001000598.1	identified by match to protein family HMM PF01339
YP_001000599.1	identified by match to protein family HMM PF02502; match to protein family HMM TIGR00689; match to protein family HMM TIGR01120
YP_001000601.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_001000603.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_001000604.1	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_001000605.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_001000606.1	PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP
YP_001000607.1	identified by match to protein family HMM PF00364; match to protein family HMM PF00682
YP_001000608.1	identified by match to protein family HMM PF00209
YP_001000609.1	identified by match to protein family HMM PF00209
YP_001000610.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0
YP_001000613.1	identified by match to protein family HMM PF03681
YP_001000620.1	identified by match to protein family HMM PF03547
YP_001000621.1	identified by match to protein family HMM PF00501; match to protein family HMM PF01553; match to protein family HMM PF07690
YP_001000623.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_001000624.1	identified by match to protein family HMM PF02687
YP_001000625.1	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_001000626.1	participates with LolB in the incorporation of lipoprotein into the outer membrane
YP_001000630.1	identified by match to protein family HMM PF00795
YP_001000631.1	identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297
YP_001000632.1	identified by match to protein family HMM PF04371
YP_001000633.1	identified by match to protein family HMM PF03724
YP_001000634.1	identified by match to protein family HMM PF00015; match to protein family HMM PF00672
YP_001000635.1	involved in de novo purine biosynthesis
YP_001000636.1	identified by match to protein family HMM PF00226
YP_001000637.1	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_001000638.1	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_001000640.1	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_001000641.1	identified by match to protein family HMM PF01809; match to protein family HMM TIGR00278
YP_001000642.1	identified by match to protein family HMM PF00825; match to protein family HMM TIGR00188
YP_001000643.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_001000644.1	identified by match to protein family HMM PF00583
YP_001000647.1	identified by match to protein family HMM PF03061; match to protein family HMM TIGR00051
YP_001000654.1	identified by match to protein family HMM PF05860; match to protein family HMM TIGR01901
YP_001000655.1	identified by match to protein family HMM PF01103; match to protein family HMM PF08479
YP_001000656.1	identified by match to protein family HMM PF08003
YP_001000659.1	identified by match to protein family HMM PF00565
YP_001000661.1	identified by match to protein family HMM PF00083; match to protein family HMM PF07690
YP_001000662.1	identified by match to protein family HMM PF00497
YP_001000664.1	identified by match to protein family HMM PF03883
YP_001000665.1	identified by match to protein family HMM PF01546; match to protein family HMM PF07687; match to protein family HMM TIGR01891
YP_001000670.1	identified by match to protein family HMM PF00037; match to protein family HMM PF02754
YP_001000671.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_001000673.1	catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation
YP_001000674.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_001000675.1	catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate
YP_001000676.1	identified by match to protein family HMM PF02527; match to protein family HMM TIGR00138
YP_001000678.1	identified by match to protein family HMM PF03601
YP_001000679.1	identified by match to protein family HMM PF00126; match to protein family HMM PF03466
YP_001000680.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria
YP_001000681.1	identified by match to protein family HMM PF00300
YP_001000682.1	identified by match to protein family HMM PF01694
YP_001000684.1	identified by match to protein family HMM PF00004; match to protein family HMM PF06480
YP_001000685.1	identified by match to protein family HMM PF00919; match to protein family HMM PF04055; match to protein family HMM TIGR00089; match to protein family HMM TIGR01579
YP_001000686.1	identified by match to protein family HMM PF00924
YP_001000687.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_001000688.1	identified by match to protein family HMM PF02080
YP_001000689.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_001000692.1	identified by match to protein family HMM PF01578
YP_001000693.1	identified by match to protein family HMM PF00005
YP_001000694.1	identified by match to protein family HMM PF00005
YP_001000695.1	identified by match to protein family HMM PF02653
YP_001000696.1	identified by match to protein family HMM PF02653
YP_001000697.1	identified by match to protein family HMM PF01094
YP_001000698.1	identified by match to protein family HMM PF01094
YP_001000701.1	identified by match to protein family HMM PF03350
YP_001000702.1	catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde
YP_001000703.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954
YP_001000705.1	identified by match to protein family HMM PF04164
YP_001000706.1	negatively supercoils closed circular double-stranded DNA
YP_001000709.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_001000710.1	identified by match to protein family HMM PF02321
YP_001000712.1	identified by match to protein family HMM PF00873
YP_001000713.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_001000714.1	Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate
YP_001000716.1	biotin carboxylase; catalyses the carboxylation of the carrier protein which then transfers the carboxyl group to form malonyl-CoA, which in turn controls the rate of fatty acid metabolism
YP_001000717.1	identified by match to protein family HMM PF01098; match to protein family HMM TIGR02614
YP_001000718.1	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_001000723.1	identified by match to protein family HMM PF00165
YP_001000724.1	identified by match to protein family HMM PF02581
YP_001000725.1	in Escherichia coli this enzyme functions in thiamine biosynthesis along with thiFSGI and iscS; with ThiFSG catalyzes the formation of thiazole phosphate from tyrosine, cysteine and 1-deoxy-D-xylulose-5-phosphate; forms a complex with ThiG; contains an iron-sulfur center
YP_001000726.1	functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate
YP_001000727.1	catalyzes the adenylation of ThiS which is involved in the formation of 5-methyl-4-(beta-hydroxyethyl)thiazole phosphate
YP_001000728.1	identified by match to protein family HMM PF02597; match to protein family HMM TIGR01683
YP_001000729.1	dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.
YP_001000730.1	identified by match to protein family HMM PF01810
YP_001000731.1	identified by match to protein family HMM PF02146
YP_001000732.1	MutS2; MutS-II; involved in blocking homologous and homeologous recombination; has ATPase activity stimulated by recombination intermediates; inhibits DNA strand exchange
YP_001000734.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_001000735.1	identified by match to protein family HMM PF00884
YP_001000738.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_001000739.1	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_001000740.1	IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme
YP_001000741.1	identified by match to protein family HMM PF02464; match to protein family HMM TIGR00199
YP_001000742.1	identified by match to protein family HMM PF00583
YP_001000743.1	identified by match to protein family HMM PF00881
YP_001000744.1	identified by match to protein family HMM PF00881
YP_001000745.1	identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560
YP_001000746.1	identified by match to protein family HMM PF02163; match to protein family HMM TIGR00054
YP_001000747.1	identified by match to protein family HMM PF04393
YP_001000748.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_001000749.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_001000750.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_001000751.1	identified by match to protein family HMM PF00004; match to protein family HMM PF02190; match to protein family HMM PF05362; match to protein family HMM PF07728; match to protein family HMM TIGR00763
YP_001000753.1	binds to flagellin and appears to stabilize flagellin during flagella assembly
YP_001000754.1	catalyzes the formation of L-proline from pyrroline-5-carboxylate
YP_001000758.1	catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane; functions in tetrapyrrole and heme biosynthesis
YP_001000759.1	identified by match to protein family HMM PF02581; match to protein family HMM TIGR00693
YP_001000760.1	identified by match to protein family HMM PF01256; match to protein family HMM TIGR00097
YP_001000761.1	identified by match to protein family HMM PF00730
YP_001000762.1	identified by match to protein family HMM PF05673
YP_001000763.1	identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF02559; match to protein family HMM PF03461; match to protein family HMM PF04851; match to protein family HMM TIGR00580
YP_001000764.1	identified by match to protein family HMM PF04519
YP_001000765.1	identified by match to protein family HMM PF01551
YP_001000766.1	identified by match to protein family HMM PF08245; match to protein family HMM TIGR01499
YP_001000769.1	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_001000770.1	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_001000771.1	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_001000772.1	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_001000773.1	Transfers the fatty acyl group on membrane lipoproteins
YP_001000774.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_001000775.1	involved in the import of serine and threonine coupled with the import of sodium
YP_001000776.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_001000777.1	identified by match to protein family HMM PF01432; match to protein family HMM TIGR02290
YP_001000779.1	identified by match to protein family HMM PF00580
YP_001000780.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_001000781.1	identified by match to protein family HMM PF02599; match to protein family HMM TIGR00202
YP_001000782.1	catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis
YP_001000783.1	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_001000785.1	identified by match to protein family HMM PF02617
YP_001000786.1	identified by match to protein family HMM PF00004; match to protein family HMM PF02861; match to protein family HMM PF07724; match to protein family HMM PF07728; match to protein family HMM TIGR02639
YP_001000787.1	leucyltransferase; phenylalanyltransferse; functions in the N-end rule pathway; transfers Leu, Phe, Met, from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys
YP_001000788.1	identified by match to protein family HMM PF00015; match to protein family HMM TIGR00229
YP_001000789.1	identified by match to protein family HMM PF01914
YP_001000790.1	this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; a fusion protein of this enzyme with MsrA and thioredoxin provides protection against oxidative stress in Neisseria gonorrhoeae
YP_001000791.1	identified by match to protein family HMM PF04305
YP_001000792.1	identified by match to protein family HMM PF01066; match to protein family HMM TIGR00473
YP_001000794.1	identified by match to protein family HMM PF00004; match to protein family HMM PF01434; match to protein family HMM PF06480; match to protein family HMM PF07728; match to protein family HMM TIGR01241
YP_001000795.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_001000796.1	identified by match to protein family HMM PF00072
YP_001000798.1	identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF04321
YP_001000799.1	identified by match to protein family HMM PF01041
YP_001000801.1	identified by match to protein family HMM PF02397
YP_001000802.1	identified by match to protein family HMM PF00534
YP_001000803.1	identified by match to protein family HMM PF02516
YP_001000804.1	identified by match to protein family HMM PF00534
YP_001000805.1	identified by match to protein family HMM PF00535
YP_001000806.1	identified by match to protein family HMM PF00534
YP_001000807.1	identified by match to protein family HMM PF00005; match to protein family HMM PF00664
YP_001000808.1	identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF04321; match to protein family HMM PF07993; match to protein family HMM TIGR01179
YP_001000809.1	identified by match to protein family HMM PF03104
YP_001000810.1	identified by match to protein family HMM PF01075; match to protein family HMM TIGR02193
YP_001000811.1	acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA; essential for survival; plays a role in cell responses to environmental changes
YP_001000812.1	identified by match to protein family HMM PF00535
YP_001000814.1	identified by match to protein family HMM PF06306
YP_001000816.1	identified by match to protein family HMM PF00535
YP_001000817.1	identified by match to protein family HMM PF06002
YP_001000818.1	identified by match to protein family HMM PF01354; match to protein family HMM PF03102
YP_001000819.1	identified by match to protein family HMM PF02350
YP_001000820.1	identified by match to protein family HMM PF06306
YP_001000821.1	identified by match to protein family HMM PF02348
YP_001000823.1	identified by match to protein family HMM PF00535
YP_001000824.1	identified by match to protein family HMM PF01075; match to protein family HMM TIGR02195
YP_001000825.1	identified by match to protein family HMM PF01755
YP_001000826.1	catalyzes the isomerization of sedoheptulose 7-phosphate to D-glycero-D-manno-heptose 7-phosphate
YP_001000827.1	identified by match to protein family HMM PF00294; match to protein family HMM PF01467; match to protein family HMM TIGR00125; match to protein family HMM TIGR02198; match to protein family HMM TIGR02199
YP_001000828.1	identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF04321; match to protein family HMM PF07993; match to protein family HMM TIGR02197
YP_001000829.1	identified by match to protein family HMM PF08645; match to protein family HMM TIGR00213; match to protein family HMM TIGR01656; match to protein family HMM TIGR01662
YP_001000830.1	identified by match to protein family HMM PF00034
YP_001000831.1	identified by match to protein family HMM PF03597; match to protein family HMM TIGR00847
YP_001000832.1	identified by match to protein family HMM PF00122; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01525
YP_001000833.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_001000834.1	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_001000836.1	identified by match to protein family HMM PF00122; match to protein family HMM PF00403; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01511; match to protein family HMM TIGR01525
YP_001000838.1	identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297
YP_001000841.1	identified by match to protein family HMM PF06738
YP_001000842.1	identified by match to protein family HMM PF00056; match to protein family HMM PF02866
YP_001000846.1	identified by match to protein family HMM PF00160
YP_001000847.1	identified by match to protein family HMM PF01709; match to protein family HMM TIGR01033
YP_001000848.1	identified by match to protein family HMM PF00893
YP_001000849.1	identified by match to protein family HMM PF00893
YP_001000850.1	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_001000851.1	identified by match to protein family HMM PF02416; match to protein family HMM TIGR01411
YP_001000852.1	Essential for recycling GMP and indirectly, cGMP
YP_001000854.1	FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus
YP_001000855.1	identified by match to protein family HMM PF00005
YP_001000856.1	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_001000857.1	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_001000858.1	identified by match to protein family HMM PF02353
YP_001000859.1	identified by match to protein family HMM PF00034
YP_001000860.1	identified by match to protein family HMM PF00032; match to protein family HMM PF00033
YP_001000861.1	identified by match to protein family HMM PF00355; match to protein family HMM TIGR01416
YP_001000862.1	identified by match to protein family HMM PF02040; match to protein family HMM PF03600
YP_001000863.1	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_001000864.1	identified by match to protein family HMM TIGR00229
YP_001000865.1	identified by match to protein family HMM PF00015
YP_001000866.1	identified by match to protein family HMM TIGR00229
YP_001000867.1	identified by match to protein family HMM PF00375
YP_001000869.1	identified by match to protein family HMM PF01384
YP_001000870.1	Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides
YP_001000871.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_001000872.1	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_001000873.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_001000874.1	identified by match to protein family HMM PF03171
YP_001000875.1	identified by match to protein family HMM PF03180
YP_001000876.1	catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine
YP_001000877.1	identified by match to protein family HMM PF02219; match to protein family HMM TIGR00676
YP_001000879.1	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_001000880.1	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_001000881.1	identified by match to protein family HMM PF00448; match to protein family HMM TIGR00064
YP_001000884.1	protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP
YP_001000886.1	identified by match to protein family HMM PF03631; match to protein family HMM TIGR00765
YP_001000887.1	identified by match to protein family HMM PF01565; match to protein family HMM PF02913
YP_001000889.1	identified by match to protein family HMM PF01551
YP_001000891.1	identified by match to protein family HMM PF02578
YP_001000892.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_001000894.1	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_001000895.1	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_001000896.1	identified by match to protein family HMM PF00512; match to protein family HMM PF02518
YP_001000897.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_001000898.1	identified by match to protein family HMM PF01814; match to protein family HMM TIGR02481
YP_001000900.1	identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518
YP_001000901.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_001000902.1	identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037
YP_001000903.1	identified by match to protein family HMM PF00226; match to protein family HMM PF01556
YP_001000904.1	identified by match to protein family HMM PF00376
YP_001000905.1	identified by match to protein family HMM PF00999; match to protein family HMM PF02254
YP_001000907.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549
YP_001000908.1	glycine--tRNA ligase beta chain; glyS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA
YP_001000909.1	identified by match to protein family HMM PF01551
YP_001000910.1	identified by match to protein family HMM PF02636
YP_001000911.1	identified by match to protein family HMM PF02541
YP_001000912.1	involved in the de novo synthesis of pyridoxine (Vitamin B6)
YP_001000913.1	catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate)
YP_001000916.1	identified by match to protein family HMM PF07690
YP_001000918.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III
YP_001000919.1	identified by match to protein family HMM PF04055
YP_001000921.1	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_001000924.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_001000926.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_001000927.1	identified by match to protein family HMM PF06271
YP_001000928.1	identified by match to protein family HMM PF04453
YP_001000929.1	identified by match to protein family HMM PF00013; match to protein family HMM PF00575; match to protein family HMM PF01138; match to protein family HMM PF03725; match to protein family HMM PF03726
YP_001000930.1	identified by match to protein family HMM PF03167
YP_001000931.1	identified by match to protein family HMM PF01361; match to protein family HMM TIGR00013
YP_001000933.1	identified by match to protein family HMM PF07690
YP_001000934.1	identified by match to protein family HMM PF01451
YP_001000935.1	identified by match to protein family HMM PF05538
YP_001000936.1	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_001000937.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_001000938.1	identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518
YP_001000939.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_001000940.1	identified by match to protein family HMM PF01750; match to protein family HMM TIGR00072
YP_001000941.1	identified by match to protein family HMM PF01292; match to protein family HMM TIGR02125
YP_001000942.1	identified by match to protein family HMM PF00374
YP_001000943.1	identified by match to protein family HMM PF01058; match to protein family HMM PF08425; match to protein family HMM TIGR00391; match to protein family HMM TIGR01409
YP_001000944.1	catalyzes the formation of 5-methylaminomethyl-2-thiouridine in position 34 of the anticodon of tRNA molecules
YP_001000945.1	identified by match to protein family HMM PF01520
YP_001000946.1	identified by match to protein family HMM PF03060
YP_001000947.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_001000948.1	identified by match to protein family HMM PF01842; match to protein family HMM PF01966; match to protein family HMM PF02824; match to protein family HMM PF04607; match to protein family HMM TIGR00691
YP_001000949.1	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_001000950.1	Catalyzes the phosphorylation of UMP to UDP
YP_001000951.1	identified by match to protein family HMM PF01551
YP_001000953.1	identified by match to protein family HMM PF00005
YP_001000954.1	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_001000955.1	identified by match to protein family HMM PF00041
YP_001000956.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005
YP_001000957.1	identified by match to protein family HMM PF01098
YP_001000958.1	identified by match to protein family HMM PF02386; match to protein family HMM TIGR00933
YP_001000959.1	identified by match to protein family HMM PF02080; match to protein family HMM PF02254
YP_001000960.1	identified by match to protein family HMM PF02621
YP_001000961.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_001000962.1	identified by match to protein family HMM PF00390; match to protein family HMM PF03949
YP_001000963.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_001000965.1	biotin carboxylase; biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA; catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism
YP_001000966.1	identified by match to protein family HMM PF00364; match to protein family HMM TIGR00531
YP_001000967.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_001000968.1	identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF07993
YP_001000969.1	identified by match to protein family HMM PF01041; match to protein family HMM PF01212
YP_001000976.1	identified by match to protein family HMM TIGR01681; match to protein family HMM TIGR01686
YP_001000977.1	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; paralogs which do not contain the N-X-R ACP-binding site motif
YP_001000980.1	identified by match to protein family HMM PF00501
YP_001000981.1	identified by match to protein family HMM PF00583
YP_001000986.1	identified by match to protein family HMM PF00483; match to protein family HMM PF02348
YP_001000988.1	identified by match to protein family HMM PF00583
YP_001000989.1	catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamide and glutamine to imidazole-glycerolphosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase
YP_001000990.1	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_001000992.1	identified by match to protein family HMM PF01354; match to protein family HMM PF03102
YP_001000993.1	identified by match to protein family HMM PF01973
YP_001000994.1	identified by match to protein family HMM PF01973
YP_001000995.1	identified by match to protein family HMM PF01973
YP_001000996.1	FlaB; structural flagella protein; in Helicobacter the flagella are composed of flagellin A and flagellin B; the amounts of each seem to be controlled by environmental conditions
YP_001000997.1	FlaA; structural flagella protein; in Helicobacter the flagella are composed of flagellin A and flagellin B; the amounts of each seem to be controlled by environmental conditions
YP_001000998.1	identified by match to protein family HMM PF01973
YP_001001000.1	identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532
YP_001001001.1	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_001001003.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_001001004.1	identified by match to protein family HMM PF01148
YP_001001006.1	identified by match to protein family HMM PF05670
YP_001001008.1	identified by match to protein family HMM PF02253
YP_001001009.1	identified by match to protein family HMM PF01032
YP_001001010.1	identified by match to protein family HMM PF01032
YP_001001011.1	identified by match to protein family HMM PF00005
YP_001001012.1	identified by match to protein family HMM PF01497
YP_001001014.1	identified by match to protein family HMM PF05016
YP_001001016.1	identified by match to protein family HMM PF02335
YP_001001017.1	identified by match to protein family HMM PF03264; match to protein family HMM TIGR03153
YP_001001018.1	catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate
YP_001001020.1	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_001001021.1	identified by match to protein family HMM PF01594
YP_001001022.1	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_001001023.1	identified by match to protein family HMM PF00082; match to protein family HMM PF03797; match to protein family HMM TIGR02601
YP_001001024.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_001001026.1	identified by match to protein family HMM PF04055; match to protein family HMM TIGR00423
YP_001001027.1	identified by match to protein family HMM PF00082; match to protein family HMM PF03797; match to protein family HMM TIGR01414; match to protein family HMM TIGR02601
YP_001001028.1	identified by match to protein family HMM PF00860; match to protein family HMM PF00916
YP_001001029.1	identified by match to protein family HMM PF00156
YP_001001030.1	identified by match to protein family HMM PF04333
YP_001001031.1	identified by match to protein family HMM PF05494
YP_001001032.1	identified by match to protein family HMM PF02460
YP_001001033.1	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_001001034.1	identified by match to protein family HMM PF07690
YP_001001035.1	identified by match to protein family HMM PF00037
YP_001001036.1	catalyzes the formation of selenocysteinyl-tRNA(Sec) from seryl-tRNA(Sec) and L-selenophosphate in selenoprotein biosynthesis
YP_001001037.1	identified by match to protein family HMM PF00009; match to protein family HMM TIGR00231; match to protein family HMM TIGR00475
YP_001001040.1	An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group
YP_001001043.1	identified by match to protein family HMM PF00199
YP_001001044.1	identified by match to protein family HMM PF00023
YP_001001046.1	identified by match to protein family HMM PF01042; match to protein family HMM TIGR00004
YP_001001047.1	identified by match to protein family HMM PF03606; match to protein family HMM TIGR00771
YP_001001048.1	identified by match to protein family HMM PF01053
YP_001001049.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_001001050.1	identified by match to protein family HMM PF03972
YP_001001052.1	identified by match to protein family HMM PF01926; match to protein family HMM PF02421; match to protein family HMM TIGR00231; match to protein family HMM TIGR00650
YP_001001053.1	identified by match to protein family HMM PF07664; match to protein family HMM PF07670
YP_001001054.1	identified by match to protein family HMM PF01058; match to protein family HMM TIGR00391
YP_001001055.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_001001056.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_001001057.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_001001058.1	identified by match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534
YP_001001059.1	identified by match to protein family HMM PF01467; match to protein family HMM TIGR00125; match to protein family HMM TIGR00482
YP_001001060.1	identified by match to protein family HMM PF02410; match to protein family HMM TIGR00090
YP_001001061.1	identified by match to protein family HMM PF06476
YP_001001062.1	identified by match to protein family HMM PF00408; match to protein family HMM PF02878; match to protein family HMM PF02879; match to protein family HMM PF02880
YP_001001063.1	interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring
YP_001001064.1	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_001001066.1	identified by match to protein family HMM PF00067
YP_001001068.1	identified by match to protein family HMM PF05159
YP_001001069.1	identified by match to protein family HMM PF05159
YP_001001070.1	converts ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; in Escherichia coli this enzyme functions in cysteine biosynthesis
YP_001001071.1	identified by match to protein family HMM PF00483
YP_001001072.1	identified by match to protein family HMM PF00117
YP_001001074.1	identified by match to protein family HMM PF01209
YP_001001078.1	identified by match to protein family HMM PF00483
YP_001001079.1	identified by match to protein family HMM TIGR00441
YP_001001080.1	identified by match to protein family HMM PF00288
YP_001001081.1	identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF04321
YP_001001082.1	identified by match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF07993
YP_001001083.1	identified by match to protein family HMM PF01370
YP_001001086.1	identified by match to protein family HMM PF00908
YP_001001088.1	identified by match to protein family HMM PF00535
YP_001001089.1	identified by match to protein family HMM PF00535
YP_001001090.1	identified by match to protein family HMM PF01501
YP_001001092.1	identified by match to protein family HMM PF05159
YP_001001093.1	identified by match to protein family HMM PF00571; match to protein family HMM PF01380; match to protein family HMM TIGR00393
YP_001001094.1	identified by match to protein family HMM PF02563
YP_001001095.1	identified by match to protein family HMM PF02706
YP_001001096.1	identified by match to protein family HMM PF00005
YP_001001097.1	identified by match to protein family HMM PF01061
YP_001001101.1	identified by match to protein family HMM PF04401
YP_001001102.1	identified by match to protein family HMM PF01171; match to protein family HMM TIGR02432
YP_001001103.1	identified by match to protein family HMM PF00919; match to protein family HMM PF04055; match to protein family HMM TIGR00089; match to protein family HMM TIGR01125
YP_001001104.1	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_001001106.1	catalyzes the modification of U13 in tRNA(Glu)
YP_001001107.1	catalyzes the formation of thiamine diphosphate from thiamine phosphate ant ATP
YP_001001110.1	identified by match to protein family HMM PF03602
YP_001001111.1	part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum
YP_001001115.1	with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook
YP_001001116.1	identified by match to protein family HMM TIGR02757
YP_001001118.1	identified by match to protein family HMM PF01925
YP_001001119.1	identified by match to protein family HMM PF00482
YP_001001120.1	identified by match to protein family HMM PF00437
YP_001001123.1	identified by match to protein family HMM PF00263; match to protein family HMM PF07655; match to protein family HMM PF07660; match to protein family HMM TIGR02519
YP_001001125.1	identified by match to protein family HMM PF00037; match to protein family HMM PF01558; match to protein family HMM PF01855; match to protein family HMM TIGR02176
YP_001001126.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549
YP_001001127.1	identified by match to protein family HMM PF00691; match to protein family HMM PF01389
YP_001001128.1	forms a direct contact with the tRNA during translation
YP_001001129.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_001001130.1	identified by match to protein family HMM PF00580
YP_001001135.1	identified by match to protein family HMM PF00034; match to protein family HMM TIGR00782
YP_001001136.1	identified by match to protein family HMM TIGR02736
YP_001001137.1	CcoO; FixO
YP_001001138.1	CcoN; FixN
YP_001001139.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_001001140.1	identified by match to protein family HMM PF02518; match to protein family HMM TIGR00229
YP_001001142.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_001001143.1	identified by match to protein family HMM PF04368
YP_001001146.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_001001147.1	identified by match to protein family HMM PF04143
YP_001001148.1	identified by match to protein family HMM PF01206
YP_001001149.1	identified by match to protein family HMM PF00474; match to protein family HMM TIGR00813; match to protein family HMM TIGR02121
YP_001001150.1	identified by match to protein family HMM PF00171; match to protein family HMM PF01619
YP_001001151.1	identified by match to protein family HMM PF02769; match to protein family HMM TIGR00476
YP_001001152.1	identified by match to protein family HMM PF01206
YP_001001153.1	identified by match to protein family HMM PF00015
YP_001001155.1	involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth
YP_001001156.1	identified by match to protein family HMM TIGR01583
YP_001001157.1	identified by match to protein family HMM PF00037
YP_001001158.1	identified by match to protein family HMM PF00384; match to protein family HMM PF01568
YP_001001159.1	identified by match to protein family HMM PF04879; match to protein family HMM TIGR01409
YP_001001160.1	identified by match to protein family HMM TIGR01409
YP_001001162.1	identified by match to protein family HMM PF00278; match to protein family HMM TIGR01047
YP_001001163.1	identified by match to protein family HMM PF00394; match to protein family HMM PF07731; match to protein family HMM PF07732; match to protein family HMM TIGR01409
YP_001001164.1	identified by match to protein family HMM PF02597
YP_001001165.1	identified by match to protein family HMM PF02391
YP_001001166.1	identified by match to protein family HMM PF00994; match to protein family HMM PF03453; match to protein family HMM PF03454; match to protein family HMM TIGR00177
YP_001001169.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_001001170.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_001001171.1	involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate
YP_001001172.1	identified by match to protein family HMM PF01832
YP_001001174.1	identified by match to protein family HMM PF00210
YP_001001175.1	catalyzes the formation of D-fructose 6-phosphate from D-glucose 6-phosphate
YP_001001176.1	identified by match to protein family HMM PF00483; match to protein family HMM TIGR01099
YP_001001177.1	Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA
YP_001001178.1	identified by match to protein family HMM PF00005
YP_001001179.1	identified by match to protein family HMM PF00528
YP_001001181.1	identified by match to protein family HMM PF03746
YP_001001182.1	identified by match to protein family HMM PF02682; match to protein family HMM TIGR00370
YP_001001183.1	identified by match to protein family HMM PF02626; match to protein family HMM TIGR00724
YP_001001184.1	identified by match to protein family HMM PF00892
YP_001001185.1	identified by match to protein family HMM PF02525
YP_001001186.1	identified by match to protein family HMM PF01638
YP_001001187.1	identified by match to protein family HMM PF08212
YP_001001188.1	identified by match to protein family HMM PF00107
YP_001001189.1	identified by match to protein family HMM PF04313; match to protein family HMM PF04851; match to protein family HMM TIGR00348
YP_001001191.1	identified by match to protein family HMM PF01420
YP_001001193.1	identified by match to protein family HMM PF04326
YP_001001194.1	identified by match to protein family HMM PF02384
YP_001001197.1	identified by match to protein family HMM PF01638
YP_001001199.1	identified by match to protein family HMM PF03773
YP_001001200.1	identified by match to protein family HMM PF01022
YP_001001202.1	identified by match to protein family HMM PF00376
YP_001001203.1	identified by match to protein family HMM PF02743
YP_001001204.1	identified by match to protein family HMM PF00015
YP_001001206.1	identified by match to protein family HMM PF00361
YP_001001207.1	identified by match to protein family HMM PF00361; match to protein family HMM TIGR01972
YP_001001208.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_001001209.1	identified by match to protein family HMM PF00420
YP_001001210.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001001211.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001001212.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001001213.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_001001216.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001001217.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_001001218.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_001001219.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_001001220.1	identified by match to protein family HMM PF00005
YP_001001221.1	identified by match to protein family HMM PF00005
YP_001001222.1	identified by match to protein family HMM PF00528
YP_001001223.1	identified by match to protein family HMM PF00528
YP_001001224.1	identified by match to protein family HMM PF00496
YP_001001225.1	identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; match to protein family HMM TIGR02166
YP_001001226.1	identified by match to protein family HMM PF00037; match to protein family HMM TIGR02951
YP_001001229.1	identified by match to protein family HMM PF00042
YP_001001230.1	efflux pump for the antibacterial peptide microcin J25
YP_001001231.1	identified by match to protein family HMM PF00083; match to protein family HMM PF07690
YP_001001232.1	identified by match to protein family HMM PF00753
YP_001001233.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_001001234.1	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_001001235.1	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_001001236.1	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_001001237.1	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_001001238.1	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_001001239.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_001001240.1	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_001001241.1	catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer
YP_001001242.1	catalyzes the formation of 3-(imidazol-4-yl)-2-oxopropyl phosphate from D-ethythro-1-(imidazol-4-yl)glycerol 3-phosphate and histidinol from histidinol phosphate
YP_001001243.1	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_001001244.1	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
YP_001001245.1	identified by match to protein family HMM PF04373
YP_001001246.1	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_001001247.1	catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribosyl)-ATP and the subsequent formation of 1-(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide from 1-(5-phosphoribosyl)-AMP in histidine biosynthesis
YP_001001249.1	identified by match to protein family HMM PF01883
YP_001001250.1	bifunctional enzyme involved in formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate and 2-C-methyl-D-erythritol 2,4-cyclodiphosphate and CMP from 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; binds divalent cations
YP_001001251.1	identified by match to protein family HMM PF00072
YP_001001253.1	identified by match to protein family HMM PF04608
YP_001001254.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_001001255.1	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_001001256.1	identified by match to protein family HMM PF01243
YP_001001257.1	identified by match to protein family HMM PF00593; match to protein family HMM PF07715
YP_001001258.1	identified by match to protein family HMM PF01032
YP_001001259.1	identified by match to protein family HMM PF00005
YP_001001260.1	identified by match to protein family HMM PF01497
YP_001001261.1	identified by match to protein family HMM PF04055
YP_001001262.1	identified by match to protein family HMM PF00083; match to protein family HMM PF07690
YP_001001263.1	identified by match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01084
YP_001001265.1	identified by match to protein family HMM PF00383; match to protein family HMM TIGR00326
YP_001001267.1	identified by match to protein family HMM PF03313; match to protein family HMM PF03315; match to protein family HMM TIGR00720
YP_001001268.1	identified by match to protein family HMM PF03222; match to protein family HMM PF03845
YP_001001271.1	identified by match to protein family HMM PF01618; match to protein family HMM TIGR02805
YP_001001272.1	identified by match to protein family HMM PF02472; match to protein family HMM TIGR02804
YP_001001273.1	identified by match to protein family HMM PF03544; match to protein family HMM TIGR01352
YP_001001277.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_001001278.1	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_001001279.1	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_001001280.1	identified by match to protein family HMM PF07719
YP_001001281.1	synthesizes RNA primers at the replication forks
YP_001001282.1	identified by match to protein family HMM PF01106
YP_001001284.1	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_001001285.1	identified by match to protein family HMM PF02575; match to protein family HMM TIGR00103
YP_001001287.1	identified by match to protein family HMM PF00348
YP_001001288.1	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_001001289.1	identified by match to protein family HMM PF02405; match to protein family HMM TIGR00056
YP_001001290.1	identified by match to protein family HMM PF00005
YP_001001291.1	identified by match to protein family HMM PF02470
YP_001001294.1	catalyzes the removal of N-terminal amino acids from peptides and arylamides; generally Co(II) however activity has been shown for some methionine aminopeptidases with Zn, Fe, or Mn
YP_001001295.1	converts L-glutamate to D-glutamate, a component of peptidoglycan
YP_001001296.1	identified by match to protein family HMM PF00877
YP_001001297.1	exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH
YP_001001298.1	identified by match to protein family HMM PF06965; match to protein family HMM TIGR00773
YP_001001301.1	identified by match to protein family HMM PF03239
YP_001001303.1	identified by match to protein family HMM PF04945
YP_001001304.1	identified by match to protein family HMM PF02687
YP_001001305.1	identified by match to protein family HMM PF02687
YP_001001306.1	identified by match to protein family HMM PF00005
YP_001001307.1	identified by match to protein family HMM PF00578; match to protein family HMM PF08534
YP_001001308.1	identified by match to protein family HMM PF08534
YP_001001309.1	identified by match to protein family HMM PF04214
YP_001001312.1	catalyzes the formation of a phosphodiester at the site of a single-strand break in duplex DNA
YP_001001315.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_001001316.1	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_001001317.1	identified by match to protein family HMM PF02642
YP_001001318.1	with proteins FliP and FliR forms the core of the central channel in the flagella export apparatus
YP_001001319.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_001001321.1	identified by match to protein family HMM PF00459
YP_001001322.1	identified by match to protein family HMM PF00285; match to protein family HMM TIGR01798
YP_001001323.1	identified by match to protein family HMM PF00999
YP_001001324.1	catalyzes the formation of biotin from dethiobiotin and sulfur
YP_001001325.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_001001326.1	identified by match to protein family HMM PF07690
YP_001001327.1	identified by match to protein family HMM PF02129; match to protein family HMM TIGR00976
YP_001001332.1	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_001001333.1	late assembly protein
YP_001001334.1	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_001001335.1	binds 5S rRNA along with protein L5 and L25
YP_001001336.1	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_001001337.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_001001338.1	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 appear to contain the zinc-binding motif
YP_001001339.1	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_001001340.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_001001341.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_001001342.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_001001343.1	one of the stabilizing components for the large ribosomal subunit
YP_001001344.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_001001345.1	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_001001346.1	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_001001347.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_001001348.1	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_001001349.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_001001350.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_001001351.1	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_001001352.1	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_001001353.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093
YP_001001354.1	identified by match to protein family HMM PF00753; match to protein family HMM PF07521; match to protein family HMM TIGR00649
YP_001001355.1	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_001001357.1	23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance
YP_001001359.1	identified by match to protein family HMM PF00583
YP_001001360.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D
YP_001001361.1	dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate
YP_001001362.1	catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis
YP_001001363.1	catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis
YP_001001366.1	NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis
YP_001001367.1	identified by match to protein family HMM PF07992
YP_001001368.1	catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis
YP_001001369.1	identified by match to protein family HMM PF01053; match to protein family HMM TIGR01326
YP_001001371.1	the hook connects flagellar basal body to the flagellar filament
YP_001001372.1	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_001004014.1	identified by match to protein family HMM PF00176; match to protein family HMM PF00271; match to protein family HMM PF02384; match to protein family HMM PF04851
YP_001004025.1	identified by match to protein family HMM PF03681
YP_001004026.1	identified by match to protein family HMM PF07927
YP_001004028.1	identified by match to protein family HMM PF00239
YP_001004032.1	identified by match to protein family HMM PF03135; match to protein family HMM PF05101
YP_001004033.1	identified by match to protein family HMM TIGR02681
YP_001004035.1	identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621
YP_001004038.1	identified by match to protein family HMM PF04610
YP_001004040.1	identified by match to protein family HMM PF04335
YP_001004041.1	identified by match to protein family HMM PF03524; match to protein family HMM TIGR02781
YP_001004042.1	identified by match to protein family HMM PF03743
YP_001004043.1	identified by match to protein family HMM PF00437; match to protein family HMM TIGR02788
YP_001004044.1	identified by match to protein family HMM PF02534
YP_001004046.1	identified by match to protein family HMM PF07424
YP_001004049.1	identified by match to protein family HMM PF01131; match to protein family HMM PF01396; match to protein family HMM PF01751; match to protein family HMM TIGR01056
YP_001004052.1	identified by match to protein family HMM PF00009; match to protein family HMM PF00679; match to protein family HMM PF03144; match to protein family HMM PF03764; match to protein family HMM TIGR00231