-- dump date   	20140619_021341
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_891211.1	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_891212.1	binds the polymerase to DNA and acts as a sliding clamp
YP_891213.1	negatively supercoils closed circular double-stranded DNA
YP_891214.1	identified by match to protein family HMM PF00563
YP_891215.1	NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis
YP_891218.1	identified by match to protein family HMM PF06429
YP_891219.1	acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod
YP_891221.1	identified by match to protein family HMM PF07690; match to protein family HMM TIGR00710
YP_891223.1	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_891226.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_891227.1	identified by match to protein family HMM PF04332
YP_891228.1	identified by match to protein family HMM PF00005
YP_891230.1	identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297
YP_891231.1	Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates
YP_891232.1	identified by match to protein family HMM PF04095
YP_891234.1	identified by match to protein family HMM PF04055; match to protein family HMM TIGR02495
YP_891235.1	identified by match to protein family HMM PF03498
YP_891236.1	identified by match to protein family HMM PF03372
YP_891237.1	identified by match to protein family HMM PF03498
YP_891238.1	identified by match to protein family HMM TIGR02532
YP_891239.1	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_891240.1	identified by match to protein family HMM PF00795
YP_891241.1	catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins
YP_891242.1	identified by match to protein family HMM PF00081; match to protein family HMM PF02777
YP_891243.1	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_891244.1	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_891245.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_891246.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_891247.1	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_891248.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_891249.1	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_891250.1	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_891251.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_891252.1	one of the stabilizing components for the large ribosomal subunit
YP_891253.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_891254.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_891255.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_891256.1	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_891257.1	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_891258.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_891259.1	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_891260.1	binds 5S rRNA along with protein L5 and L25
YP_891261.1	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_891262.1	late assembly protein
YP_891263.1	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_891264.1	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_891265.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_891266.1	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_891267.1	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_891268.1	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_891269.1	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_891270.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_891271.1	identified by match to protein family HMM PF01106
YP_891273.1	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_891274.1	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_891275.1	identified by match to protein family HMM PF00015
YP_891276.1	identified by match to protein family HMM PF02575; match to protein family HMM TIGR00103
YP_891278.1	identified by match to protein family HMM PF00348
YP_891279.1	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_891280.1	NAD-linked
YP_891281.1	identified by match to protein family HMM PF04328
YP_891282.1	identified by match to protein family HMM PF02554
YP_891283.1	identified by match to protein family HMM PF02597; match to protein family HMM TIGR01683
YP_891284.1	catalyzes the adenylation of ThiS which is involved in the formation of 5-methyl-4-(beta-hydroxyethyl)thiazole phosphate
YP_891285.1	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_891286.1	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_891287.1	identified by match to protein family HMM PF01205
YP_891288.1	identified by match to protein family HMM PF00483; match to protein family HMM TIGR01099
YP_891289.1	catalyzes the formation of D-fructose 6-phosphate from D-glucose 6-phosphate
YP_891290.1	identified by match to protein family HMM PF00210
YP_891291.1	identified by match to protein family HMM PF04264
YP_891293.1	identified by match to protein family HMM TIGR00347
YP_891295.1	identified by match to protein family HMM PF04301
YP_891296.1	identified by match to protein family HMM PF00155
YP_891298.1	catalyzes the formation of thiamine diphosphate from thiamine phosphate ant ATP
YP_891299.1	catalyzes the modification of U13 in tRNA(Glu)
YP_891301.1	flagellin specific chaperone
YP_891302.1	Also called hook-associated protein 2; involved in flagellin assembly
YP_891303.1	possibly involved in flagella export
YP_891305.1	identified by match to protein family HMM PF03602; match to protein family HMM TIGR00095
YP_891306.1	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_891310.1	with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook
YP_891311.1	identified by match to protein family HMM TIGR02757
YP_891312.1	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_891313.1	identified by match to protein family HMM PF00483; match to protein family HMM PF01050; match to protein family HMM TIGR01479
YP_891314.1	identified by match to protein family HMM PF02568; match to protein family HMM PF06508; match to protein family HMM TIGR00364
YP_891315.1	charges one glutamine molecule and pairs it with tRNA(Gln)
YP_891316.1	identified by match to protein family HMM PF02325
YP_891317.1	identified by match to protein family HMM PF01464
YP_891320.1	An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group
YP_891321.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_891322.1	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_891323.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_891324.1	identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001
YP_891325.1	identified by match to protein family HMM PF01547
YP_891326.1	identified by match to protein family HMM PF00528
YP_891327.1	identified by match to protein family HMM PF02321; match to protein family HMM TIGR01845
YP_891328.1	identified by match to protein family HMM PF00873; match to protein family HMM TIGR00915
YP_891329.1	identified by match to protein family HMM PF00529; match to protein family HMM TIGR01730
YP_891330.1	identified by match to protein family HMM PF00440
YP_891331.1	identified by match to protein family HMM PF00037; match to protein family HMM TIGR02745
YP_891332.1	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_891335.1	identified by match to protein family HMM PF01058
YP_891336.1	electron transfer protein for hydrogenase-3; the formate hydrogenlyase complex comprises of a formate dehydrogenase, unidentified electron carriers and hydrogenase-3; in this non-energy conserving pathway, molecular hydrogen and carbodioxide are released from formate
YP_891337.1	identified by match to protein family HMM PF00329; match to protein family HMM PF00346
YP_891338.1	identified by match to protein family HMM PF00361
YP_891340.1	interacts with formate dehydrogenase to produce an active formate hydrogenlyase complex which cleaves formate to dihydrogen and carbon dioxide
YP_891341.1	identified by match to protein family HMM PF00146
YP_891342.1	identified by match to protein family HMM PF00361
YP_891343.1	identified by match to protein family HMM PF00037
YP_891344.1	identified by match to protein family HMM PF00221
YP_891346.1	identified by match to protein family HMM PF00890; match to protein family HMM PF01266; match to protein family HMM TIGR01409; match to protein family HMM TIGR01813
YP_891348.1	identified by match to protein family HMM PF03264
YP_891349.1	identified by match to protein family HMM PF02518; match to protein family HMM PF02743
YP_891350.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_891351.1	MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis
YP_891354.1	identified by match to protein family HMM PF04214
YP_891355.1	identified by match to protein family HMM PF03605; match to protein family HMM TIGR00770
YP_891356.1	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_891357.1	identified by match to protein family HMM PF01435
YP_891358.1	identified by match to protein family HMM PF02652; match to protein family HMM TIGR00795
YP_891359.1	identified by match to protein family HMM PF00571; match to protein family HMM PF01595; match to protein family HMM PF03471
YP_891362.1	identified by match to protein family HMM PF00507
YP_891363.1	identified by match to protein family HMM PF01058; match to protein family HMM TIGR01957
YP_891364.1	identified by match to protein family HMM PF00329; match to protein family HMM PF00346
YP_891365.1	identified by match to protein family HMM PF01257
YP_891366.1	identified by match to protein family HMM PF01512
YP_891367.1	identified by match to protein family HMM PF00111
YP_891368.1	identified by match to protein family HMM PF00146
YP_891369.1	identified by match to protein family HMM PF00037
YP_891370.1	identified by match to protein family HMM PF00499
YP_891371.1	identified by match to protein family HMM PF00420
YP_891372.1	identified by match to protein family HMM PF00361; match to protein family HMM PF00662; match to protein family HMM TIGR01974
YP_891373.1	identified by match to protein family HMM PF00361; match to protein family HMM TIGR01972
YP_891374.1	identified by match to protein family HMM PF00361
YP_891376.1	catalyzes the ATP-dependent transport of cobalt
YP_891378.1	identified by match to protein family HMM PF02361
YP_891379.1	identified by match to protein family HMM PF00005; match to protein family HMM PF02463
YP_891380.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_891381.1	catalyzes the formation of biotin from dethiobiotin and sulfur
YP_891382.1	identified by match to protein family HMM PF00999
YP_891383.1	identified by match to protein family HMM PF00285; match to protein family HMM TIGR01798
YP_891384.1	identified by match to protein family HMM PF00459
YP_891385.1	identified by match to protein family HMM PF01547; match to protein family HMM TIGR00975
YP_891386.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR02138
YP_891387.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR00974
YP_891388.1	identified by match to protein family HMM PF00005; match to protein family HMM TIGR00972
YP_891389.1	identified by match to protein family HMM PF00083; match to protein family HMM PF07690
YP_891390.1	identified by match to protein family HMM PF00015
YP_891392.1	identified by match to protein family HMM PF00583
YP_891394.1	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_891395.1	identified by match to protein family HMM PF00015; match to protein family HMM PF00672; match to protein family HMM PF02743
YP_891398.1	identified by match to protein family HMM PF02597
YP_891399.1	identified by match to protein family HMM PF05670
YP_891400.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis
YP_891402.1	identified by match to protein family HMM PF02253
YP_891405.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_891406.1	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_891407.1	identified by match to protein family HMM PF02642
YP_891408.1	with proteins FliP and FliR forms the core of the central channel in the flagella export apparatus
YP_891409.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_891413.1	identified by match to protein family HMM PF01148
YP_891414.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_891415.1	identified by match to protein family HMM PF03352
YP_891416.1	identified by match to protein family HMM PF00860; match to protein family HMM TIGR00801
YP_891417.1	identified by match to protein family HMM PF02557; match to protein family HMM TIGR01409
YP_891419.1	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_891421.1	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_891422.1	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_891425.1	together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z
YP_891426.1	identified by match to protein family HMM PF04055
YP_891427.1	identified by match to protein family HMM PF00465
YP_891431.1	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_891433.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_891434.1	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_891435.1	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_891436.1	identified by match to protein family HMM PF00037
YP_891437.1	identified by match to protein family HMM PF00334
YP_891439.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_891440.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_891441.1	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_891444.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX
YP_891446.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_891447.1	identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518
YP_891448.1	identified by match to protein family HMM PF00037
YP_891449.1	identified by match to protein family HMM PF02541
YP_891451.1	identified by match to protein family HMM PF01207
YP_891453.1	identified by match to protein family HMM PF01258
YP_891454.1	similar to jhp_0883; identified by match to protein family HMM PF02590
YP_891455.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits
YP_891456.1	identified by match to protein family HMM PF00578
YP_891458.1	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_891459.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_891460.1	Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone
YP_891462.1	identified by match to protein family HMM PF07158
YP_891464.1	identified by match to protein family HMM PF00005
YP_891465.1	identified by match to protein family HMM PF01061
YP_891466.1	identified by match to protein family HMM PF01061
YP_891467.1	identified by match to protein family HMM PF01475
YP_891468.1	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_891469.1	binds to and inhibits the function of flagella specific ATPase FliI
YP_891470.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_891471.1	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_891472.1	catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis
YP_891473.1	identified by match to protein family HMM PF00800; match to protein family HMM PF01817; match to protein family HMM PF01842; match to protein family HMM TIGR01807
YP_891474.1	identified by match to protein family HMM TIGR01460
YP_891475.1	identified by match to protein family HMM PF00278; match to protein family HMM PF02784; match to protein family HMM TIGR01048
YP_891476.1	identified by match to protein family HMM PF03739
YP_891478.1	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_891479.1	identified by match to protein family HMM PF00296
YP_891480.1	identified by match to protein family HMM PF01497
YP_891481.1	identified by match to protein family HMM PF00950; match to protein family HMM PF01032
YP_891482.1	identified by match to protein family HMM PF00005
YP_891484.1	identified by match to protein family HMM PF01618; match to protein family HMM TIGR02805
YP_891485.1	identified by match to protein family HMM PF02472; match to protein family HMM TIGR02804
YP_891486.1	identified by match to protein family HMM TIGR01352
YP_891487.1	identified by match to protein family HMM PF03435
YP_891489.1	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_891490.1	identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096
YP_891491.1	identified by match to protein family HMM PF00588; match to protein family HMM PF08032; match to protein family HMM TIGR00186
YP_891494.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_891495.1	catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine
YP_891496.1	similar to jhp_0762; identified by match to protein family HMM PF02021
YP_891497.1	identified by match to protein family HMM PF00085; match to protein family HMM TIGR01068
YP_891498.1	identified by match to protein family HMM PF00070; match to protein family HMM PF07992; match to protein family HMM TIGR01292
YP_891500.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_891501.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_891504.1	identified by match to protein family HMM PF01502; match to protein family HMM PF01503
YP_891505.1	identified by match to protein family HMM PF01145
YP_891506.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_891507.1	identified by match to protein family HMM PF01381
YP_891512.1	identified by match to protein family HMM PF01361
YP_891513.1	identified by match to protein family HMM PF00578
YP_891514.1	identified by match to protein family HMM PF05359
YP_891515.1	identified by match to protein family HMM PF02677
YP_891516.1	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_891517.1	catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis
YP_891518.1	binds and unfolds substrates as part of the ClpXP protease
YP_891519.1	functions in MreBCD complex in some organisms
YP_891520.1	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_891521.1	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_891522.1	identified by match to protein family HMM PF01729
YP_891524.1	identified by match to protein family HMM PF00015; match to protein family HMM PF00989; match to protein family HMM TIGR00229
YP_891526.1	identified by match to protein family HMM PF00899
YP_891527.1	catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate
YP_891528.1	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_891529.1	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_891530.1	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_891532.1	identified by match to protein family HMM PF00072; match to protein family HMM PF01584
YP_891533.1	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_891534.1	identified by match to protein family HMM PF01584
YP_891535.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR00338; match to protein family HMM TIGR01488
YP_891536.1	Important for the balance of metabolites in the pentose-phosphate pathway
YP_891537.1	identified by match to protein family HMM PF00437; match to protein family HMM TIGR01420
YP_891538.1	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_891539.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_891540.1	identified by match to protein family HMM PF00278; match to protein family HMM TIGR01047
YP_891541.1	identified by match to protein family HMM PF01206
YP_891542.1	identified by match to protein family HMM PF02769; match to protein family HMM TIGR00476
YP_891543.1	identified by match to protein family HMM PF00881
YP_891544.1	membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export
YP_891545.1	identified by match to protein family HMM PF00999; match to protein family HMM PF06965; match to protein family HMM TIGR00773
YP_891546.1	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_891548.1	identified by match to protein family HMM PF00939; match to protein family HMM TIGR00785
YP_891549.1	identified by match to protein family HMM PF01925
YP_891550.1	identified by match to protein family HMM PF01925
YP_891551.1	identified by match to protein family HMM PF03625
YP_891552.1	identified by match to protein family HMM PF00425
YP_891553.1	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_891554.1	identified by match to protein family HMM PF00697
YP_891555.1	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_891556.1	catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis
YP_891558.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_891561.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR02141
YP_891562.1	identified by match to protein family HMM PF00005
YP_891564.1	identified by match to protein family HMM PF01547; match to protein family HMM TIGR01256
YP_891565.1	identified by match to protein family HMM PF00126; match to protein family HMM PF03459; match to protein family HMM TIGR00638
YP_891566.1	identified by match to protein family HMM PF04333
YP_891567.1	identified by match to protein family HMM PF05494
YP_891569.1	identified by match to protein family HMM PF04972
YP_891570.1	identified by match to protein family HMM PF00563; match to protein family HMM PF00989; match to protein family HMM PF00990; match to protein family HMM TIGR00229; match to protein family HMM TIGR00254
YP_891571.1	May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine
YP_891572.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_891575.1	identified by match to protein family HMM PF04368
YP_891576.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_891578.1	identified by match to protein family HMM PF00989; match to protein family HMM PF02518; match to protein family HMM TIGR00229
YP_891579.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_891580.1	CcoN; FixN
YP_891581.1	CcoO; FixO
YP_891582.1	identified by match to protein family HMM TIGR02736
YP_891583.1	identified by match to protein family HMM PF00034; match to protein family HMM TIGR00782
YP_891588.1	identified by match to protein family HMM PF00580
YP_891589.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_891590.1	forms a direct contact with the tRNA during translation
YP_891591.1	identified by match to protein family HMM PF00691
YP_891592.1	identified by match to protein family HMM PF00924
YP_891593.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549
YP_891594.1	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_891598.1	identified by match to protein family HMM PF05538
YP_891599.1	identified by match to protein family HMM PF05538
YP_891600.1	identified by match to protein family HMM PF00034
YP_891601.1	identified by match to protein family HMM PF01094
YP_891602.1	identified by match to protein family HMM PF02653
YP_891603.1	identified by match to protein family HMM PF02653
YP_891604.1	identified by match to protein family HMM PF00005
YP_891605.1	identified by match to protein family HMM PF00005
YP_891606.1	identified by match to protein family HMM PF01578
YP_891608.1	identified by match to protein family HMM PF04608
YP_891610.1	identified by match to protein family HMM PF00072
YP_891611.1	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_891612.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_891615.1	identified by match to protein family HMM PF00005; match to protein family HMM PF02463
YP_891616.1	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_891617.1	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_891618.1	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_891619.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_891621.1	identified by match to protein family HMM PF00817
YP_891623.1	identified by match to protein family HMM PF00583
YP_891624.1	identified by match to protein family HMM PF03222
YP_891625.1	identified by match to protein family HMM PF01709; match to protein family HMM TIGR01033
YP_891626.1	identified by match to protein family HMM PF00160
YP_891627.1	identified by match to protein family HMM PF00375
YP_891628.1	identified by match to protein family HMM PF00375
YP_891629.1	identified by match to protein family HMM PF00027; match to protein family HMM PF00325
YP_891630.1	identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM TIGR01409
YP_891631.1	identified by match to protein family HMM PF00512; match to protein family HMM PF02518
YP_891632.1	identified by match to protein family HMM PF00072
YP_891635.1	identified by match to protein family HMM PF00593
YP_891636.1	identified by match to protein family HMM PF05935
YP_891637.1	identified by match to protein family HMM PF00350
YP_891638.1	identified by match to protein family HMM PF00350
YP_891640.1	identified by match to protein family HMM PF00116
YP_891643.1	identified by match to protein family HMM PF00037
YP_891646.1	identified by match to protein family HMM PF00037; match to protein family HMM TIGR02163
YP_891647.1	identified by match to protein family HMM PF00005
YP_891650.1	identified by match to protein family HMM PF00512; match to protein family HMM PF00672
YP_891651.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_891652.1	identified by match to protein family HMM PF01292
YP_891656.1	identified by match to protein family HMM PF02321
YP_891657.1	identified by match to protein family HMM PF00529; match to protein family HMM TIGR01843
YP_891658.1	identified by match to protein family HMM PF00005; match to protein family HMM TIGR01842
YP_891659.1	identified by match to protein family HMM PF07277
YP_891665.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_891667.1	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_891668.1	identified by match to protein family HMM PF01594
YP_891669.1	identified by match to protein family HMM PF00005
YP_891670.1	identified by match to protein family HMM PF02470
YP_891672.1	identified by match to protein family HMM PF02130; match to protein family HMM TIGR00043
YP_891674.1	identified by match to protein family HMM PF05016; match to protein family HMM TIGR02385
YP_891677.1	identified by match to protein family HMM PF07804; match to protein family HMM PF07805; match to protein family HMM TIGR03071
YP_891680.1	identified by match to protein family HMM PF01637; match to protein family HMM PF03008
YP_891685.1	identified by match to protein family HMM PF00534
YP_891686.1	identified by match to protein family HMM PF00534
YP_891688.1	identified by match to protein family HMM PF00005
YP_891689.1	identified by match to protein family HMM PF01061
YP_891690.1	identified by match to protein family HMM PF00534
YP_891691.1	identified by match to protein family HMM PF02397; match to protein family HMM TIGR03025
YP_891692.1	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_891693.1	identified by match to protein family HMM PF00448; match to protein family HMM TIGR00064
YP_891695.1	identified by match to protein family HMM PF01812; match to protein family HMM TIGR02727
YP_891696.1	protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP
YP_891700.1	identified by match to protein family HMM PF00633
YP_891701.1	identified by match to protein family HMM PF00015
YP_891702.1	identified by match to protein family HMM PF00202; match to protein family HMM TIGR00508
YP_891703.1	identified by match to protein family HMM PF00730; match to protein family HMM TIGR01083
YP_891704.1	identified by match to protein family HMM PF00639
YP_891705.1	catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate
YP_891709.1	catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer
YP_891710.1	identified by match to protein family HMM PF00669
YP_891711.1	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_891712.1	identified by match to protein family HMM PF00460
YP_891713.1	makes up the distal portion of the flagellar basal body rod
YP_891714.1	identified by match to protein family HMM PF03239
YP_891716.1	identified by match to protein family HMM PF04945
YP_891717.1	identified by match to protein family HMM PF02687
YP_891718.1	identified by match to protein family HMM PF02687
YP_891719.1	identified by match to protein family HMM PF00005
YP_891721.1	identified by match to protein family HMM PF04371
YP_891722.1	identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297
YP_891723.1	identified by match to protein family HMM PF00795
YP_891724.1	identified by match to protein family HMM PF03616; match to protein family HMM TIGR00210
YP_891725.1	identified by match to protein family HMM PF01863
YP_891726.1	identified by match to protein family HMM PF01554; match to protein family HMM TIGR00797
YP_891727.1	identified by match to protein family HMM PF00512; match to protein family HMM PF02518
YP_891728.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_891729.1	identified by match to protein family HMM PF00083; match to protein family HMM PF07690
YP_891730.1	identified by match to protein family HMM PF00005; match to protein family HMM PF02463
YP_891731.1	identified by match to protein family HMM PF00209
YP_891732.1	identified by match to protein family HMM PF01435
YP_891733.1	identified by match to protein family HMM PF05175; match to protein family HMM TIGR00536
YP_891738.1	identified by match to protein family HMM PF00583
YP_891739.1	identified by match to protein family HMM PF00909; match to protein family HMM TIGR00836
YP_891740.1	identified by match to protein family HMM PF00543
YP_891741.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_891742.1	identified by match to protein family HMM PF00825; match to protein family HMM TIGR00188
YP_891743.1	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_891745.1	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_891746.1	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_891747.1	identified by match to protein family HMM PF00226
YP_891748.1	involved in de novo purine biosynthesis
YP_891751.1	identified by match to protein family HMM PF01883
YP_891752.1	identified by match to protein family HMM PF00015; match to protein family HMM PF00672
YP_891753.1	identified by match to protein family HMM PF01063
YP_891757.1	identified by match to protein family HMM PF01795; match to protein family HMM TIGR00006
YP_891758.1	identified by match to protein family HMM PF00596
YP_891760.1	identified by match to protein family HMM PF02491; match to protein family HMM TIGR01174
YP_891761.1	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_891762.1	identified by match to protein family HMM PF00877
YP_891765.1	participates with LolB in the incorporation of lipoprotein into the outer membrane
YP_891766.1	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_891767.1	identified by match to protein family HMM PF02687
YP_891770.1	identified by match to protein family HMM PF07690
YP_891771.1	identified by match to protein family HMM PF00156
YP_891772.1	identified by match to protein family HMM PF00860; match to protein family HMM PF00916
YP_891773.1	identified by match to protein family HMM PF04055; match to protein family HMM TIGR00423
YP_891774.1	identified by match to protein family HMM PF01966
YP_891775.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_891776.1	identified by match to protein family HMM PF04143
YP_891777.1	identified by match to protein family HMM PF01206
YP_891779.1	identified by match to protein family HMM PF01177; match to protein family HMM TIGR00067
YP_891780.1	identified by match to protein family HMM PF01977; match to protein family HMM TIGR00148
YP_891781.1	identified by match to protein family HMM PF00633
YP_891782.1	identified by match to protein family HMM PF00990; match to protein family HMM PF01814; match to protein family HMM TIGR00254; match to protein family HMM TIGR02481
YP_891784.1	identified by match to protein family HMM PF02464; match to protein family HMM TIGR00199
YP_891786.1	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_891787.1	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_891788.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_891789.1	identified by match to protein family HMM PF00561; match to protein family HMM TIGR01392
YP_891792.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_891794.1	identified by match to protein family HMM PF00724
YP_891795.1	identified by match to protein family HMM PF00005
YP_891796.1	identified by match to protein family HMM PF00528
YP_891797.1	identified by match to protein family HMM PF03180
YP_891799.1	identified by match to protein family HMM PF02566
YP_891800.1	MutS2; MutS-II; involved in blocking homologous and homeologous recombination; has ATPase activity stimulated by recombination intermediates; inhibits DNA strand exchange
YP_891801.1	identified by match to protein family HMM PF00563; match to protein family HMM PF00990
YP_891802.1	identified by match to protein family HMM PF01810
YP_891803.1	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_891804.1	identified by match to protein family HMM PF01266; match to protein family HMM PF06039
YP_891806.1	identified by match to protein family HMM PF00224; match to protein family HMM PF02887; match to protein family HMM TIGR01064
YP_891807.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_891808.1	catalyzes branch migration in Holliday junction intermediates
YP_891809.1	identified by match to protein family HMM PF01474; match to protein family HMM TIGR01358
YP_891810.1	identified by match to protein family HMM TIGR00407
YP_891811.1	identified by match to protein family HMM PF00070; match to protein family HMM PF07992
YP_891813.1	identified by match to protein family HMM PF05175
YP_891814.1	identified by match to protein family HMM PF03692
YP_891816.1	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_891817.1	identified by match to protein family HMM PF01230
YP_891818.1	identified by match to protein family HMM PF03883
YP_891824.1	identified by match to protein family HMM PF03237
YP_891825.1	identified by match to protein family HMM PF04860
YP_891834.1	identified by match to protein family HMM TIGR01877
YP_891837.1	identified by match to protein family HMM TIGR02592; match to protein family HMM TIGR02593
YP_891838.1	identified by match to protein family HMM PF00271; match to protein family HMM TIGR01587
YP_891839.1	identified by match to protein family HMM PF01930
YP_891840.1	identified by match to protein family HMM PF01867; match to protein family HMM TIGR00287
YP_891841.1	identified by match to protein family HMM TIGR01573
YP_891851.1	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_891853.1	Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate
YP_891854.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_891855.1	involved in the de novo synthesis of pyridoxine (Vitamin B6)
YP_891856.1	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_891857.1	identified by match to protein family HMM PF01384
YP_891858.1	identified by match to protein family HMM PF00669
YP_891859.1	identified by match to protein family HMM PF01580
YP_891862.1	identified by match to protein family HMM PF00348
YP_891863.1	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_891864.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_891866.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_891867.1	identified by match to protein family HMM PF03631; match to protein family HMM TIGR00765
YP_891868.1	identified by match to protein family HMM PF01565; match to protein family HMM PF02913
YP_891871.1	identified by match to protein family HMM PF01551
YP_891872.1	identified by match to protein family HMM PF00571; match to protein family HMM PF01769; match to protein family HMM PF03448; match to protein family HMM TIGR00400
YP_891873.1	identified by match to protein family HMM PF00293; match to protein family HMM TIGR00052
YP_891875.1	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_891876.1	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_891877.1	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_891878.1	identified by match to protein family HMM PF00905; match to protein family HMM PF03717
YP_891879.1	forms a junction between the M-ring and FlgB during flagella biosynthesis
YP_891880.1	with FlgF and B makes up the proximal portion of the flagellar basal body rod
YP_891881.1	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_891882.1	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_891884.1	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_891885.1	identified by match to protein family HMM PF02617
YP_891887.1	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_891888.1	catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis
YP_891889.1	identified by match to protein family HMM PF02599; match to protein family HMM TIGR00202
YP_891890.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_891891.1	identified by match to protein family HMM PF00580
YP_891892.1	identified by match to protein family HMM PF00126
YP_891894.1	identified by match to protein family HMM PF01432
YP_891895.1	involved in the import of serine and threonine coupled with the import of sodium
YP_891896.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_891897.1	identified by match to protein family HMM PF01297
YP_891898.1	identified by match to protein family HMM PF00005
YP_891899.1	identified by match to protein family HMM PF00950
YP_891900.1	identified by match to protein family HMM PF00950
YP_891901.1	Transfers the fatty acyl group on membrane lipoproteins
YP_891902.1	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_891903.1	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_891904.1	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_891906.1	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_891908.1	identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254
YP_891909.1	identified by match to protein family HMM TIGR01499
YP_891910.1	identified by match to protein family HMM PF01551
YP_891911.1	identified by match to protein family HMM PF04519
YP_891912.1	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_891915.1	identified by match to protein family HMM PF00730
YP_891916.1	identified by match to protein family HMM PF04076
YP_891917.1	identified by match to protein family HMM PF02629
YP_891918.1	catalyzes the formation of 2-oxobutanoate from L-threonine
YP_891919.1	identified by match to protein family HMM PF05594; match to protein family HMM PF05860; match to protein family HMM TIGR01901
YP_891920.1	identified by match to protein family HMM PF03865
YP_891922.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_891923.1	identified by match to protein family HMM PF03739
YP_891924.1	identified by match to protein family HMM PF06750
YP_891925.1	identified by match to protein family HMM PF01255; match to protein family HMM TIGR00055
YP_891927.1	catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine
YP_891928.1	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_891929.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_891931.1	identified by match to protein family HMM PF03547
YP_891932.1	3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate
YP_891933.1	identified by match to protein family HMM PF00529; match to protein family HMM TIGR01730
YP_891934.1	identified by match to protein family HMM PF00005; match to protein family HMM PF02687
YP_891935.1	identified by match to protein family HMM PF02321
YP_891936.1	identified by match to protein family HMM PF03772; match to protein family HMM TIGR00360
YP_891937.1	identified by match to protein family HMM PF00512; match to protein family HMM PF00672
YP_891938.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_891939.1	identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037
YP_891940.1	identified by match to protein family HMM PF00226; match to protein family HMM PF01556
YP_891941.1	identified by match to protein family HMM PF00376
YP_891942.1	identified by match to protein family HMM PF00999; match to protein family HMM PF02254
YP_891943.1	the Vibrio parahaemolyticus gene VP2867 was found to be a potassium/proton antiporter; can rapidly extrude potassium against a potassium gradient at alkaline pH when cloned and expressed in Escherichia coli
YP_891945.1	identified by match to protein family HMM PF01925
YP_891946.1	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_891948.1	identified by match to protein family HMM PF02581
YP_891949.1	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_891950.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_891951.1	identified by match to protein family HMM PF00933
YP_891953.1	identified by match to protein family HMM PF00892; match to protein family HMM TIGR00688
YP_891954.1	identified by match to protein family HMM PF00005
YP_891955.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_891956.1	identified by match to protein family HMM PF00497
YP_891957.1	identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560
YP_891958.1	Acts on the hydroxyl group at position 7 of the steroid frame
YP_891959.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_891960.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_891961.1	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_891962.1	identified by match to protein family HMM PF00005; match to protein family HMM PF00664
YP_891963.1	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_891964.1	identified by match to protein family HMM PF03023; match to protein family HMM TIGR01695
YP_891966.1	identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF04851
YP_891968.1	identified by match to protein family HMM PF03205; match to protein family HMM TIGR00176
YP_891969.1	catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate
YP_891971.1	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_891973.1	identified by match to protein family HMM PF00027; match to protein family HMM PF00325
YP_891974.1	identified by match to protein family HMM PF03264
YP_891976.1	identified by match to protein family HMM PF04055; match to protein family HMM TIGR00423
YP_891978.1	identified by match to protein family HMM PF04332; match to protein family HMM PF07690
YP_891979.1	identified by match to protein family HMM PF01739
YP_891980.1	identified by match to protein family HMM PF01339
YP_891982.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_891983.1	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_891987.1	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_891988.1	identified by match to protein family HMM PF01515; match to protein family HMM TIGR00651
YP_891989.1	part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod
YP_891990.1	identified by match to protein family HMM PF03713
YP_891991.1	catalyzes the formation of 2-acetolactate from pyruvate, leucine resistant; also known as acetolactate synthase 3 large subunit
YP_891992.1	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_891993.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_891996.1	identified by match to protein family HMM PF01729; match to protein family HMM PF02749; match to protein family HMM TIGR00078
YP_891997.1	identified by match to protein family HMM PF00551; match to protein family HMM TIGR00655
YP_891998.1	identified by match to protein family HMM PF00588
YP_891999.1	identified by match to protein family HMM PF03372
YP_892001.1	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_892002.1	identified by match to protein family HMM PF02086
YP_892005.1	identified by match to protein family HMM PF01235; match to protein family HMM TIGR00835
YP_892006.1	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_892013.1	identified by match to protein family HMM PF01551
YP_892015.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_892016.1	identified by match to protein family HMM PF00512; match to protein family HMM PF02518
YP_892017.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_892018.1	identified by match to protein family HMM PF00589
YP_892019.1	identified by match to protein family HMM PF01098
YP_892020.1	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_892021.1	identified by match to protein family HMM PF00216
YP_892022.1	identified by match to protein family HMM PF01618; match to protein family HMM TIGR02805
YP_892023.1	identified by match to protein family HMM PF02472; match to protein family HMM TIGR02804
YP_892024.1	identified by match to protein family HMM PF03544; match to protein family HMM TIGR01352
YP_892025.1	identified by match to protein family HMM PF01479
YP_892026.1	identified by match to protein family HMM PF02367; match to protein family HMM TIGR00150
YP_892027.1	identified by match to protein family HMM PF00005
YP_892028.1	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_892029.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_892030.1	identified by match to protein family HMM PF00924
YP_892031.1	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_892032.1	identified by match to protein family HMM PF00004; match to protein family HMM PF01434; match to protein family HMM PF06480
YP_892033.1	identified by match to protein family HMM PF00994; match to protein family HMM TIGR00177
YP_892034.1	identified by match to protein family HMM PF01168; match to protein family HMM TIGR00044
YP_892035.1	identified by match to protein family HMM PF02163; match to protein family HMM TIGR00054
YP_892036.1	catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate
YP_892037.1	3'-5' exonuclease of DNA polymerase III
YP_892038.1	binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity
YP_892039.1	identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532
YP_892040.1	identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532
YP_892041.1	identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532
YP_892046.1	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_892047.1	identified by match to protein family HMM PF03929
YP_892048.1	identified by match to protein family HMM PF00593; match to protein family HMM PF07715; match to protein family HMM TIGR01783
YP_892049.1	identified by match to protein family HMM PF01554
YP_892050.1	catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate
YP_892052.1	catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine
YP_892054.1	identified by match to protein family HMM PF00300
YP_892055.1	identified by match to protein family HMM PF04305
YP_892056.1	identified by match to protein family HMM PF01694
YP_892057.1	identified by match to protein family HMM PF02754
YP_892058.1	identified by match to protein family HMM PF00037; match to protein family HMM TIGR00273
YP_892059.1	identified by match to protein family HMM PF02589
YP_892061.1	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_892062.1	identified by match to protein family HMM PF00994; match to protein family HMM PF03453; match to protein family HMM TIGR00177
YP_892063.1	required for the assembly of the flagellar basal body P-ring
YP_892064.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_892065.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_892066.1	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_892067.1	catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis
YP_892068.1	identified by match to protein family HMM PF00132; match to protein family HMM TIGR01172
YP_892069.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_892070.1	identified by match to protein family HMM PF00535
YP_892071.1	identified by match to protein family HMM PF05787
YP_892072.1	identified by match to protein family HMM PF00258
YP_892074.1	identified by match to protein family HMM PF03401
YP_892076.1	identified by match to protein family HMM PF01558
YP_892077.1	identified by match to protein family HMM PF02775
YP_892078.1	identified by match to protein family HMM PF01855
YP_892079.1	identified by match to protein family HMM PF00037
YP_892080.1	identified by match to protein family HMM PF00549; match to protein family HMM PF02629; match to protein family HMM TIGR01019
YP_892081.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_892082.1	identified by match to protein family HMM PF00056; match to protein family HMM PF00070; match to protein family HMM PF02866
YP_892083.1	identified by match to protein family HMM PF03971; match to protein family HMM TIGR00178
YP_892084.1	identified by match to protein family HMM PF03595
YP_892085.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549
YP_892087.1	identified by match to protein family HMM PF00171; match to protein family HMM TIGR01780
YP_892088.1	catalyzes the reduction of hydroxylamine to ammonia and water
YP_892089.1	identified by match to protein family HMM PF01041; match to protein family HMM PF01053; match to protein family HMM PF01212; match to protein family HMM TIGR01326
YP_892090.1	identified by match to protein family HMM PF02082
YP_892091.1	identified by match to protein family HMM PF00291; match to protein family HMM TIGR01136; match to protein family HMM TIGR01139
YP_892092.1	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_892093.1	interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring
YP_892094.1	identified by match to protein family HMM PF01557
YP_892095.1	catalyzes the formation of N-acetyl-l-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine
YP_892096.1	identified by match to protein family HMM PF03458
YP_892097.1	identified by match to protein family HMM PF02618
YP_892099.1	identified by match to protein family HMM PF01155
YP_892100.1	identified by match to protein family HMM PF00586; match to protein family HMM PF02769; match to protein family HMM TIGR02124
YP_892101.1	identified by match to protein family HMM PF01924; match to protein family HMM TIGR00075
YP_892102.1	identified by match to protein family HMM PF01455; match to protein family HMM TIGR00074
YP_892103.1	identified by match to protein family HMM PF02492; match to protein family HMM TIGR00073
YP_892104.1	Inhibits transcription at high concentrations of nickel
YP_892105.1	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_892107.1	identified by match to protein family HMM PF01750; match to protein family HMM TIGR00072
YP_892108.1	identified by match to protein family HMM PF01292; match to protein family HMM TIGR02125
YP_892109.1	identified by match to protein family HMM PF00374
YP_892110.1	identified by match to protein family HMM PF01058; match to protein family HMM TIGR00391; match to protein family HMM TIGR01409
YP_892111.1	identified by match to protein family HMM PF05437
YP_892112.1	identified by match to protein family HMM PF03591
YP_892113.1	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_892114.1	identified by match to protein family HMM PF00595; match to protein family HMM PF03572; match to protein family HMM TIGR00225
YP_892115.1	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_892116.1	identified by match to protein family HMM PF02700; match to protein family HMM TIGR00302
YP_892117.1	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_892119.1	identified by match to protein family HMM PF01553; match to protein family HMM TIGR00530
YP_892120.1	identified by match to protein family HMM PF02537; match to protein family HMM TIGR00494
YP_892121.1	identified by match to protein family HMM PF03498
YP_892122.1	identified by match to protein family HMM PF03498
YP_892123.1	identified by match to protein family HMM PF03498
YP_892124.1	identified by match to protein family HMM PF03372
YP_892125.1	identified by match to protein family HMM PF03498
YP_892126.1	molecular chaperone
YP_892127.1	identified by match to protein family HMM PF00581
YP_892129.1	identified by match to protein family HMM PF00580
YP_892133.1	identified by match to protein family HMM PF00206; match to protein family HMM TIGR00979
YP_892134.1	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_892135.1	identified by match to protein family HMM PF00005
YP_892136.1	identified by match to protein family HMM PF00528
YP_892137.1	identified by match to protein family HMM TIGR00097
YP_892138.1	identified by match to protein family HMM PF03180
YP_892139.1	required for 70S ribosome assembly
YP_892140.1	identified by match to protein family HMM PF02080; match to protein family HMM PF02254; match to protein family HMM PF07885
YP_892141.1	bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate
YP_892142.1	identified by match to protein family HMM PF04325
YP_892143.1	identified by match to protein family HMM PF00015
YP_892144.1	catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs
YP_892145.1	identified by match to protein family HMM PF00106; match to protein family HMM PF01370
YP_892146.1	identified by match to protein family HMM PF00023
YP_892147.1	identified by match to protein family HMM PF02080
YP_892148.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_892150.1	unwinds double stranded DNA
YP_892151.1	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_892152.1	identified by match to protein family HMM PF01863
YP_892153.1	identified by match to protein family HMM PF04313; match to protein family HMM PF04851; match to protein family HMM TIGR00348
YP_892156.1	identified by match to protein family HMM PF01420
YP_892158.1	identified by match to protein family HMM PF02384; match to protein family HMM TIGR00497
YP_892159.1	identified by match to protein family HMM PF01420
YP_892163.1	catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate
YP_892164.1	identified by match to protein family HMM PF01035; match to protein family HMM TIGR00589
YP_892165.1	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_892166.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_892167.1	heat shock protein involved in degradation of misfolded proteins
YP_892168.1	heat shock protein involved in degradation of misfolded proteins
YP_892169.1	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_892173.1	identified by match to protein family HMM PF00263; match to protein family HMM PF07655; match to protein family HMM TIGR02519
YP_892176.1	identified by match to protein family HMM PF00437; match to protein family HMM PF05157
YP_892177.1	identified by match to protein family HMM PF00482
YP_892178.1	identified by match to protein family HMM PF00989; match to protein family HMM TIGR00229
YP_892179.1	identified by match to protein family HMM PF02637
YP_892180.1	identified by match to protein family HMM PF02541
YP_892181.1	identified by match to protein family HMM PF01743
YP_892184.1	catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis
YP_892185.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis
YP_892186.1	identified by match to protein family HMM PF01810
YP_892187.1	identified by match to protein family HMM PF01810
YP_892189.1	identified by match to protein family HMM PF00710; match to protein family HMM TIGR00520
YP_892190.1	identified by match to protein family HMM PF02646
YP_892191.1	identified by match to protein family HMM PF03547
YP_892192.1	identified by match to protein family HMM PF03831
YP_892193.1	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_892195.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_892196.1	identified by match to protein family HMM PF00905; match to protein family HMM PF00912; match to protein family HMM TIGR02074
YP_892198.1	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_892199.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_892200.1	identified by match to protein family HMM PF01782; match to protein family HMM PF05239; match to protein family HMM TIGR02273
YP_892202.1	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_892203.1	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_892204.1	identified by match to protein family HMM PF00939; match to protein family HMM PF03600
YP_892205.1	identified by match to protein family HMM PF00015
YP_892206.1	identified by match to protein family HMM PF00849
YP_892207.1	catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A
YP_892209.1	identified by match to protein family HMM PF02591
YP_892210.1	identified by match to protein family HMM PF01784; match to protein family HMM TIGR00486
YP_892211.1	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_892213.1	identified by match to protein family HMM PF00731; match to protein family HMM TIGR01162
YP_892214.1	identified by match to protein family HMM PF01136
YP_892216.1	identified by match to protein family HMM PF02811; match to protein family HMM TIGR01856
YP_892217.1	identified by match to protein family HMM PF00120; match to protein family HMM PF03951; match to protein family HMM TIGR00653
YP_892219.1	identified by match to protein family HMM PF00023
YP_892220.1	identified by match to protein family HMM PF00199
YP_892221.1	identified by match to protein family HMM PF00004; match to protein family HMM PF05362; match to protein family HMM PF07728; match to protein family HMM TIGR00763
YP_892223.1	identified by match to protein family HMM PF01614
YP_892224.1	identified by match to protein family HMM PF00701
YP_892225.1	identified by match to protein family HMM PF04292; match to protein family HMM PF04295
YP_892226.1	identified by match to protein family HMM PF00106
YP_892227.1	identified by match to protein family HMM PF07690; match to protein family HMM TIGR00885
YP_892228.1	identified by match to protein family HMM PF04909; match to protein family HMM PF05336
YP_892229.1	binds to flagellin and appears to stabilize flagellin during flagella assembly
YP_892230.1	identified by match to protein family HMM TIGR02532
YP_892231.1	identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532
YP_892233.1	identified by match to protein family HMM PF02482; match to protein family HMM TIGR00741
YP_892234.1	identified by match to protein family HMM PF05343; match to protein family HMM PF07687
YP_892236.1	identified by match to protein family HMM PF08003
YP_892238.1	identified by match to protein family HMM PF00753
YP_892239.1	identified by match to protein family HMM PF02540; match to protein family HMM TIGR00552
YP_892240.1	identified by match to protein family HMM PF01041; match to protein family HMM PF01212
YP_892241.1	transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate
YP_892242.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate
YP_892243.1	identified by match to protein family HMM PF00291; match to protein family HMM PF03091; match to protein family HMM TIGR00260
YP_892244.1	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_892246.1	identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254
YP_892247.1	identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254
YP_892248.1	identified by match to protein family HMM PF00085; match to protein family HMM PF02683
YP_892249.1	identified by match to protein family HMM PF03976
YP_892250.1	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_892251.1	identified by match to protein family HMM PF01025
YP_892252.1	Acts as a negative regulator of the grpE-dnaK-dnaJ and groELS class I heat shock operons by preventing heat-shock induction
YP_892256.1	membrane protein involved in the flagellar export apparatus
YP_892257.1	identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738
YP_892258.1	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_892259.1	catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine
YP_892261.1	identified by match to protein family HMM TIGR01488; match to protein family HMM TIGR01490
YP_892262.1	identified by match to protein family HMM PF00005
YP_892263.1	identified by match to protein family HMM PF00528
YP_892264.1	identified by match to protein family HMM PF00528
YP_892267.1	identified by match to protein family HMM PF02390; match to protein family HMM TIGR00740
YP_892268.1	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_892269.1	identified by match to protein family HMM PF01479; match to protein family HMM PF01728
YP_892270.1	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_892271.1	identified by match to protein family HMM PF00809; match to protein family HMM TIGR01496
YP_892272.1	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_892274.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.
YP_892275.1	hydrolyzes diadenosine polyphosphate
YP_892276.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_892277.1	mediates the export of protein precursors bearing twin-arginine signal peptides
YP_892278.1	identified by match to protein family HMM PF00902; match to protein family HMM TIGR00945
YP_892279.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_892281.1	identified by match to protein family HMM PF01189
YP_892282.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_892283.1	identified by match to protein family HMM PF02481
YP_892284.1	identified by match to protein family HMM PF04748
YP_892285.1	catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis
YP_892287.1	identified by match to protein family HMM PF00773; match to protein family HMM PF08206
YP_892288.1	required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA
YP_892289.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_892290.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_892291.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_892292.1	identified by match to protein family HMM PF00226; match to protein family HMM PF00684; match to protein family HMM PF01556; match to protein family HMM TIGR02349
YP_892293.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_892294.1	identified by match to protein family HMM PF00512; match to protein family HMM PF00672
YP_892295.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_892296.1	AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate
YP_892297.1	identified by match to protein family HMM PF05036
YP_892299.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_892300.1	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_892301.1	identified by match to protein family HMM PF01475
YP_892302.1	identified by match to protein family HMM PF02674
YP_892303.1	identified by match to protein family HMM PF00437; match to protein family HMM TIGR01420
YP_892304.1	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_892308.1	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_892309.1	short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ
YP_892310.1	identified by match to protein family HMM PF05525; match to protein family HMM TIGR00796
YP_892311.1	identified by match to protein family HMM PF00149
YP_892312.1	catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine
YP_892315.1	identified by match to protein family HMM PF00037
YP_892316.1	identified by match to protein family HMM PF03892
YP_892317.1	part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA
YP_892318.1	part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; secreted by twin arginine translocation pathway
YP_892319.1	periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC
YP_892320.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_892321.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_892322.1	PEB1
YP_892323.1	identified by match to protein family HMM PF00005
YP_892324.1	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_892325.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_892327.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_892329.1	identified by match to protein family HMM PF02502; match to protein family HMM TIGR00689; match to protein family HMM TIGR01120
YP_892330.1	identified by match to protein family HMM PF02163
YP_892331.1	identified by match to protein family HMM PF00717; match to protein family HMM TIGR02227
YP_892332.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_892334.1	Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway
YP_892337.1	identified by match to protein family HMM PF07690
YP_892339.1	identified by match to protein family HMM TIGR00789
YP_892340.1	identified by match to protein family HMM PF00905; match to protein family HMM PF03717
YP_892342.1	catalyzes the formation of N-acetyl-L-glutamate from acetyl-CoA and L-glutamate
YP_892343.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_892344.1	identified by match to protein family HMM PF03968
YP_892346.1	identified by match to protein family HMM TIGR01670
YP_892347.1	catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis
YP_892348.1	identified by match to protein family HMM PF03330; match to protein family HMM PF05036; match to protein family HMM TIGR00413
YP_892349.1	identified by match to protein family HMM PF01464; match to protein family HMM PF01476
YP_892350.1	identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010
YP_892351.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00990; match to protein family HMM TIGR00254
YP_892352.1	identified by match to protein family HMM PF02463
YP_892353.1	catalyzes the phosphorylation of NAD to NADP
YP_892354.1	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_892355.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_892356.1	identified by match to protein family HMM PF00719
YP_892359.1	identified by match to protein family HMM PF00005
YP_892360.1	identified by match to protein family HMM PF01032
YP_892361.1	identified by match to protein family HMM PF01497
YP_892364.1	identified by match to protein family HMM PF00593; match to protein family HMM PF07715
YP_892365.1	identified by match to protein family HMM PF00165
YP_892366.1	catalyzes the formation of 5-methylaminomethyl-2-thiouridine in position 34 of the anticodon of tRNA molecules
YP_892367.1	identified by match to protein family HMM PF01520
YP_892368.1	identified by match to protein family HMM PF03060
YP_892369.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_892370.1	identified by 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_892371.1	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_892372.1	Catalyzes the phosphorylation of UMP to UDP
YP_892373.1	identified by match to protein family HMM PF01551
YP_892375.1	identified by match to protein family HMM PF00005
YP_892376.1	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_892377.1	identified by match to protein family HMM PF00041
YP_892378.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005
YP_892379.1	identified by match to protein family HMM PF01098
YP_892380.1	identified by match to protein family HMM PF02630
YP_892381.1	identified by match to protein family HMM PF00015
YP_892382.1	identified by match to protein family HMM PF01638
YP_892384.1	identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297
YP_892385.1	identified by match to protein family HMM PF00015; match to protein family HMM PF00672
YP_892386.1	identified by match to protein family HMM PF00474; match to protein family HMM TIGR00813; match to protein family HMM TIGR02121
YP_892387.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_892388.1	identified by match to protein family HMM PF00005
YP_892389.1	identified by match to protein family HMM PF00497
YP_892390.1	identified by match to protein family HMM PF00497
YP_892391.1	identified by match to protein family HMM PF02581
YP_892392.1	identified by match to protein family HMM PF02673; match to protein family HMM TIGR00753
YP_892393.1	identified by match to protein family HMM PF00266
YP_892394.1	identified by match to protein family HMM PF03008
YP_892395.1	identified by match to protein family HMM PF00512; match to protein family HMM PF02518
YP_892396.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_892397.1	identified by match to protein family HMM PF00076
YP_892398.1	identified by match to protein family HMM PF00171; match to protein family HMM PF01619
YP_892399.1	identified by match to protein family HMM PF00474; match to protein family HMM TIGR00813; match to protein family HMM TIGR02121
YP_892401.1	identified by match to protein family HMM PF02335
YP_892402.1	identified by match to protein family HMM PF01965; match to protein family HMM TIGR01383
YP_892403.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_892404.1	catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate
YP_892406.1	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_892407.1	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_892408.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_892409.1	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_892410.1	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_892411.1	identified by match to protein family HMM PF01230
YP_892413.1	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_892415.1	identified by match to protein family HMM PF04453
YP_892416.1	identified by match to protein family HMM PF06271
YP_892417.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_892418.1	catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane; functions in tetrapyrrole and heme biosynthesis
YP_892420.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_892422.1	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_892424.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF02518
YP_892425.1	identified by match to protein family HMM PF00072
YP_892430.1	identified by match to protein family HMM PF02690
YP_892432.1	identified by match to protein family HMM PF04341
YP_892433.1	member of the sodium:solute symporter family; cotranscribed with the acs gene which encodes acetyl coenzyme A synthase; mutations affect acetate uptake
YP_892434.1	identified by match to protein family HMM PF03061
YP_892435.1	identified by match to protein family HMM PF01625; match to protein family HMM PF01641; match to protein family HMM TIGR00357; match to protein family HMM TIGR00401
YP_892437.1	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_892438.1	similar to P. aerophilum
YP_892439.1	identified by match to protein family HMM PF00165; match to protein family HMM PF06719
YP_892440.1	identified by match to protein family HMM PF00465
YP_892442.1	identified by match to protein family HMM PF00165
YP_892447.1	identified by match to protein family HMM PF00209
YP_892448.1	identified by match to protein family HMM PF00364; match to protein family HMM PF00682
YP_892449.1	PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP
YP_892450.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_892451.1	identified by match to protein family HMM PF04023
YP_892453.1	identified by match to protein family HMM PF02525
YP_892457.1	identified by match to protein family HMM PF00394; match to protein family HMM PF07731; match to protein family HMM PF07732
YP_892458.1	identified by match to protein family HMM PF00015; match to protein family HMM PF02743
YP_892460.1	identified by match to protein family HMM PF00015; match to protein family HMM PF00672; match to protein family HMM PF02743
YP_892463.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_892464.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_892465.2	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_892467.1	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_892468.1	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_892469.1	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_892470.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_892471.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_892472.1	binds directly to 23S ribosomal RNA
YP_892473.1	Modulates Rho-dependent transcription termination
YP_892474.1	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_892475.1	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_892476.1	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_892477.1	identified by match to protein family HMM PF00080
YP_892478.1	type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase
YP_892479.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_892480.1	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_892481.1	identified by match to protein family HMM PF00893
YP_892482.1	identified by match to protein family HMM PF00893
YP_892483.1	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_892484.1	identified by match to protein family HMM PF00892
YP_892485.1	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_892486.1	identified by match to protein family HMM PF01202
YP_892487.1	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_892488.1	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_892489.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_892490.1	catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis
YP_892491.1	identified by match to protein family HMM PF01066; match to protein family HMM TIGR00473
YP_892492.1	identified by match to protein family HMM PF02666
YP_892493.1	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_892494.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_892495.1	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_892496.1	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_892498.1	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_892499.1	identified by match to protein family HMM PF01041; match to protein family HMM PF01212
YP_892500.1	identified by match to protein family HMM PF02525
YP_892501.1	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_892502.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_892503.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_892504.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_892505.1	carries the fatty acid chain in fatty acid biosynthesis
YP_892506.1	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_892507.1	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_892510.1	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_892511.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_892512.1	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_892513.1	identified by match to protein family HMM PF01171; match to protein family HMM TIGR02432
YP_892517.1	identified by match to protein family HMM PF04028
YP_892518.1	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_892520.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_892521.1	identified by match to protein family HMM PF00132
YP_892522.1	identified by match to protein family HMM PF02397
YP_892523.1	identified by match to protein family HMM PF00534
YP_892524.1	identified by match to protein family HMM PF02516
YP_892525.1	identified by match to protein family HMM PF00534
YP_892526.1	identified by match to protein family HMM PF00534
YP_892527.1	identified by match to protein family HMM PF00534
YP_892528.1	identified by match to protein family HMM PF01943
YP_892529.1	identified by match to protein family HMM PF00984; match to protein family HMM PF03720; match to protein family HMM PF03721; match to protein family HMM TIGR03026
YP_892530.1	identified by match to protein family HMM PF00535
YP_892532.1	identified by match to protein family HMM PF04138
YP_892533.1	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_892534.1	identified by match to protein family HMM PF01420; match to protein family HMM PF02384
YP_892536.1	catalyzes the formation of a phosphodiester at the site of a single-strand break in duplex DNA
YP_892537.1	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
YP_892538.1	identified by match to protein family HMM PF00984; match to protein family HMM PF03720; match to protein family HMM PF03721; match to protein family HMM TIGR03026
YP_892540.1	identified by match to protein family HMM PF01075; match to protein family HMM TIGR02193
YP_892541.1	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_892542.1	identified by match to protein family HMM PF00535
YP_892543.1	identified by match to protein family HMM PF01075
YP_892544.1	identified by match to protein family HMM PF01522
YP_892545.1	identified by match to protein family HMM PF00534
YP_892548.1	identified by match to protein family HMM PF00534
YP_892549.1	identified by match to protein family HMM PF01075; match to protein family HMM TIGR02195
YP_892550.1	identified by match to protein family HMM PF01380; match to protein family HMM TIGR00441
YP_892551.1	identified by match to protein family HMM PF01177; match to protein family HMM TIGR00035
YP_892552.1	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_892553.1	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 TIGR02197
YP_892554.1	identified by match to protein family HMM TIGR00213; match to protein family HMM TIGR01656; match to protein family HMM TIGR01662
YP_892555.1	identified by match to protein family HMM PF00034
YP_892556.1	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_892557.1	identified by match to protein family HMM PF00034
YP_892558.1	identified by match to protein family HMM PF03597; match to protein family HMM TIGR00847
YP_892559.1	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_892560.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_892561.1	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_892565.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_892566.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_892567.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_892568.1	identified by match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534
YP_892569.1	identified by match to protein family HMM PF01467; match to protein family HMM TIGR00482
YP_892570.1	identified by match to protein family HMM PF02410; match to protein family HMM TIGR00090
YP_892571.1	identified by match to protein family HMM PF03601; match to protein family HMM TIGR00698
YP_892572.1	identified by match to protein family HMM PF00126; match to protein family HMM PF03466
YP_892573.1	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_892574.1	identified by match to protein family HMM PF02416; match to protein family HMM TIGR01411
YP_892575.1	Essential for recycling GMP and indirectly, cGMP
YP_892577.1	FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus
YP_892578.1	identified by match to protein family HMM PF00593; match to protein family HMM PF07715; match to protein family HMM TIGR01783
YP_892579.1	identified by match to protein family HMM PF00005
YP_892580.1	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_892581.1	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_892583.1	identified by match to protein family HMM PF02578; match to protein family HMM TIGR00726
YP_892584.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_892585.1	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_892587.1	identified by match to protein family HMM PF00355; match to protein family HMM TIGR01409; match to protein family HMM TIGR01416
YP_892588.1	identified by match to protein family HMM PF00032; match to protein family HMM PF00033
YP_892591.1	identified by match to protein family HMM PF04055
YP_892592.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III
YP_892593.1	identified by match to protein family HMM PF03350
YP_892594.1	catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde
YP_892595.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00158
YP_892597.1	identified by match to protein family HMM PF04164
YP_892598.1	negatively supercoils closed circular double-stranded DNA
YP_892601.1	identified by match to protein family HMM PF00583
YP_892602.1	identified by match to protein family HMM PF00501
YP_892606.1	identified by match to protein family HMM PF01361; match to protein family HMM TIGR00013
YP_892607.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_892608.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_892609.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_892610.1	identified by match to protein family HMM PF01979; match to protein family HMM TIGR00857
YP_892614.1	identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532
YP_892616.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_892617.1	identified by match to protein family HMM TIGR01583
YP_892619.1	identified by match to protein family HMM PF03641; match to protein family HMM TIGR00730
YP_892620.1	identified by match to protein family HMM PF00070; match to protein family HMM PF07992; match to protein family HMM TIGR01318
YP_892621.1	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_892622.1	identified by match to protein family HMM PF00383; match to protein family HMM TIGR00326
YP_892625.1	similar to Tmden_0678; identified by match to protein family HMM PF02576
YP_892626.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_892627.1	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_892629.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_892631.1	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_892632.1	identified by match to protein family HMM PF02567; match to protein family HMM TIGR00654
YP_892633.1	identified by match to protein family HMM PF01551
YP_892634.1	catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate
YP_892635.1	identified by match to protein family HMM PF01103; match to protein family HMM PF07244
YP_892636.1	identified by match to protein family HMM PF03473
YP_892637.1	identified by match to protein family HMM PF01343; match to protein family HMM TIGR00706
YP_892638.1	Catalyzes the hydrolytic cleavage of a carbon-halogen bond in N-ethylammeline
YP_892639.1	catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis
YP_892640.1	identified by match to protein family HMM PF00557
YP_892641.1	identified by match to protein family HMM PF01288; match to protein family HMM TIGR01498
YP_892642.1	positive regulator of class III flagellar genes
YP_892643.1	identified by match to protein family HMM PF01656
YP_892645.1	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_892646.1	with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation
YP_892647.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_892648.1	identified by match to protein family HMM PF01171; match to protein family HMM PF06508
YP_892649.1	enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine
YP_892650.1	identified by match to protein family HMM TIGR00128
YP_892651.1	identified by match to protein family HMM PF00254
YP_892652.1	identified by match to protein family HMM PF07719
YP_892653.1	identified by match to protein family HMM PF00691
YP_892654.1	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_892656.1	identified by match to protein family HMM PF02472
YP_892657.1	identified by match to protein family HMM PF01618
YP_892658.1	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_892659.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_892660.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_892661.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_892662.1	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_892663.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_892664.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B' is part of the membrane proton channel.
YP_892665.1	identified by match to protein family HMM PF02195; match to protein family HMM TIGR00180
YP_892666.1	identified by match to protein family HMM PF01656
YP_892667.1	catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon
YP_892668.1	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_892669.1	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_892670.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_892671.1	involved in the peptidyltransferase reaction during translation
YP_892672.1	identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061
YP_892673.1	identified by match to protein family HMM PF03150
YP_892674.1	identified by match to protein family HMM PF00037
YP_892675.1	identified by match to protein family HMM PF00384; match to protein family HMM PF01568
YP_892676.1	identified by match to protein family HMM TIGR01409
YP_892678.1	identified by match to protein family HMM PF00037
YP_892679.1	catalyzes the formation of selenocysteinyl-tRNA(Sec) from seryl-tRNA(Sec) and L-selenophosphate in selenoprotein biosynthesis
YP_892680.1	identified by match to protein family HMM PF00009; match to protein family HMM PF03144; match to protein family HMM TIGR00231; match to protein family HMM TIGR00475
YP_892682.1	identified by match to protein family HMM PF02348
YP_892683.1	identified by match to protein family HMM PF01261
YP_892689.1	identified by match to protein family HMM PF01354; match to protein family HMM PF03102
YP_892690.1	converts 2-oxoglutarate to glutamate; in Escherichia coli this enzyme plays a role in glutamate synthesis when the cell is under energy restriction; uses NADPH; forms a homohexamer
YP_892691.1	identified by match to protein family HMM PF02621
YP_892692.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_892693.1	identified by match to protein family HMM PF00390; match to protein family HMM PF03949
YP_892694.1	identified by match to protein family HMM PF01047
YP_892695.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_892697.1	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_892698.1	identified by match to protein family HMM PF00364; match to protein family HMM TIGR00531
YP_892699.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_892700.1	identified by match to protein family HMM PF01041; match to protein family HMM PF01212
YP_892701.1	identified by match to protein family HMM PF00037; match to protein family HMM PF02754
YP_892702.1	catalyzes the formation of L-proline from pyrroline-5-carboxylate
YP_892704.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_892706.1	identified by match to protein family HMM PF00185; match to protein family HMM PF02729; match to protein family HMM TIGR00658
YP_892707.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_892708.1	catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate
YP_892709.1	identified by match to protein family HMM PF02527; match to protein family HMM TIGR00138
YP_892712.1	identified by match to protein family HMM PF01435
YP_892713.1	converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer
YP_892716.1	identified by match to protein family HMM PF04314
YP_892718.1	identified by match to protein family HMM PF04055
YP_892719.1	identified by match to protein family HMM PF04055
YP_892720.1	identified by match to protein family HMM PF00456
YP_892721.1	identified by match to protein family HMM TIGR01444
YP_892722.1	identified by match to protein family HMM PF02779; match to protein family HMM PF02780
YP_892724.1	identified by match to protein family HMM PF01596
YP_892725.1	identified by match to protein family HMM PF04055
YP_892726.1	identified by match to protein family HMM PF04055
YP_892733.1	identified by match to protein family HMM PF04055
YP_892734.1	identified by match to protein family HMM PF03275
YP_892741.1	identified by match to protein family HMM PF00310; match to protein family HMM PF00733; match to protein family HMM TIGR01536
YP_892742.1	identified by match to protein family HMM PF00534
YP_892745.1	identified by match to protein family HMM PF00534
YP_892746.1	identified by match to protein family HMM PF00310; match to protein family HMM PF00733; match to protein family HMM TIGR01536
YP_892747.1	identified by match to protein family HMM PF04007
YP_892756.1	converts ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; in Escherichia coli this enzyme functions in cysteine biosynthesis
YP_892759.1	identified by match to protein family HMM PF00117
YP_892760.1	identified by match to protein family HMM PF00483
YP_892761.1	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_892762.1	identified by match to protein family HMM PF00583
YP_892763.1	FlaB; structural flagella protein; in Helicobacter flagella are composed of flagellin A and flagellin B; the amounts of each seem to be controlled by environmental conditions
YP_892764.1	FlaB; structural flagella protein; in Helicobacter flagella are composed of flagellin A and flagellin B; the amounts of each seem to be controlled by environmental conditions
YP_892766.1	identified by match to protein family HMM PF01973
YP_892768.1	identified by match to protein family HMM PF01594
YP_892769.1	identified by match to protein family HMM PF02386; match to protein family HMM TIGR00933
YP_892770.1	identified by match to protein family HMM PF02254
YP_892771.1	catalyzes the formation of fumarate from aspartate
YP_892772.1	functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to dcuB
YP_892773.1	identified by match to protein family HMM PF00015
YP_892774.1	identified by match to protein family HMM PF02600
YP_892776.1	identified by match to protein family HMM PF00593; match to protein family HMM PF07715
YP_892777.1	identified by match to protein family HMM PF01618; match to protein family HMM TIGR02805
YP_892778.1	identified by match to protein family HMM PF02472; match to protein family HMM TIGR02804
YP_892779.1	identified by match to protein family HMM PF03544; match to protein family HMM TIGR01352
YP_892780.1	identified by match to protein family HMM PF00496
YP_892781.1	identified by match to protein family HMM PF00528
YP_892782.1	identified by match to protein family HMM PF00528
YP_892783.1	identified by match to protein family HMM PF00005
YP_892784.1	identified by match to protein family HMM PF02040; match to protein family HMM PF03600
YP_892788.1	identified by match to protein family HMM PF03738
YP_892789.1	identified by match to protein family HMM PF02441; match to protein family HMM TIGR00421
YP_892790.1	Involved in the metabolism of aromatic amino acids
YP_892791.1	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_892793.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_892794.1	identified by match to protein family HMM PF00004
YP_892795.1	activates fatty acids by binding to coenzyme A
YP_892796.1	identified by match to protein family HMM PF03349
YP_892797.1	Assists in DNA repair by cleaving phosphodiester bonds at apurinic or apyrimidinic sties to produce new 5' ends that are base-free deoxyribose 5-phosphate residues
YP_892802.1	identified by match to protein family HMM PF03787
YP_892806.1	identified by match to protein family HMM PF03741
YP_892807.1	identified by match to protein family HMM PF00551; match to protein family HMM TIGR00639
YP_892808.1	similar to N-terminus; 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_892809.1	identified by match to protein family HMM PF01078; match to protein family HMM PF07728; match to protein family HMM TIGR00368
YP_892810.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_892811.1	identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254
YP_892812.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_892813.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_892814.1	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_892815.1	involved in type III protein export during flagellum assembly
YP_892816.1	identified by match to protein family HMM PF00266; match to protein family HMM PF01212
YP_892817.1	identified by match to protein family HMM PF01106; match to protein family HMM PF01592; match to protein family HMM PF04324
YP_892818.1	identified by match to protein family HMM PF00015; match to protein family HMM PF02743
YP_892819.1	identified by match to protein family HMM PF01814; match to protein family HMM TIGR02481
YP_892820.1	identified by match to protein family HMM PF05154
YP_892821.1	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_892822.1	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_892825.1	identified by match to protein family HMM PF05016
YP_892830.1	identified by match to protein family HMM PF00589
YP_892832.1	identified by match to protein family HMM PF03653
YP_892833.1	identified by match to protein family HMM PF05154
YP_892834.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_892835.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_892836.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_892837.1	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_892838.1	identified by match to protein family HMM PF04237
YP_892839.1	identified by match to protein family HMM PF00857
YP_892840.1	identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633
YP_892841.1	identified by match to protein family HMM PF00884; match to protein family HMM PF08019
YP_892842.1	identified by match to protein family HMM PF01219
YP_892844.1	identified by match to protein family HMM PF02659
YP_892845.1	identified by match to protein family HMM PF00892
YP_892846.1	identified by match to protein family HMM PF00950; match to protein family HMM PF01032
YP_892847.1	identified by match to protein family HMM PF00005
YP_892848.1	identified by match to protein family HMM PF03824
YP_892849.1	identified by match to protein family HMM PF01297
YP_892852.1	identified by match to protein family HMM PF03150
YP_892853.1	identified by match to protein family HMM PF00563; match to protein family HMM PF00989; match to protein family HMM PF00990; match to protein family HMM TIGR00229
YP_892854.1	identified by match to protein family HMM PF00484
YP_892855.1	identified by match to protein family HMM PF00924
YP_892859.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_892860.1	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_892861.1	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_892862.1	identified by match to protein family HMM PF07719
YP_892863.1	synthesizes RNA primers at the replication forks
YP_892864.1	identified by match to protein family HMM PF00764
YP_892866.1	identified by match to protein family HMM PF04402
YP_892867.1	identified by match to protein family HMM PF03553; match to protein family HMM PF03600; match to protein family HMM PF06808
YP_892869.1	identified by match to protein family HMM PF03062
YP_892870.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_892871.1	identified by match to protein family HMM PF00149; match to protein family HMM PF02872
YP_892872.1	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_892873.1	identified by match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644
YP_892874.1	identified by match to protein family HMM PF06965; match to protein family HMM TIGR00773
YP_892875.1	identified by match to protein family HMM PF00005
YP_892876.1	identified by match to protein family HMM PF01243
YP_892878.1	identified by match to protein family HMM PF00593; match to protein family HMM PF07715
YP_892879.1	identified by match to protein family HMM PF01032
YP_892880.1	identified by match to protein family HMM PF00005
YP_892881.1	identified by match to protein family HMM PF01497
YP_892884.1	the hook connects flagellar basal body to the flagellar filament
YP_892885.1	identified by match to protein family HMM PF01832
YP_892886.1	involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate
YP_892887.1	identified by match to protein family HMM PF01121; match to protein family HMM TIGR00152
YP_892888.1	identified by match to protein family HMM PF01042; match to protein family HMM TIGR00004
YP_892889.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_892890.1	identified by match to protein family HMM PF01734
YP_892891.1	identified by match to protein family HMM PF00004
YP_892892.1	identified by match to protein family HMM PF00892
YP_892893.1	identified by match to protein family HMM PF00578
YP_892894.1	identified by match to protein family HMM PF06271
YP_892895.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_892896.1	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_892897.1	identified by match to protein family HMM PF01522
YP_892898.1	identified by match to protein family HMM PF03840; match to protein family HMM TIGR00810
YP_892899.1	identified by match to protein family HMM PF01027
YP_892901.1	identified by match to protein family HMM PF00082; match to protein family HMM PF03797
YP_892902.1	identified by match to protein family HMM PF02525
YP_892908.1	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_892909.1	identified by match to protein family HMM PF00732
YP_892911.1	identified by match to protein family HMM PF07681
YP_892913.1	identified by match to protein family HMM PF00881
YP_892916.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093
YP_892917.1	identified by match to protein family HMM PF00571; match to protein family HMM PF01380; match to protein family HMM TIGR00393
YP_892918.1	identified by match to protein family HMM PF00753; match to protein family HMM PF07521; match to protein family HMM TIGR00649
YP_892919.1	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_892920.1	identified by match to protein family HMM PF05977; match to protein family HMM PF07690
YP_892921.1	identified by match to protein family HMM PF00977; match to protein family HMM TIGR00735
YP_892923.1	23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance
YP_892924.1	identified by match to protein family HMM PF04993
YP_892925.1	similar to jhp_0321; identified by match to protein family HMM PF00849
YP_892926.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_892927.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_892928.1	identified by match to protein family HMM PF00324
YP_892929.1	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