-- dump date   	20111121_010649
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_002364640.1	identified by match to protein family HMM PF07094
YP_002364641.1	identified by match to protein family HMM PF05606
YP_002364642.1	identified by match to protein family HMM PF07115
YP_002364643.1	identified by match to protein family HMM PF03434
YP_002364644.1	identified by match to protein family HMM PF05246
YP_002364645.1	identified by match to protein family HMM PF05085
YP_002364646.1	identified by match to protein family HMM PF05102; match to protein family HMM TIGR01606
YP_002364648.1	identified by match to protein family HMM PF02999
YP_002364650.1	identified by match to protein family HMM PF02524
YP_002364651.1	identified by match to protein family HMM PF03304
YP_002364652.1	identified by glimmer; putative
YP_002364653.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002364656.1	identified by match to protein family HMM PF02524
YP_002364657.1	identified by match to protein family HMM PF03196
YP_002364658.1	identified by match to protein family HMM PF00589
YP_002364660.1	identified by match to protein family HMM PF04645
YP_002364661.1	identified by match to protein family HMM PF03237; match to protein family HMM TIGR01547
YP_002364662.1	identified by match to protein family HMM PF06381
YP_002364663.1	identified by match to protein family HMM PF07094
YP_002364664.1	identified by match to protein family HMM PF02989
YP_002364665.1	identified by match to protein family HMM PF02989
YP_002364666.1	identified by match to protein family HMM PF02989
YP_002364671.1	identified by match to protein family HMM PF05561
YP_002364672.1	identified by match to protein family HMM PF05619
YP_002364673.1	identified by match to protein family HMM PF07316
YP_002364674.1	identified by match to protein family HMM PF07341
YP_002364675.1	identified by match to protein family HMM PF07032
YP_002364676.1	identified by match to protein family HMM PF05537
YP_002364677.1	identified by match to protein family HMM PF05632
YP_002364678.1	identified by match to protein family HMM PF05113
YP_002364679.1	identified by match to protein family HMM PF05606
YP_002364680.1	identified by match to protein family HMM PF07115
YP_002364681.1	identified by match to protein family HMM PF03434
YP_002364682.1	identified by match to protein family HMM PF05246
YP_002364683.1	identified by match to protein family HMM PF05085
YP_002364684.1	identified by match to protein family HMM TIGR01606
YP_002364685.1	identified by glimmer; putative
YP_002364686.1	identified by match to protein family HMM PF02999
YP_002364687.1	identified by glimmer; putative
YP_002364688.1	identified by glimmer; putative
YP_002364689.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002364692.1	identified by match to protein family HMM PF02524
YP_002364693.1	identified by match to protein family HMM PF03112; match to protein family HMM PF09588
YP_002364694.1	identified by match to protein family HMM PF03196
YP_002364695.1	identified by match to protein family HMM PF00589
YP_002364697.1	identified by match to protein family HMM PF07268
YP_002364698.1	identified by match to protein family HMM PF04645
YP_002364699.1	identified by match to protein family HMM PF03237; match to protein family HMM TIGR01547
YP_002364752.1	identified by match to protein family HMM PF07094
YP_002364753.1	identified by match to protein family HMM PF02989
YP_002364754.1	identified by match to protein family HMM PF02989
YP_002364755.1	identified by match to protein family HMM PF02989
YP_002364758.1	identified by match to protein family HMM PF07405
YP_002364760.1	identified by match to protein family HMM PF05561
YP_002364761.1	identified by match to protein family HMM PF07316
YP_002364762.1	identified by match to protein family HMM PF07032
YP_002364763.1	identified by match to protein family HMM PF05537
YP_002364764.1	identified by match to protein family HMM PF05632
YP_002364765.1	identified by match to protein family HMM PF05113
YP_002364766.1	identified by match to protein family HMM PF07115
YP_002364767.1	identified by match to protein family HMM PF03434
YP_002364768.1	identified by glimmer; putative
YP_002364769.1	identified by match to protein family HMM PF05102; match to protein family HMM TIGR01606
YP_002364770.1	identified by match to protein family HMM PF05289
YP_002364771.1	identified by glimmer; putative
YP_002364772.1	identified by match to protein family HMM PF02999
YP_002364773.1	identified by match to protein family HMM PF02524
YP_002364774.1	identified by match to protein family HMM PF03304
YP_002364775.1	identified by glimmer; putative
YP_002364776.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002364779.1	identified by match to protein family HMM PF02524
YP_002364780.1	identified by match to protein family HMM PF03112; match to protein family HMM PF09588
YP_002364781.1	identified by match to protein family HMM PF03196
YP_002364782.1	identified by match to protein family HMM PF00589
YP_002364783.1	identified by match to protein family HMM PF02471
YP_002364784.1	identified by match to protein family HMM PF06780
YP_002364785.1	identified by match to protein family HMM PF04867
YP_002364786.1	identified by match to protein family HMM PF04645
YP_002364833.1	identified by match to protein family HMM PF02378; match to protein family HMM TIGR00359; match to protein family HMM TIGR00410
YP_002364834.1	identified by match to protein family HMM PF02255
YP_002364835.1	identified by match to protein family HMM PF02302; match to protein family HMM TIGR00853
YP_002364836.1	identified by match to protein family HMM PF05913
YP_002364838.1	identified by match to protein family HMM PF02414
YP_002364839.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002364841.1	identified by match to protein family HMM PF01672
YP_002364843.1	identified by match to protein family HMM PF00496
YP_002364844.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_002364845.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_002364846.1	identified by glimmer; putative
YP_002364847.1	identified by match to protein family HMM PF01441
YP_002364848.1	identified by glimmer; putative
YP_002364849.1	identified by match to protein family HMM PF00860
YP_002364850.1	identified by match to protein family HMM PF00860
YP_002364853.1	identified by match to protein family HMM PF06114
YP_002364855.1	identified by match to protein family HMM PF00023
YP_002374536.1	identified by match to protein family HMM PF00933
YP_002374537.1	identified by glimmer
YP_002374538.1	identified by match to protein family HMM PF02878
YP_002374539.1	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_002374540.1	identified by match to protein family HMM PF01594
YP_002374542.1	identified by match to protein family HMM PF02457; match to protein family HMM TIGR00159
YP_002374543.1	identified by match to protein family HMM PF07949
YP_002374544.1	identified by match to protein family HMM PF01648; match to protein family HMM TIGR00556
YP_002374546.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_002374548.1	identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF04851; match to protein family HMM TIGR00595
YP_002374549.1	functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor
YP_002374551.1	identified by match to protein family HMM PF02588
YP_002374552.1	identified by match to protein family HMM PF00849; match to protein family HMM TIGR00005
YP_002374554.1	catalyzes the formation of fructose 1,6-bisphosphate from fructose 6-phosphate and diphosphate
YP_002374555.1	identified by match to protein family HMM PF02547; match to protein family HMM TIGR00113
YP_002374556.1	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_002374557.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_002374559.1	identified by match to protein family HMM PF01709; match to protein family HMM TIGR01033
YP_002374560.1	identified by match to protein family HMM PF00763; match to protein family HMM PF02882
YP_002374563.1	identified by match to protein family HMM PF02639
YP_002374564.1	identified by match to protein family HMM TIGR02227
YP_002374565.1	identified by match to protein family HMM PF00717; match to protein family HMM TIGR02227
YP_002374567.1	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_002374568.1	identified by match to protein family HMM PF05628
YP_002374569.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_002374570.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_002374571.1	identified by match to protein family HMM PF01553; match to protein family HMM TIGR00530
YP_002374574.1	identified by match to protein family HMM PF01739; match to protein family HMM PF03705
YP_002374575.1	identified by match to protein family HMM PF01895; match to protein family HMM TIGR02135
YP_002374578.1	identified by match to protein family HMM PF02463
YP_002374579.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_002374581.1	identified by match to protein family HMM PF02592; match to protein family HMM TIGR00697
YP_002374582.1	identified by match to protein family HMM PF02592; match to protein family HMM TIGR00697
YP_002374583.1	identified by match to protein family HMM PF00588
YP_002374584.1	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_002374585.1	identified by match to protein family HMM PF03840; match to protein family HMM TIGR00810
YP_002374586.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_002374587.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_002374588.1	identified by match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534
YP_002374589.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_002374590.1	identified by match to protein family HMM PF00571; match to protein family HMM PF03471
YP_002374591.1	identified by match to protein family HMM PF02130; match to protein family HMM TIGR00043
YP_002374592.1	identified by match to protein family HMM PF00085; match to protein family HMM TIGR01068
YP_002374593.1	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_002374594.1	identified by match to protein family HMM PF03793
YP_002374595.1	identified by match to protein family HMM PF00551; match to protein family HMM PF02911; match to protein family HMM TIGR00460
YP_002374597.1	identified by match to protein family HMM PF00557; match to protein family HMM PF01321
YP_002374598.1	identified by match to protein family HMM PF00702; match to protein family HMM PF08282; match to protein family HMM TIGR00099; match to protein family HMM TIGR01484
YP_002374599.1	identified by match to protein family HMM PF02073
YP_002374600.1	identified by match to protein family HMM PF02681
YP_002374604.1	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_002374606.1	identified by match to protein family HMM PF00448; match to protein family HMM TIGR00064
YP_002374608.1	identified by match to protein family HMM PF02687
YP_002374609.1	identified by match to protein family HMM PF00005
YP_002374610.1	identified by match to protein family HMM PF02687
YP_002374613.1	identified by match to protein family HMM PF00266; match to protein family HMM PF01212
YP_002374615.1	identified by match to protein family HMM PF01078; match to protein family HMM TIGR00368
YP_002374616.1	identified by match to protein family HMM PF00056; match to protein family HMM PF02866; match to protein family HMM TIGR01771
YP_002374617.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_002374619.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the K subunit is a nonenzymatic component which binds the dimeric form by interacting with the G and E subunits
YP_002374620.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the D subunit is part of the catalytic core of the ATP synthase complex
YP_002374621.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the B subunit is part of the catalytic core of the ATP synthase complex
YP_002374622.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the A subunit is part of the catalytic core of the ATP synthase complex
YP_002374624.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the E subunit is part of the catalytic core of the ATP synthase complex
YP_002374626.1	identified by match to protein family HMM PF00488; match to protein family HMM PF01713; match to protein family HMM TIGR01069
YP_002374627.1	identified by match to protein family HMM PF03193; match to protein family HMM TIGR00157
YP_002374628.1	identified by match to protein family HMM PF01177; match to protein family HMM TIGR00067
YP_002374629.1	catalyzes a two-step reaction, first charging an asparagine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_002374632.1	identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037
YP_002374633.1	identified by match to protein family HMM PF00557; match to protein family HMM TIGR00500
YP_002374634.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_002374635.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_002374636.1	identified by match to protein family HMM PF00639; match to protein family HMM PF09312
YP_002374637.1	identified by match to protein family HMM PF00108; match to protein family HMM PF02803; match to protein family HMM TIGR01930
YP_002374639.1	identified by match to protein family HMM PF00772; match to protein family HMM PF03796; match to protein family HMM TIGR00665
YP_002374640.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_002374641.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_002374642.1	identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621
YP_002374643.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_002374644.1	identified by match to protein family HMM PF00367; match to protein family HMM PF02378
YP_002374645.1	identified by match to protein family HMM PF03006; match to protein family HMM TIGR01065
YP_002374646.1	identified by match to protein family HMM PF02163; match to protein family HMM TIGR00054
YP_002374647.1	identified by match to protein family HMM PF01148
YP_002374648.1	catalyzes the formation of UDP pyrophosphate from isopentenyl pyrophosphate
YP_002374649.1	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_002374650.1	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_002374651.1	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_002374655.1	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_002374656.1	identified by match to protein family HMM PF02224; match to protein family HMM TIGR00017
YP_002374657.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093
YP_002374659.1	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_002374660.1	contains N-terminal domain of unknown function fused to transcription elongation factor; GreA is necessary for efficient RNA polymerization through arresting sites; cleaves the nascent transcript and allows resumption of transcription elongation
YP_002374662.1	identified by match to protein family HMM PF07719
YP_002374663.1	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_002374664.1	identified by match to protein family HMM PF00905; match to protein family HMM PF03717; match to protein family HMM PF03793
YP_002374665.1	identified by match to protein family HMM PF00501
YP_002374668.1	identified by match to protein family HMM PF00873
YP_002374669.1	identified by match to protein family HMM TIGR01730
YP_002374670.1	identified by match to protein family HMM PF02321
YP_002374671.1	identified by glimmer
YP_002374672.1	identified by match to protein family HMM PF04069
YP_002374673.1	identified by match to protein family HMM PF00528
YP_002374674.1	identified by match to protein family HMM PF00005
YP_002374675.1	structural flagella protein
YP_002374676.1	involved in flagellin assembly
YP_002374677.1	identified by match to protein family HMM PF01979; match to protein family HMM TIGR00221
YP_002374678.1	catalyzes the reversible formation of fructose 6-phosphate from glucosamine 6-phosphate
YP_002374679.1	identified by match to protein family HMM PF00081; match to protein family HMM PF02777
YP_002374680.1	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_002374681.1	identified by glimmer
YP_002374687.1	identified by match to protein family HMM PF00842; match to protein family HMM PF01168; match to protein family HMM TIGR00492
YP_002374691.1	identified by match to protein family HMM PF01699; match to protein family HMM TIGR00367
YP_002374693.1	amylomaltase; acts to release glucose from maltodextrins
YP_002374694.1	identified by match to protein family HMM PF00691
YP_002374695.1	identified by match to protein family HMM PF01258
YP_002374696.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_002374698.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_002374699.1	identified by match to protein family HMM PF00092
YP_002374700.1	identified by glimmer
YP_002374701.1	identified by match to protein family HMM PF00092
YP_002374704.1	identified by match to protein family HMM PF07726; match to protein family HMM PF07728
YP_002374705.1	identified by match to protein family HMM PF02527; match to protein family HMM TIGR00138
YP_002374706.1	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_002374707.1	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_002374709.1	with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook
YP_002374710.1	With FlgK acts as a hook filament junction protein to join the flagellar filament to the hook
YP_002374711.1	binds to flagellin and appears to stabilize flagellin during flagella assembly
YP_002374712.1	identified by match to protein family HMM PF02599; match to protein family HMM TIGR00202
YP_002374713.1	identified by match to protein family HMM PF00814
YP_002374714.1	identified by match to protein family HMM PF02367; match to protein family HMM TIGR00150
YP_002374716.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_002374717.1	identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001
YP_002374718.1	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_002374719.1	identified by glimmer
YP_002374722.1	identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010
YP_002374723.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_002374724.1	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_002374725.1	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_002374727.1	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_002374728.1	identified by match to protein family HMM PF01225; match to protein family HMM PF02875; match to protein family HMM PF08245; match to protein family HMM TIGR01085
YP_002374729.1	identified by match to protein family HMM PF00571; match to protein family HMM PF01595; match to protein family HMM PF03471
YP_002374730.1	identified by match to protein family HMM PF01145; match to protein family HMM TIGR01933
YP_002374731.1	identified by match to protein family HMM PF01145; match to protein family HMM TIGR01932
YP_002374732.1	identified by match to protein family HMM PF03602; match to protein family HMM TIGR00095
YP_002374733.1	identified by match to protein family HMM PF00483
YP_002374734.1	identified by match to protein family HMM PF00515
YP_002374735.1	identified by match to protein family HMM PF00515; match to protein family HMM PF01846; match to protein family HMM PF07719
YP_002374736.1	identified by match to protein family HMM PF01119; match to protein family HMM PF02518; match to protein family HMM PF08676; match to protein family HMM TIGR00585
YP_002374737.1	identified by match to protein family HMM PF02414
YP_002374739.1	identified by match to protein family HMM PF01132; match to protein family HMM PF08207; match to protein family HMM PF09285; match to protein family HMM TIGR00038
YP_002374740.1	identified by match to protein family HMM PF01547
YP_002374741.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR02138
YP_002374742.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR00974
YP_002374743.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_002374744.1	identified by match to protein family HMM PF02535
YP_002374745.1	catalyzes a two-step reaction, first charging an alanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_002374746.1	identified by match to protein family HMM PF01706
YP_002374748.1	identified by match to protein family HMM PF01207; match to protein family HMM TIGR00742
YP_002374749.1	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_002374751.1	identified by match to protein family HMM PF05193; match to protein family HMM PF08367
YP_002374752.1	RpmE2; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome
YP_002374753.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_002374754.1	identified by match to protein family HMM PF04519
YP_002374755.1	identified by match to protein family HMM PF00216
YP_002374756.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_002374758.1	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_002374759.1	identified by match to protein family HMM PF01436
YP_002374760.1	identified by glimmer
YP_002374762.1	identified by match to protein family HMM PF01712
YP_002374763.1	identified by match to protein family HMM PF00230; match to protein family HMM TIGR00861
YP_002374764.1	identified by match to protein family HMM PF00370; match to protein family HMM PF02782; match to protein family HMM TIGR01311
YP_002374766.1	identified by match to protein family HMM PF01266
YP_002374767.1	identified by match to protein family HMM PF03885
YP_002374768.1	identified by match to protein family HMM PF04519
YP_002374769.1	identified by match to protein family HMM PF01551
YP_002374770.1	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_002374771.1	identified by match to protein family HMM PF01432; match to protein family HMM PF08439; match to protein family HMM TIGR00181
YP_002374772.1	identified by match to protein family HMM PF01066
YP_002374774.1	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_002374776.1	identified by match to protein family HMM PF00004; match to protein family HMM PF02190; match to protein family HMM PF05362; match to protein family HMM PF07728; match to protein family HMM TIGR00763
YP_002374777.1	identified by match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644
YP_002374778.1	identified by match to protein family HMM PF01551
YP_002374779.1	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_002374780.1	identified by match to protein family HMM PF01580; match to protein family HMM PF09397
YP_002374781.1	BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters UDP disphosphate which reduces the pool of lipid carrier available to the cell
YP_002374782.1	identified by match to protein family HMM PF01464
YP_002374784.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_002374785.1	identified by match to protein family HMM PF01476; match to protein family HMM PF01551
YP_002374786.1	identified by match to protein family HMM TIGR02227
YP_002374787.1	identified by match to protein family HMM PF00012
YP_002374790.1	identified by match to protein family HMM PF03961
YP_002374792.1	identified by match to protein family HMM PF01656
YP_002374793.1	Positive regulator of class III flagellar genes
YP_002374794.1	membrane protein involved in the flagellar export apparatus
YP_002374795.1	membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export
YP_002374796.1	identified by match to protein family HMM PF01311; match to protein family HMM TIGR01400
YP_002374797.1	identified by match to protein family HMM PF01313; match to protein family HMM TIGR01402
YP_002374798.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_002374799.1	possible structural component of the flagellum that anchors the rod to the membrane
YP_002374800.1	identified by match to protein family HMM PF01052; match to protein family HMM TIGR02480
YP_002374801.1	with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation
YP_002374802.1	interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring
YP_002374803.1	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_002374804.1	identified by match to protein family HMM PF01618
YP_002374805.1	identified by match to protein family HMM PF06289
YP_002374806.1	the hook connects flagellar basal body to the flagellar filament
YP_002374807.1	acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod
YP_002374808.1	identified by match to protein family HMM PF02120
YP_002374811.1	identified by match to protein family HMM PF00006; match to protein family HMM PF02874; match to protein family HMM TIGR01026; match to protein family HMM TIGR03498
YP_002374812.1	binds to and inhibits the function of flagella specific ATPase FliI
YP_002374813.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_002374814.1	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_002374815.1	forms a junction between the M-ring and FlgB during flagella biosynthesis
YP_002374816.1	with FlgF and B makes up the proximal portion of the flagellar basal body rod
YP_002374817.1	with FlgF and C makes up the proximal portion of the flagellar basal body rod
YP_002374818.1	heat shock protein involved in degradation of misfolded proteins
YP_002374819.1	heat shock protein involved in degradation of misfolded proteins
YP_002374820.1	identified by match to protein family HMM PF02481; match to protein family HMM TIGR00732
YP_002374821.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_002374822.1	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_002374823.1	identified by match to protein family HMM PF02491; match to protein family HMM TIGR01174
YP_002374824.1	identified by match to protein family HMM PF08478
YP_002374825.1	identified by match to protein family HMM PF01098; match to protein family HMM TIGR02614
YP_002374826.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_002374827.1	identified by match to protein family HMM PF02875; match to protein family HMM PF08245; match to protein family HMM TIGR01143
YP_002374829.1	identified by match to protein family HMM PF01795; match to protein family HMM TIGR00006
YP_002374833.1	identified by match to protein family HMM PF01513
YP_002374834.1	identified by match to protein family HMM PF01584
YP_002374835.1	identified by match to protein family HMM PF01728
YP_002374836.1	identified by match to protein family HMM PF00348
YP_002374838.1	identified by match to protein family HMM PF02653
YP_002374839.1	identified by match to protein family HMM PF02653
YP_002374840.1	identified by match to protein family HMM PF00005
YP_002374841.1	identified by match to protein family HMM PF02608
YP_002374843.1	identified by match to protein family HMM PF01476
YP_002374844.1	identified by glimmer
YP_002374849.1	identified by match to protein family HMM PF00496
YP_002374850.1	identified by match to protein family HMM PF00496
YP_002374851.1	identified by match to protein family HMM PF00496
YP_002374853.1	identified by match to protein family HMM PF00528
YP_002374854.1	identified by match to protein family HMM PF00528
YP_002374855.1	identified by match to protein family HMM PF00005; match to protein family HMM PF08352
YP_002374857.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_002374858.1	forms a direct contact with the tRNA during translation
YP_002374859.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_002374861.1	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_002374862.1	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_002374863.1	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_002374864.1	identified by match to protein family HMM PF00580
YP_002374867.1	identified by match to protein family HMM PF05670; match to protein family HMM PF05833
YP_002374868.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_002374870.1	required for 70S ribosome assembly
YP_002374875.1	identified by match to protein family HMM PF02559
YP_002374877.1	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_002374878.1	identified by match to protein family HMM PF00595; match to protein family HMM PF03572; match to protein family HMM TIGR00225
YP_002374879.1	identified by match to protein family HMM PF01656
YP_002374880.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_002374881.1	identified by match to protein family HMM PF00563
YP_002374882.1	catalyzes the formation of methylglyoxal from glycerone phosphate
YP_002374884.1	catalyzes the removal of amino acids from the N termini of peptides
YP_002374885.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_002374886.1	identified by match to protein family HMM PF00004
YP_002374887.1	identified by match to protein family HMM PF00579; match to protein family HMM PF01479; match to protein family HMM TIGR00234
YP_002374888.1	Catalyzes a two-step reaction, first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_002374889.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_002374891.1	identified by match to protein family HMM PF01966
YP_002374892.1	identified by match to protein family HMM PF01048; match to protein family HMM TIGR01704
YP_002374893.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_002374894.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_002374896.1	identified by match to protein family HMM PF01230
YP_002374897.1	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_002374899.1	identified by match to protein family HMM PF02608
YP_002374900.1	identified by match to protein family HMM PF02608
YP_002374901.1	identified by match to protein family HMM PF02608
YP_002374902.1	identified by match to protein family HMM PF02608
YP_002374903.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_002374904.1	interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance
YP_002374905.1	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Subunit beta' binds to sigma factor allowing it to bind to the -10 region of the promoter
YP_002374906.1	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_002374907.1	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_002374908.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_002374909.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_002374910.1	binds directly to 23S ribosomal RNA
YP_002374911.1	identified by match to protein family HMM PF00467; match to protein family HMM PF02357; match to protein family HMM TIGR00922
YP_002374912.1	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_002374915.1	identified by match to protein family HMM PF00023
YP_002374917.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_002374922.1	identified by match to protein family HMM PF01238; match to protein family HMM TIGR00218
YP_002374923.1	identified by match to protein family HMM PF00359; match to protein family HMM PF02378; match to protein family HMM PF02379; match to protein family HMM TIGR00829; match to protein family HMM TIGR00848; match to protein family HMM TIGR01427
YP_002374925.1	identified by match to protein family HMM PF01223
YP_002374928.1	identified by match to protein family HMM PF01739; match to protein family HMM PF03705
YP_002374929.1	identified by match to protein family HMM PF01339
YP_002374930.1	identified by match to protein family HMM PF01963; match to protein family HMM TIGR00261
YP_002374931.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_002374933.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00990; match to protein family HMM TIGR00254
YP_002374934.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF02518
YP_002374935.1	identified by match to protein family HMM PF00702; match to protein family HMM PF05116; match to protein family HMM PF08282; match to protein family HMM TIGR00099; match to protein family HMM TIGR01484
YP_002374936.1	identified by match to protein family HMM PF02245; match to protein family HMM TIGR00567
YP_002374938.1	identified by match to protein family HMM PF05014
YP_002374939.1	identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096
YP_002374941.1	identified by match to protein family HMM PF08973
YP_002374942.1	identified by match to protein family HMM PF01205; match to protein family HMM TIGR00257
YP_002374943.1	identified by match to protein family HMM PF01656
YP_002374945.1	identified by match to protein family HMM PF02195; match to protein family HMM TIGR00180
YP_002374946.1	identified by match to protein family HMM PF00521; match to protein family HMM PF03989; match to protein family HMM TIGR01063
YP_002374947.1	identified by match to protein family HMM PF00204; match to protein family HMM PF00986; match to protein family HMM PF01751; match to protein family HMM PF02518; match to protein family HMM TIGR01059
YP_002374948.1	identified by match to protein family HMM PF00308; match to protein family HMM PF08299; match to protein family HMM TIGR00362
YP_002374949.1	identified by match to protein family HMM PF00712; match to protein family HMM PF02767; match to protein family HMM PF02768; match to protein family HMM TIGR00663
YP_002374951.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_002374952.1	identified by match to protein family HMM TIGR00188
YP_002374953.1	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_002374954.1	identified by match to protein family HMM PF01424
YP_002374955.1	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_002374956.1	catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate
YP_002374957.1	identified by glimmer
YP_002374958.1	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_002374959.1	identified by match to protein family HMM PF00999
YP_002374960.1	identified by match to protein family HMM PF00381; match to protein family HMM TIGR01003
YP_002374962.1	identified by match to protein family HMM PF00309; match to protein family HMM PF04552; match to protein family HMM PF04963; match to protein family HMM TIGR02395
YP_002374963.1	identified by match to protein family HMM PF02417
YP_002374964.1	identified by match to protein family HMM PF02417
YP_002374965.1	identified by match to protein family HMM PF00924
YP_002374966.1	identified by match to protein family HMM PF00534
YP_002374967.1	identified by match to protein family HMM PF06144
YP_002374968.1	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_002374969.1	identified by match to protein family HMM PF00041
YP_002374970.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_002374972.1	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_002374973.1	identified by match to protein family HMM PF02575; match to protein family HMM TIGR00103
YP_002374974.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_002374977.1	identified by match to protein family HMM PF00005
YP_002374978.1	identified by match to protein family HMM PF02578; match to protein family HMM TIGR00726
YP_002374979.1	identified by match to protein family HMM PF01784; match to protein family HMM TIGR00486
YP_002374980.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_002374983.1	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_002374984.1	identified by match to protein family HMM PF01554; match to protein family HMM TIGR00797
YP_002374986.1	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_002374987.1	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_002374988.1	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_002374989.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_002374990.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_002374991.1	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_002374992.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_002374993.1	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_002374994.1	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_002374995.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_002374996.1	one of the stabilizing components for the large ribosomal subunit
YP_002374997.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_002374998.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_002374999.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_002375000.1	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_002375001.1	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_002375002.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_002375003.1	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_002375004.1	binds 5S rRNA along with protein L5 and L25
YP_002375005.1	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_002375006.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_002375007.1	late assembly protein
YP_002375008.1	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_002375009.1	smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group have the motif
YP_002375010.1	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_002375011.1	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_002375012.1	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_002375013.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_002375014.1	protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP
YP_002375015.1	identified by match to protein family HMM PF00149; match to protein family HMM TIGR00282
YP_002375016.1	identified by match to protein family HMM PF01728; match to protein family HMM TIGR00478
YP_002375018.1	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_002375020.1	identified by match to protein family HMM PF00702
YP_002375022.1	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 2 subfamily
YP_002375023.1	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 1 subfamily
YP_002375024.1	identified by match to protein family HMM PF00070; match to protein family HMM PF07992; match to protein family HMM TIGR01292
YP_002375025.1	identified by match to protein family HMM PF00588; match to protein family HMM PF08032; match to protein family HMM TIGR00186
YP_002375026.1	chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion
YP_002375027.1	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_002375028.1	identified by match to protein family HMM PF01025
YP_002375029.1	identified by glimmer
YP_002375030.1	identified by match to protein family HMM PF02540; match to protein family HMM TIGR00552
YP_002375031.1	identified by match to protein family HMM PF00459
YP_002375034.1	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_002375035.1	identified by match to protein family HMM PF00248
YP_002375036.1	identified by glimmer
YP_002375039.1	identified by match to protein family HMM PF00753
YP_002375040.1	identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633
YP_002375042.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_002375043.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_002375044.1	identified by match to protein family HMM PF04519
YP_002375045.1	identified by match to protein family HMM PF01027
YP_002375046.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_002375050.1	Catalyzes the formation of PRPP from ATP and ribose 5-phosphate
YP_002375051.1	identified by match to protein family HMM PF00370
YP_002375052.1	identified by match to protein family HMM PF05036
YP_002375053.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_002375054.1	identified by match to protein family HMM PF00476; match to protein family HMM PF01367; match to protein family HMM PF01612; match to protein family HMM PF02739; match to protein family HMM TIGR00593
YP_002375056.1	identified by match to protein family HMM PF02561; match to protein family HMM TIGR00208
YP_002375057.1	identified by match to protein family HMM PF00072
YP_002375058.1	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_002375063.1	identified by match to protein family HMM PF00381; match to protein family HMM TIGR01003
YP_002375064.1	identified by match to protein family HMM PF00391; match to protein family HMM PF02896; match to protein family HMM PF05524; match to protein family HMM TIGR01417
YP_002375065.1	functions in phosphoenolpyruvate-(PEP)-dependent phosphotransferase (PTS) system; functions in the transport and phosphorylation of glucose
YP_002375066.1	molecular chaperone
YP_002375067.1	catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate
YP_002375069.1	identified by glimmer
YP_002375072.1	identified by match to protein family HMM PF01584
YP_002375074.1	identified by 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_002375075.1	identified by match to protein family HMM PF01339
YP_002375077.1	identified by match to protein family HMM PF00072
YP_002375078.1	Catalyzes the phosphorylation of UMP to UDP
YP_002375079.1	identified by glimmer
YP_002375080.1	identified by match to protein family HMM PF00535
YP_002375081.1	identified by match to protein family HMM PF00005
YP_002375083.1	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_002375086.1	identified by match to protein family HMM PF00015
YP_002375087.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_002375088.1	identified by match to protein family HMM PF02325
YP_002375089.1	catalyzes branch migration in Holliday junction intermediates
YP_002375090.1	identified by match to protein family HMM PF02557
YP_002375091.1	identified by match to protein family HMM PF01554; match to protein family HMM TIGR00797
YP_002375092.1	identified by match to protein family HMM PF01554; match to protein family HMM TIGR00797
YP_002375093.1	identified by match to protein family HMM PF02875; match to protein family HMM PF08245; match to protein family HMM TIGR01087
YP_002375094.1	identified by match to protein family HMM PF02388
YP_002375095.1	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_002375096.1	identified by match to protein family HMM PF01048; match to protein family HMM TIGR01704
YP_002375097.1	identified by match to protein family HMM PF01515; match to protein family HMM TIGR00651
YP_002375098.1	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_002375099.1	identified by match to protein family HMM PF03772; match to protein family HMM TIGR00360
YP_002375100.1	identified by match to protein family HMM PF02517
YP_002375101.1	identified by match to protein family HMM PF00501
YP_002375102.1	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_002375104.1	identified by match to protein family HMM PF00015
YP_002375105.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_002375106.1	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_002375107.1	identified by match to protein family HMM PF01833
YP_002375108.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_002375109.1	identified by match to protein family HMM PF00226
YP_002375110.1	p66
YP_002375111.1	identified by match to protein family HMM PF02652; match to protein family HMM TIGR00795
YP_002375112.1	identified by match to protein family HMM PF00768; match to protein family HMM PF07943
YP_002375113.1	catalyzes the conversion of glutamine residues to glutamate on methyl-accepting chemotaxis receptors
YP_002375114.1	identified by match to protein family HMM PF00580
YP_002375115.1	identified by match to protein family HMM PF01546; match to protein family HMM PF07687; match to protein family HMM TIGR01893
YP_002375116.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_002375117.1	binds and unfolds substrates as part of the ClpXP protease
YP_002375118.1	identified by match to protein family HMM PF00004; match to protein family HMM PF02190; match to protein family HMM PF05362; match to protein family HMM PF07728; match to protein family HMM TIGR00763
YP_002375120.1	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_002375121.1	identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297
YP_002375122.1	identified by match to protein family HMM PF01368; match to protein family HMM PF02272
YP_002375123.1	identified by match to protein family HMM PF00933
YP_002375124.1	identified by match to protein family HMM PF01965; match to protein family HMM TIGR01383
YP_002375125.1	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_002375126.1	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_002375128.1	identified by match to protein family HMM PF01476; match to protein family HMM PF01520
YP_002375129.1	catalyzes the removal of amino acids from the N termini of peptides
YP_002375131.1	identified by match to protein family HMM PF00359; match to protein family HMM PF02378; match to protein family HMM PF02379; match to protein family HMM TIGR00829; match to protein family HMM TIGR00848; match to protein family HMM TIGR01427
YP_002375132.1	identified by match to protein family HMM PF00294; match to protein family HMM TIGR03168
YP_002375133.1	identified by match to protein family HMM TIGR01447
YP_002375134.1	identified by match to protein family HMM PF00580; match to protein family HMM TIGR00609
YP_002375136.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate
YP_002375137.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_002375138.1	identified by match to protein family HMM PF03553
YP_002375139.1	identified by match to protein family HMM PF03553; match to protein family HMM PF03600
YP_002375140.1	identified by match to protein family HMM PF01547
YP_002375141.1	identified by match to protein family HMM PF00528
YP_002375142.1	identified by match to protein family HMM PF00528
YP_002375143.1	identified by match to protein family HMM PF00005; match to protein family HMM PF08402
YP_002375144.1	essential GTPase; functions in ribosome assembly; binds a unique part of the 23S rRNA; interacts with ribosomal protein L25(Ctc)
YP_002375145.1	Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate
YP_002375146.1	identified by match to protein family HMM PF00367; match to protein family HMM PF02378; match to protein family HMM TIGR00826; match to protein family HMM TIGR00852
YP_002375148.1	identified by match to protein family HMM PF01475
YP_002375150.1	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_002375152.1	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_002375153.1	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_002375155.1	identified by match to protein family HMM PF00226; match to protein family HMM PF01556
YP_002375157.1	identified by match to protein family HMM PF06026; match to protein family HMM TIGR00021
YP_002375158.1	2,3-bisphosphoglycerate-dependent; catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate
YP_002375159.1	class I; LysRS1; 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 this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine
YP_002375160.1	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_002375163.1	identified by match to protein family HMM PF02643
YP_002375166.1	identified by match to protein family HMM PF01520
YP_002375168.1	identified by match to protein family HMM PF04620
YP_002375169.1	identified by match to protein family HMM PF01584; match to protein family HMM PF01627; match to protein family HMM PF02518; match to protein family HMM PF02895; match to protein family HMM PF07194
YP_002375170.1	identified by match to protein family HMM PF01584; match to protein family HMM PF01739; match to protein family HMM PF03705
YP_002375171.1	identified by match to protein family HMM PF04509
YP_002375172.1	identified by match to protein family HMM PF00072
YP_002375176.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549
YP_002375177.1	identified by match to protein family HMM PF00005
YP_002375178.1	identified by match to protein family HMM PF02653
YP_002375179.1	identified by match to protein family HMM PF02653
YP_002375180.1	identified by match to protein family HMM PF00015; match to protein family HMM PF00672
YP_002375181.1	identified by match to protein family HMM PF00015; match to protein family HMM PF00672
YP_002375182.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_002375183.1	identified by match to protein family HMM PF01154; match to protein family HMM PF08540; match to protein family HMM TIGR01835
YP_002375184.1	catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate
YP_002375185.1	identified by match to protein family HMM TIGR00532
YP_002375186.1	identified by match to protein family HMM PF00288; match to protein family HMM PF08544; match to protein family HMM TIGR01240
YP_002375187.1	identified by match to protein family HMM PF00288
YP_002375188.1	identified by match to protein family HMM PF00288; match to protein family HMM PF08544; match to protein family HMM TIGR00549
YP_002375189.1	identified by match to protein family HMM PF00188
YP_002375190.1	identified by match to protein family HMM PF00210
YP_002375191.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_002375193.1	identified by match to protein family HMM PF00480
YP_002375194.1	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_002375195.1	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_002375197.1	Essential for efficient processing of 16S rRNA
YP_002375198.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_002375199.1	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_002375202.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_002375203.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_002375204.1	carries the fatty acid chain in fatty acid biosynthesis
YP_002375205.1	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_002375206.1	identified by match to protein family HMM PF01743
YP_002375209.1	identified by match to protein family HMM PF02618; match to protein family HMM TIGR00247
YP_002375210.1	identified by match to protein family HMM PF01751; match to protein family HMM PF01807; match to protein family HMM PF08275; match to protein family HMM TIGR01391
YP_002375211.1	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_002375212.1	identified by match to protein family HMM PF02591
YP_002375213.1	functions in MreBCD complex in some organisms
YP_002375214.1	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_002375216.1	identified by match to protein family HMM PF00905; match to protein family HMM PF03717; match to protein family HMM TIGR03423
YP_002375217.1	identified by match to protein family HMM PF01098; match to protein family HMM TIGR02210
YP_002375218.1	catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr)
YP_002375219.1	identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560
YP_002375221.1	identified by match to protein family HMM PF01928; match to protein family HMM TIGR00318
YP_002375222.1	identified by match to protein family HMM PF02386; match to protein family HMM TIGR00933
YP_002375223.1	identified by match to protein family HMM PF02080; match to protein family HMM PF02254
YP_002375225.1	catalyzes the formation of fructose 1,6-bisphosphate from fructose 6-phosphate and diphosphate
YP_002375226.1	CoADR; specific for coenzyme A disulfide; requires NADH; involved in protecting cells against reactive oxygen species by recycling coenzyme A disulfide which can reduce hydrogen peroxide
YP_002375227.1	identified by match to protein family HMM PF00375
YP_002375228.1	identified by glimmer
YP_002375229.1	functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family
YP_002375230.1	identified by match to protein family HMM PF02195
YP_002375231.1	identified by match to protein family HMM PF00905; match to protein family HMM PF00912; match to protein family HMM TIGR02074
YP_002375233.1	identified by match to protein family HMM PF01300; match to protein family HMM PF03481; match to protein family HMM TIGR00057
YP_002375234.1	identified by match to protein family HMM PF03330; match to protein family HMM PF05036; match to protein family HMM TIGR00413
YP_002375235.1	identified by match to protein family HMM PF01207
YP_002375236.1	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_002375238.1	identified by match to protein family HMM PF05430
YP_002375239.1	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_002375240.1	identified by match to protein family HMM PF00005
YP_002375242.1	p83/100; identified by match to protein family HMM PF05262
YP_002375244.1	identified by match to protein family HMM PF00633; match to protein family HMM PF00730
YP_002375245.1	identified by match to protein family HMM PF00528
YP_002375246.1	identified by match to protein family HMM PF00528
YP_002375247.1	identified by match to protein family HMM PF04977
YP_002375252.1	identified by match to protein family HMM PF01061
YP_002375253.1	identified by match to protein family HMM PF00005
YP_002375254.1	member of metallo-beta-lactamase family; the purified enzyme from Escherichia coli forms dimeric zinc phosphodiesterase; in Bacillus subtilis this protein is a 3'-tRNA processing endoribonuclease and is essential while in Escherichia coli it is not; associates with two zinc ions
YP_002375255.1	identified by match to protein family HMM PF01266
YP_002375256.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_002375258.1	identified by match to protein family HMM PF04018
YP_002375259.1	identified by match to protein family HMM PF03819
YP_002375260.1	identified by match to protein family HMM PF01476; match to protein family HMM PF01551
YP_002375262.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954; match to protein family HMM PF07728
YP_002375264.1	identified by match to protein family HMM PF02674
YP_002375265.1	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_002375267.1	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_002375268.1	identified by match to protein family HMM PF04748
YP_002375269.1	identified by match to protein family HMM PF04542; match to protein family HMM PF04545; match to protein family HMM PF04967; match to protein family HMM TIGR02937
YP_002375270.1	identified by glimmer
YP_002375271.1	part of the basal body which consists of four rings L, P, S, and M mounted on a central rod
YP_002375273.1	makes up the distal portion of the flagellar basal body rod
YP_002375274.1	identified by match to protein family HMM PF00460; match to protein family HMM PF06429; match to protein family HMM TIGR03506
YP_002375276.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_002375277.1	identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061
YP_002375278.1	identified by match to protein family HMM PF04327
YP_002375279.1	involved in the peptidyltransferase reaction during translation
YP_002375280.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_002375281.1	identified by match to protein family HMM PF01467; match to protein family HMM TIGR00125; match to protein family HMM TIGR00482
YP_002375283.1	identified by match to protein family HMM PF02410
YP_002375284.1	stage V sporulation protein G; essential for spore formation and a negative regulator of asymmetric septation in Bacillus; involved in methicillin-resistance, biofilm formation and capsular polysaccharide synthesis in Staphylococcus
YP_002375285.1	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_002375286.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_002375287.1	identified by match to protein family HMM PF01171; match to protein family HMM TIGR02432
YP_002375288.1	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_002375292.1	identified by match to protein family HMM PF02223; match to protein family HMM TIGR00041
YP_002375293.1	identified by match to protein family HMM PF04357
YP_002375294.1	identified by match to protein family HMM PF01103; match to protein family HMM PF07244; match to protein family HMM TIGR03303
YP_002375295.1	identified by match to protein family HMM PF03938
YP_002375296.1	This protein performs the mismatch recognition step during the DNA repair process
YP_002375297.1	identified by match to protein family HMM TIGR00201
YP_002375298.1	identified by match to protein family HMM PF02576
YP_002375299.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_002375300.1	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_002375301.1	identified by match to protein family HMM PF02033; match to protein family HMM TIGR00082
YP_002375302.1	identified by match to protein family HMM PF01509; match to protein family HMM TIGR00431
YP_002375303.1	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_002375304.1	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; match to protein family HMM TIGR03591
YP_002375305.1	identified by match to protein family HMM PF03739
YP_002375306.1	identified by match to protein family HMM PF03739
YP_002375307.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_002375308.1	identified by match to protein family HMM PF03023; match to protein family HMM TIGR01695
YP_002375310.1	identified by match to protein family HMM PF02441; match to protein family HMM PF04127; match to protein family HMM TIGR00521
YP_002375312.1	mediates high affinitiy panthothenate transport which is stimulated by the presence of sodium ions; member of SSS family of sodium/solute symporters; the imported panthothenate is phosphorylated by panthothenate kinase
YP_002375313.1	identified by match to protein family HMM PF00849
YP_002375315.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_002375316.1	identified by match to protein family HMM PF03755; match to protein family HMM PF08340; match to protein family HMM TIGR00255
YP_002375317.1	catalyzes the formation of (d)CDP from ATP and (d)CMP
YP_002375318.1	identified by match to protein family HMM TIGR00690
YP_002375319.1	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_002375324.1	identified by match to protein family HMM PF00271; match to protein family HMM PF04408; match to protein family HMM PF07717
YP_002375325.1	identified by match to protein family HMM PF01131; match to protein family HMM PF01751; match to protein family HMM TIGR01051
YP_002375326.1	identified by match to protein family HMM PF00149; match to protein family HMM TIGR00619
YP_002375327.1	identified by match to protein family HMM PF02463
YP_002375329.1	IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 2 subfamily; some organisms carry two different copies of this enzyme; in some organisms, the type 2 subfamily is associated with resistance to the antibiotic pseudomonic acid (mupirocin)
YP_002375330.1	identified by match to protein family HMM PF00004; match to protein family HMM PF07724
YP_002375331.1	identified by match to protein family HMM PF02878; match to protein family HMM PF02879; match to protein family HMM PF02880
YP_002375332.1	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_002375333.1	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_002375335.1	identified by glimmer
YP_002375338.1	catalyzes the degradation of arginine to citruline and ammonia
YP_002375339.1	catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation
YP_002375342.1	identified by match to protein family HMM PF04313
YP_002380596.1	identified by match to protein family HMM PF07094
YP_002380597.1	identified by match to protein family HMM PF02989
YP_002380598.1	identified by match to protein family HMM PF02989
YP_002380599.1	identified by match to protein family HMM PF02989
YP_002380602.1	identified by match to protein family HMM PF07405
YP_002380604.1	identified by match to protein family HMM PF05561
YP_002380605.1	identified by match to protein family HMM PF05619
YP_002380606.1	identified by match to protein family HMM PF07316
YP_002380607.1	identified by match to protein family HMM PF07341
YP_002380608.1	identified by match to protein family HMM PF07032
YP_002380609.1	identified by match to protein family HMM PF05537
YP_002380610.1	identified by match to protein family HMM PF05632
YP_002380611.1	identified by match to protein family HMM PF05113
YP_002380612.1	identified by match to protein family HMM PF05606
YP_002380613.1	identified by match to protein family HMM PF05085
YP_002380614.1	identified by match to protein family HMM PF05102; match to protein family HMM TIGR01606
YP_002380615.1	identified by match to protein family HMM PF05289
YP_002380617.1	identified by match to protein family HMM PF02999
YP_002380618.1	identified by match to protein family HMM PF02524
YP_002380619.1	identified by match to protein family HMM PF03304
YP_002380620.1	identified by glimmer; putative
YP_002380621.1	identified by glimmer; putative
YP_002380622.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002380625.1	identified by match to protein family HMM PF02524
YP_002380626.1	identified by match to protein family HMM PF03112; match to protein family HMM PF09588
YP_002380627.1	identified by match to protein family HMM PF03196
YP_002380628.1	identified by match to protein family HMM PF00589
YP_002380629.1	identified by match to protein family HMM PF06780
YP_002380630.1	identified by match to protein family HMM PF04867
YP_002380631.1	identified by match to protein family HMM PF04645
YP_002380678.1	identified by match to protein family HMM PF07094
YP_002380679.1	identified by match to protein family HMM PF02989
YP_002380680.1	identified by match to protein family HMM PF02989
YP_002380681.1	identified by match to protein family HMM PF02989
YP_002380684.1	identified by match to protein family HMM PF07405
YP_002380686.1	identified by match to protein family HMM PF05561
YP_002380687.1	identified by match to protein family HMM PF05619
YP_002380688.1	identified by match to protein family HMM PF07316
YP_002380689.1	identified by match to protein family HMM PF07341
YP_002380690.1	identified by match to protein family HMM PF07032
YP_002380691.1	identified by match to protein family HMM PF05537
YP_002380692.1	identified by match to protein family HMM PF05632
YP_002380693.1	identified by match to protein family HMM PF05113
YP_002380694.1	identified by match to protein family HMM PF05606
YP_002380695.1	identified by match to protein family HMM PF07115
YP_002380696.1	identified by match to protein family HMM PF03434
YP_002380697.1	identified by match to protein family HMM PF05246
YP_002380698.1	identified by match to protein family HMM PF05085
YP_002380699.1	identified by match to protein family HMM PF05102; match to protein family HMM TIGR01606
YP_002380700.1	identified by match to protein family HMM PF05289
YP_002380702.1	identified by match to protein family HMM PF02999
YP_002380703.1	identified by match to protein family HMM PF03978
YP_002380704.1	identified by match to protein family HMM PF03304
YP_002380706.1	identified by glimmer; putative
YP_002380707.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002380710.1	identified by match to protein family HMM PF02524
YP_002380711.1	identified by match to protein family HMM PF03112; match to protein family HMM PF09588
YP_002380712.1	identified by match to protein family HMM PF03196
YP_002380713.1	identified by match to protein family HMM PF00589
YP_002380715.1	identified by match to protein family HMM PF04867
YP_002380716.1	identified by match to protein family HMM PF04645
YP_002380717.1	identified by match to protein family HMM PF07094
YP_002380718.1	identified by match to protein family HMM PF02989
YP_002380719.1	identified by match to protein family HMM PF02989
YP_002380720.1	identified by match to protein family HMM PF02989
YP_002380723.1	identified by match to protein family HMM PF07405
YP_002380725.1	identified by match to protein family HMM PF05561
YP_002380726.1	identified by match to protein family HMM PF05619
YP_002380727.1	identified by match to protein family HMM PF07316
YP_002380728.1	identified by match to protein family HMM PF07341
YP_002380729.1	identified by match to protein family HMM PF07032
YP_002380730.1	identified by match to protein family HMM PF05537
YP_002380731.1	identified by match to protein family HMM PF05632
YP_002380732.1	identified by match to protein family HMM PF05113
YP_002380733.1	identified by match to protein family HMM PF05606
YP_002380734.1	identified by match to protein family HMM PF07115
YP_002380735.1	identified by match to protein family HMM PF03434
YP_002380736.1	identified by match to protein family HMM PF05246
YP_002380737.1	identified by match to protein family HMM PF05085
YP_002380738.1	identified by match to protein family HMM PF05102; match to protein family HMM TIGR01606
YP_002380739.1	identified by match to protein family HMM PF05289
YP_002380741.1	identified by match to protein family HMM PF02999
YP_002380742.1	identified by match to protein family HMM PF02524
YP_002380743.1	identified by match to protein family HMM PF03304
YP_002380745.1	identified by glimmer; putative
YP_002380746.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002380749.1	identified by match to protein family HMM PF03112; match to protein family HMM PF09588
YP_002380750.1	identified by match to protein family HMM PF03196
YP_002380751.1	identified by match to protein family HMM PF00589
YP_002380753.1	identified by match to protein family HMM PF06780
YP_002380755.1	identified by match to protein family HMM PF04867
YP_002380756.1	identified by match to protein family HMM PF04645
YP_002455211.1	identified by match to protein family HMM PF04402
YP_002455212.1	identified by match to protein family HMM PF01979; match to protein family HMM TIGR01178
YP_002455215.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002455216.1	identified by match to protein family HMM PF02414
YP_002455225.1	identified by glimmer; putative
YP_002455228.1	identified by glimmer; putative
YP_002455233.1	identified by glimmer; putative
YP_002455234.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002455235.1	identified by match to protein family HMM PF01656
YP_002455236.1	identified by match to protein family HMM PF01672
YP_002455237.1	identified by match to protein family HMM PF00015; match to protein family HMM TIGR02675
YP_002455248.1	identified by match to protein family HMM PF04466; match to protein family HMM TIGR01547
YP_002455249.1	identified by glimmer; putative
YP_002455257.1	identified by match to protein family HMM PF02414
YP_002455259.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002455260.1	identified by match to protein family HMM PF03796
YP_002455261.1	identified by match to protein family HMM PF02524
YP_002455263.1	identified by match to protein family HMM PF02414
YP_002455264.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002455265.1	identified by match to protein family HMM PF01656
YP_002455266.1	identified by match to protein family HMM PF01672
YP_002455268.1	identified by glimmer; putative
YP_002455269.1	identified by glimmer; putative
YP_002455272.1	identified by glimmer; putative
YP_002455273.1	identified by glimmer; putative
YP_002455274.1	identified by glimmer; putative
YP_002455276.1	identified by match to protein family HMM PF05628
YP_002455277.1	identified by match to protein family HMM PF01385
YP_002455279.1	identified by match to protein family HMM PF05714
YP_002455280.1	identified by match to protein family HMM PF01672
YP_002455282.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002455283.1	identified by match to protein family HMM PF02414
YP_002455284.1	identified by glimmer; putative
YP_002455288.1	identified by match to protein family HMM PF02524
YP_002455289.1	identified by glimmer; putative
YP_002455291.1	identified by match to protein family HMM PF04313
YP_002455300.1	identified by glimmer; putative
YP_002455302.1	identified by glimmer; putative
YP_002455304.1	identified by glimmer; putative
YP_002455307.1	identified by match to protein family HMM PF02414
YP_002455308.1	identified by glimmer; putative
YP_002455312.1	identified by match to protein family HMM PF04313
YP_002455317.1	identified by glimmer; putative
YP_002455323.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002455324.1	identified by match to protein family HMM PF02414
YP_002455325.1	identified by match to protein family HMM PF00857
YP_002455326.1	identified by glimmer; putative
YP_002455328.1	identified by match to protein family HMM PF05714
YP_002455329.1	identified by match to protein family HMM PF05628
YP_002455334.1	identified by match to protein family HMM PF07115
YP_002455335.1	identified by match to protein family HMM PF03434
YP_002455336.1	identified by match to protein family HMM PF05246
YP_002455337.1	identified by match to protein family HMM PF05085
YP_002455338.1	identified by match to protein family HMM PF05102; match to protein family HMM TIGR01606
YP_002455340.1	identified by match to protein family HMM PF02999
YP_002455341.1	identified by match to protein family HMM PF00820
YP_002455342.1	identified by match to protein family HMM PF00820
YP_002455343.1	identified by match to protein family HMM PF02414
YP_002455346.1	identified by match to protein family HMM PF03196
YP_002455347.1	identified by match to protein family HMM PF02352
YP_002455348.1	identified by match to protein family HMM PF02352
YP_002455350.1	identified by match to protein family HMM PF03237; match to protein family HMM TIGR01547
YP_002455352.1	identified by match to protein family HMM PF00496
YP_002455355.1	identified by match to protein family HMM PF06381
YP_002455356.1	identified by match to protein family HMM PF02989
YP_002455359.1	identified by match to protein family HMM PF05561
YP_002455360.1	identified by match to protein family HMM PF05619
YP_002455361.1	identified by match to protein family HMM PF07316
YP_002455362.1	identified by match to protein family HMM PF07341
YP_002455363.1	identified by match to protein family HMM PF07032
YP_002455364.1	identified by match to protein family HMM PF05632
YP_002455382.1	identified by match to protein family HMM PF03532
YP_002455383.1	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_002455387.1	identified by glimmer; putative
YP_002455389.1	identified by match to protein family HMM PF01048; match to protein family HMM TIGR01704
YP_002455392.1	identified by match to protein family HMM PF05714
YP_002455394.1	identified by glimmer; putative
YP_002455395.1	belongs to a borrelia family of proteins of unknown function; identified by match to protein family HMM PF02890
YP_002455398.1	identified by match to protein family HMM PF05714
YP_002455399.1	identified by match to protein family HMM PF05714
YP_002455400.1	identified by match to protein family HMM PF05628