-- dump date   	20111121_015457
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_002284414.1	identified by match to protein family HMM PF00308; match to protein family HMM PF08299; match to protein family HMM TIGR00362
YP_002284415.1	RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome
YP_002284416.1	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_002284417.1	identified by match to protein family HMM PF05175; match to protein family HMM TIGR00536
YP_002284419.1	identified by match to protein family HMM PF02502; match to protein family HMM TIGR00689
YP_002284422.1	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_002284423.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_002284424.1	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_002284425.1	identified by match to protein family HMM PF02608
YP_002284426.1	identified by match to protein family HMM PF02653
YP_002284427.1	identified by match to protein family HMM PF02653
YP_002284428.1	identified by match to protein family HMM PF00005
YP_002284429.1	identified by match to protein family HMM PF02608
YP_002284430.1	identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010
YP_002284431.1	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_002284433.1	identified by match to protein family HMM PF02223; match to protein family HMM TIGR00041
YP_002284434.1	identified by match to protein family HMM PF00561
YP_002284435.1	identified by match to protein family HMM PF01032
YP_002284436.1	identified by match to protein family HMM PF01032
YP_002284438.1	identified by match to protein family HMM PF01032
YP_002284439.1	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_002284442.1	identified by match to protein family HMM PF00575; match to protein family HMM PF09371
YP_002284444.1	identified by glimmer; putative
YP_002284445.1	identified by glimmer; putative
YP_002284449.1	identified by match to protein family HMM PF02384
YP_002284450.1	identified by match to protein family HMM PF00271; match to protein family HMM PF04313; match to protein family HMM PF04851; match to protein family HMM TIGR00348
YP_002284451.1	identified by match to protein family HMM PF01420
YP_002284452.1	identified by match to protein family HMM PF01420
YP_002284453.1	identified by match to protein family HMM PF01420
YP_002284454.1	identified by match to protein family HMM PF01420
YP_002284455.1	identified by match to protein family HMM PF04326; match to protein family HMM PF08220
YP_002284456.1	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_002284457.1	identified by match to protein family HMM PF02527; match to protein family HMM TIGR00138
YP_002284458.1	identified by glimmer; putative
YP_002284461.1	identified by match to protein family HMM PF04200
YP_002284463.1	identified by match to protein family HMM PF04200
YP_002284471.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a catalytic subunit
YP_002284472.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the beta chain is a regulatory subunit
YP_002284474.1	identified by match to protein family HMM PF03372
YP_002284475.1	identified by match to protein family HMM TIGR00810
YP_002284476.1	identified by match to protein family HMM PF00575; match to protein family HMM PF00773; match to protein family HMM PF08206; match to protein family HMM TIGR00358; match to protein family HMM TIGR02063
YP_002284477.1	identified by glimmer; putative
YP_002284478.1	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_002284479.1	identified by match to protein family HMM PF00005
YP_002284480.1	identified by match to protein family HMM PF00005; match to protein family HMM PF00664
YP_002284482.1	class II; LysRS2; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri, LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1
YP_002284484.1	identified by match to protein family HMM PF01432; match to protein family HMM PF08439; match to protein family HMM TIGR00181
YP_002284485.1	identified by match to protein family HMM PF01515
YP_002284488.1	identified by similarity to SP:P15031; match to protein family HMM PF00005
YP_002284489.1	identified by match to protein family HMM PF00950; match to protein family HMM PF01032
YP_002284491.1	identified by match to protein family HMM PF00571; match to protein family HMM PF01595
YP_002284492.1	identified by match to protein family HMM PF02650; match to protein family HMM TIGR00647
YP_002284493.1	identified by match to protein family HMM PF00070; match to protein family HMM PF01134; match to protein family HMM PF03486; match to protein family HMM PF07992
YP_002284494.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_002284495.1	catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system
YP_002284496.1	identified by match to protein family HMM PF01171; match to protein family HMM TIGR02432
YP_002284497.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_002284498.1	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_002284500.1	negatively supercoils closed circular double-stranded DNA
YP_002284501.1	negatively supercoils closed circular double-stranded DNA
YP_002284502.1	identified by match to protein family HMM PF02464; match to protein family HMM TIGR00199
YP_002284503.1	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_002284504.1	identified by match to protein family HMM PF01966; match to protein family HMM PF08668; match to protein family HMM TIGR00277
YP_002284506.1	identified by glimmer; putative
YP_002284508.1	identified by glimmer; putative
YP_002284512.1	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_002284513.1	identified by match to protein family HMM PF02575; match to protein family HMM TIGR00103
YP_002284514.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_002284515.1	identified by similarity to RF:XP_001579764.1
YP_002284516.1	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_002284518.1	identified by match to protein family HMM PF00005
YP_002284522.1	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_002284524.1	identified by match to protein family HMM PF00156; match to protein family HMM TIGR01203
YP_002284525.1	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_002284526.1	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_002284527.1	identified by glimmer; putative
YP_002284529.1	identified by match to protein family HMM PF00005; match to protein family HMM PF08402
YP_002284530.1	identified by match to protein family HMM PF00528
YP_002284531.1	identified by match to protein family HMM PF00528
YP_002284532.1	identified by match to protein family HMM PF02030
YP_002284535.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479
YP_002284536.1	identified by match to protein family HMM PF00186
YP_002284537.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549
YP_002284538.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_002284539.1	identified by match to protein family HMM PF00579; match to protein family HMM PF01479; match to protein family HMM TIGR00234
YP_002284540.1	identified by match to protein family HMM PF00005
YP_002284541.1	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_002284542.1	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_002284543.1	identified by match to protein family HMM PF00533; match to protein family HMM PF01653; match to protein family HMM PF03119; match to protein family HMM PF03120; match to protein family HMM TIGR00575
YP_002284545.1	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_002284546.1	identified by match to protein family HMM PF00588; match to protein family HMM PF08032; match to protein family HMM TIGR00186
YP_002284550.1	identified by match to protein family HMM PF02823; match to protein family HMM TIGR01216
YP_002284551.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_002284552.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_002284554.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_002284556.1	identified by match to protein family HMM PF00213; match to protein family HMM TIGR01145
YP_002284557.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_002284558.1	identified by glimmer; putative
YP_002284559.1	identified by match to protein family HMM PF00137
YP_002284560.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0
YP_002284563.1	identified by match to protein family HMM PF02463; match to protein family HMM PF06470
YP_002284564.1	identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM TIGR00064
YP_002284565.1	identified by match to protein family HMM PF04297
YP_002284570.1	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_002284571.1	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_002284572.1	identified by match to protein family HMM PF03960; match to protein family HMM TIGR01617
YP_002284573.1	identified by match to protein family HMM PF01513
YP_002284574.1	identified by similarity to GB:BAC44251.1
YP_002284576.1	identified by similarity to SP:Q9PQW3; match to protein family HMM PF02590
YP_002284577.1	identified by match to protein family HMM PF00121
YP_002284578.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_002284580.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_002284581.1	identified by match to protein family HMM PF00365
YP_002284582.1	identified by match to protein family HMM PF00224; match to protein family HMM TIGR01064
YP_002284583.1	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_002284584.1	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_002284586.1	identified by match to protein family HMM PF02645; match to protein family HMM TIGR00762
YP_002284587.1	identified by match to protein family HMM PF01588
YP_002284588.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_002284589.1	identified by match to protein family HMM PF01751; match to protein family HMM TIGR00334
YP_002284590.1	identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096
YP_002284591.1	identified by match to protein family HMM PF00004; match to protein family HMM PF07728
YP_002284592.1	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_002284594.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR00974
YP_002284595.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_002284596.1	identified by match to protein family HMM PF01895
YP_002284598.1	identified by match to protein family HMM PF00122; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01525
YP_002284600.1	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_002284601.1	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_002284602.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_002284603.1	identified by match to protein family HMM PF02734; match to protein family HMM TIGR03599
YP_002284606.1	required for 70S ribosome assembly
YP_002284607.1	identified by glimmer; putative
YP_002284608.1	involved in the peptidyltransferase reaction during translation
YP_002284609.1	identified by match to protein family HMM PF04327
YP_002284610.1	identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061
YP_002284611.1	identified by match to protein family HMM PF00625; match to protein family HMM TIGR03263
YP_002284613.1	identified by match to protein family HMM PF00481
YP_002284614.1	identified by match to protein family HMM PF00069
YP_002284615.1	identified by match to protein family HMM PF03193; match to protein family HMM TIGR00157
YP_002284616.1	identified by match to protein family HMM PF00909
YP_002284617.1	identified by match to protein family HMM PF00909
YP_002284619.1	identified by match to protein family HMM PF01268
YP_002284620.1	identified by match to protein family HMM PF00589
YP_002284621.1	identified by match to protein family HMM PF00324
YP_002284625.1	identified by match to protein family HMM PF02608
YP_002284626.1	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_002284627.1	identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001
YP_002284628.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_002284629.1	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_002284630.1	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_002284631.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_002284632.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_002284633.1	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_002284634.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_002284635.1	fusion of L22 and COG4933
YP_002284636.1	identified by match to protein family HMM PF00189; match to protein family HMM PF00417; match to protein family HMM PF07650; match to protein family HMM TIGR01009
YP_002284637.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_002284638.1	one of the stabilizing components for the large ribosomal subunit
YP_002284639.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_002284640.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_002284641.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_002284642.1	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_002284643.1	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_002284644.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_002284645.1	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_002284646.1	binds 5S rRNA along with protein L5 and L25
YP_002284647.1	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_002284648.1	late assembly protein
YP_002284649.1	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_002284650.1	identified by match to protein family HMM PF00406; match to protein family HMM PF05191; match to protein family HMM TIGR01351
YP_002284651.1	identified by match to protein family HMM PF00557; match to protein family HMM TIGR00500
YP_002284652.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_002284653.1	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_002284654.1	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_002284655.1	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_002284656.1	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_002284657.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_002284662.1	identified by match to protein family HMM PF01205
YP_002284664.1	identified by match to protein family HMM PF00122; match to protein family HMM PF00689; match to protein family HMM PF00690; match to protein family HMM PF00702; match to protein family HMM TIGR01494
YP_002284665.1	identified by match to protein family HMM PF03672
YP_002284666.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_002284667.1	identified by match to protein family HMM PF00133; match to protein family HMM PF08264; match to protein family HMM PF09334; match to protein family HMM TIGR00422
YP_002284668.1	identified by match to protein family HMM PF00588
YP_002284669.1	identified by match to protein family HMM PF02390; match to protein family HMM TIGR00091
YP_002284672.1	identified by match to protein family HMM PF01230
YP_002284674.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_002284677.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate
YP_002284678.1	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_002284679.1	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_002284680.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_002284681.1	identified by match to protein family HMM PF05343
YP_002284682.1	identified by match to protein family HMM PF01048; match to protein family HMM TIGR00107
YP_002284683.1	identified by match to protein family HMM PF00216
YP_002284684.1	identified by match to protein family HMM PF01966; match to protein family HMM PF04607; match to protein family HMM TIGR00691
YP_002284685.1	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_002284686.1	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_002284687.1	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_002284689.1	this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress
YP_002284691.1	identified by match to protein family HMM PF00255
YP_002284692.1	identified by match to protein family HMM PF00657
YP_002284693.1	identified by match to protein family HMM PF00657
YP_002284695.1	identified by match to protein family HMM PF01709; match to protein family HMM TIGR01033
YP_002284697.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_002284699.1	identified by match to protein family HMM TIGR01951
YP_002284700.1	identified by match to protein family HMM PF04452; match to protein family HMM TIGR00046
YP_002284702.1	necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus
YP_002284703.1	identified by match to protein family HMM PF05175
YP_002284704.1	Assists in DNA repair by cleaving phosphodiester bonds at apurinic or apyrimidinic sties to produce new 5' ends that are base-free deoxyribose 5-phosphate residues
YP_002284708.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_002284709.1	identified by match to protein family HMM PF00583
YP_002284710.1	identified by match to protein family HMM PF00814
YP_002284711.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005
YP_002284712.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_002284713.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_002284716.1	identified by match to protein family HMM PF02687
YP_002284717.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_002284718.1	identified by match to protein family HMM PF04296
YP_002284719.1	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_002284720.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_002284723.1	identified by match to protein family HMM PF01863
YP_002284724.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_002284725.1	identified by match to protein family HMM PF04011
YP_002284727.1	identified by match to protein family HMM PF00588; match to protein family HMM PF08032
YP_002284728.1	identified by match to protein family HMM PF06144
YP_002284732.1	functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor
YP_002284733.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_002284737.1	identified by match to protein family HMM PF02882
YP_002284739.1	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_002284740.1	identified by match to protein family HMM TIGR00481
YP_002284742.1	identified by match to protein family HMM PF02224; match to protein family HMM TIGR00017
YP_002284744.1	identified by match to protein family HMM PF01553
YP_002284745.1	identified by match to protein family HMM PF02616
YP_002284746.1	functions during chromosome segregation; may form a condensin-like structure with SMC and ScpA; forms a homodimer
YP_002284747.1	identified by match to protein family HMM PF00254; match to protein family HMM PF05697; match to protein family HMM PF05698; match to protein family HMM TIGR00115
YP_002284748.1	identified by match to protein family HMM PF00004; match to protein family HMM PF05362; match to protein family HMM PF07728; match to protein family HMM TIGR00763
YP_002284749.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
YP_002284750.1	identified by match to protein family HMM PF04816
YP_002284751.1	identified by match to protein family HMM PF01784
YP_002284754.1	identified by match to protein family HMM PF01509; match to protein family HMM TIGR00431
YP_002284755.1	identified by match to protein family HMM PF01687; match to protein family HMM PF06574
YP_002284757.1	identified by match to protein family HMM PF01032
YP_002284759.1	identified by match to protein family HMM PF01032
YP_002284760.1	identified by match to protein family HMM PF01032
YP_002284764.1	identified by match to protein family HMM PF00171
YP_002284765.1	catalyzes the formation of asparagine from aspartate and ammonia
YP_002284766.1	identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560
YP_002284767.1	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_002284770.1	identified by match to protein family HMM PF00591; match to protein family HMM PF02885; match to protein family HMM PF07831; match to protein family HMM TIGR02644
YP_002284771.1	Catalyzes a two-step reaction, first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_002284772.1	identified by match to protein family HMM PF03652; match to protein family HMM TIGR00250
YP_002284773.1	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_002284775.1	identified by glimmer; putative
YP_002284777.1	identified by glimmer; putative
YP_002284779.1	identified by match to protein family HMM PF03237; match to protein family HMM TIGR01547
YP_002284785.1	identified by similarity to GB:AAF30569.1
YP_002284792.1	identified by match to protein family HMM PF03837; match to protein family HMM TIGR01913
YP_002284801.1	identified by match to protein family HMM PF00589
YP_002284802.1	identified by glimmer; putative
YP_002284803.1	identified by glimmer; putative
YP_002284806.1	identified by glimmer; putative
YP_002284812.1	identified by glimmer; putative
YP_002284813.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; required for leading strand synthesis; PolC exhibits 3' to 5' exonuclease activity
YP_002284816.1	identified by match to protein family HMM PF02525
YP_002284817.1	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_002284818.1	identified by match to protein family HMM PF01210; match to protein family HMM PF07479
YP_002284819.1	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_002284820.1	identified by match to protein family HMM PF03772; match to protein family HMM TIGR00360
YP_002284821.1	identified by match to protein family HMM PF02381; match to protein family HMM TIGR00242
YP_002284822.1	identified by match to protein family HMM PF01795; match to protein family HMM TIGR00006
YP_002284824.1	identified by match to protein family HMM PF07751
YP_002284827.1	identified by match to protein family HMM PF00004; match to protein family HMM PF07724; match to protein family HMM PF07728
YP_002284829.1	Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids
YP_002284833.1	identified by match to protein family HMM PF01351
YP_002284835.1	identified by match to protein family HMM PF01032
YP_002284836.1	identified by match to protein family HMM PF01032
YP_002284838.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_002284841.1	identified by match to protein family HMM PF02660; match to protein family HMM TIGR00023
YP_002284843.1	identified by match to protein family HMM PF01025
YP_002284844.1	identified by match to protein family HMM PF00226; match to protein family HMM PF00684; match to protein family HMM PF01556; match to protein family HMM TIGR02349
YP_002284847.1	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; some organisms carry two different copies of this enzyme
YP_002284848.1	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_002284849.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_002284850.1	Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases
YP_002284851.1	identified by match to protein family HMM PF01367; match to protein family HMM PF02739
YP_002284852.1	catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time. Proposed to be responsible for the synthesis of the lagging strand; in the low GC gram positive bacteria this enzyme is less processive and more error prone than its counterpart in other bacteria.
YP_002284854.1	identified by match to protein family HMM PF01368; match to protein family HMM PF02272
YP_002284855.1	Required for the synthesis of the thiazole moiety
YP_002284858.1	Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons
YP_002284860.1	identified by match to protein family HMM PF04167
YP_002284864.1	identified by match to protein family HMM PF00210
YP_002284865.1	identified by match to protein family HMM PF01774
YP_002284866.1	identified by match to protein family HMM PF02492; match to protein family HMM TIGR00101
YP_002284867.1	identified by match to protein family HMM PF01730
YP_002284868.1	involved in the assembly of the urease metallocenter; possible nickel donor
YP_002284869.1	ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 ureC (alpha) and 3 ureAB (gamma/beta) subunits
YP_002284870.1	identified by match to protein family HMM PF00699; match to protein family HMM TIGR00192
YP_002284871.1	UreA, with UreB and UreC catalyzes the hydrolysis of urea into ammonia and carbon dioxide; nickel metalloenzyme; accessory proteins UreD, UreE, UreF, and UreG are necessary for assembly of the metallocenter
YP_002284872.1	identified by match to protein family HMM PF00005
YP_002284873.1	identified by match to protein family HMM PF01479; match to protein family HMM PF01728
YP_002284874.1	identified by match to protein family HMM PF00817
YP_002284875.1	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_002284876.1	identified by match to protein family HMM PF07499
YP_002284879.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_002284880.1	identified by match to protein family HMM PF01592
YP_002284881.1	identified by match to protein family HMM PF00266
YP_002284883.1	identified by match to protein family HMM PF00834
YP_002284885.1	identified by glimmer; putative
YP_002284887.1	identified by glimmer; putative
YP_002284889.1	identified by glimmer; putative
YP_002284890.1	identified by similarity to GB:CAE77662.1
YP_002284891.1	identified by match to protein family HMM PF00004
YP_002284892.1	catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a tetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily
YP_002284893.1	catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily
YP_002284895.1	identified by match to protein family HMM PF02540; match to protein family HMM TIGR00552
YP_002284896.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_002284898.1	identified by glimmer; putative
YP_002284899.1	identified by match to protein family HMM PF00551; match to protein family HMM PF02911; match to protein family HMM TIGR00460
YP_002284901.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_002284902.1	identified by match to protein family HMM PF00521; match to protein family HMM PF03989; match to protein family HMM TIGR01061
YP_002284904.1	identified by glimmer; putative
YP_002284906.1	identified by match to protein family HMM PF07198
YP_002284908.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_002284909.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_002284910.1	identified by match to protein family HMM PF00521; match to protein family HMM PF03989; match to protein family HMM TIGR01061
YP_002284911.1	identified by match to protein family HMM TIGR03597
YP_002284912.1	catalyzes the reversible adenylation of nicotinate mononucleotide to nicotinic acid adenine dinucleotide
YP_002284913.1	identified by match to protein family HMM PF01048; match to protein family HMM TIGR01704
YP_002284915.1	identified by match to protein family HMM PF07198
YP_002284917.1	identified by match to protein family HMM PF04851
YP_002284918.1	identified by match to protein family HMM PF01555
YP_002284920.1	identified by match to protein family HMM PF02608
YP_002284921.1	identified by match to protein family HMM PF07198
YP_002284923.1	identified by match to protein family HMM PF00871; match to protein family HMM TIGR00016
YP_002284925.1	identified by match to protein family HMM PF03372
YP_002284927.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_002284929.1	identified by match to protein family HMM PF03129
YP_002284930.1	identified by match to protein family HMM PF00041; match to protein family HMM PF07198
YP_002284934.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_002284936.1	identified by glimmer; putative
YP_002284937.1	identified by match to protein family HMM PF02130; match to protein family HMM TIGR00043
YP_002284938.1	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_002284939.1	identified by match to protein family HMM TIGR00613
YP_002284940.1	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_002284941.1	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_002284942.1	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_002284944.1	identified by match to protein family HMM PF00149; match to protein family HMM TIGR00282
YP_002284945.1	identified by match to protein family HMM PF00580
YP_002284947.1	identified by match to protein family HMM PF00535
YP_002284951.1	identified by match to protein family HMM PF00550
YP_002284952.1	identified by match to protein family HMM PF00145; match to protein family HMM TIGR00675
YP_002284954.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_002284955.1	identified by match to protein family HMM PF01580
YP_002284957.1	identified by match to protein family HMM PF00005; match to protein family HMM PF03412
YP_002284959.1	identified by match to protein family HMM PF01148
YP_002284960.1	identified by match to protein family HMM PF01765; match to protein family HMM TIGR00496
YP_002284961.1	identified by match to protein family HMM PF00696; match to protein family HMM TIGR02075
YP_002284962.1	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_002284963.1	identified by match to protein family HMM PF01032
YP_002284964.1	identified by match to protein family HMM PF01032
YP_002284967.1	identified by similarity to GB:ACA32698.1; match to protein family HMM PF07198
YP_002284970.1	identified by match to protein family HMM PF01432; match to protein family HMM PF08439; match to protein family HMM TIGR00181
YP_002284971.1	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_002284972.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_002284973.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_002284974.1	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_002284975.1	identified by match to protein family HMM PF03767
YP_002284977.1	identified by glimmer; putative
YP_002284978.1	identified by match to protein family HMM PF02878; match to protein family HMM PF02879
YP_002284979.1	identified by match to protein family HMM PF00383; match to protein family HMM TIGR01354
YP_002284980.1	identified by match to protein family HMM PF00557; match to protein family HMM PF01321
YP_002284981.1	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_002284982.1	catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_002284983.1	identified by match to protein family HMM PF02645; match to protein family HMM TIGR00762
YP_002284984.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_002284985.1	identified by match to protein family HMM PF02361
YP_002284986.1	with CbiNQ forms the ABC transporter for cobalt import; Mycoplasmas have two adjacent copies of this gene
YP_002284987.1	with CbiNQ forms the ABC transporter for cobalt import; Mycoplasmas have two adjacent copies of this gene
YP_002284988.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_002284989.1	binds directly to 23S ribosomal RNA
YP_002284990.1	identified by match to protein family HMM PF02687
YP_002284991.1	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_002284992.1	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_002284994.1	in some Mycoplasma, this protein is fused to aspartyl/glutamyl-tRNA amidotransferase subunit C domain
YP_002284995.1	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_002284997.1	identified by match to protein family HMM PF03796
YP_002284998.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_002284999.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_002285000.1	identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621
YP_002285001.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_002285002.1	identified by match to protein family HMM PF00583
YP_002285007.1	identified by match to protein family HMM PF00496
YP_002285009.1	identified by match to protein family HMM PF00005; match to protein family HMM PF08352
YP_002285010.1	identified by match to protein family HMM PF00005; match to protein family HMM PF08352; match to protein family HMM TIGR01727
YP_002285011.1	identified by match to protein family HMM PF00528
YP_002285012.1	identified by match to protein family HMM PF00528
YP_002285016.1	identified by match to protein family HMM PF02588
YP_002285017.1	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_002285018.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_002285019.1	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_002285020.1	identified by 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_002285021.1	identified by match to protein family HMM PF00753; match to protein family HMM PF07521
YP_002285022.1	identified by glimmer; putative
YP_002285027.1	identified by match to protein family HMM PF07885
YP_002285030.1	forms a direct contact with the tRNA during translation
YP_002285031.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_002285032.1	identified by glimmer; putative
YP_002285033.1	identified by glimmer; putative
YP_002285034.1	identified by match to protein family HMM PF00324
YP_002285035.1	identified by match to protein family HMM TIGR00964
YP_002285036.1	identified by match to protein family HMM PF02357; match to protein family HMM TIGR01956
YP_002285037.1	identified by match to protein family HMM PF00270; match to protein family HMM PF00271
YP_002285038.1	identified by match to protein family HMM PF01554
YP_002285039.1	identified by match to protein family HMM PF01554
YP_002285040.1	catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate
YP_002285041.1	catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase
YP_002285042.1	identified by match to protein family HMM PF00381; match to protein family HMM TIGR01003
YP_002285043.1	identified by match to protein family HMM PF00614
YP_002285044.1	identified by match to protein family HMM PF00085; match to protein family HMM PF05768
YP_002285045.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_002285047.1	identified by match to protein family HMM PF01926; match to protein family HMM TIGR03596
YP_002285049.1	catalyzes the formation of thymidine 5'-phosphate from thymidine
YP_002285050.1	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_002285051.1	identified by match to protein family HMM PF01116; match to protein family HMM TIGR00167; match to protein family HMM TIGR01859
YP_002285052.1	participates in both the initiation and recycling phases of transcription; in the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling
YP_002285053.1	identified by match to protein family HMM PF01966
YP_002285054.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_002285055.1	identified by match to protein family HMM PF00288
YP_002285056.1	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_002285057.1	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_002285058.1	identified by match to protein family HMM PF00825; match to protein family HMM TIGR00188
YP_002285059.1	in Escherichia coli transcription of this gene is enhanced by polyamines