-- dump date 20111121_012026 -- class Genbank::Feature -- table feature -- table main -- field 1 id -- field 2 type -- field 3 name -- field 4 contig -- field 5 start_pos -- field 6 end_pos -- field 7 strand -- field 8 description -- field 9 chrom_position -- field 10 organism -- field 11 GeneID -- header -- id type name contig start_pos end_pos strand description chrom_position organism GeneID 585035000001 SEQ_END SEQ_END NC_011742.1 5032268 5032268 DR NC_011742.1; contig end 5032268..5032268 Escherichia coli S88 585035000002 SEQ_END SEQ_END NC_011747.1 133853 133853 DR NC_011747.1; contig end 133853..133853 Escherichia coli S88 YP_002389853.1 CDS thrL NC_011742.1 190 255 D involved in threonine biosynthesis; controls the expression of the thrLABC operon; thr operon leader peptide 190..255 Escherichia coli S88 7131897 YP_002389854.1 CDS thrA NC_011742.1 336 2798 D multifunctional homotetrameric enzyme that catalyzes the phosphorylation of aspartate to form aspartyl-4-phosphate as well as conversion of aspartate semialdehyde to homoserine; functions in a number of amino acid biosynthetic pathways; bifunctional aspartokinase I/homeserine dehydrogenase I 336..2798 Escherichia coli S88 7131306 YP_002389855.1 CDS thrB NC_011742.1 2800 3732 D catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate; homoserine kinase 2800..3732 Escherichia coli S88 7131303 YP_002389856.1 CDS thrC NC_011742.1 3733 5019 D catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase 3733..5019 Escherichia coli S88 7131304 YP_002389857.1 CDS yaaX NC_011742.1 5233 5529 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein 5233..5529 Escherichia coli S88 7131305 YP_002389858.1 CDS yaaA NC_011742.1 5569 6345 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(5569..6345) Escherichia coli S88 7130256 YP_002389859.1 CDS yaaJ NC_011742.1 6415 7845 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative amino acid sodium/proton transporter complement(6415..7845) Escherichia coli S88 7130251 YP_002389860.1 CDS talB NC_011742.1 8124 9077 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8332529, 92334977, 11298760, 7592346, 8805555, 9007983, 9298646; Product type e : enzyme; transaldolase B 8124..9077 Escherichia coli S88 7130254 YP_002389861.1 CDS mogA NC_011742.1 9192 9779 D forms a trimer; related to eukaryotic protein gephyrin; functions during molybdenum cofactor biosynthesis; molybdenum cofactor biosynthesis protein MogA 9192..9779 Escherichia coli S88 7131258 YP_002389862.1 CDS yaaH NC_011742.1 9984 10550 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(9984..10550) Escherichia coli S88 7128863 YP_002389863.1 CDS htpY NC_011742.1 10699 11412 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8478327; Product type r : regulator; hypothetical protein complement(10699..11412) Escherichia coli S88 7130252 YP_002389864.1 CDS yaaI NC_011742.1 11438 11842 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(11438..11842) Escherichia coli S88 7131401 YP_002389865.1 CDS dnaK NC_011742.1 12214 14130 D 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; molecular chaperone DnaK 12214..14130 Escherichia coli S88 7130253 YP_002389866.1 CDS dnaJ NC_011742.1 14219 15349 D 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; chaperone protein DnaJ 14219..15349 Escherichia coli S88 7133503 YP_002389867.1 CDS mokC NC_011742.1 15454 15663 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90136075, 92048480, 92048481, 99291074; Product type r : regulator; regulatory protein for HokC, overlaps CDS of hokC complement(15454..15663) Escherichia coli S88 7130225 YP_002389868.1 CDS ECS88_0017 NC_011742.1 16218 16979 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein 16218..16979 Escherichia coli S88 7130620 YP_002389869.1 CDS ECS88_0018 NC_011742.1 16963 18492 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative Cerebroside-sulfatase 16963..18492 Escherichia coli S88 7133187 YP_002389870.1 CDS ECS88_0019 NC_011742.1 18615 19880 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 18615..19880 Escherichia coli S88 7133188 YP_002389871.1 CDS nhaA NC_011742.1 20115 21281 D exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH; pH-dependent sodium/proton antiporter 20115..21281 Escherichia coli S88 7133189 YP_002389872.1 CDS nhaR NC_011742.1 21341 22246 D Na+/H+ antiporter regulatory protein; activates the genes nhaA and osmC; transcriptional activator NhaR 21341..22246 Escherichia coli S88 7129706 YP_002389873.1 CDS rpsT NC_011742.1 22342 22605 R binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 complement(22342..22605) Escherichia coli S88 7129708 YP_002389874.1 CDS yaaY NC_011742.1 22708 22926 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 22708..22926 Escherichia coli S88 7133803 YP_002389875.1 CDS ribF NC_011742.1 22934 23875 D catalyzes the formation of FMN from riboflavin and the formation of FAD from FMN; in Bacillus the ribC gene has both flavokinase and FAD synthetase activities; bifunctional riboflavin kinase/FMN adenylyltransferase 22934..23875 Escherichia coli S88 7130257 YP_002389876.1 CDS ileS NC_011742.1 23918 26734 D IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme; isoleucyl-tRNA synthetase 23918..26734 Escherichia coli S88 7132719 YP_002389877.1 CDS lspA NC_011742.1 26734 27228 D lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase 26734..27228 Escherichia coli S88 7131618 YP_002389878.1 CDS fkpB NC_011742.1 27336 27785 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 97332650, 2011499; Product type e : enzyme; FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase) 27336..27785 Escherichia coli S88 7129390 YP_002389879.1 CDS ispH NC_011742.1 27787 28737 D catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway; 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 27787..28737 Escherichia coli S88 7129510 YP_002389880.1 CDS rihC NC_011742.1 28803 29717 D catalyzes the hydrolysis of both purine and pyrimidine ribonucleosides; ribonucleoside hydrolase RihC 28803..29717 Escherichia coli S88 7130424 YP_002389881.1 CDS ECS88_0030 NC_011742.1 29740 30105 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 29740..30105 Escherichia coli S88 7132722 YP_002389882.1 CDS dapB NC_011742.1 30266 31087 D catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase 30266..31087 Escherichia coli S88 7133190 YP_002389883.1 CDS carA NC_011742.1 31542 32690 D catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers; carbamoyl phosphate synthase small subunit 31542..32690 Escherichia coli S88 7130565 YP_002389884.1 CDS carB NC_011742.1 32708 35929 D four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity; carbamoyl phosphate synthase large subunit 32708..35929 Escherichia coli S88 7129159 YP_002389885.1 CDS ECS88_0034 NC_011742.1 35993 36196 D Evidence 6 : Doubtful CDS; hypothetical protein 35993..36196 Escherichia coli S88 7129160 YP_002389886.1 CDS ECS88_0035 NC_011742.1 36102 36611 D Evidence 2b : Function of strongly homologous gene; Product type e : enzyme; transposase IS605 family, IS200 group 36102..36611 Escherichia coli S88 7133191 YP_002389887.1 CDS caiF NC_011742.1 36901 37296 D regulator of carnitine metabolism; induces the caiTABCDE and fixABCX operons; DNA-binding transcriptional activator CaiF 36901..37296 Escherichia coli S88 7133192 YP_002389888.1 CDS caiE NC_011742.1 37415 38005 R involved in the synthesis of a cofactor required for carnitine dehydratase and carnitine racemase activities; carnitine operon protein CaiE complement(37415..38005) Escherichia coli S88 7129156 YP_002389889.1 CDS caiD NC_011742.1 38011 38904 R catalyzes the dehydration of L-carnitinyl-CoA to crotonobetainyl-CoA; carnitinyl-CoA dehydratase complement(38011..38904) Escherichia coli S88 7129155 YP_002389890.1 CDS caiC NC_011742.1 38905 40473 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15731894, 97189569, 7815937; Product type e : enzyme; putative crotonobetaine/carnitine-CoA ligase complement(38905..40473) Escherichia coli S88 7129154 YP_002389891.1 CDS caiB NC_011742.1 40531 41748 R catalyzes formation of L-carnitinyl-CoA by transfering the CoA moiety from gamma-butyrobetainyl-CoA, also catalyzes the formation of crotonobetainyl-CoA by transfer of CoA from gamma-butyrobetainyl-CoA or L-carnitinyl-CoA to crotonobetaine; crotonobetainyl-CoA:carnitine CoA-transferase complement(40531..41748) Escherichia coli S88 7129153 YP_002389892.1 CDS caiA NC_011742.1 41876 43018 R catalyzes the reduction of crotonobetainyl-CoA to gamma-butyrobetainyl-CoA; crotonobetainyl-CoA dehydrogenase complement(41876..43018) Escherichia coli S88 7129152 YP_002389893.1 CDS caiT NC_011742.1 43049 44563 R catalyzes the exchange of L-carnitine for gamma-butyrobetaine in carnitine metabolism; L-carnitine/gamma-butyrobetaine antiporter complement(43049..44563) Escherichia coli S88 7129151 YP_002389894.1 CDS fixA NC_011742.1 45036 45806 D required for anaerobic carnitine reduction, may act to transfer electrons to crotonobetaine reductase; putative electron transfer flavoprotein FixA 45036..45806 Escherichia coli S88 7129157 YP_002389895.1 CDS fixB NC_011742.1 45821 46762 D involved in electron transfer during carnitine metabolism; putative electron transfer flavoprotein FixB 45821..46762 Escherichia coli S88 7129504 YP_002389896.1 CDS fixC NC_011742.1 46813 48099 D FAD/NAD(P)-binding domain; possibly part of an electron transfer system required for anaerobic carnitine reduction; putative oxidoreductase FixC 46813..48099 Escherichia coli S88 7129505 YP_002389897.1 CDS fixX NC_011742.1 48096 48383 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 96066354, 12081978; Product type pc : putative carrier; putative 4Fe-4S ferredoxin 48096..48383 Escherichia coli S88 7129506 YP_002389898.1 CDS yaaU NC_011742.1 48442 49773 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 48442..49773 Escherichia coli S88 7129507 YP_002389899.1 CDS kefF NC_011742.1 49881 50411 D Required for full activity of KefC, a potassium-proton antiporter; glutathione-regulated potassium-efflux system ancillary protein KefF 49881..50411 Escherichia coli S88 7130255 YP_002389900.1 CDS kefC NC_011742.1 50404 52266 D transport system that facilitates potassium-efflux; glutathione-regulated potassium-efflux system protein KefC 50404..52266 Escherichia coli S88 7130456 YP_002389901.1 CDS folA NC_011742.1 52458 52937 D catalyzes the reduction of dihydrofolate to tetrahydrofolate; dihydrofolate reductase 52458..52937 Escherichia coli S88 7130455 YP_002389902.1 CDS ECS88_0052 NC_011742.1 53023 53256 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative antitoxin of gyrase inhibiting toxin-antitoxin system 53023..53256 Escherichia coli S88 7132813 YP_002389903.1 CDS apaH NC_011742.1 53571 54419 R hydrolyzes P(1),P(4)-bis(5'-adenosyl) tetraphosphate to form 2 ADP; diadenosine tetraphosphatase complement(53571..54419) Escherichia coli S88 7133194 YP_002389904.1 CDS apaG NC_011742.1 54426 54803 R protein associated with Co2+ and Mg2+ efflux; ApaG complement(54426..54803) Escherichia coli S88 7133073 YP_002389905.1 CDS ksgA NC_011742.1 54806 55627 R 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; dimethyladenosine transferase complement(54806..55627) Escherichia coli S88 7133072 YP_002389906.1 CDS pdxA NC_011742.1 55624 56613 R catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate); 4-hydroxythreonine-4-phosphate dehydrogenase complement(55624..56613) Escherichia coli S88 7130468 YP_002389907.1 CDS surA NC_011742.1 56613 57899 R Chaperone involved in the folding of extracytoplasmic proteins, especially OmpA, OmpF and LamB; peptidyl-prolyl cis-trans isomerase SurA complement(56613..57899) Escherichia coli S88 7133181 YP_002389908.1 CDS imp NC_011742.1 57952 60306 R determines N-hexane tolerance and is involved in outer membrane permeability; organic solvent tolerance protein complement(57952..60306) Escherichia coli S88 7131251 YP_002389909.1 CDS djlA NC_011742.1 60561 61376 D functions as a co-chaperone with DnaK; involved in regulation of colanic acid capsule; inner membrane protein; dimerized via transmembrane domain; J-like domain is cytoplasmic and can functionally substitute for DnaJ; stimulates synthesis of colanic acid mucoid capsule through the RcsB/C signal transduction system; Dna-J like membrane chaperone protein 60561..61376 Escherichia coli S88 7131631 YP_002389910.1 CDS rluA NC_011742.1 61526 62185 R catalyzes the synthesis of pseudouridine from uracil-746 in 23S ribosomal RNA and from uracil-32 in the anticodon stem and loop of transfer RNAs; 23S rRNA/tRNA pseudouridine synthase A complement(61526..62185) Escherichia coli S88 7130211 YP_002389911.1 CDS hepA NC_011742.1 62197 65103 R transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA; ATP-dependent helicase HepA complement(62197..65103) Escherichia coli S88 7132731 YP_002389912.1 CDS polB NC_011742.1 65267 67618 R Has polymerase, DNA-binding and 3'-5' exonuclease activities. In Aeropyrum pernix this protein is sensitive to aphidicolin and stable at 95#C; DNA polymerase II complement(65267..67618) Escherichia coli S88 7128908 YP_002389913.1 CDS araD NC_011742.1 67693 68388 R catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate in the anaerobic catabolism of L-ascorbate; links the arabinose metabolic pathway to the pentose phosphate pathway and allows the bacteria to use arabinose as an energy source; L-ribulose-5-phosphate 4-epimerase complement(67693..68388) Escherichia coli S88 7130740 YP_002389914.1 CDS araA NC_011742.1 68673 70175 R catalyzes the formation of L-ribulose from L-arabinose in L-arabinose catabolism; L-arabinose isomerase complement(68673..70175) Escherichia coli S88 7133083 YP_002389915.1 CDS araB NC_011742.1 70186 71886 R catalyzes the phosphorylation of ribulose to ribulose 5-phosphate; ribulokinase complement(70186..71886) Escherichia coli S88 7133080 YP_002389916.1 CDS araC NC_011742.1 72225 73070 D positive and negative regulator; regulates the araBAD and araFGH operons and other genes involved in the transport and catabolism of L-arabinose; DNA-binding transcriptional regulator AraC 72225..73070 Escherichia coli S88 7133081 YP_002389917.1 CDS ECS88_0068 NC_011742.1 73582 74433 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 73582..74433 Escherichia coli S88 7133082 YP_002389918.1 CDS ECS88_0069 NC_011742.1 74440 74862 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 74440..74862 Escherichia coli S88 7131228 YP_002389919.1 CDS yabI NC_011742.1 75017 75781 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 75017..75781 Escherichia coli S88 7129028 YP_002389920.1 CDS thiQ NC_011742.1 75895 76593 R with TbpA and ThiP is part of the thiamine and TPP transport system; thiamine transporter ATP-binding subunit complement(75895..76593) Escherichia coli S88 7130258 YP_002389921.1 CDS thiP NC_011742.1 76577 78187 R permease; with TbpA and ThiQ functions in transport of thiamine and thiamine pyrophosphate into the cell; repressed in presence of exogenous thiamine; thiamine transporter membrane protein complement(76577..78187) Escherichia coli S88 7131301 YP_002389922.1 CDS tbpA NC_011742.1 78163 79146 R part of the thiamine and TPP transport system tbpA-thiPQ; thiamine transporter substrate binding subunit complement(78163..79146) Escherichia coli S88 7131300 YP_002389923.1 CDS sgrR NC_011742.1 79310 80965 R activates sgrS under glucose-phosphate stress conditions; transcriptional regulator SgrR complement(79310..80965) Escherichia coli S88 7129857 YP_002389924.1 CDS ECS88_0075 NC_011742.1 80934 81185 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 80934..81185 Escherichia coli S88 7130597 YP_002389925.1 CDS leuD NC_011742.1 81293 81898 R catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit complement(81293..81898) Escherichia coli S88 7130598 YP_002389926.1 CDS leuC NC_011742.1 81909 83309 R dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit complement(81909..83309) Escherichia coli S88 7130487 YP_002389927.1 CDS leuB NC_011742.1 83312 84403 R catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase complement(83312..84403) Escherichia coli S88 7130486 YP_002389928.1 CDS leuA NC_011742.1 84403 85974 R catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase complement(84403..85974) Escherichia coli S88 7130485 YP_002389929.1 CDS leuL NC_011742.1 86066 86152 R involved in attenuation control of the leuABCD operon in leucine biosynthesis; leu operon leader peptide complement(86066..86152) Escherichia coli S88 7130484 YP_002389930.1 CDS leuO NC_011742.1 86810 87754 D activator for leuABCD operon; member of LysR family of transcriptional activators; leucine transcriptional activator 86810..87754 Escherichia coli S88 7130488 YP_002389931.1 CDS ilvI NC_011742.1 88072 89796 D catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; acetolactate synthase 3 catalytic subunit 88072..89796 Escherichia coli S88 7130489 YP_002389932.1 CDS ilvH NC_011742.1 89799 90290 D with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit; acetolactate synthase 3 regulatory subunit 89799..90290 Escherichia coli S88 7131626 YP_002389933.1 CDS fruR NC_011742.1 90470 91474 D binds D-fructose as an inducer; involved in regulation of operons for central pathways of carbon metabolism; DNA-binding transcriptional regulator FruR 90470..91474 Escherichia coli S88 7131625 YP_002389934.1 CDS mraZ NC_011742.1 92076 92534 D MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ 92076..92534 Escherichia coli S88 7132838 YP_002389935.1 CDS mraW NC_011742.1 92536 93477 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20042184, 10493123, 2187182, 6350821; Product type e : enzyme; S-adenosyl-methyltransferase MraW 92536..93477 Escherichia coli S88 7129604 YP_002389936.1 CDS ftsL NC_011742.1 93474 93839 D membrane bound cell division protein at septum containing leucine zipper motif; cell division protein FtsL 93474..93839 Escherichia coli S88 7129602 YP_002389937.1 CDS ftsI NC_011742.1 93855 95621 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91072213, 92202178, 94095121, 9603865, 9614966, 1332942, 1447153, 2198024, 2677607, 2681146, 3049550, 3911028, 6350821; Product type e : enzyme; transpeptidase involved in septal peptidoglycan synthesis (penicillin-binding protein 3) 93855..95621 Escherichia coli S88 7132852 YP_002389938.1 CDS murE NC_011742.1 95608 97095 D involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate; UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase 95608..97095 Escherichia coli S88 7132850 YP_002389939.1 CDS murF NC_011742.1 97092 98450 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88273095, 90248455, 91310568, 97128642, 11090285, 2668880, 9166795; Product type e : enzyme; UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase 97092..98450 Escherichia coli S88 7129634 YP_002389940.1 CDS mraY NC_011742.1 98444 99526 D First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase 98444..99526 Escherichia coli S88 7129635 YP_002389941.1 CDS murD NC_011742.1 99529 100845 D UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase 99529..100845 Escherichia coli S88 7129603 YP_002389942.1 CDS ftsW NC_011742.1 100845 102089 D integral membrane protein involved in stabilizing FstZ ring during cell division; cell division protein FtsW 100845..102089 Escherichia coli S88 7129633 YP_002389943.1 CDS murG NC_011742.1 102086 103153 D UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis; undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase 102086..103153 Escherichia coli S88 7132855 YP_002389944.1 CDS murC NC_011742.1 103207 104682 D Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis; UDP-N-acetylmuramate--L-alanine ligase 103207..104682 Escherichia coli S88 7129636 YP_002389945.1 CDS ddl NC_011742.1 104675 105595 D 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; D-alanine--D-alanine ligase 104675..105595 Escherichia coli S88 7129632 YP_002389946.1 CDS ftsQ NC_011742.1 105597 106427 D involved in septum formation; cell division protein FtsQ 105597..106427 Escherichia coli S88 7130176 YP_002389947.1 CDS ftsA NC_011742.1 106424 107686 D ATP-binding involved in recruitment of FtsK to Z ring; essential cell division protein; colocalizes with FtsZ through direct interaction to the septal ring structure; structurally similar to eukaryotic actin; binds directly to the cell membrane; cell division protein FtsA 106424..107686 Escherichia coli S88 7132854 YP_002389948.1 CDS ftsZ NC_011742.1 107747 108898 D 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; cell division protein FtsZ 107747..108898 Escherichia coli S88 7132846 YP_002389949.1 CDS lpxC NC_011742.1 108999 109916 D zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis; UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase 108999..109916 Escherichia coli S88 7132145 YP_002389950.1 CDS secM NC_011742.1 110147 110659 D secM translational pause allows for the initiation of secA translation; SecA regulator SecM 110147..110659 Escherichia coli S88 7129382 YP_002389951.1 CDS secA NC_011742.1 110721 113426 D 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; preprotein translocase subunit SecA 110721..113426 Escherichia coli S88 7131384 YP_002389952.1 CDS mutT NC_011742.1 113486 113884 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10218109, 89264540, 90136514, 91225007, 97444511, 1309939, 2841285, 3033442, 3288626, 7578113, 9063868; Product type e : enzyme; nucleoside triphosphate pyrophosphohydrolase 113486..113884 Escherichia coli S88 7131378 YP_002389953.1 CDS yacG NC_011742.1 113972 114169 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 12211008, 3033442; zinc-binding protein complement(113972..114169) Escherichia coli S88 7129643 YP_002389954.1 CDS yacF NC_011742.1 114179 114922 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(114179..114922) Escherichia coli S88 7130261 YP_002389955.1 CDS coaE NC_011742.1 114922 115542 R catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis; dephospho-CoA kinase complement(114922..115542) Escherichia coli S88 7130260 YP_002389956.1 CDS guaC NC_011742.1 115767 116810 D catalyzes the NADPH-dependent deamination of GMP to inosine monophosphate; guanosine 5'-monophosphate oxidoreductase 115767..116810 Escherichia coli S88 7131940 YP_002389957.1 CDS hofC NC_011742.1 116845 118047 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96099298, 2904262, 7959070; Product type s : structure; type IV pilin biogenesis protein complement(116845..118047) Escherichia coli S88 7128876 YP_002389958.1 CDS hofB NC_011742.1 118037 119422 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 96099298, 7959070; Product type pt : putative transporter; hypothetical protein complement(118037..119422) Escherichia coli S88 7128938 YP_002389959.1 CDS ppdD NC_011742.1 119432 119872 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 20100782, 20271862, 96099298, 7959070; Product type ps : putative structure; putative major pilin subunit complement(119432..119872) Escherichia coli S88 7128937 YP_002389960.1 CDS nadC NC_011742.1 120076 120969 R catalyzes the formation of pyridine-2,3-dicarboxylate and 5-phospho-alpha-D-ribose 1-diphosphate from nictinate D-ribonucleotide; quinolinate phosphoribosyltransferase complement(120076..120969) Escherichia coli S88 7130757 YP_002389961.1 CDS ampD NC_011742.1 121057 121608 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90113890, 95047240, 2607970, 7959070; Product type e : enzyme; N-acetyl-anhydromuranmyl-L-alanine amidase 121057..121608 Escherichia coli S88 7129652 YP_002389962.1 CDS ampE NC_011742.1 121605 122459 D involved in regulation of beta-lactamase; putative signaling protein; regulatory protein AmpE 121605..122459 Escherichia coli S88 7133062 YP_002389963.1 CDS aroP NC_011742.1 122502 123872 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1104763, 90174991, 9150230; Product type t : transporter; aromatic amino acid transporter complement(122502..123872) Escherichia coli S88 7133063 YP_002389964.1 CDS ECS88_0115 NC_011742.1 124400 126181 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 10702359; hypothetical protein 124400..126181 Escherichia coli S88 7129932 YP_002389965.1 CDS ECS88_0116 NC_011742.1 126184 126468 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; Putative Colicin E7 immunity protein (ImmE7) (Microcin E7 immunity protein) 126184..126468 Escherichia coli S88 7129030 YP_002389966.1 CDS ECS88_0118 NC_011742.1 126876 127166 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; Putative Colicin E7 immunity protein (ImmE7) (Microcin E7 immunity protein) 126876..127166 Escherichia coli S88 7129032 YP_002389967.1 CDS ECS88_0120 NC_011742.1 127569 127865 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; Putative Colicin E7 immunity protein (ImmE7) (Microcin E7 immunity protein) 127569..127865 Escherichia coli S88 7129034 YP_002389968.1 CDS pdhR NC_011742.1 128321 129085 D activates lctPRD operon; autoregulates itself through repression of pdhR-aceEF-lpdA operon; regulates pyruvate dehydrogenase complex; transcriptional regulator PdhR 128321..129085 Escherichia coli S88 7129035 YP_002389969.1 CDS ECS88_0122 NC_011742.1 129082 129264 R Evidence 6 : Doubtful CDS; hypothetical protein complement(129082..129264) Escherichia coli S88 7133501 YP_002389970.1 CDS aceE NC_011742.1 129246 131909 D E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC; pyruvate dehydrogenase subunit E1 129246..131909 Escherichia coli S88 7129036 YP_002389971.1 CDS aceF NC_011742.1 131924 133816 D E2 component of pyruvate dehydrogenase multienzyme complex; in Escherichia coli AceF contains three N-terminal lipoyl domains; dihydrolipoamide acetyltransferase 131924..133816 Escherichia coli S88 7132032 YP_002389972.1 CDS lpd NC_011742.1 134023 135447 D E3 component of pyruvate and 2-oxoglutarate dehydrogenase complex; catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase 134023..135447 Escherichia coli S88 7132033 YP_002389973.1 CDS yacH NC_011742.1 135689 137446 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(135689..137446) Escherichia coli S88 7129375 YP_002389974.1 CDS acnB NC_011742.1 137801 140398 D catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase 137801..140398 Escherichia coli S88 7130262 YP_002389975.1 CDS yacL NC_011742.1 140573 140935 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 2666401, 7567469; hypothetical protein 140573..140935 Escherichia coli S88 7132037 YP_002389976.1 CDS speD NC_011742.1 140973 141767 R S-adenosylmethionine provides the aminopropyl moiety required for spermidine biosynthesis from putrescine; S-adenosylmethionine decarboxylase complement(140973..141767) Escherichia coli S88 7130263 YP_002389977.1 CDS speE NC_011742.1 141783 142649 R catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine; spermidine synthase complement(141783..142649) Escherichia coli S88 7130627 YP_002389978.1 CDS yacC NC_011742.1 142755 143273 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 2666401; hypothetical protein complement(142755..143273) Escherichia coli S88 7130628 YP_002389979.1 CDS cueO NC_011742.1 143268 144818 D laccase; copper-stimulated phenoloxidase and ferroxidase which may be involved in copper detoxification; multicopper oxidase 143268..144818 Escherichia coli S88 7130259 YP_002389980.1 CDS gcd NC_011742.1 144865 147255 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10359647, 11604400, 14612441, 91035240, 93123180, 93286127; Product type e : enzyme; glucose dehydrogenase complement(144865..147255) Escherichia coli S88 7130507 YP_002389981.1 CDS hpt NC_011742.1 147461 147997 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 13808016, 339828, 6787390, 6801015, 12070315; Product type e : enzyme; hypoxanthine phosphoribosyltransferase 147461..147997 Escherichia coli S88 7132193 YP_002389982.1 CDS can NC_011742.1 148038 148700 R catalyzes the interconversion of bicarbonate and carbon dioxide; carbonic anhydrase complement(148038..148700) Escherichia coli S88 7128946 YP_002389983.1 CDS yadG NC_011742.1 148809 149735 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter subunit: ATP-binding component of ABC superfamily 148809..149735 Escherichia coli S88 7129158 YP_002389984.1 CDS yadH NC_011742.1 149732 150502 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10474187; Product type pt : putative transporter; putative transporter subunit: membrane component of ABC superfamily 149732..150502 Escherichia coli S88 7130267 YP_002389985.1 CDS yadI NC_011742.1 150607 151047 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative PTS Enzyme IIA 150607..151047 Escherichia coli S88 7130268 YP_002389986.1 CDS yadE NC_011742.1 151111 152340 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative exported polysaccharide deacetylase 151111..152340 Escherichia coli S88 7130269 YP_002389987.1 CDS panD NC_011742.1 152344 152724 R Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5); aspartate alpha-decarboxylase complement(152344..152724) Escherichia coli S88 7130266 YP_002389988.1 CDS yadD NC_011742.1 152998 153882 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11319082; Product type pe : putative enzyme; putative transposase 152998..153882 Escherichia coli S88 7133159 YP_002389989.1 CDS panC NC_011742.1 153964 154815 R catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine; pantoate--beta-alanine ligase complement(153964..154815) Escherichia coli S88 7130265 YP_002389990.1 CDS panB NC_011742.1 154827 155621 R catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate; 3-methyl-2-oxobutanoate hydroxymethyltransferase complement(154827..155621) Escherichia coli S88 7133158 YP_002389991.1 CDS ECS88_0145 NC_011742.1 155733 157022 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8096212; Product type ps : putative structure; putative fimbrial-like adhesin protein complement(155733..157022) Escherichia coli S88 7133157 YP_002389992.1 CDS ECS88_0146 NC_011742.1 157048 157644 R Evidence 2b : Function of strongly homologous gene; Product type ps : putative structure; protein yadK, putative fimbrial-like adhesin complement(157048..157644) Escherichia coli S88 7129037 YP_002389993.1 CDS ECS88_0147 NC_011742.1 157671 158285 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative fimbrial-like adhesin protein YadL complement(157671..158285) Escherichia coli S88 7129038 YP_002389994.1 CDS ECS88_0148 NC_011742.1 158291 158857 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative fimbrial-like adhesin protein YadM complement(158291..158857) Escherichia coli S88 7129039 YP_002389995.1 CDS htrE NC_011742.1 158874 161462 R similar to the fimbrial usher protein PapC; putative outer membrane usher protein complement(158874..161462) Escherichia coli S88 7129040 YP_002389996.1 CDS ecpD NC_011742.1 161497 162237 R Evidence 2b : Function of strongly homologous gene; PubMedId : 93352405, 8102362, 15561151; Product type f : factor; putative chaperone protein EcpD complement(161497..162237) Escherichia coli S88 7131402 YP_002389997.1 CDS yadN NC_011742.1 162346 162960 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative fimbrial-like adhesin exported protein complement(162346..162960) Escherichia coli S88 7132380 YP_002389998.1 CDS folK NC_011742.1 163298 163777 R catalyzes the formation of 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate from 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine and ATP; 2-amino-4-hydroxy-6-hydroxymethyldihyropteridine pyrophosphokinase complement(163298..163777) Escherichia coli S88 7130270 YP_002389999.1 CDS pcnB NC_011742.1 163774 165192 R Polymerase that creates the 3' poly(A) tail found in some mRNA's; poly(A) polymerase I complement(163774..165192) Escherichia coli S88 7132818 YP_002390000.1 CDS yadB NC_011742.1 165231 166157 R this tRNA synthetase lacks the tRNA anticodon interaction domain; instead this enzyme modifies tRNA(Asp) with glutamate by esterifying glutamate to the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of queosine generating a modified nucleoside at the first anticodon position of tRNAAsp; the modified tRNA does not bind elongation factor Tu; glutamyl-Q tRNA(Asp) synthetase complement(165231..166157) Escherichia coli S88 7133179 YP_002390001.1 CDS dksA NC_011742.1 166194 166649 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15294157, 90202727, 2013578, 9298646, 9600841; Product type r : regulator; RNA polymerase-binding transcription factor complement(166194..166649) Escherichia coli S88 7130264 YP_002390002.1 CDS sfsA NC_011742.1 166827 167531 R Regulatory factor involved in maltose metabolism; sugar fermentation stimulation protein A complement(166827..167531) Escherichia coli S88 7130214 YP_002390003.1 CDS ligT NC_011742.1 167546 168076 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 97094878; Product type e : enzyme; 2'-5' RNA ligase complement(167546..168076) Escherichia coli S88 7130585 YP_002390004.1 CDS hrpB NC_011742.1 168150 170579 D similar in sequence to the ATP-dependent RNA helicase HrpA; ATP-dependent RNA helicase HrpB 168150..170579 Escherichia coli S88 7129355 YP_002390005.1 CDS mrcB NC_011742.1 170673 173207 D bifunctional periplasmic enzyme; contains transglycosylase and transpeptidase activity; major enzyme for peptidoglycan biosynthesis in Escherichia coli; transmembrane protein; forms dimers; three variants, one of which may be a degradation product, while the other appears to result from an alternative initiation site, are found within the cell; penicillin-binding protein 1b 170673..173207 Escherichia coli S88 7131390 YP_002390006.1 CDS fhuA NC_011742.1 173427 175670 D involved with the transport of ferrichrome across the outer membrane; binds the ferrichrome-iron ligand and interacts with the TonB protein; ferrichrome outer membrane transporter 173427..175670 Escherichia coli S88 7129606 YP_002390007.1 CDS fhuC NC_011742.1 175721 176518 D part of the FhuBCD ATP-dependent iron (III) hydroxamate transporter; iron-hydroxamate transporter ATP-binding subunit 175721..176518 Escherichia coli S88 7129482 YP_002390008.1 CDS fhuD NC_011742.1 176518 177408 D Part of the FhuBCD ATP-dependent iron (III) hydroxamate transporter; binds to all hydroxamate siderophores; iron-hydroxamate transporter substrate-binding subunit 176518..177408 Escherichia coli S88 7129484 YP_002390009.1 CDS fhuB NC_011742.1 177405 179387 D part of the FhuBCD ATP-dependent iron (III) hydroxamate transporter involved in the high-affinity transport of Fe(3+)-ferrichrome; iron-hydroxamate transporter permease subunit 177405..179387 Escherichia coli S88 7129485 YP_002390010.1 CDS hemL NC_011742.1 179422 180702 R Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway; glutamate-1-semialdehyde aminotransferase complement(179422..180702) Escherichia coli S88 7129483 YP_002390011.1 CDS clcA NC_011742.1 180927 182348 D Acts as an electrical shunt for an outwardly-directed proton pump that is linked to amino acid decarboxylation; chloride channel protein 180927..182348 Escherichia coli S88 7128904 YP_002390012.1 CDS yadR NC_011742.1 182430 182774 D essential respiratory protein A; may be involved in the transfer of iron-sulfur clusters; essential for growth using oxygen or alternate electron acceptors; iron-sulfur cluster insertion protein ErpA 182430..182774 Escherichia coli S88 7131925 YP_002390013.1 CDS yadS NC_011742.1 182821 183444 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(182821..183444) Escherichia coli S88 7130271 YP_002390014.1 CDS btuF NC_011742.1 183482 184282 R solute binding component of the vitamin B12 transport system BtuCDF; vitamin B12-transporter protein BtuF complement(183482..184282) Escherichia coli S88 7130272 YP_002390015.1 CDS pfs NC_011742.1 184275 184973 R enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine; 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase complement(184275..184973) Escherichia coli S88 7129140 YP_002390016.1 CDS dgt NC_011742.1 185057 186574 D forms a homotetramer; requires magnesium for activity; catalyzes the hydrolysis of dGTP to form deoxyguanosine and triphosphate; deoxyguanosinetriphosphate triphosphohydrolase 185057..186574 Escherichia coli S88 7133684 YP_002390017.1 CDS degP NC_011742.1 186704 188128 D protease Do; required at high temperature; degrades damaged proteins; serine endoprotease 186704..188128 Escherichia coli S88 7130199 YP_002390018.1 CDS cdaR NC_011742.1 188306 189436 D regulates the expression of the operons for the enzymes involved in galactarate, glucarate and glycerate utilization; carbohydrate diacid transcriptional activator CdaR 188306..189436 Escherichia coli S88 7130181 YP_002390019.1 CDS yaeH NC_011742.1 189490 189876 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(189490..189876) Escherichia coli S88 7129175 YP_002390020.1 CDS dapD NC_011742.1 190188 191012 R catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway; 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase complement(190188..191012) Escherichia coli S88 7130275 YP_002390021.1 CDS glnD NC_011742.1 191043 193715 R catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein; PII uridylyl-transferase complement(191043..193715) Escherichia coli S88 7130566 YP_002390022.1 CDS map NC_011742.1 193777 194571 R catalyzes the removal of N-terminal amino acids from peptides and arylamides; generally Co(II) however activity has been shown for some methionine aminopeptidases with Zn, Fe, or Mn; methionine aminopeptidase complement(193777..194571) Escherichia coli S88 7130006 YP_002390023.1 CDS rpsB NC_011742.1 194939 195664 D 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; 30S ribosomal protein S2 194939..195664 Escherichia coli S88 7131254 YP_002390024.1 CDS tsf NC_011742.1 195799 196650 D 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; elongation factor Ts 195799..196650 Escherichia coli S88 7133785 YP_002390025.1 CDS pyrH NC_011742.1 196797 197522 D Catalyzes the phosphorylation of UMP to UDP; uridylate kinase 196797..197522 Escherichia coli S88 7130358 YP_002390026.1 CDS frr NC_011742.1 197672 198229 D 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; ribosome recycling factor 197672..198229 Escherichia coli S88 7131769 YP_002390027.1 CDS dxr NC_011742.1 198321 199517 D catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate; 1-deoxy-D-xylulose 5-phosphate reductoisomerase 198321..199517 Escherichia coli S88 7132833 YP_002390028.1 CDS ispU NC_011742.1 199703 200464 D catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate; undecaprenyl pyrophosphate synthase 199703..200464 Escherichia coli S88 7132369 YP_002390029.1 CDS cdsA NC_011742.1 200477 201334 D catalyzes the synthesis of CDP-diglyceride from CTP and phosphatidate; CDP-diglyceride synthase 200477..201334 Escherichia coli S88 7130425 YP_002390030.1 CDS yaeL NC_011742.1 201346 202698 D catalyzes the cleavage of RseA which activates the sigmaE-mediated stress response; zinc metallopeptidase RseP 201346..202698 Escherichia coli S88 7129178 YP_002390031.1 CDS yaeT NC_011742.1 202728 205160 D part of a complex with YfgL, YfiO, and NlpB involved in outer membrane protein biosynthesis; involved in the assembly of outer membrane proteins; outer membrane protein assembly factor YaeT 202728..205160 Escherichia coli S88 7130277 YP_002390032.1 CDS hlpA NC_011742.1 205282 205767 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15101556, 90201355, 97032152, 99386928, 1987124, 2843433, 9298646, 2167239; Product type f : factor; periplasmic chaperone 205282..205767 Escherichia coli S88 7130281 YP_002390033.1 CDS lpxD NC_011742.1 205771 206796 D adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis; UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase 205771..206796 Escherichia coli S88 7128933 YP_002390034.1 CDS fabZ NC_011742.1 206901 207356 D in Pseudomonas aeruginosa this enzyme is a trimer of dimers; essential for membrane formation; performs third step of type II fatty acid biosynthesis; catalyzes dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP; (3R)-hydroxymyristoyl-ACP dehydratase 206901..207356 Escherichia coli S88 7129383 YP_002390035.1 CDS lpxA NC_011742.1 207360 208148 D catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis; UDP-N-acetylglucosamine acyltransferase 207360..208148 Escherichia coli S88 7129439 YP_002390036.1 CDS lpxB NC_011742.1 208148 209296 D catalyzes the formation of lipid A disaccharide from UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate, lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM; lipid-A-disaccharide synthase 208148..209296 Escherichia coli S88 7129380 YP_002390037.1 CDS rnhB NC_011742.1 209293 209889 D RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids; ribonuclease HII 209293..209889 Escherichia coli S88 7129381 YP_002390038.1 CDS dnaE NC_011742.1 209926 213408 D catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase; DNA polymerase III subunit alpha 209926..213408 Escherichia coli S88 7132749 YP_002390039.1 CDS accA NC_011742.1 213421 214380 D catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein; acetyl-CoA carboxylase carboxyltransferase subunit alpha 213421..214380 Escherichia coli S88 7130223 YP_002390040.1 CDS ldcC NC_011742.1 214478 216619 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 97480927, 98195734, 98357244, 9226257, 9723924; Product type e : enzyme; lysine decarboxylase 2, constitutive 214478..216619 Escherichia coli S88 7132026 YP_002390041.1 CDS yaeR NC_011742.1 216676 217065 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein 216676..217065 Escherichia coli S88 7130476 YP_002390042.1 CDS tilS NC_011742.1 217130 218428 D Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU; ATP-dependent; responsible for modifying the wobble-base of the CAU anticodon of tRNAIle such that it exhibits proper recognition of the AUA codon rather than the AUG codon and is in turn properly recognized by isoleucyl-tRNA synthetase; tRNA(Ile)-lysidine synthetase 217130..218428 Escherichia coli S88 7130280 YP_002390043.1 CDS rof NC_011742.1 218476 218736 R Suppresses temperature-sensitive mutations in essential genes by modulating rho-dependent transcription termination; Rho-binding antiterminator complement(218476..218736) Escherichia coli S88 7133474 YP_002390044.1 CDS yaeP NC_011742.1 218723 218923 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(218723..218923) Escherichia coli S88 7132756 YP_002390045.1 CDS yaeQ NC_011742.1 219089 219634 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 219089..219634 Escherichia coli S88 7130278 YP_002390046.1 CDS yaeJ NC_011742.1 219631 220053 D Evidence 4 : Homologs of previously reported genes of unknown function; peptidyl-tRNA hydrolase domain protein 219631..220053 Escherichia coli S88 7130279 YP_002390047.1 CDS nlpE NC_011742.1 220067 220777 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11830644, 95362641, 95362642; Product type lp : lipoprotein; lipoprotein involved with copper homeostasis and adhesion 220067..220777 Escherichia coli S88 7130276 YP_002390048.1 CDS yaeF NC_011742.1 220933 221757 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; hypothetical protein complement(220933..221757) Escherichia coli S88 7129724 YP_002390049.1 CDS proS NC_011742.1 221810 223528 R catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase complement(221810..223528) Escherichia coli S88 7130274 YP_002390050.1 CDS yaeB NC_011742.1 223639 224346 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(223639..224346) Escherichia coli S88 7130789 YP_002390051.1 CDS rcsF NC_011742.1 224343 224747 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 93094132; Product type pr : putative regulator; outer membrane lipoprotein complement(224343..224747) Escherichia coli S88 7130273 YP_002390052.1 CDS metQ NC_011742.1 224865 225680 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12169620, 12218041, 12819857, 1459951; Product type t : transporter; DL-methionine transporter substrate-binding subunit complement(224865..225680) Escherichia coli S88 7131798 YP_002390053.1 CDS metI NC_011742.1 225720 226373 R part of the MetNIQ methionine uptake system; DL-methionine transporter permease subunit complement(225720..226373) Escherichia coli S88 7128823 YP_002390054.1 CDS metN NC_011742.1 226366 227397 R part of the metNIQ transport system for methionine; DL-methionine transporter ATP-binding subunit complement(226366..227397) Escherichia coli S88 7128817 YP_002390055.1 CDS gmhB NC_011742.1 227585 228157 D Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate intermediate into D-glycero-beta-D-manno-heptose 1-phosphate; D,D-heptose 1,7-bisphosphate phosphatase 227585..228157 Escherichia coli S88 7128822 YP_002390056.1 CDS dkgB NC_011742.1 233914 234717 D catalyzes the reduction of 2,5-diketo-D-gluconic acid to 2-keto-L-gulonic acid; 2,5-diketo-D-gluconate reductase B 233914..234717 Escherichia coli S88 7129888 YP_002390057.1 CDS yafC NC_011742.1 234714 235628 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(234714..235628) Escherichia coli S88 7130213 YP_002390058.1 CDS yafD NC_011742.1 235869 236669 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 1663890; hypothetical protein 235869..236669 Escherichia coli S88 7130282 YP_002390059.1 CDS yafE NC_011742.1 236747 237517 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative S-adenosyl-L-methionine-dependent methyltransferase 236747..237517 Escherichia coli S88 7130283 YP_002390060.1 CDS mltD NC_011742.1 237564 238922 R catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine residues; may play a role in recycling muropeptides during cell division and/or cell elongation; in Helicobacter pylori MltD is a endolytic transglycosylase involved mainly in the rearrangement of the peptidoglycan layer of the bacterial cell wall; membrane-bound lytic murein transglycosylase D complement(237564..238922) Escherichia coli S88 7130284 YP_002390061.1 CDS gloB NC_011742.1 238994 239749 R catalyzes the hydrolysis of S-D-lactoylglutathione to D-lactic acid and reduced glutathione; plays an important role in cellular detoxification using glutathione; hydroxyacylglutathione hydrolase complement(238994..239749) Escherichia coli S88 7128845 YP_002390062.1 CDS yafS NC_011742.1 239783 240505 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative S-adenosyl-L-methionine-dependent methyltransferase 239783..240505 Escherichia coli S88 7130016 YP_002390063.1 CDS rnhA NC_011742.1 240502 240969 R An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids; ribonuclease H complement(240502..240969) Escherichia coli S88 7130292 YP_002390064.1 CDS dnaQ NC_011742.1 241034 241765 D 3'-5' exonuclease of DNA polymerase III; DNA polymerase III subunit epsilon 241034..241765 Escherichia coli S88 7132748 YP_002390065.1 CDS yafT NC_011742.1 242303 243088 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative aminopeptidase 242303..243088 Escherichia coli S88 7129899 YP_002390066.1 CDS ECS88_0232 NC_011742.1 243428 243928 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(243428..243928) Escherichia coli S88 7130293 YP_002390067.1 CDS ECS88_0233 NC_011742.1 243925 245424 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(243925..245424) Escherichia coli S88 7129041 YP_002390068.1 CDS ECS88_0234 NC_011742.1 245294 248821 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; hypothetical protein complement(245294..248821) Escherichia coli S88 7129042 YP_002390069.1 CDS ECS88_0235 NC_011742.1 248841 250349 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec29, contains a TPR-like_helical domain complement(248841..250349) Escherichia coli S88 7129043 YP_002390070.1 CDS ECS88_0236 NC_011742.1 250288 251031 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec28 complement(250288..251031) Escherichia coli S88 7129044 YP_002390071.1 CDS ECS88_0237 NC_011742.1 251028 253787 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative ATP-dependent Clp proteinase Aec27 ATP-binding chain, with chaperone activity complement(251028..253787) Escherichia coli S88 7129045 YP_002390072.1 CDS ECS88_0238 NC_011742.1 253797 254561 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; Putative membrane protein Aec26 complement(253797..254561) Escherichia coli S88 7129046 YP_002390073.1 CDS ECS88_0239 NC_011742.1 254566 255912 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec25 complement(254566..255912) Escherichia coli S88 7129047 YP_002390074.1 CDS ECS88_0240 NC_011742.1 255915 256439 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec24; putative lipoprotein complement(255915..256439) Escherichia coli S88 7129048 YP_002390075.1 CDS ECS88_0241 NC_011742.1 256436 257878 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec23, contains FHA domain complement(256436..257878) Escherichia coli S88 7129049 YP_002390076.1 CDS ECS88_0242 NC_011742.1 257733 258782 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec22 complement(257733..258782) Escherichia coli S88 7129050 YP_002390077.1 CDS ECS88_0243 NC_011742.1 258746 260605 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec21 complement(258746..260605) Escherichia coli S88 7129051 YP_002390078.1 CDS ECS88_0244 NC_011742.1 260593 261018 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec19 complement(260593..261018) Escherichia coli S88 7129052 YP_002390079.1 CDS ECS88_0245 NC_011742.1 261023 262507 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec18 complement(261023..262507) Escherichia coli S88 7129053 YP_002390080.1 CDS ECS88_0246 NC_011742.1 262530 263084 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec17 complement(262530..263084) Escherichia coli S88 7129054 YP_002390081.1 CDS ECS88_0247 NC_011742.1 263739 264257 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 263739..264257 Escherichia coli S88 7129055 YP_002390082.1 CDS ECS88_0248 NC_011742.1 264478 266460 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec15, putative VgrG/E protein associated with Rhs elements 264478..266460 Escherichia coli S88 7129056 YP_002390083.1 CDS ECS88_0249 NC_011742.1 266567 267613 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec14 266567..267613 Escherichia coli S88 7129057 YP_002390084.1 CDS ECS88_0250 NC_011742.1 267606 269045 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein (fused Aec13 and Aec 12) 267606..269045 Escherichia coli S88 7129058 YP_002390085.1 CDS ECS88_0251 NC_011742.1 269020 269310 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec11 269020..269310 Escherichia coli S88 7129059 YP_002390086.1 CDS ECS88_0252 NC_011742.1 269568 269747 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative H-repeat associated protein 269568..269747 Escherichia coli S88 7129060 YP_002390087.1 CDS ECS88_0253 NC_011742.1 269847 270332 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative transposase 269847..270332 Escherichia coli S88 7129061 YP_002390088.1 CDS ECS88_0254 NC_011742.1 270561 271064 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 270561..271064 Escherichia coli S88 7129062 YP_002390089.1 CDS ECS88_0255 NC_011742.1 271134 271646 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein Aec7 271134..271646 Escherichia coli S88 7129063 YP_002390090.1 CDS yafV NC_011742.1 271917 272687 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8526497; Product type pe : putative enzyme; hypothetical protein complement(271917..272687) Escherichia coli S88 7129064 YP_002390091.1 CDS ivy NC_011742.1 272841 273314 D inactivates vertebrate C-type lysozyme; C-lysozyme inhibitor 272841..273314 Escherichia coli S88 7130294 YP_002390092.1 CDS fadE NC_011742.1 273357 275801 R functions in fatty acid oxidation; converts acyl-CoA and FAD to FADH2 and delta2-enoyl-CoA; acyl-CoA dehydrogenase complement(273357..275801) Escherichia coli S88 7130429 YP_002390093.1 CDS gmhA NC_011742.1 276041 276619 D catalyzes the isomerization of sedoheptulose 7-phosphate to D-glycero-D-manno-heptose 7-phosphate; phosphoheptose isomerase 276041..276619 Escherichia coli S88 7129443 YP_002390094.1 CDS yafJ NC_011742.1 276824 277591 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative glutamine amidotransferases class-II 276824..277591 Escherichia coli S88 7129374 YP_002390095.1 CDS yafK NC_011742.1 277562 278302 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(277562..278302) Escherichia coli S88 7130285 YP_002390096.1 CDS yafL NC_011742.1 278605 279363 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative exported hydrolase 278605..279363 Escherichia coli S88 7130286 YP_002390097.1 CDS yafM NC_011742.1 279539 280036 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 279539..280036 Escherichia coli S88 7130287 YP_002390098.1 CDS fhiA NC_011742.1 280356 282095 R Evidence 7 : Gene remnant; Product type s : structure; flagellar system protein complement(280356..282095) Escherichia coli S88 7130288 YP_002390099.1 CDS mbhA NC_011742.1 281935 282825 D Evidence 2b : Function of strongly homologous gene; PubMedId : 15687208; Product type s : structure; hypothetical protein 281935..282825 Escherichia coli S88 7129480 YP_002390100.1 CDS dinB NC_011742.1 282896 283951 D involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function; DNA polymerase IV 282896..283951 Escherichia coli S88 7129429 YP_002390101.1 CDS yafN NC_011742.1 284003 284296 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12813093, 14594833; Product type pf : putative factor; putative antitoxin of the YafO-YafN toxin-antitoxin system 284003..284296 Escherichia coli S88 7130205 YP_002390102.1 CDS yafO NC_011742.1 284299 284697 D YafO overproduction induces toxicity; it is believed to be the toxin of a toxin-antitoxin pair; unknown function; putative toxin YafO 284299..284697 Escherichia coli S88 7130289 YP_002390103.1 CDS yafP NC_011742.1 284707 285159 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12813093; Product type pe : putative enzyme; hypothetical protein 284707..285159 Escherichia coli S88 7130290 YP_002390104.1 CDS ECS88_0270 NC_011742.1 285337 286488 D mutations in this gene result in a compromised ability for drug-inducible mexXY expression; expression is inducible by the same ribosome-targeting agents that induce mexXY; hypothetical protein 285337..286488 Escherichia coli S88 7130291 YP_002390105.1 CDS prfH NC_011742.1 286599 287099 D similar to release factor 1 and 2; peptide chain release factor-like protein 286599..287099 Escherichia coli S88 7129065 YP_002390106.1 CDS pepD NC_011742.1 287156 288613 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1695895, 21101837, 88121730, 92204123, 2651887; Product type e : enzyme; aminoacyl-histidine dipeptidase (peptidase D) complement(287156..288613) Escherichia coli S88 7130775 YP_002390107.1 CDS gpt NC_011742.1 288874 289332 D catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively; xanthine-guanine phosphoribosyltransferase 288874..289332 Escherichia coli S88 7133671 YP_002390108.1 CDS frsA NC_011742.1 289424 290668 D forms a 1:1 complex with the unphosphorylated from of enzyme IIAGlc; FrsA may promote fermentation; fermentation/respiration switch protein 289424..290668 Escherichia coli S88 7130065 YP_002390109.1 CDS crl NC_011742.1 290726 291127 D involved in the expression of csgBA which is involved in curli formation; interacts with sigmaS; DNA-binding transcriptional regulator Crl 290726..291127 Escherichia coli S88 7132834 YP_002390110.1 CDS phoE NC_011742.1 291237 292292 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89178658, 89380253, 92219258, 98090453, 1380671, 1848301, 1848682, 6089111, 6341601, 7679770; Product type t : transporter; outer membrane phosphoporin protein E complement(291237..292292) Escherichia coli S88 7131964 YP_002390111.1 CDS proB NC_011742.1 292581 293684 D catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis; gamma-glutamyl kinase 292581..293684 Escherichia coli S88 7133724 YP_002390112.1 CDS proA NC_011742.1 293696 294949 D Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase 293696..294949 Escherichia coli S88 7130785 YP_002390113.1 CDS ECS88_0279 NC_011742.1 295294 295632 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; CP4-like integrase 295294..295632 Escherichia coli S88 7129910 YP_002390114.1 CDS vat NC_011742.1 296717 300847 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12933851, 16081954; Product type e : enzyme; Vacuolating autotransporter toxin complement(296717..300847) Escherichia coli S88 7129066 YP_002390115.1 CDS ECS88_0281 NC_011742.1 301440 301655 D Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase InsA (ORF1) IS1 301440..301655 Escherichia coli S88 7132472 YP_002390116.1 CDS ECS88_0282 NC_011742.1 301957 302133 D Evidence 7 : Gene remnant; Product type pe : putative enzyme; transposase InsB (ORF1) IS1 (Fragment) 301957..302133 Escherichia coli S88 7129067 YP_002390117.1 CDS ECS88_0283 NC_011742.1 302512 302742 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 302512..302742 Escherichia coli S88 7129068 YP_002390118.1 CDS yagU NC_011742.1 302957 303571 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 302957..303571 Escherichia coli S88 7129069 YP_002390119.1 CDS yagV NC_011742.1 304456 305166 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(304456..305166) Escherichia coli S88 7130295 YP_002390120.1 CDS yagW NC_011742.1 305135 306778 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative surface or exported protein complement(305135..306778) Escherichia coli S88 7130296 YP_002390121.1 CDS yagX NC_011742.1 306768 309293 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(306768..309293) Escherichia coli S88 7130297 YP_002390122.1 CDS yagY NC_011742.1 309319 309987 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(309319..309987) Escherichia coli S88 7130298 YP_002390123.1 CDS ecpA NC_011742.1 310044 310631 R Evidence 2b : Function of strongly homologous gene; PubMedId : 17563352, 11466275; Product type s : structure; common pilus ECP complement(310044..310631) Escherichia coli S88 7130299 YP_002390124.1 CDS ykgK NC_011742.1 310705 311295 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator complement(310705..311295) Escherichia coli S88 7132379 YP_002390125.1 CDS rpmE2 NC_011742.1 312471 312734 R 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; 50S ribosomal protein L31 type B complement(312471..312734) Escherichia coli S88 7131100 YP_002390126.1 CDS ECS88_0294 NC_011742.1 313674 314816 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative NADH-dependent flavin oxidoreductase complement(313674..314816) Escherichia coli S88 7131101 YP_002390127.1 CDS ECS88_0295 NC_011742.1 314988 315908 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(314988..315908) Escherichia coli S88 7129070 YP_002390128.1 CDS ECS88_0296 NC_011742.1 316002 316991 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative LysR-like transcriptional regulator 316002..316991 Escherichia coli S88 7129071 YP_002390129.1 CDS ECS88_0297 NC_011742.1 317116 318084 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator, lysR family 317116..318084 Escherichia coli S88 7129072 YP_002390130.1 CDS ECS88_0298 NC_011742.1 318115 319104 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative aldo-keto reductase complement(318115..319104) Escherichia coli S88 7129073 YP_002390131.1 CDS ECS88_0299 NC_011742.1 319131 319982 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 17575004; Product type pe : putative enzyme; putative aldo-keto reductase complement(319131..319982) Escherichia coli S88 7129074 YP_002390132.1 CDS ECS88_0300 NC_011742.1 320548 324798 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative adhesin 320548..324798 Escherichia coli S88 7129075 YP_002390133.1 CDS ykgA NC_011742.1 324923 325780 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; Putatve transcriptional regulator ykgA complement(324923..325780) Escherichia coli S88 7129076 YP_002390134.1 CDS ECS88_0302 NC_011742.1 326013 326897 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative reductase 326013..326897 Escherichia coli S88 7131091 YP_002390135.1 CDS ykgB NC_011742.1 327057 327650 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(327057..327650) Escherichia coli S88 7129077 YP_002390136.1 CDS ykgI NC_011742.1 327662 327898 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(327662..327898) Escherichia coli S88 7131092 YP_002390137.1 CDS ykgC NC_011742.1 328007 329332 R Involved in disulfide oxidoreductase activity and electron transport; pyridine nucleotide-disulfide oxidoreductase complement(328007..329332) Escherichia coli S88 7131099 YP_002390138.1 CDS ykgD NC_011742.1 329559 330413 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative AraC-type DNA-binding transcriptional regulator 329559..330413 Escherichia coli S88 7131093 YP_002390139.1 CDS ykgE NC_011742.1 330940 331659 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative hydroxyacid oxidoreductase (Fe-S centre) 330940..331659 Escherichia coli S88 7131094 YP_002390140.1 CDS ykgF NC_011742.1 331670 333097 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase subunit with NAD(P)-binding domain and ferridoxin-like domain 331670..333097 Escherichia coli S88 7131095 YP_002390141.1 CDS ykgG NC_011742.1 333090 333785 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 333090..333785 Escherichia coli S88 7131096 YP_002390142.1 CDS ECS88_0310 NC_011742.1 333859 334056 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(333859..334056) Escherichia coli S88 7131097 YP_002390143.1 CDS ykgH NC_011742.1 334028 334696 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(334028..334696) Escherichia coli S88 7129078 YP_002390144.1 CDS ECS88_0312 NC_011742.1 334880 337210 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; Putative adhesin; putative outer membrane autotransporter barrel complement(334880..337210) Escherichia coli S88 7131098 YP_002390145.1 CDS ECS88_0313 NC_011742.1 337219 337980 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(337219..337980) Escherichia coli S88 7129079 YP_002390146.1 CDS ECS88_0315 NC_011742.1 338134 338928 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcription regulator; LuxR-type HTH domain complement(338134..338928) Escherichia coli S88 7129080 YP_002390147.1 CDS ECS88_0317 NC_011742.1 339258 339860 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; Putative DNA recombinase complement(339258..339860) Escherichia coli S88 7129081 YP_002390148.1 CDS ECS88_0318 NC_011742.1 340586 340867 D Evidence 6 : Doubtful CDS; hypothetical protein 340586..340867 Escherichia coli S88 7129082 YP_002390149.1 CDS betA NC_011742.1 340892 342580 R catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine; choline dehydrogenase complement(340892..342580) Escherichia coli S88 7129083 YP_002390150.1 CDS betB NC_011742.1 342594 344066 R catalyzes the formation of betaine from betaine aldehyde; betaine aldehyde dehydrogenase complement(342594..344066) Escherichia coli S88 7130002 YP_002390151.1 CDS betI NC_011742.1 344080 344667 R HTH-type; bet1; Repressor involved in choline regulation of the bet genes; transcriptional regulator BetI complement(344080..344667) Escherichia coli S88 7130003 YP_002390152.1 CDS betT NC_011742.1 344796 346829 D proton-motive-force-driven choline transporter; choline transport protein BetT 344796..346829 Escherichia coli S88 7129108 YP_002390153.1 CDS ECS88_0323 NC_011742.1 347198 347386 R Evidence 6 : Doubtful CDS; hypothetical protein complement(347198..347386) Escherichia coli S88 7129110 YP_002390154.1 CDS yahA NC_011742.1 347707 348795 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15995192; Product type e : enzyme; cyclic di-GMP phosphodiesterase 347707..348795 Escherichia coli S88 7129084 YP_002390155.1 CDS yahB NC_011742.1 348837 349769 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(348837..349769) Escherichia coli S88 7130300 YP_002390156.1 CDS yahC NC_011742.1 349861 350358 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(349861..350358) Escherichia coli S88 7130301 YP_002390157.1 CDS yahD NC_011742.1 350616 351221 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative protein with ankyrin domain 350616..351221 Escherichia coli S88 7130302 YP_002390158.1 CDS yahE NC_011742.1 351261 352124 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 351261..352124 Escherichia coli S88 7130303 YP_002390159.1 CDS yahF NC_011742.1 352114 353661 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative enzyme with acyl-CoA domain 352114..353661 Escherichia coli S88 7130304 YP_002390160.1 CDS yahG NC_011742.1 353661 355079 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 353661..355079 Escherichia coli S88 7130305 YP_002390161.1 CDS yahI NC_011742.1 355233 356183 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7711027, 11523892; Product type pe : putative enzyme; putative carbamate kinase 355233..356183 Escherichia coli S88 7130306 YP_002390162.1 CDS yahJ NC_011742.1 356193 357575 D metallo-dependent hydrolase superfamily; deaminase with metallo-dependent hydrolase domain; putative deaminase 356193..357575 Escherichia coli S88 7130307 YP_002390163.1 CDS ECS88_0333 NC_011742.1 357843 358283 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 357843..358283 Escherichia coli S88 7130308 YP_002390164.1 CDS ECS88_0334 NC_011742.1 358534 359520 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative periplasmic binding protein, substrate ribose (sugar-binding protein), ABC-type transport system 358534..359520 Escherichia coli S88 7129085 YP_002390165.1 CDS ECS88_0335 NC_011742.1 359554 361053 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; Putative ATP-binding component of ABC sugar transport system 359554..361053 Escherichia coli S88 7129086 YP_002390166.1 CDS ECS88_0336 NC_011742.1 361046 362017 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative permease component of sugar ABC transport system 361046..362017 Escherichia coli S88 7129087 YP_002390167.1 CDS ECS88_0337 NC_011742.1 361984 362970 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative permease component of sugar ABC transport system 361984..362970 Escherichia coli S88 7129088 YP_002390168.1 CDS yahK NC_011742.1 363057 364106 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase, Zn-dependent and NAD(P)-binding 363057..364106 Escherichia coli S88 7129089 YP_002390169.1 CDS yahM NC_011742.1 364728 364973 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 364728..364973 Escherichia coli S88 7129921 YP_002390170.1 CDS yahN NC_011742.1 364990 365661 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12879215; Product type t : transporter; neutral amino-acid efflux system complement(364990..365661) Escherichia coli S88 7130310 YP_002390171.1 CDS yahO NC_011742.1 365808 366083 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 365808..366083 Escherichia coli S88 7130311 YP_002390172.1 CDS prpR NC_011742.1 366184 367770 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9325432, 15805526; Product type r : regulator; DNA-binding transcriptional activator complement(366184..367770) Escherichia coli S88 7130312 YP_002390173.1 CDS prpB NC_011742.1 368009 368899 D catalyzes the formation of pyruvate and succinate from 2-methylisocitrate; 2-methylisocitrate lyase 368009..368899 Escherichia coli S88 7130798 YP_002390174.1 CDS prpC NC_011742.1 368944 370113 D catalyzes the synthesis of 2-methylcitrate from propionyl-CoA and oxaloacetate; also catalyzes the condensation of oxaloacetate with acetyl-CoA but with a lower specificity; methylcitrate synthase 368944..370113 Escherichia coli S88 7130794 YP_002390175.1 CDS prpD NC_011742.1 370147 371598 D functions in propionate metabolism; involved in isomerization of (2S,3S)-methylcitrate to (2R,3S)-methylisocitrate; also encodes minor aconitase or dehydratase activity; aconitase C; 2-methylcitrate dehydratase 370147..371598 Escherichia coli S88 7130795 YP_002390176.1 CDS prpE NC_011742.1 371638 373524 D catalyzes the formation of propionyl-CoA using propionate as a substrate; PrpE from Ralstonia solanacearum can produce acetyl-, propionyl-, butyryl- and acrylyl-coenzyme A, and Salmonella enterica produces propionyl- and butyryl-coenzyme A; not expressed in Escherichia coli when grown on propionate/minimal media; ATP-dependent; propionyl-CoA synthetase 371638..373524 Escherichia coli S88 7130796 YP_002390177.1 CDS codB NC_011742.1 373849 375108 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92349961; Product type t : transporter; cytosine permease 373849..375108 Escherichia coli S88 7130797 YP_002390178.1 CDS codA NC_011742.1 375098 376381 D Catalyzes the deamination of cytosine to uracil and ammonia; cytosine deaminase 375098..376381 Escherichia coli S88 7131946 YP_002390179.1 CDS lacA NC_011742.1 376502 377113 R transfers acetyl group from acetyl-CoA to the 6-hydroxyl of galactopyranosides; exact physiological role is unknown; galactoside O-acetyltransferase complement(376502..377113) Escherichia coli S88 7131945 YP_002390180.1 CDS lacY NC_011742.1 377179 378432 R lactose/proton symporter; mediates lactose/proton symport through the membrane by utilizing the proton gradient to drive transport of galactosides; member of major facilitator superfamily; functions as a monomer with 12 transmembrane segments; galactoside permease complement(377179..378432) Escherichia coli S88 7130470 YP_002390181.1 CDS lacZ NC_011742.1 378484 381558 R forms a homotetramer; hydrolyzes lactose disaccharide to galactose and glucose; converts lactose to allolactose which is the natural inducer of the lac operon; beta-D-galactosidase complement(378484..381558) Escherichia coli S88 7130472 YP_002390182.1 CDS lacI NC_011742.1 381681 382763 R transcriptional repressor of lac operon; forms a homotetramer as a dimer of dimers; binds specific sites in lac operon resulting in DNA looping between the operators; binds allolactose as inducer; lac repressor complement(381681..382763) Escherichia coli S88 7130473 YP_002390183.1 CDS yaiL NC_011742.1 382965 383504 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15115803, 12878731, 13129938; Product type e : enzyme; nucleoprotein/polynucleotide-associated enzyme 382965..383504 Escherichia coli S88 7130471 YP_002390184.1 CDS frmB NC_011742.1 383730 384563 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16567800, 15466022; Product type e : enzyme; S-formylglutathione hydrolase complement(383730..384563) Escherichia coli S88 7130318 YP_002390185.1 CDS frmA NC_011742.1 384656 385765 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15466022, 87172301, 1731906; Product type e : enzyme; alcohol dehydrogenase class III/glutathione-dependent formaldehyde dehydrogenase complement(384656..385765) Escherichia coli S88 7132830 YP_002390186.1 CDS frmR NC_011742.1 385800 386075 R formaldehyde-induced negative regulator of the frmRAB operon; regulator protein FrmR complement(385800..386075) Escherichia coli S88 7132829 YP_002390187.1 CDS yaiO NC_011742.1 386264 387037 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(386264..387037) Escherichia coli S88 7132832 YP_002390188.1 CDS yaiX NC_011742.1 387039 387749 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative transferase complement(387039..387749) Escherichia coli S88 7130319 YP_002390189.1 CDS yaiP NC_011742.1 387598 388794 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative membrane-associated glycosyltransferase complement(387598..388794) Escherichia coli S88 7130324 YP_002390190.1 CDS yaiS NC_011742.1 388804 389475 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(388804..389475) Escherichia coli S88 7130320 YP_002390191.1 CDS tauA NC_011742.1 390083 391045 D with TauB and TauC is responsible for taurine uptake.; taurine transporter substrate binding subunit 390083..391045 Escherichia coli S88 7130321 YP_002390192.1 CDS tauB NC_011742.1 391058 391825 D Part of the ABC transporter complex tauABC involved in taurine import; taurine transporter ATP-binding subunit 391058..391825 Escherichia coli S88 7131267 YP_002390193.1 CDS tauC NC_011742.1 391822 392649 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9401024, 96404792; Product type t : transporter; taurine transporter subunit 391822..392649 Escherichia coli S88 7131268 YP_002390194.1 CDS tauD NC_011742.1 392646 393497 D catalyzes the conversion of taurine (2-aminoethanesulfonate) to sulfite and aminoacetaldehyde concurrently with the conversion of alpha-ketoglutarate to succinate and carbon dioxide; non-heme iron oxidase; allows the use of taurine as an alternative sulfur source; forms homodimers; taurine dioxygenase 392646..393497 Escherichia coli S88 7131269 YP_002390195.1 CDS hemB NC_011742.1 393537 394511 R catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase complement(393537..394511) Escherichia coli S88 7131270 YP_002390196.1 CDS ECS88_0367 NC_011742.1 395037 398024 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative flagellin-like structural protein 395037..398024 Escherichia coli S88 7128897 YP_002390197.1 CDS yaiV NC_011742.1 398065 398733 D Evidence 4 : Homologs of previously reported genes of unknown function; putative DNA-binding transcriptional regulator 398065..398733 Escherichia coli S88 7129090 YP_002390198.1 CDS ampH NC_011742.1 398734 399891 R this protein has no known enzymatic function; beta-lactam binding protein AmpH complement(398734..399891) Escherichia coli S88 7130322 YP_002390199.1 CDS ECS88_0370 NC_011742.1 400029 400223 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 400029..400223 Escherichia coli S88 7133065 YP_002390200.1 CDS sbmA NC_011742.1 400243 401463 D in Escherichia coli SbmA is involved in uptake of microcin J25; functions along with FhuA, TonB, and ExbB/D in this capacity; in Sinorhizobium meliloti, BacA is essential and required for symbiosis; defects appear to affect the cell envelope; transport protein 400243..401463 Escherichia coli S88 7129091 YP_002390201.1 CDS yaiW NC_011742.1 401476 402570 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative lipoprotein 401476..402570 Escherichia coli S88 7131367 YP_002390202.1 CDS yaiY NC_011742.1 402629 402937 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(402629..402937) Escherichia coli S88 7130323 YP_002390203.1 CDS yaiZ NC_011742.1 403065 403409 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 403065..403409 Escherichia coli S88 7130325 YP_002390204.1 CDS ddl NC_011742.1 403433 404527 R 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; D-alanyl-alanine synthetase A complement(403433..404527) Escherichia coli S88 7130326 YP_002390205.1 CDS yaiB NC_011742.1 404989 405249 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 404989..405249 Escherichia coli S88 7130175 YP_002390206.1 CDS phoA NC_011742.1 405350 406765 D Evidence 1b : Function experimentally demonstrated in the studied species; Product type e : enzyme; alkaline phosphatase 405350..406765 Escherichia coli S88 7130314 YP_002390207.1 CDS psiF NC_011742.1 406884 407204 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3533724, 2160940; Product type f : factor; hypothetical protein 406884..407204 Escherichia coli S88 7133722 YP_002390208.1 CDS adrA NC_011742.1 407306 408421 D catalyzes the conversion of 2 GTP into c-di-GMP; adrA overexpression induces cellulose biosynthesis, cell adherence to abiotic surfaces and swimming and swarming motility; AdrA acts post-transcriptionally on the bcsABZC operon activating cellulose biosynthesis; diguanylate cyclase AdrA 407306..408421 Escherichia coli S88 7130802 YP_002390209.1 CDS proC NC_011742.1 408438 409247 R catalyzes the formation of L-proline from pyrroline-5-carboxylate; pyrroline-5-carboxylate reductase complement(408438..409247) Escherichia coli S88 7130315 YP_002390210.1 CDS yaiI NC_011742.1 409367 409825 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 409367..409825 Escherichia coli S88 7130786 YP_002390211.1 CDS aroL NC_011742.1 410008 410532 D type II enzyme similar to type I but differentially regulated and with a lower Km; catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis; shikimate kinase II 410008..410532 Escherichia coli S88 7130317 YP_002390212.1 CDS yaiA NC_011742.1 410582 410773 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 410582..410773 Escherichia coli S88 7129930 YP_002390213.1 CDS aroM NC_011742.1 411031 411708 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 86085675, 3001025; hypothetical protein 411031..411708 Escherichia coli S88 7130313 YP_002390214.1 CDS yaiE NC_011742.1 411780 412064 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 411780..412064 Escherichia coli S88 7129931 YP_002390215.1 CDS ykiA NC_011742.1 412272 412553 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 412272..412553 Escherichia coli S88 7130316 YP_002390216.1 CDS rdgC NC_011742.1 412711 413622 R Required for efficient pilin antigenic variation; recombination associated protein complement(412711..413622) Escherichia coli S88 7131102 YP_002390217.1 CDS mak NC_011742.1 413747 414655 D catalyzes phosphorylation of fructose; cytosolic enzyme; fructokinase 413747..414655 Escherichia coli S88 7131799 YP_002390218.1 CDS araJ NC_011742.1 414924 416108 R member of the major facilitator superfamily (MFS) of transporters; unknown function; may be associated with transport or processing of arabinose polymers; MFS transport protein AraJ complement(414924..416108) Escherichia coli S88 7129405 YP_002390219.1 CDS sbcC NC_011742.1 416234 419377 R with SbcD cleaves DNA hairpin structures; also has 5' single-strand endonuclease activity; exonuclease subunit SbcC complement(416234..419377) Escherichia coli S88 7133088 YP_002390220.1 CDS sbcD NC_011742.1 419374 420576 R with SbcC cleaves DNA hairpin structure, also has 5' single-strand endonuclease activity; exonuclease subunit SbcD complement(419374..420576) Escherichia coli S88 7131365 YP_002390221.1 CDS phoB NC_011742.1 420766 421455 D two component response regulator for the phosphate regulon; PhoR phosphorylates PhoB; transcriptional regulator PhoB 420766..421455 Escherichia coli S88 7131366 YP_002390222.1 CDS phoR NC_011742.1 421513 422808 D membrane-associated histidine protein kinase that phosphorylates phoB in response to environmental signals as part of the two-component phosphate regulatory system phoR/phoB; phosphate regulon sensor protein 421513..422808 Escherichia coli S88 7133723 YP_002390223.1 CDS brnQ NC_011742.1 423215 424534 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 3078876, 6998958, 3550103, 7984428; Product type t : transporter; branched chain amino acid transporter (LIV-II) 423215..424534 Escherichia coli S88 7133728 YP_002390224.1 CDS proY NC_011742.1 424610 425983 D cryptic permease that may be involved in the transport of proline across the inner membrane; in Salmonella typhimurium, the proY gene is silent unless overexpressed on a multicopy plasmid or activated by a proZ mutation; putative proline-specific permease 424610..425983 Escherichia coli S88 7129133 YP_002390225.1 CDS malZ NC_011742.1 426139 427956 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92184757, 1706703, 1918057; Product type e : enzyme; maltodextrin glucosidase 426139..427956 Escherichia coli S88 7130793 YP_002390226.1 CDS acpH NC_011742.1 427961 428542 R Converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine prosthetic group from ACP; acyl carrier protein phosphodiesterase complement(427961..428542) Escherichia coli S88 7129418 YP_002390227.1 CDS queA NC_011742.1 428761 429831 D Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step; S-adenosylmethionine:tRNA ribosyltransferase-isomerase 428761..429831 Escherichia coli S88 7132038 YP_002390228.1 CDS tgt NC_011742.1 429886 431013 D Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr); queuine tRNA-ribosyltransferase 429886..431013 Escherichia coli S88 7131775 YP_002390229.1 CDS yajC NC_011742.1 431036 431368 D member of preprotein translocase; forms a heterotrimer with SecD and SecF; links the SecD/SecF/YajC/YidC complex with the SecY/SecE/SecG complex; preprotein translocase subunit YajC 431036..431368 Escherichia coli S88 7131290 YP_002390230.1 CDS secD NC_011742.1 431396 433243 D 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; preprotein translocase subunit SecD 431396..433243 Escherichia coli S88 7130327 YP_002390231.1 CDS secF NC_011742.1 433254 434225 D 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; preprotein translocase subunit SecF 433254..434225 Escherichia coli S88 7131380 YP_002390232.1 CDS yajD NC_011742.1 434355 434702 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 434355..434702 Escherichia coli S88 7131382 YP_002390233.1 CDS tsx NC_011742.1 434740 435624 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91092502, 91358319, 93352541; Product type m : membrane component; nucleoside channel phage T6/colicin K receptor complement(434740..435624) Escherichia coli S88 7130328 YP_002390234.1 CDS yajI NC_011742.1 435922 436461 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; hypothetical protein complement(435922..436461) Escherichia coli S88 7130361 YP_002390235.1 CDS nrdR NC_011742.1 436612 437061 D Evidence 2b : Function of strongly homologous gene; Product type r : regulator; transcriptional regulator NrdR 436612..437061 Escherichia coli S88 7131147 YP_002390236.1 CDS ribD NC_011742.1 437065 438168 D riboflavin biosynthesis protein which catalyzes the deamination and reduction steps in the riboflavin biosynthesis pathway; catalyzes the formation of 5-amino-6-(5-phosphoribosylamino)uracil from 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and the formation of 5-amino-6-(5-phosphoribosylamino)uracil from 5-amino-6-(5-phosphoribitylamino)uracil; bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase 437065..438168 Escherichia coli S88 7129740 YP_002390237.1 CDS ribH NC_011742.1 438257 438727 D RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not; 6,7-dimethyl-8-ribityllumazine synthase 438257..438727 Escherichia coli S88 7132717 YP_002390238.1 CDS nusB NC_011742.1 438747 439166 D Regulates rRNA biosynthesis by transcriptional antitermination; transcription antitermination protein NusB 438747..439166 Escherichia coli S88 7132718 YP_002390239.1 CDS thiL NC_011742.1 439244 440221 D catalyzes the formation of thiamine diphosphate from thiamine phosphate ant ATP; thiamine monophosphate kinase 439244..440221 Escherichia coli S88 7133117 YP_002390240.1 CDS pgpA NC_011742.1 440199 440717 D hydrolyzes phosphatidylglycerophosphate to produce phosphatidylglycerol and phosphate; phosphatidylglycerophosphatase A 440199..440717 Escherichia coli S88 7131298 YP_002390241.1 CDS yajO NC_011742.1 440771 441745 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15292217, 16077126; Product type e : enzyme; aldoketo-oxidoreductase, NADP-binding complement(440771..441745) Escherichia coli S88 7133694 YP_002390242.1 CDS dxs NC_011742.1 441800 443662 R catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase complement(441800..443662) Escherichia coli S88 7131149 YP_002390243.1 CDS ispA NC_011742.1 443687 444586 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89291702, 91210228; Product type e : enzyme; geranyltranstransferase complement(443687..444586) Escherichia coli S88 7132370 YP_002390244.1 CDS xseB NC_011742.1 444586 444828 R catalyzes the bidirectional exonucleolytic cleavage of DNA; exodeoxyribonuclease VII small subunit complement(444586..444828) Escherichia coli S88 7130418 YP_002390245.1 CDS thiI NC_011742.1 445034 446482 D Required for the synthesis of the thiazole moiety; thiamine biosynthesis protein ThiI 445034..446482 Escherichia coli S88 7132523 YP_002390246.1 CDS yajL NC_011742.1 446536 447126 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 97039868, 99173753, 99311269; DJ-1 family protein complement(446536..447126) Escherichia coli S88 7131297 YP_002390247.1 CDS panE NC_011742.1 447089 448000 R ketopantoate reductase; catalyzes the NADPH reduction of ketopantoate to pantoate; functions in pantothenate (vitamin B5) biosynthesis; 2-dehydropantoate 2-reductase complement(447089..448000) Escherichia coli S88 7131148 YP_002390248.1 CDS yajQ NC_011742.1 448168 448659 D putative nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ; the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription; putative nucleotide-binding protein 448168..448659 Escherichia coli S88 7133160 YP_002390249.1 CDS yajR NC_011742.1 448787 450151 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter, major facilitator family complement(448787..450151) Escherichia coli S88 7131150 YP_002390250.1 CDS cyoE NC_011742.1 450300 451190 R converts protoheme IX and farnesyl diphosphate to heme O; protoheme IX farnesyltransferase complement(450300..451190) Escherichia coli S88 7131151 YP_002390251.1 CDS cyoD NC_011742.1 451202 451531 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90330636, 90366572, 92345252, 9378722, 98021084, 11017202, 2162835; Product type c : carrier; cytochrome o ubiquinol oxidase subunit IV complement(451202..451531) Escherichia coli S88 7130532 YP_002390252.1 CDS cyoC NC_011742.1 451531 452145 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90330636, 92345252, 93349845, 9378722, 98021084, 11017202, 2162835, 2168206; Product type c : carrier; cytochrome o ubiquinol oxidase subunit III complement(451531..452145) Escherichia coli S88 7130531 YP_002390253.1 CDS cyoB NC_011742.1 452135 454126 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90330636, 92345252, 93349845, 9378722, 98021084, 11017202, 2162835, 2168206; Product type c : carrier; cytochrome o ubiquinol oxidase subunit I complement(452135..454126) Escherichia coli S88 7130530 YP_002390254.1 CDS cyoA NC_011742.1 454148 455113 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92112945, 92371427, 9378722, 98021084, 11017202, 1322173, 2162835, 2162837, 2165491, 2168206, 8231804, 8618822; Product type c : carrier; cytochrome o ubiquinol oxidase subunit II complement(454148..455113) Escherichia coli S88 7130529 YP_002390255.1 CDS ampG NC_011742.1 455572 457047 R in Escherichia coli this protein is a permease involved in peptidoglycan recycling; member of major facilitator superfamily; MFS; inner membrane protein; muropeptide transporter complement(455572..457047) Escherichia coli S88 7130528 YP_002390256.1 CDS yajG NC_011742.1 457091 457669 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; hypothetical protein complement(457091..457669) Escherichia coli S88 7133064 YP_002390257.1 CDS bolA NC_011742.1 457974 458291 D positive transcriptional regulator of morphogenetic pathway; controlling several genes involved in oxidative stress, acid stress, heat shock, osmotic shock, and carbon-starvation stress; transcriptional regulator BolA 457974..458291 Escherichia coli S88 7133387 YP_002390258.1 CDS ECS88_0432 NC_011742.1 458225 458488 D Evidence 6 : Doubtful CDS; hypothetical protein 458225..458488 Escherichia coli S88 7129131 YP_002390259.1 CDS tig NC_011742.1 458635 459924 D Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer; trigger factor 458635..459924 Escherichia coli S88 7129092 YP_002390260.1 CDS clpP NC_011742.1 460179 460802 D hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit 460179..460802 Escherichia coli S88 7133473 YP_002390261.1 CDS clpX NC_011742.1 460928 462202 D binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX 460928..462202 Escherichia coli S88 7131930 YP_002390262.1 CDS lon NC_011742.1 462390 464744 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10094703, 14665623, 8939438, 91072263, 97137085, 2984174, 3042779, 3289547, 7988699, 8226758, 8294008; Product type e : enzyme; DNA-binding ATP-dependent protease La 462390..464744 Escherichia coli S88 7130637 YP_002390263.1 CDS hupB NC_011742.1 464953 465225 D histone-like DNA-binding protein; transcriptional regulator HU subunit beta 464953..465225 Escherichia coli S88 7129373 YP_002390264.1 CDS ppiD NC_011742.1 465417 467288 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9670013; Product type e : enzyme; peptidyl-prolyl cis-trans isomerase (rotamase D) 465417..467288 Escherichia coli S88 7131405 YP_002390265.1 CDS ybaV NC_011742.1 467439 467810 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 467439..467810 Escherichia coli S88 7130763 YP_002390266.1 CDS ybaW NC_011742.1 467916 468314 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 467916..468314 Escherichia coli S88 7131165 YP_002390267.1 CDS queC NC_011742.1 468366 469061 R YbaX; catalyzes the transformation of GTP to 7-cyano-7-deazaguanine (preQ0), as one of the early reactions of quenosine biosynthesis; quenosine is a modified nucleoside that occurs at the wobble position of GUN anticodons in tRNAs for Asn, Asp, Tyr, and His; queuosine biosynthesis protein QueC complement(468366..469061) Escherichia coli S88 7131166 YP_002390268.1 CDS ybaE NC_011742.1 469126 470826 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(469126..470826) Escherichia coli S88 7131776 YP_002390269.1 CDS cof NC_011742.1 470926 471744 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15292217; Product type e : enzyme; thiamin pyrimidine pyrophosphate hydrolase 470926..471744 Escherichia coli S88 7131154 YP_002390270.1 CDS ybaO NC_011742.1 471669 472355 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator (Lrp-like) 471669..472355 Escherichia coli S88 7131947 YP_002390271.1 CDS mdlA NC_011742.1 472385 474157 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 94124004, 10850996; Product type pt : putative transporter; putative multidrug transporter membrane\ATP-binding components 472385..474157 Escherichia coli S88 7131160 YP_002390272.1 CDS mdlB NC_011742.1 474150 475931 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 94124004; Product type pt : putative transporter; putative multidrug transporter membrane\ATP-binding components 474150..475931 Escherichia coli S88 7129432 YP_002390273.1 CDS glnK NC_011742.1 476112 476450 D indirectly regulates nitrogen metabolism; at high nitrogen levels P-II 2 prevents the phosphorylation of NR-I, the transcriptional activator of the glutamine synthetase gene (glnA); at low nitrogen levels P-II 2 is uridylylated to form PII-UMP and interacts with an adenylyltransferase (GlnE) that activates GlnA; functionally it is equivalent to protein P-II (GlnB), but itsexpression is driven by the presence of uridylyltransferase, nitrogen regulator I, and the absence of ammonia.; nitrogen regulatory protein P-II 2 476112..476450 Escherichia coli S88 7129433 YP_002390274.1 CDS amtB NC_011742.1 476480 477766 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 22020597, 9618533, 10931328, 1645722, 7984428; Product type t : transporter; ammonium transporter 476480..477766 Escherichia coli S88 7130010 YP_002390275.1 CDS tesB NC_011742.1 477815 478675 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 86139906, 91250410, 10876240; Product type e : enzyme; acyl-CoA thioesterase II complement(477815..478675) Escherichia coli S88 7133066 YP_002390276.1 CDS ybaY NC_011742.1 478893 479465 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative lipoprotein 478893..479465 Escherichia coli S88 7131284 YP_002390277.1 CDS ybaZ NC_011742.1 479496 479885 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative methylated DNA-protein cysteine alkyltransferase complement(479496..479885) Escherichia coli S88 7131167 YP_002390278.1 CDS ECS88_0452 NC_011742.1 479789 480127 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 479789..480127 Escherichia coli S88 7131168 YP_002390279.1 CDS ybaA NC_011742.1 480186 480539 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 480186..480539 Escherichia coli S88 7129479 YP_002390280.1 CDS ylaB NC_011742.1 480581 482131 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(480581..482131) Escherichia coli S88 7131152 YP_002390281.1 CDS ylaC NC_011742.1 482295 482765 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(482295..482765) Escherichia coli S88 7131103 YP_002390282.1 CDS maa NC_011742.1 482881 483432 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 82180540, 91310703, 9600841; Product type e : enzyme; maltose O-acetyltransferase complement(482881..483432) Escherichia coli S88 7131104 YP_002390283.1 CDS hha NC_011742.1 483606 484070 R Evidence 2b : Function of strongly homologous gene; PubMedId : 1956303, 1484495; Product type f : factor; modulator of gene expression, with H-NS complement(483606..484070) Escherichia coli S88 7129401 YP_002390284.1 CDS ybaJ NC_011742.1 483850 484224 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 1956303, 7984428, 14645275; hypothetical protein complement(483850..484224) Escherichia coli S88 7128915 YP_002390285.1 CDS acrB NC_011742.1 484769 487918 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12351840, 12654283, 15111118, 15155734, 21450803, 94012493, 10920254, 7651136; Product type t : transporter; multidrug efflux system protein complement(484769..487918) Escherichia coli S88 7131155 YP_002390286.1 CDS acrA NC_011742.1 487941 489134 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15155734, 21450803, 383699, 390095, 94012493, 10920254, 7651136; Product type t : transporter; multidrug efflux system complement(487941..489134) Escherichia coli S88 7132043 YP_002390287.1 CDS acrR NC_011742.1 489276 489923 D regulates the acrAB operon which is involved in susceptibility to dephalothin and cephaloridine; DNA-binding transcriptional repressor AcrR 489276..489923 Escherichia coli S88 7132042 YP_002390288.1 CDS kefA NC_011742.1 490051 493413 D small mechanosensitive ion channel (MscS) that opens in response to stretch forces in the membrane lipid bilayer; maintains cell turgor through accumulation and release of potassium; large protein class of MscS; potassium efflux protein KefA 490051..493413 Escherichia coli S88 7132047 YP_002390289.1 CDS ybaM NC_011742.1 493625 493786 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(493625..493786) Escherichia coli S88 7130453 YP_002390290.1 CDS priC NC_011742.1 493800 494327 R PriC; protein involved in DNA replication; part of the primosome, a protein complex required to restart stalled replication forks; binds the complex formed by PriA, PriB and DNA; PriC-dependent primosome requires a gap to restart DNA replication; stimulates Rep activity at stalled forks; primosomal replication protein N'' complement(493800..494327) Escherichia coli S88 7131158 YP_002390291.1 CDS ybaN NC_011742.1 494397 494774 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 494397..494774 Escherichia coli S88 7130778 YP_002390292.1 CDS apt NC_011742.1 494927 495478 D catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase 494927..495478 Escherichia coli S88 7131159 YP_002390293.1 CDS dnaX NC_011742.1 495607 497538 D 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; DNA polymerase III subunits gamma and tau 495607..497538 Escherichia coli S88 7133078 YP_002390294.1 CDS ybaB NC_011742.1 497591 497920 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 15322138, 1698765, 2674903; hypothetical protein 497591..497920 Escherichia coli S88 7130230 YP_002390295.1 CDS recR NC_011742.1 497920 498525 D involved in a recombinational process of DNA repair, independent of the recBC complex; recombination protein RecR 497920..498525 Escherichia coli S88 7131153 YP_002390296.1 CDS htpG NC_011742.1 498635 500509 D molecular chaperone; heat shock protein 90 498635..500509 Escherichia coli S88 7131814 YP_002390297.1 CDS adk NC_011742.1 500690 501334 D essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase 500690..501334 Escherichia coli S88 7131399 YP_002390298.1 CDS hemH NC_011742.1 501466 502428 D protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic; ferrochelatase 501466..502428 Escherichia coli S88 7132058 YP_002390299.1 CDS aes NC_011742.1 502425 503384 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9401025, 98244813, 2051480, 7721718; Product type e : enzyme; acetyl esterase complement(502425..503384) Escherichia coli S88 7128903 YP_002390300.1 CDS gsk NC_011742.1 503536 504840 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90155203, 95238302, 2051480; Product type e : enzyme; inosine/guanosine kinase 503536..504840 Escherichia coli S88 7133025 YP_002390301.1 CDS ybaL NC_011742.1 504970 506646 R YbaL; member of the CPA-2 family of antiporters; uncharacterized protein; putative cation:proton antiport protein complement(504970..506646) Escherichia coli S88 7130078 YP_002390302.1 CDS fsr NC_011742.1 506885 508105 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21450803, 97074653, 8917080; Product type t : transporter; fosmidomycin efflux system, member of the major facilitator superfamily complement(506885..508105) Escherichia coli S88 7131157 YP_002390303.1 CDS ushA NC_011742.1 508323 509975 D catalyzes the degradation of periplasmic UDP-glucose to uridine, glucose-1-phosphate and inorganic phosphate; specific for uridine nucleotides; bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor 508323..509975 Escherichia coli S88 7132844 YP_002390304.1 CDS ECS88_0478 NC_011742.1 510013 510516 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(510013..510516) Escherichia coli S88 7131329 YP_002390305.1 CDS ECS88_0479 NC_011742.1 510513 511313 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(510513..511313) Escherichia coli S88 7129094 YP_002390306.1 CDS ybaK NC_011742.1 511337 511816 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(511337..511816) Escherichia coli S88 7129095 YP_002390307.1 CDS ybaP NC_011742.1 512020 512814 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(512020..512814) Escherichia coli S88 7130647 YP_002390308.1 CDS ECS88_0483 NC_011742.1 512917 513249 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative RelE/ParE family protein, cytotoxic translational repressor of toxin-antitoxin stability system 512917..513249 Escherichia coli S88 7131161 YP_002390309.1 CDS ybaQ NC_011742.1 513285 513626 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 513285..513626 Escherichia coli S88 7129096 YP_002390310.1 CDS copA NC_011742.1 513684 516188 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12351646, 20105527, 11167016, 11500054, 9868784; Product type t : transporter; copper exporting ATPase complement(513684..516188) Escherichia coli S88 7131162 YP_002390311.1 CDS ybaS NC_011742.1 516450 517382 D catalyzes the formation of glutamate from glutamine; glutaminase 516450..517382 Escherichia coli S88 7131948 YP_002390312.1 CDS ybaT NC_011742.1 517385 518677 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative nitrogen-containing metabolite transporter 517385..518677 Escherichia coli S88 7131163 YP_002390313.1 CDS cueR NC_011742.1 518802 519209 D activator of copper-responsive regulon genes; DNA-binding transcriptional regulator CueR 518802..519209 Escherichia coli S88 7131164 YP_002390314.1 CDS ECS88_0489 NC_011742.1 519213 519416 R hypothetical protein complement(519213..519416) Escherichia coli S88 7130508 YP_002390315.1 CDS ECS88_0490 NC_011742.1 519413 519835 R hypothetical protein complement(519413..519835) Escherichia coli S88 7129097 YP_002390316.1 CDS ECS88_0491 NC_011742.1 519921 520937 R hypothetical protein complement(519921..520937) Escherichia coli S88 7129098 YP_002390317.1 CDS ECS88_0492 NC_011742.1 521304 521666 D hypothetical protein 521304..521666 Escherichia coli S88 7129099 YP_002390318.1 CDS ybbJ NC_011742.1 521769 522224 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(521769..522224) Escherichia coli S88 7129100 YP_002390319.1 CDS ybbK NC_011742.1 522224 523141 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative protease, membrane anchored complement(522224..523141) Escherichia coli S88 7131171 YP_002390320.1 CDS ybbL NC_011742.1 523287 523964 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ABC transporter ATP-binding protein YbbL 523287..523964 Escherichia coli S88 7131172 YP_002390321.1 CDS ybbM NC_011742.1 523951 524730 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative permease of an ABC transporter 523951..524730 Escherichia coli S88 7131173 YP_002390322.1 CDS ybbN NC_011742.1 524793 525647 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative thioredoxin domain-containing protein complement(524793..525647) Escherichia coli S88 7131174 YP_002390323.1 CDS ybbO NC_011742.1 525708 526517 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; short chain dehydrogenase complement(525708..526517) Escherichia coli S88 7131175 YP_002390324.1 CDS tesA NC_011742.1 526507 527133 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91270121, 91324311, 93163029, 93252782, 94179121, 99353977, 1864840, 8432696, 8098033; Product type e : enzyme; multifunctional acyl-CoA thioesterase I and protease I and lysophospholipase L1 complement(526507..527133) Escherichia coli S88 7131176 YP_002390325.1 CDS ybbA NC_011742.1 527101 527787 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ABC transporter ATP-binding protein YbbA 527101..527787 Escherichia coli S88 7131283 YP_002390326.1 CDS ybbP NC_011742.1 527784 530198 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type t : transporter; putative ABC transporter permease 527784..530198 Escherichia coli S88 7131169 YP_002390327.1 CDS ybbB NC_011742.1 530257 531351 R catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA; tRNA 2-selenouridine synthase complement(530257..531351) Escherichia coli S88 7131177 YP_002390328.1 CDS ybbS NC_011742.1 531420 532346 R activator of the allDC-ylbA operon involved in allantoin utilization; DNA-binding transcriptional activator AllS complement(531420..532346) Escherichia coli S88 7131170 YP_002390329.1 CDS allA NC_011742.1 532576 533058 D catalyzes the formation of glyoxylate from (S)-ureidoglycolate; ureidoglycolate hydrolase 532576..533058 Escherichia coli S88 7131178 YP_002390330.1 CDS allR NC_011742.1 533136 533951 D regulates operons involved in the utilization of allantoin; DNA-binding transcriptional repressor AllR 533136..533951 Escherichia coli S88 7133044 YP_002390331.1 CDS gcl NC_011742.1 534041 535822 D catalyzes the formation of 2-hydroxy-3-oxopropanoate (tartronate semialdehyde) from two molecules of glyoxylate; glyoxylate carboligase 534041..535822 Escherichia coli S88 7133048 YP_002390332.1 CDS hyi NC_011742.1 535835 536611 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20029625, 8440684; Product type e : enzyme; hydroxypyruvate isomerase 535835..536611 Escherichia coli S88 7132194 YP_002390333.1 CDS glxR NC_011742.1 536711 537589 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20069628; Product type e : enzyme; tartronate semialdehyde reductase, NADH-dependent 536711..537589 Escherichia coli S88 7131592 YP_002390334.1 CDS ybbW NC_011742.1 537759 539213 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 1293888; Product type t : transporter; allantoin permease 537759..539213 Escherichia coli S88 7130040 YP_002390335.1 CDS allB NC_011742.1 539273 540634 D Plays a crucial role on both purine and pyrimidine metabolism; allantoinase 539273..540634 Escherichia coli S88 7131179 YP_002390336.1 CDS ybbY NC_011742.1 540690 541991 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative purine permease YbbY 540690..541991 Escherichia coli S88 7133045 YP_002390337.1 CDS glxK NC_011742.1 542013 543158 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20069628; Product type e : enzyme; glycerate kinase II 542013..543158 Escherichia coli S88 7131180 YP_002390338.1 CDS ylbA NC_011742.1 543287 544072 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(543287..544072) Escherichia coli S88 7130039 YP_002390339.1 CDS allC NC_011742.1 544083 545318 R allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide; allantoate amidohydrolase complement(544083..545318) Escherichia coli S88 7131105 YP_002390340.1 CDS allD NC_011742.1 545340 546389 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12460564, 20069628, 69151449; Product type e : enzyme; ureidoglycolate dehydrogenase complement(545340..546389) Escherichia coli S88 7133046 YP_002390341.1 CDS fdrA NC_011742.1 546706 548373 D multicopy suppressor of dominant negative ftsH mutations; membrane protein FdrA 546706..548373 Escherichia coli S88 7133047 YP_002390342.1 CDS ylbE NC_011742.1 548383 549642 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 548383..549642 Escherichia coli S88 7129460 YP_002390343.1 CDS ylbF NC_011742.1 549653 550468 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 549653..550468 Escherichia coli S88 7131106 YP_002390344.1 CDS ybcF NC_011742.1 550465 551358 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2464576, 2644189, 7920643, 7940673, 7984428; Product type pe : putative enzyme; carbamate kinase 550465..551358 Escherichia coli S88 7131107 YP_002390345.1 CDS purK NC_011742.1 551511 552578 R With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway; phosphoribosylaminoimidazole carboxylase ATPase subunit complement(551511..552578) Escherichia coli S88 7131181 YP_002390346.1 CDS purE NC_011742.1 552575 553084 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10074353, 8117684, 89123018, 89123019, 92287929, 10574791; Product type e : enzyme; N5-carboxyaminoimidazole ribonucleotide mutase complement(552575..553084) Escherichia coli S88 7131751 YP_002390347.1 CDS ECS88_0523 NC_011742.1 553180 553509 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; hypothetical protein complement(553180..553509) Escherichia coli S88 7131748 YP_002390348.1 CDS lpxH NC_011742.1 553620 554342 R catalyzes the formation of 2,3=diacylglucosamine 1-phosphate from UDP-2,3=diacylglucosamine; UDP-2,3-diacylglucosamine hydrolase complement(553620..554342) Escherichia coli S88 7129101 YP_002390349.1 CDS ppiB NC_011742.1 554345 554839 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90272647, 91175755, 1606970, 1864365, 8601841, 9298646, 9600841; Product type e : enzyme; peptidyl-prolyl cis-trans isomerase B (rotamase B) complement(554345..554839) Escherichia coli S88 7129384 YP_002390350.1 CDS cysS NC_011742.1 555013 556398 D 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; cysteinyl-tRNA synthetase 555013..556398 Escherichia coli S88 7130761 YP_002390351.1 CDS ybcI NC_011742.1 556434 556955 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(556434..556955) Escherichia coli S88 7130547 YP_002390352.1 CDS ybcJ NC_011742.1 557063 557275 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12837795, 1748668, 7567469; Product type pr : putative regulator; hypothetical protein complement(557063..557275) Escherichia coli S88 7131183 YP_002390353.1 CDS folD NC_011742.1 557277 558143 R catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate; bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase complement(557277..558143) Escherichia coli S88 7131184 YP_002390354.1 CDS ECS88_0530 NC_011742.1 558193 558381 D Evidence 6 : Doubtful CDS; hypothetical protein 558193..558381 Escherichia coli S88 7132816 YP_002390355.1 CDS intD NC_011742.1 558506 559669 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 90036709, 2183007; Product type pe : putative enzyme; putative integrase; DLP12 prophage complement(558506..559669) Escherichia coli S88 7131989 YP_002390356.1 CDS ECS88_0532 NC_011742.1 559525 559980 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Excisionase from phage origin complement(559525..559980) Escherichia coli S88 7131652 YP_002390357.1 CDS yfdT NC_011742.1 559896 560201 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage complement(559896..560201) Escherichia coli S88 7129103 YP_002390358.1 CDS yfdS NC_011742.1 560201 560563 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage complement(560201..560563) Escherichia coli S88 7129840 YP_002390359.1 CDS yfdR NC_011742.1 560554 561090 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage complement(560554..561090) Escherichia coli S88 7129838 YP_002390360.1 CDS yfdQ NC_011742.1 561218 562042 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage complement(561218..562042) Escherichia coli S88 7129835 YP_002390361.1 CDS ECS88_0537 NC_011742.1 562108 562656 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein complement(562108..562656) Escherichia coli S88 7129832 YP_002390362.1 CDS ECS88_0538 NC_011742.1 562859 563113 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein complement(562859..563113) Escherichia coli S88 7129104 YP_002390363.1 CDS ECS88_0539 NC_011742.1 563193 563885 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative repressor protein CI complement(563193..563885) Escherichia coli S88 7129105 YP_002390364.1 CDS ECS88_0540 NC_011742.1 563983 564243 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative lambda repressor-like DNA-binding domains 563983..564243 Escherichia coli S88 7129106 YP_002390365.1 CDS ymfL NC_011742.1 564236 564793 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative nucleic acid-binding protein; e14 prophage 564236..564793 Escherichia coli S88 7129107 YP_002390366.1 CDS ECS88_0543 NC_011742.1 564790 565938 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative antirepressor from phage 564790..565938 Escherichia coli S88 7131127 YP_002390367.1 CDS ECS88_0544 NC_011742.1 565935 566801 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; Putative antirepressor from phage 565935..566801 Escherichia coli S88 7130577 YP_002390368.1 CDS ECS88_0545 NC_011742.1 566798 567022 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 566798..567022 Escherichia coli S88 7130659 YP_002390369.1 CDS ECS88_0546 NC_011742.1 566980 567837 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative replication protein from phage 566980..567837 Escherichia coli S88 7130660 YP_002390370.1 CDS yfdN NC_011742.1 567834 568328 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage 567834..568328 Escherichia coli S88 7130661 YP_002390371.1 CDS ECS88_0548 NC_011742.1 568295 568981 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage AdoMet-dependent methyltransferase 568295..568981 Escherichia coli S88 7129829 YP_002390372.1 CDS ECS88_0549 NC_011742.1 568978 569304 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative LexA repressor 568978..569304 Escherichia coli S88 7130662 YP_002390373.1 CDS ECS88_0550 NC_011742.1 569301 569696 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative Crossover junction endodeoxyribonuclease 569301..569696 Escherichia coli S88 7130663 YP_002390374.1 CDS ECS88_0551 NC_011742.1 569847 570674 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 569847..570674 Escherichia coli S88 7130664 YP_002390375.1 CDS ECS88_0552 NC_011742.1 570676 571671 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 570676..571671 Escherichia coli S88 7130665 YP_002390376.1 CDS ECS88_0553 NC_011742.1 571674 572060 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative Antitermination protein Q 571674..572060 Escherichia coli S88 7130666 YP_002390377.1 CDS ECS88_0554 NC_011742.1 572109 572753 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 572109..572753 Escherichia coli S88 7130667 YP_002390378.1 CDS ECS88_0555 NC_011742.1 573032 573229 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 573032..573229 Escherichia coli S88 7130668 YP_002390379.1 CDS ECS88_0556 NC_011742.1 573364 574071 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative ARAC-type regulatory protein from phage origin 573364..574071 Escherichia coli S88 7130669 YP_002390380.1 CDS ECS88_0557 NC_011742.1 574841 576802 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 574841..576802 Escherichia coli S88 7129867 YP_002390381.1 CDS ECS88_0558 NC_011742.1 576939 577121 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 576939..577121 Escherichia coli S88 7130671 YP_002390382.1 CDS ECS88_0559 NC_011742.1 576985 577428 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 576985..577428 Escherichia coli S88 7130672 YP_002390383.1 CDS essD NC_011742.1 577504 577719 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2019562; Product type pe : putative enzyme; putative phage lysis protein S; DLP12 prophage 577504..577719 Escherichia coli S88 7130673 YP_002390384.1 CDS ECS88_0561 NC_011742.1 577721 578074 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 577721..578074 Escherichia coli S88 7132418 YP_002390385.1 CDS ydfQ NC_011742.1 578138 578671 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative membrane-associated lysozyme; Qin prophage 578138..578671 Escherichia coli S88 7130674 YP_002390386.1 CDS ECS88_0563 NC_011742.1 578795 578968 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 578795..578968 Escherichia coli S88 7129336 YP_002390387.1 CDS ECS88_0564 NC_011742.1 578970 579407 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative endopeptidase (Protein gp15) 578970..579407 Escherichia coli S88 7130675 YP_002390388.1 CDS ECS88_0565 NC_011742.1 579609 580130 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 579609..580130 Escherichia coli S88 7130676 YP_002390389.1 CDS ECS88_0566 NC_011742.1 580821 580979 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 580821..580979 Escherichia coli S88 7130677 YP_002390390.1 CDS ECS88_0568 NC_011742.1 581313 581468 R Evidence 6 : Doubtful CDS; hypothetical protein complement(581313..581468) Escherichia coli S88 7133615 YP_002390391.1 CDS ECS88_0569 NC_011742.1 581693 582241 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Terminase small subunit (Gp1) 581693..582241 Escherichia coli S88 7130679 YP_002390392.1 CDS ECS88_0572 NC_011742.1 584123 584329 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head stabilization protein (Head protein GP3) 584123..584329 Escherichia coli S88 7130682 YP_002390393.1 CDS ECS88_0573 NC_011742.1 584296 585918 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Portal protein (Head protein Gp4) 584296..585918 Escherichia coli S88 7130683 YP_002390394.1 CDS ECS88_0574 NC_011742.1 585908 587413 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head-tail preconnector protein GP5 [Contains: Scaffold protein GP6 (Head protein GP6)] 585908..587413 Escherichia coli S88 7130684 YP_002390395.1 CDS ECS88_0575 NC_011742.1 587450 587797 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head decoration protein (Head protein GPshp) 587450..587797 Escherichia coli S88 7130685 YP_002390396.1 CDS ECS88_0576 NC_011742.1 587855 588883 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major head protein (Head protein gp7) 587855..588883 Escherichia coli S88 7130686 YP_002390397.1 CDS ECS88_0577 NC_011742.1 588887 589309 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 588887..589309 Escherichia coli S88 7130687 YP_002390398.1 CDS ECS88_0578 NC_011742.1 589266 589655 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail attachment protein (Head protein gp8) 589266..589655 Escherichia coli S88 7130688 YP_002390399.1 CDS ECS88_0579 NC_011742.1 589601 590245 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein Z (GpZ) 589601..590245 Escherichia coli S88 7130689 YP_002390400.1 CDS ECS88_0580 NC_011742.1 590242 590637 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein U 590242..590637 Escherichia coli S88 7130690 YP_002390401.1 CDS ECS88_0581 NC_011742.1 590615 591385 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major tail protein V 590615..591385 Escherichia coli S88 7130691 YP_002390402.1 CDS ECS88_0582 NC_011742.1 591401 591823 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein G 591401..591823 Escherichia coli S88 7130692 YP_002390403.1 CDS ECS88_0583 NC_011742.1 591805 592239 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein T 591805..592239 Escherichia coli S88 7130693 YP_002390404.1 CDS ECS88_0584 NC_011742.1 592232 594793 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein precursor H 592232..594793 Escherichia coli S88 7130694 YP_002390405.1 CDS ECS88_0586 NC_011742.1 594790 595119 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein M 594790..595119 Escherichia coli S88 7130695 YP_002390406.1 CDS ECS88_0587 NC_011742.1 595119 595817 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein L 595119..595817 Escherichia coli S88 7130696 YP_002390407.1 CDS ECS88_0588 NC_011742.1 595567 596571 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; tail fiber component K 595567..596571 Escherichia coli S88 7130697 YP_002390408.1 CDS ECS88_0589 NC_011742.1 596469 597149 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail assembly protein I 596469..597149 Escherichia coli S88 7130698 YP_002390409.1 CDS ECS88_0590 NC_011742.1 597493 601185 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Host specificity protein J 597493..601185 Escherichia coli S88 7130699 YP_002390410.1 CDS ECS88_0591 NC_011742.1 601253 601852 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; Putative Lom-like outer membrane protein of prophage 601253..601852 Escherichia coli S88 7130700 YP_002390411.1 CDS ECS88_0592 NC_011742.1 602004 604064 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 602004..604064 Escherichia coli S88 7130701 YP_002390412.1 CDS ECS88_0593 NC_011742.1 604061 604339 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 604061..604339 Escherichia coli S88 7130702 YP_002390413.1 CDS ECS88_0594 NC_011742.1 604349 604642 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 604349..604642 Escherichia coli S88 7130703 YP_002390414.1 CDS ybcY NC_011742.1 604835 605419 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative AdoMet-dependent methyltransferase; DLP12 prophage complement(604835..605419) Escherichia coli S88 7130704 YP_002390415.1 CDS ECS88_0596 NC_011742.1 606049 607533 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative exported protein; putative protease complement(606049..607533) Escherichia coli S88 7131189 YP_002390416.1 CDS ompT NC_011742.1 607720 608673 R outer membrane protease; involved in virulence in many organisms; OmpT; IcsP; SopA; Pla; PgtE; omptin; in Escherichia coli OmpT can degrade antimicrobial peptides; in Yersinia Pla activates plasminogen during infection; in Shigella flexneria SopA cleaves the autotransporter IcsA; outer membrane protease complement(607720..608673) Escherichia coli S88 7130705 YP_002390417.1 CDS tfaQ NC_011742.1 609782 610138 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail fiber assembly protein 609782..610138 Escherichia coli S88 7130707 YP_002390418.1 CDS ybcY NC_011742.1 610193 610777 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative AdoMet-dependent methyltransferase; DLP12 prophage complement(610193..610777) Escherichia coli S88 7131287 YP_002390419.1 CDS ompT NC_011742.1 611093 612046 R outer membrane protease; involved in virulence in many organisms; OmpT; IcsP; SopA; Pla; PgtE; omptin; in Escherichia coli OmpT can degrade antimicrobial peptides; in Yersinia Pla activates plasminogen during infection; in Shigella flexneria SopA cleaves the autotransporter IcsA; outer membrane protease complement(611093..612046) Escherichia coli S88 7131190 YP_002390420.1 CDS ybcH NC_011742.1 612704 613594 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(612704..613594) Escherichia coli S88 7133130 YP_002390421.1 CDS nfrA NC_011742.1 613595 616567 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89359086, 94042873, 94042874; Product type m : membrane component; bacteriophage N4 receptor, outer membrane subunit complement(613595..616567) Escherichia coli S88 7131182 YP_002390422.1 CDS nfrB NC_011742.1 616554 618791 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89359086, 94042873, 94042874; Product type m : membrane component; bacteriophage N4 adsorption protein B complement(616554..618791) Escherichia coli S88 7129703 YP_002390423.1 CDS cusS NC_011742.1 618941 620383 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20461235, 11283292, 11399769; Product type r : regulator; sensor kinase CusS complement(618941..620383) Escherichia coli S88 7129704 YP_002390424.1 CDS cusR NC_011742.1 620373 621056 R response regulator in two-component regulatory system with CusS; regulates the copper efflux system; DNA-binding transcriptional activator CusR complement(620373..621056) Escherichia coli S88 7130514 YP_002390425.1 CDS cusC NC_011742.1 621213 622595 D with CusA, CusB and CusF is part of a cation efflux system that mediates resistance to copper and silver; copper/silver efflux system outer membrane protein CusC 621213..622595 Escherichia coli S88 7130513 YP_002390426.1 CDS cusF NC_011742.1 622619 622951 D Evidence 2b : Function of strongly homologous gene; PubMedId : 21125583, 11283292, 11399769, 12813074; Product type f : factor; periplasmic copper-binding protein 622619..622951 Escherichia coli S88 7130511 YP_002390427.1 CDS cusB NC_011742.1 622967 624190 D with CusA, CusC and CusF is part of a cation efflux system that mediates resistance to copper and silver; copper/silver efflux system membrane fusion protein CusB 622967..624190 Escherichia coli S88 7130512 YP_002390428.1 CDS cusA NC_011742.1 624202 627345 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20461235, 21125583, 21178899, 21450803, 11399769, 12813074, 1711024, 7984428; Product type t : transporter; copper/silver efflux system, membrane component 624202..627345 Escherichia coli S88 7130510 YP_002390429.1 CDS pheP NC_011742.1 627447 628823 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91267923, 94042931, 8626334; Product type t : transporter; phenylalanine transporter 627447..628823 Escherichia coli S88 7130509 YP_002390430.1 CDS ybdG NC_011742.1 628905 630152 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative membrane protein; putative channel complement(628905..630152) Escherichia coli S88 7133704 YP_002390431.1 CDS nfnB NC_011742.1 630260 630913 R catalyzes the reduction of nitroaromatic compounds such as nitrofurazone, quinones and the anti-tumor agent CB1954; NAD(P)H-dependent; oxygen insensitive; dihydropteridine reductase complement(630260..630913) Escherichia coli S88 7131196 YP_002390432.1 CDS ybdF NC_011742.1 630992 631375 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(630992..631375) Escherichia coli S88 7129701 YP_002390433.1 CDS ybdJ NC_011742.1 631440 631688 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(631440..631688) Escherichia coli S88 7131195 YP_002390434.1 CDS ybdK NC_011742.1 631754 632872 R ATP-dependent; carboxylate-amine ligase with weak glutamate--cysteine ligase activity; carboxylate-amine ligase complement(631754..632872) Escherichia coli S88 7131198 YP_002390435.1 CDS hokE NC_011742.1 633326 633478 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 99291074; Product type f : factor; toxic polypeptide, small 633326..633478 Escherichia coli S88 7131199 YP_002390436.1 CDS entD NC_011742.1 633600 634229 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89313305, 90132534, 91035252, 8939709, 9214294; Product type e : enzyme; phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex complement(633600..634229) Escherichia coli S88 7128940 YP_002390437.1 CDS fepA NC_011742.1 634395 636635 R Fep; Cbt; Cbr; FeuB; FepA; PfeA; IroN; BfeA; outer membrane receptor of ferric enterobactin and colicins B and D; interacts with the TonB-ExbBD complex which catalyzes the translocation of the siderophore to the periplasmic space; outer membrane receptor FepA complement(634395..636635) Escherichia coli S88 7132403 YP_002390438.1 CDS fes NC_011742.1 636956 638080 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92291125, 94198561, 2974033; Product type e : enzyme; enterobactin/ferric enterobactin esterase 636956..638080 Escherichia coli S88 7129471 YP_002390439.1 CDS ybdZ NC_011742.1 638083 638301 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 638083..638301 Escherichia coli S88 7129477 YP_002390440.1 CDS entF NC_011742.1 638298 642179 D with EntB, EntD, and EntE forms the multienzyme complex enterobactin synthase; EntF is the serine activating enzyme which catalyzes the formation of the amide and ester bonds of the cyclic enterobactin; enterobactin synthase subunit F 638298..642179 Escherichia coli S88 7131203 YP_002390441.1 CDS fepE NC_011742.1 642395 643528 D part of the ferric enterobactin transport system; necessary for enetrobactin uptake; ferric enterobactin transport protein FepE 642395..643528 Escherichia coli S88 7132405 YP_002390442.1 CDS fepC NC_011742.1 643525 644340 R with FepBDE is involved in the transport of ferric enterobactin; iron-enterobactin transporter ATP-binding protein complement(643525..644340) Escherichia coli S88 7129475 YP_002390443.1 CDS fepG NC_011742.1 644337 645329 R with FepBCD is involved in the transport of ferric enterobactin; iron-enterobactin transporter permease complement(644337..645329) Escherichia coli S88 7129473 YP_002390444.1 CDS fepD NC_011742.1 645326 646330 R with FepBCG is involved in the transport of ferric enterobactin; iron-enterobactin transporter membrane protein complement(645326..646330) Escherichia coli S88 7129476 YP_002390445.1 CDS ybdA NC_011742.1 646441 647691 D protein p43; inner membrane protein that exports enterobactin to the periplasmic space; member of the major facilitator superfamily (MFS) of transporters; enterobactin exporter EntS 646441..647691 Escherichia coli S88 7129474 YP_002390446.1 CDS fepB NC_011742.1 647695 648651 R with FepCDG is involved in the transport of ferric enterobactin; iron-enterobactin transporter periplasmic binding protein complement(647695..648651) Escherichia coli S88 7131192 YP_002390447.1 CDS entC NC_011742.1 648840 650015 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89123153, 90165423, 90241936, 2110093, 2139473; Product type e : enzyme; isochorismate synthase 1 648840..650015 Escherichia coli S88 7129472 YP_002390448.1 CDS entE NC_011742.1 650025 651635 D bifunctional 2,3-dihydroxybenzoate-AMP ligase/S-dihydroxybenzoyltransferase; activates the carboxylate group of 2,3-dihydroxy-benzoate forming (2,3-dihydroxybenzoyl)adenylate then catalyzes the acylation of holo-entB with 2,3-dihydroxy-benzoate adenylate; enterobactin synthase subunit E 650025..651635 Escherichia coli S88 7132402 YP_002390449.1 CDS entB NC_011742.1 651649 652506 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20183918, 90241937, 91035252, 9485415, 97361959, 2521621, 2521622; Product type e : enzyme; isochorismatase 651649..652506 Escherichia coli S88 7132404 YP_002390450.1 CDS entA NC_011742.1 652506 653252 D catalyzes the formation of 2,3-dihydroxybenzoate from 2,3-dihydro-2,3-dihydroxybenzoate; involved in the biosynthesis of siderophores, enterobactin, bacillibactin or vibriobactin; 2,3-dihydroxybenzoate-2,3-dehydrogenase 652506..653252 Escherichia coli S88 7132401 YP_002390451.1 CDS ybdB NC_011742.1 653255 653668 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2521621, 2521622, 15808744; Product type pe : putative enzyme; hypothetical protein 653255..653668 Escherichia coli S88 7132400 YP_002390452.1 CDS cstA NC_011742.1 653849 655954 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91162636, 2521622; Product type pf : putative factor; carbon starvation protein 653849..655954 Escherichia coli S88 7131193 YP_002390453.1 CDS ybdD NC_011742.1 656067 656264 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 656067..656264 Escherichia coli S88 7130506 YP_002390454.1 CDS ybdH NC_011742.1 656274 657362 R member of the iron-containing alcohol dehydrogenase family; unknown function; hypothetical protein complement(656274..657362) Escherichia coli S88 7131194 YP_002390455.1 CDS ibrB NC_011742.1 658642 659271 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12057959; Product type r : regulator; immunoglobulin-binding regulator complement(658642..659271) Escherichia coli S88 7131201 YP_002390456.1 CDS ibrA NC_011742.1 659244 660464 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12057959; Product type r : regulator; immunoglobulin-binding regulator complement(659244..660464) Escherichia coli S88 7131608 YP_002390457.1 CDS ybdO NC_011742.1 660611 661549 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator, LysR-type complement(660611..661549) Escherichia coli S88 7131606 YP_002390458.1 CDS dsbG NC_011742.1 661718 662464 R Involved in disulfide bond formation; disulfide isomerase/thiol-disulfide oxidase complement(661718..662464) Escherichia coli S88 7131202 YP_002390459.1 CDS ahpC NC_011742.1 662836 663399 D with AhpF catalyzes the conversion of alkyl hydroperoxides to their corresponding alcohols; AhpC reduced the hydroperoxide substrate; alkyl hydroperoxide reductase subunit C 662836..663399 Escherichia coli S88 7130242 YP_002390460.1 CDS ahpF NC_011742.1 663570 665135 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89197774, 1592833; Product type e : enzyme; alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)-binding 663570..665135 Escherichia coli S88 7133035 YP_002390461.1 CDS uspG NC_011742.1 665256 665684 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12732303, 12071968; Product type f : factor; universal stress protein UP12 complement(665256..665684) Escherichia coli S88 7133036 YP_002390462.1 CDS ECS88_0650 NC_011742.1 665808 665897 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(665808..665897) Escherichia coli S88 7132456 YP_002390463.1 CDS rnk NC_011742.1 666040 666450 R Regulates the synthesis of nucleoside triphosphates for nucleic acid synthesis, CTP for lipid synthesis, and GTP for protein elongation; nucleoside diphosphate kinase regulator complement(666040..666450) Escherichia coli S88 7130708 YP_002390464.1 CDS rna NC_011742.1 666680 667486 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90151658, 90264307, 2253883, 8188249; Product type e : enzyme; ribonuclease I complement(666680..667486) Escherichia coli S88 7132750 YP_002390465.1 CDS citT NC_011742.1 667600 669063 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9696764; Product type t : transporter; citrate:succinate antiporter complement(667600..669063) Escherichia coli S88 7132740 YP_002390466.1 CDS citG NC_011742.1 669114 669992 R catalyzes the formation of 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA from ATP and 3-dephospho-CoA; triphosphoribosyl-dephospho-CoA synthase complement(669114..669992) Escherichia coli S88 7131923 YP_002390467.1 CDS citX NC_011742.1 669967 670518 R 2'-(5''-phosphoribosyl)-3'-dephospho-CoA transferase; holo-citrate lyase synthase; CitG forms the prosthetic group precursor 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA which is then transferred to apo-ACP by CitX to produce holo-ACP and pyrophosphate; 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA:apo- citrate lyase complement(669967..670518) Escherichia coli S88 7131922 YP_002390468.1 CDS citF NC_011742.1 670522 672054 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 84024606, 87214225; Product type e : enzyme; citrate lyase, citrate-ACP transferase (alpha) subunit complement(670522..672054) Escherichia coli S88 7131924 YP_002390469.1 CDS citE NC_011742.1 672065 672973 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 84024606, 87214225; Product type e : enzyme; citrate lyase, citryl-ACP lyase (beta) subunit complement(672065..672973) Escherichia coli S88 7131921 YP_002390470.1 CDS citD NC_011742.1 672970 673266 R acyl carrier protein; with CitE and CitF catalyzes the formation of oxaloacetate from citrate; citrate lyase subunit gamma complement(672970..673266) Escherichia coli S88 7131920 YP_002390471.1 CDS citC NC_011742.1 673281 674339 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 84024606, 87214225; Product type e : enzyme; citrate lyase synthetase complement(673281..674339) Escherichia coli S88 7131919 YP_002390472.1 CDS citA NC_011742.1 674718 676376 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11889485, 21885746, 9701802; Product type r : regulator; sensory histidine kinase in two-component regulatory system with citB 674718..676376 Escherichia coli S88 7131918 YP_002390473.1 CDS dpiA NC_011742.1 676345 677025 D regulates the expression of citAB in citrate fermentation; two-component response regulator DpiA 676345..677025 Escherichia coli S88 7131916 YP_002390474.1 CDS dcuC NC_011742.1 677066 678451 R responsible for the transport of C4-dicarboxylates during anaerobic growth; C4-dicarboxylate transporter DcuC complement(677066..678451) Escherichia coli S88 7131917 YP_002390475.1 CDS pagP NC_011742.1 679038 679598 D catalyzes the transfer of palmitate to lipid A; palmitoyl transferase 679038..679598 Escherichia coli S88 7130171 YP_002390476.1 CDS cspE NC_011742.1 679773 679982 D member of the CspA family; constitutively expressed RNA/ssDNA-binding protein; functions in helping cells adapt to low temperature; aids nucleic acid melting; participates in gene regulation; can act as a transcription antiterminator; cold shock protein CspE 679773..679982 Escherichia coli S88 7131958 YP_002390477.1 CDS crcB NC_011742.1 680036 680419 R may be involved in chromosome condensation; overexpression in Escherichia coli protects against decondensation by camphor; overexpressing the protein results in an increase in supercoiling; camphor resistance protein CrcB complement(680036..680419) Escherichia coli S88 7130497 YP_002390478.1 CDS ybeM NC_011742.1 680740 681303 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative amidase 680740..681303 Escherichia coli S88 7131959 YP_002390479.1 CDS tatE NC_011742.1 681432 681635 D TatE; similar to TatA and found in some proteobacteria; part of system that translocates proteins with a conserved twin arginine motif across the inner membrane; capable of translocating folded substrates typically those with bound cofactors; similar to a protein import system in thylakoid membranes; twin arginine translocase protein E 681432..681635 Escherichia coli S88 7131209 YP_002390480.1 CDS lipA NC_011742.1 681735 682700 R catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group; lipoyl synthase complement(681735..682700) Escherichia coli S88 7131266 YP_002390481.1 CDS lipB NC_011742.1 683520 684161 R lipoyl/octanoyltransferase; catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein; lipoate-protein ligase B complement(683520..684161) Escherichia coli S88 7131207 YP_002390482.1 CDS ybeD NC_011742.1 684262 684525 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 8444795; hypothetical protein complement(684262..684525) Escherichia coli S88 7129357 YP_002390483.1 CDS dacA NC_011742.1 684635 685846 R penicillin-binding protein 5; removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors; D-alanyl-D-alanine carboxypeptidase fraction A complement(684635..685846) Escherichia coli S88 7131206 YP_002390484.1 CDS rlpA NC_011742.1 685986 687074 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88058785, 2644207; Product type lp : lipoprotein; rare lipoprotein A complement(685986..687074) Escherichia coli S88 7130553 YP_002390485.1 CDS mrdB NC_011742.1 687085 688197 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89123070, 90036736, 91072213, 3316191; Product type cp : cell process; cell wall shape-determining protein complement(687085..688197) Escherichia coli S88 7132729 YP_002390486.1 CDS mrdA NC_011742.1 688200 690101 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 86196149, 87030266, 89174517, 2644207; Product type e : enzyme; penicillin-binding protein 2 complement(688200..690101) Escherichia coli S88 7129608 YP_002390487.1 CDS ybeA NC_011742.1 690132 690599 R SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA; rRNA large subunit methyltransferase complement(690132..690599) Escherichia coli S88 7129607 YP_002390488.1 CDS ybeB NC_011742.1 690603 690920 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(690603..690920) Escherichia coli S88 7131204 YP_002390489.1 CDS phpB NC_011742.1 691180 691791 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7929373; Product type pe : putative enzyme; putative phosphatase with phosphoglycerate mutase domain complement(691180..691791) Escherichia coli S88 7131205 YP_002390490.1 CDS nadD NC_011742.1 691815 692456 R transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria; nicotinic acid mononucleotide adenylyltransferase complement(691815..692456) Escherichia coli S88 7133731 YP_002390491.1 CDS holA NC_011742.1 692458 693489 R required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA; DNA polymerase III subunit delta complement(692458..693489) Escherichia coli S88 7129653 YP_002390492.1 CDS rlpB NC_011742.1 693489 694070 R rare lipoprotein B; involved in the assembly of LPS in the outer membrane; LPS-assembly lipoprotein RlpB complement(693489..694070) Escherichia coli S88 7128941 YP_002390493.1 CDS leuS NC_011742.1 694085 696667 R 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; leucyl-tRNA synthetase complement(694085..696667) Escherichia coli S88 7132730 YP_002390494.1 CDS ybeL NC_011742.1 696902 697384 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 11373298, 12105207, 3320963, 7567469; hypothetical protein 696902..697384 Escherichia coli S88 7130490 YP_002390495.1 CDS rihA NC_011742.1 697429 698364 R Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively; pyrimidine-specific; ribonucleoside hydrolase 1 complement(697429..698364) Escherichia coli S88 7131208 YP_002390496.1 CDS gltL NC_011742.1 698482 699207 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11121068; Product type t : transporter; glutamate and aspartate transporter subunit ; ATP-binding component of ABC superfamily complement(698482..699207) Escherichia coli S88 7132720 YP_002390497.1 CDS gltK NC_011742.1 699207 699881 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11121068; Product type t : transporter; glutamate and aspartate transporter subunit ; membrane component of ABC superfamily complement(699207..699881) Escherichia coli S88 7130035 YP_002390498.1 CDS gltJ NC_011742.1 699881 700621 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11121068; Product type t : transporter; glutamate and aspartate transporter subunit ; membrane component of ABC superfamily complement(699881..700621) Escherichia coli S88 7130034 YP_002390499.1 CDS gltI NC_011742.1 700791 701699 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1091636, 1091635, 10493123, 8740179, 10972807; Product type t : transporter; glutamate and aspartate transporter subunit complement(700791..701699) Escherichia coli S88 7129854 YP_002390500.1 CDS ECS88_0691 NC_011742.1 702153 704030 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 702153..704030 Escherichia coli S88 7130032 YP_002390501.1 CDS lnt NC_011742.1 704157 705698 R Transfers the fatty acyl group on membrane lipoproteins; apolipoprotein N-acyltransferase complement(704157..705698) Escherichia coli S88 7130709 YP_002390502.1 CDS ybeX NC_011742.1 705723 706601 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1779764; Product type pt : putative transporter; putative protein involved in divalent ion export complement(705723..706601) Escherichia coli S88 7129367 YP_002390503.1 CDS ybeY NC_011742.1 706691 707158 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16511207; Product type pe : putative enzyme; putative metalloprotease complement(706691..707158) Escherichia coli S88 7131210 YP_002390504.1 CDS ybeZ NC_011742.1 707155 708234 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12762842; Product type pe : putative enzyme; putative enzyme with nucleoside triphosphate hydrolase domain complement(707155..708234) Escherichia coli S88 7131211 YP_002390505.1 CDS miaB NC_011742.1 708348 709772 R catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A); (dimethylallyl)adenosine tRNA methylthiotransferase complement(708348..709772) Escherichia coli S88 7131212 YP_002390506.1 CDS ubiF NC_011742.1 709918 711093 D catalyzes the formation of 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol from 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol; functions in the biosynthesis of ubiquinone or coenzyme Q; 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase 709918..711093 Escherichia coli S88 7128832 YP_002390508.1 CDS asnB NC_011742.1 712334 713998 R functions in asparagine biosynthesis; converts glutamine, aspartate, ATP, and water to glutamate, asparagine, pyrophosphate and AMP; asparagine synthetase B complement(712334..713998) Escherichia coli S88 7132006 YP_002390509.1 CDS nagD NC_011742.1 714254 715006 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16430214, 89343637; Product type e : enzyme; UMP phosphatase complement(714254..715006) Escherichia coli S88 7129947 YP_002390510.1 CDS nagC NC_011742.1 715054 716274 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15066032, 90136533, 91171292, 92114782, 92356048, 2190615, 2668691, 7545108; Product type r : regulator; DNA-binding transcriptional dual regulator, repressor of N-acetylglucosamine complement(715054..716274) Escherichia coli S88 7129659 YP_002390511.1 CDS nagA NC_011742.1 716283 717431 R catalyzes the formation of glucosamine 6-phosphate from N-acetylglucosamine 6-phosphate; N-acetylglucosamine-6-phosphate deacetylase complement(716283..717431) Escherichia coli S88 7129658 YP_002390512.1 CDS nagB NC_011742.1 717491 718291 R catalyzes the reversible formation of fructose 6-phosphate from glucosamine 6-phosphate; glucosamine-6-phosphate deaminase complement(717491..718291) Escherichia coli S88 7129656 YP_002390513.1 CDS nagE NC_011742.1 718624 720570 D phosphoenolpyruvate-dependent sugar phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIB is phosphorylated by IIA and then transfers the phosphoryl group to the sugar; IIC forms the translocation channel; PTS system N-acetyl glucosamine specific transporter subunits IIABC 718624..720570 Escherichia coli S88 7129657 YP_002390514.1 CDS ECS88_0707 NC_011742.1 721952 722422 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(721952..722422) Escherichia coli S88 7130712 YP_002390515.1 CDS ECS88_0708 NC_011742.1 722419 723588 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; Putative Glycosyl hydrolase, BNR repeat complement(722419..723588) Escherichia coli S88 7130713 YP_002390516.1 CDS dapA NC_011742.1 724434 725321 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative dihydrodipicolinate synthase complement(724434..725321) Escherichia coli S88 7129532 YP_002390517.1 CDS ECS88_0712 NC_011742.1 725325 726482 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative alcohol dehydrogenase complement(725325..726482) Escherichia coli S88 7130563 YP_002390518.1 CDS ECS88_0713 NC_011742.1 726610 727887 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 726610..727887 Escherichia coli S88 7130715 YP_002390519.1 CDS pdxA NC_011742.1 727880 728866 D catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate); 4-hydroxythreonine-4-phosphate dehydrogenase 2 727880..728866 Escherichia coli S88 7130716 YP_002390520.1 CDS ECS88_0715 NC_011742.1 728868 729629 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator, DeoR-family 728868..729629 Escherichia coli S88 7130717 YP_002390521.1 CDS glnS NC_011742.1 729849 731513 D catalyzes a two-step reaction, first charging a glutamine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; glutaminyl-tRNA synthetase 729849..731513 Escherichia coli S88 7130718 YP_002390522.1 CDS ybfM NC_011742.1 731962 733368 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2118530, 9636669; Product type pt : putative transporter; putative outer membrane porin 731962..733368 Escherichia coli S88 7130014 YP_002390523.1 CDS ybfN NC_011742.1 733418 733744 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; putative lipoprotein 733418..733744 Escherichia coli S88 7131216 YP_002390524.1 CDS fur NC_011742.1 733828 734274 R negatively regulates a number of operons that encode enzymes involved in iron transport; activated by manganese; forms a homodimer; ferric uptake regulator complement(733828..734274) Escherichia coli S88 7131217 YP_002390525.1 CDS ECS88_0720 NC_011742.1 734319 734573 D Evidence 6 : Doubtful CDS; hypothetical protein 734319..734573 Escherichia coli S88 7132156 YP_002390526.1 CDS fldA NC_011742.1 734563 735093 R An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group; flavodoxin FldA complement(734563..735093) Escherichia coli S88 7130719 YP_002390527.1 CDS ybfE NC_011742.1 735233 735526 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20223640, 12427949; Product type cp : cell process; LexA regulated protein complement(735233..735526) Escherichia coli S88 7129511 YP_002390528.1 CDS ybfF NC_011742.1 735666 736430 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15808744; Product type pe : putative enzyme; hypothetical protein complement(735666..736430) Escherichia coli S88 7131214 YP_002390529.1 CDS seqA NC_011742.1 736615 737160 D negative modulator of the initiation of chromosome replication; replication initiation regulator SeqA 736615..737160 Escherichia coli S88 7131215 YP_002390530.1 CDS pgm NC_011742.1 737186 738826 D catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate; phosphoglucomutase 737186..738826 Escherichia coli S88 7130576 YP_002390531.1 CDS potE NC_011742.1 738883 740202 R catalyzes the uptake of putrescine via a proton symport mechanism, as well as the efflux of putrescine by a putrescine/ornithine antiport system; putrescine transporter complement(738883..740202) Escherichia coli S88 7133693 YP_002390532.1 CDS speF NC_011742.1 740199 742397 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92041955; Product type e : enzyme; ornithine decarboxylase complement(740199..742397) Escherichia coli S88 7130745 YP_002390533.1 CDS kdpE NC_011742.1 743086 743763 R response regulator in two-component regulatory system with KdpD; regulates the kdp operon involved in potassium transport; DNA-binding transcriptional activator KdpE complement(743086..743763) Escherichia coli S88 7130629 YP_002390534.1 CDS kdpD NC_011742.1 743760 746444 R sensory histidine kinase in two-component regulatory system with KdpE; signal sensing protein; sensor protein KdpD complement(743760..746444) Escherichia coli S88 7130444 YP_002390535.1 CDS kdpC NC_011742.1 746437 747009 R One of the components of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions. The C subunit may be involved in assembly of the KDP complex; potassium-transporting ATPase subunit C complement(746437..747009) Escherichia coli S88 7130443 YP_002390536.1 CDS kdpB NC_011742.1 747018 749066 R One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; potassium-transporting ATPase subunit B complement(747018..749066) Escherichia coli S88 7130442 YP_002390537.1 CDS kdpA NC_011742.1 749089 750762 R catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; potassium-transporting ATPase subunit A complement(749089..750762) Escherichia coli S88 7130441 YP_002390538.1 CDS kdpF NC_011742.1 750762 750965 R Evidence 2b : Function of strongly homologous gene; PubMedId : 6146979; Product type f : factor; potassium ion accessory transporter subunit complement(750762..750965) Escherichia coli S88 7130440 YP_002390539.1 CDS ybfA NC_011742.1 751164 751370 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 751164..751370 Escherichia coli S88 7130445 YP_002390540.1 CDS ybgA NC_011742.1 751471 751980 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 6325460, 8387990; hypothetical protein 751471..751980 Escherichia coli S88 7131213 YP_002390541.1 CDS phr NC_011742.1 751977 753395 D UV-induced DNA repair; converts cyclobutane-type pyrimidine dimers created during exposure to UV ratiation to monomers; light dependent; deoxyribodipyrimidine photolyase 751977..753395 Escherichia coli S88 7131218 YP_002390542.1 CDS ybgH NC_011742.1 753437 754918 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15175316; Product type pt : putative transporter; putative transporter complement(753437..754918) Escherichia coli S88 7133732 YP_002390543.1 CDS ybgI NC_011742.1 755189 755932 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 14519207; putative hydrolase-oxidase 755189..755932 Escherichia coli S88 7131222 YP_002390544.1 CDS ybgJ NC_011742.1 755955 756611 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative hydrolase subunit 755955..756611 Escherichia coli S88 7131223 YP_002390545.1 CDS ybgK NC_011742.1 756605 757537 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative hydrolase subunit 756605..757537 Escherichia coli S88 7131224 YP_002390546.1 CDS ybgL NC_011742.1 757527 758261 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1729609; Product type pe : putative enzyme; LamB/YcsF family protein 757527..758261 Escherichia coli S88 7131225 YP_002390547.1 CDS nei NC_011742.1 758297 759088 D 5-formyluracil/5-hydroxymethyluracil DNA glycosylase; involved in base excision repair of DNA damaged by oxidation or by mutagenic agents; acts as DNA glycosylase that recognizes and removes damaged bases with a preference for oxidized pyrimidines; has apurinic/apyrimidinic lyase activity; endonuclease VIII 758297..759088 Escherichia coli S88 7131226 YP_002390548.1 CDS abrB NC_011742.1 759085 760131 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8002588; Product type ph : phenotype; hypothetical protein complement(759085..760131) Escherichia coli S88 7129692 YP_002390549.1 CDS gltA NC_011742.1 760805 762088 R type II enzyme; in Escherichia coli this enzyme forms a trimer of dimers which is allosterically inhibited by NADH and competitively inhibited by alpha-ketoglutarate; allosteric inhibition is lost when Cys206 is chemically modified which also affects hexamer formation; forms oxaloacetate and acetyl-CoA and water from citrate and coenzyme A; functions in TCA cycle, glyoxylate cycle and respiration; enzyme from Helicobacter pylori is not inhibited by NADH; type II citrate synthase complement(760805..762088) Escherichia coli S88 7131227 YP_002390550.1 CDS sdhC NC_011742.1 762797 763186 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6237244, 89076355, 89123360, 9521736, 99414342, 11259408, 3309132, 6383359, 9822661; Product type m : membrane component; succinate dehydrogenase cytochrome b556 large membrane subunit 762797..763186 Escherichia coli S88 7130029 YP_002390551.1 CDS sdhD NC_011742.1 763180 763527 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 82124790, 89076355, 9521736, 99414342, 6383359; Product type m : membrane component; succinate dehydrogenase cytochrome b556 small membrane subunit 763180..763527 Escherichia coli S88 7131375 YP_002390552.1 CDS sdhA NC_011742.1 763527 765293 D part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; succinate dehydrogenase flavoprotein subunit 763527..765293 Escherichia coli S88 7131376 YP_002390553.1 CDS sdhB NC_011742.1 765309 766025 D part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase; succinate dehydrogenase iron-sulfur subunit 765309..766025 Escherichia coli S88 7131373 YP_002390554.1 CDS sucA NC_011742.1 766386 769187 D SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide; 2-oxoglutarate dehydrogenase E1 component 766386..769187 Escherichia coli S88 7131374 YP_002390555.1 CDS sucB NC_011742.1 769202 770419 D component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA; dihydrolipoamide succinyltransferase 769202..770419 Escherichia coli S88 7131233 YP_002390556.1 CDS sucC NC_011742.1 770513 771679 D catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta 770513..771679 Escherichia coli S88 7131235 YP_002390557.1 CDS sucD NC_011742.1 771679 772548 D Catalyzes the only substrate-level phosphorylation in the TCA cycle; succinyl-CoA synthetase subunit alpha 771679..772548 Escherichia coli S88 7131237 YP_002390558.1 CDS ECS88_0755 NC_011742.1 772788 773903 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, TPR repeat protein 772788..773903 Escherichia coli S88 7131330 YP_002390559.1 CDS cydA NC_011742.1 775233 776801 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87299685, 89255232, 91035243, 1689724, 1724280, 2843510, 3138232; Product type c : carrier; cytochrome d terminal oxidase, subunit I 775233..776801 Escherichia coli S88 7130720 YP_002390560.1 CDS cydB NC_011742.1 776817 777956 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87299685, 89255232, 91035243, 2843510, 3138232; Product type c : carrier; cytochrome d terminal oxidase, subunit II 776817..777956 Escherichia coli S88 7130524 YP_002390561.1 CDS ybgE NC_011742.1 778084 778377 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 778084..778377 Escherichia coli S88 7130525 YP_002390562.1 CDS ybgC NC_011742.1 778527 778931 D catalyzes the hydrolysis of short chain aliphatic acyl-CoA thioesters; physiological role remains unknown; involved in phospholipid metabolism; part of the Tol/Pal system of proteins that are critical for maintaining the integrity of the cell envelope components; acyl-CoA thioester hydrolase YbgC 778527..778931 Escherichia coli S88 7131220 YP_002390563.1 CDS tolQ NC_011742.1 778928 779620 D membrane spanning protein in TolA-TolQ-TolR complex; involved in the tonB-independent uptake of group A colicins; colicin uptake protein TolQ 778928..779620 Escherichia coli S88 7131219 YP_002390564.1 CDS tolR NC_011742.1 779624 780052 D membrane spanning protein in TolA-TolQ-TolR complex; involved in the tonB-independent uptake of group A colicins; colicin uptake protein TolR 779624..780052 Escherichia coli S88 7133487 YP_002390565.1 CDS tolA NC_011742.1 780117 781367 D inner membrane component of 7 member Tol-Pal envelope-spanning complex; involved in maintaining cell envelope integrity; utilized by colicins and filamentous phages for import; interacts with TolB, Pal, and through TolB to various outer membrane porins; cell envelope integrity inner membrane protein TolA 780117..781367 Escherichia coli S88 7133488 YP_002390566.1 CDS tolB NC_011742.1 781500 782792 D forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA; translocation protein TolB 781500..782792 Escherichia coli S88 7133484 YP_002390567.1 CDS pal NC_011742.1 782827 783348 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11790745, 87133578, 92244043, 99403391, 11173492, 2687247; Product type lp : lipoprotein; peptidoglycan-associated outer membrane lipoprotein 782827..783348 Escherichia coli S88 7133485 YP_002390568.1 CDS ybgF NC_011742.1 783358 784149 D periplasmic protein that interacts with TolA; the tol-pal system is probably involved in maintaining cell envelope integrity; tol-pal system protein YbgF 783358..784149 Escherichia coli S88 7133156 YP_002390569.1 CDS nadA NC_011742.1 785295 786338 D 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate; quinolinate synthetase 785295..786338 Escherichia coli S88 7129874 YP_002390570.1 CDS pnuC NC_011742.1 786376 787095 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 219824, 90330519; Product type t : transporter; nicotinamide mononucleotide transporter 786376..787095 Escherichia coli S88 7129650 YP_002390571.1 CDS zitB NC_011742.1 787092 788033 R involved in zinc efflux across the cytoplasmic membrane; zinc transporter ZitB complement(787092..788033) Escherichia coli S88 7130578 YP_002390572.1 CDS ybgS NC_011742.1 788147 788527 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(788147..788527) Escherichia coli S88 7131885 YP_002390573.1 CDS aroG NC_011742.1 788843 789895 D catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive; phospho-2-dehydro-3-deoxyheptonate aldolase 788843..789895 Escherichia coli S88 7130086 YP_002390574.1 CDS gpmA NC_011742.1 790062 790814 R 2,3-bisphosphoglycerate-dependent; catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate; phosphoglyceromutase complement(790062..790814) Escherichia coli S88 7129927 YP_002390575.1 CDS galM NC_011742.1 791017 792057 R catalyzes the conversion of alpha-aldose to the beta-anomer; active on D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose; links the metabolism of lactose and galactose; aldose 1-epimerase complement(791017..792057) Escherichia coli S88 7130061 YP_002390576.1 CDS galK NC_011742.1 792051 793199 R catalyzes the formation of alpha-D-galactose 1-phosphate from D-galactose in galactose metabolism; galactokinase complement(792051..793199) Escherichia coli S88 7132173 YP_002390577.1 CDS galT NC_011742.1 793203 794249 R catalyzes the interconversion of UDP-galactose and galactose-1-P with UDP-galactose and glucose-1-P; galactose-1-phosphate uridylyltransferase complement(793203..794249) Escherichia coli S88 7132172 YP_002390578.1 CDS galE NC_011742.1 794259 795275 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89274199, 92253563, 92338916, 3022232, 6301942, 8564363, 8611559, 8931134, 9174344, 9271499, 9708982; Product type e : enzyme; UDP-galactose-4-epimerase complement(794259..795275) Escherichia coli S88 7132177 YP_002390579.1 CDS modF NC_011742.1 795538 797010 R contains 2 ATP-binding cassettes; involved in the transport of molybdenum; putative molybdenum transport ATP-binding protein ModF complement(795538..797010) Escherichia coli S88 7132170 YP_002390580.1 CDS modE NC_011742.1 797078 797866 R represses the modABCD operon and activates the moaABCD and napFDAGHBC operons; DNA-binding transcriptional regulator ModE complement(797078..797866) Escherichia coli S88 7128860 YP_002390581.1 CDS ybhT NC_011742.1 797995 798144 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 797995..798144 Escherichia coli S88 7128859 YP_002390582.1 CDS modA NC_011742.1 798311 799084 D with ModCB is involved in the high-affinity transport of molybdate; molybdate transporter periplasmic protein 798311..799084 Escherichia coli S88 7130106 YP_002390583.1 CDS modB NC_011742.1 799084 799773 D part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE; molybdate ABC transporter permease protein 799084..799773 Escherichia coli S88 7128855 YP_002390584.1 CDS modC NC_011742.1 799776 800834 D Part of the ABC transporter complex modABC involved in molybdenum import; molybdate transporter ATP-binding protein 799776..800834 Escherichia coli S88 7128856 YP_002390585.1 CDS ybhA NC_011742.1 800835 801653 R YbhA; catalyzes the dephosphorylation of pyridoxal phosphate, fructose 1,6-bisphosphate, erythrose 4-phosphate and p-nitrophenyl phosphate; purine and pyrimidine nucleotides are secondary substrates; phosphotransferase activity observed when using monophosphates as phosphate donor; member of the haloacid dehalogenase-like hydrolases superfamily; phosphotransferase complement(800835..801653) Escherichia coli S88 7128857 YP_002390586.1 CDS pgl NC_011742.1 801808 802803 D catalyzes the hydrolysis of 6-phosphogluconolactone to 6-phosphogluconate; 6-phosphogluconolactonase 801808..802803 Escherichia coli S88 7130087 YP_002390587.1 CDS ybhD NC_011742.1 802844 803860 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(802844..803860) Escherichia coli S88 7133692 YP_002390588.1 CDS ybhH NC_011742.1 803981 805033 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 803981..805033 Escherichia coli S88 7130090 YP_002390589.1 CDS ybhJ NC_011742.1 806725 808986 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11782506; Product type pe : putative enzyme; hypothetical protein 806725..808986 Escherichia coli S88 7130095 YP_002390590.1 CDS ybhC NC_011742.1 809127 810410 R outer membrane lipoprotein that catalyzes the hydrolysis of the thioester bond in palmitoyl-CoA; YbhC localizes to the cellular poles; member of pectinesterase family; putative pectinesterase complement(809127..810410) Escherichia coli S88 7130096 YP_002390591.1 CDS ybhB NC_011742.1 810562 811038 R YbhB; similar to rat and human kinase inhibitory proteins; putative kinase inhibitor protein complement(810562..811038) Escherichia coli S88 7130089 YP_002390592.1 CDS bioA NC_011742.1 811097 812386 R catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate; adenosylmethionine--8-amino-7-oxononanoate transaminase complement(811097..812386) Escherichia coli S88 7130088 YP_002390593.1 CDS bioB NC_011742.1 812473 813513 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11834738, 12475249, 14704425, 14967041, 20250955, 89066784, 94170810, 94190882, 97382445, 11686925; Product type e : enzyme; biotin synthase 812473..813513 Escherichia coli S88 7129120 YP_002390594.1 CDS bioF NC_011742.1 813510 814664 D catalyzes the formation of 8-amino-7-oxononanoate from 6-carboxyhexanoyl-CoA and L-alanine; 8-amino-7-oxononanoate synthase 813510..814664 Escherichia coli S88 7129121 YP_002390595.1 CDS bioC NC_011742.1 814651 815406 D putative methyltransferase; acyl carrier protein involved in an unidentified step in the synthesis of pimeloyl-CoA, a biotin precursor; member of the bio operon (bioABFCD); in Escherichia coli, bioC-null mutants require biotin for growth; biotin biosynthesis protein BioC 814651..815406 Escherichia coli S88 7129124 YP_002390596.1 CDS bioD NC_011742.1 815399 816076 D DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium; dithiobiotin synthetase 815399..816076 Escherichia coli S88 7129122 YP_002390597.1 CDS uvrB NC_011742.1 816655 818676 D 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; excinuclease ABC subunit B 816655..818676 Escherichia coli S88 7129123 YP_002390598.1 CDS ybhK NC_011742.1 818714 819622 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16272399; Product type pe : putative enzyme; putative transferase with NAD(P)-binding Rossmann-fold domain; UPF0052 family complement(818714..819622) Escherichia coli S88 7132459 YP_002390599.1 CDS moaA NC_011742.1 820019 821008 D together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z; molybdenum cofactor biosynthesis protein A 820019..821008 Escherichia coli S88 7130097 YP_002390600.1 CDS moaB NC_011742.1 821030 821542 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93368423; Product type pf : putative factor; molybdopterin biosynthesis protein B 821030..821542 Escherichia coli S88 7128848 YP_002390601.1 CDS moaC NC_011742.1 821545 822030 D MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis; molybdenum cofactor biosynthesis protein MoaC 821545..822030 Escherichia coli S88 7128849 YP_002390602.1 CDS moaD NC_011742.1 822023 822268 D catalyzes the conversion of molybdopterin precursor Z into molybdopterin; molybdopterin synthase small subunit 822023..822268 Escherichia coli S88 7128850 YP_002390603.1 CDS moaE NC_011742.1 822270 822722 D catalyzes the conversion of molybdopterin precursor Z into molybdopterin; molybdopterin guanine dinucleotide biosynthesis protein MoaE 822270..822722 Escherichia coli S88 7128851 YP_002390604.1 CDS ybhL NC_011742.1 822859 823563 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 822859..823563 Escherichia coli S88 7128852 YP_002390605.1 CDS ybhM NC_011742.1 823769 824482 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 823769..824482 Escherichia coli S88 7130098 YP_002390606.1 CDS ybhN NC_011742.1 824518 825474 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(824518..825474) Escherichia coli S88 7130099 YP_002390607.1 CDS ybhO NC_011742.1 825474 826715 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20102623, 10634942; Product type e : enzyme; cardiolipin synthase 2 complement(825474..826715) Escherichia coli S88 7130100 YP_002390608.1 CDS ybhP NC_011742.1 826712 827473 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative metal-dependent hydrolase complement(826712..827473) Escherichia coli S88 7130101 YP_002390609.1 CDS ybhQ NC_011742.1 827606 828016 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 827606..828016 Escherichia coli S88 7130102 YP_002390610.1 CDS ybhR NC_011742.1 827978 829084 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter subunit: permease component of ABC superfamily complement(827978..829084) Escherichia coli S88 7130103 YP_002390611.1 CDS ybhS NC_011742.1 829095 830228 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter subunit: permease component of ABC superfamily complement(829095..830228) Escherichia coli S88 7130104 YP_002390612.1 CDS ybhF NC_011742.1 830221 831957 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter fused subunits of ABC superfamily: ATP-binding components complement(830221..831957) Escherichia coli S88 7130105 YP_002390613.1 CDS ybhG NC_011742.1 831950 832948 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16092522; Product type pt : putative transporter; hypothetical protein complement(831950..832948) Escherichia coli S88 7130091 YP_002390614.1 CDS ybiH NC_011742.1 832948 833619 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(832948..833619) Escherichia coli S88 7130092 YP_002390615.1 CDS rhlE NC_011742.1 833848 835209 D this helicase is not essential cell growth; ATP-dependent RNA helicase RhlE 833848..835209 Escherichia coli S88 7130110 YP_002390616.1 CDS ybiA NC_011742.1 835442 835747 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(835442..835747) Escherichia coli S88 7132708 YP_002390617.1 CDS dinG NC_011742.1 835746 837896 D helicase involved in DNA repair and perhaps also replication; ATP-dependent DNA helicase DinG 835746..837896 Escherichia coli S88 7130107 YP_002390618.1 CDS ybiB NC_011742.1 837924 838886 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; glycosyl transferase family protein 837924..838886 Escherichia coli S88 7130208 YP_002390619.1 CDS ybiC NC_011742.1 839027 840112 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8405966; Product type pe : putative enzyme; hypothetical protein 839027..840112 Escherichia coli S88 7130108 YP_002390620.1 CDS ybiJ NC_011742.1 840340 840600 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(840340..840600) Escherichia coli S88 7130109 YP_002390621.1 CDS ybiI NC_011742.1 840865 841131 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(840865..841131) Escherichia coli S88 7130112 YP_002390622.1 CDS ybiX NC_011742.1 841205 841882 R Evidence 4 : Homologs of previously reported genes of unknown function; putative hydroxylase complement(841205..841882) Escherichia coli S88 7130111 YP_002390623.1 CDS fiu NC_011742.1 842098 844380 R Fiu; YbiL; porin involved in the uptake of iron complexed with catecholate siderophores (e.g. dihydroxybenzoylserine, dihydroxybenzoate) and beta lactam agents; Fiu interacts with TonB which provides the energy required for transport across the outer membrane; acts as a receptor for iron-siderophores and microcins E492, M, and H47; outer membrane protein; catecholate siderophore receptor Fiu complement(842098..844380) Escherichia coli S88 7130122 YP_002390624.1 CDS ybiM NC_011742.1 844645 845049 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(844645..845049) Escherichia coli S88 7129503 YP_002390625.1 CDS ybiN NC_011742.1 845181 846107 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative SAM-dependent methyltransferase 845181..846107 Escherichia coli S88 7130113 YP_002390626.1 CDS ybiO NC_011742.1 846104 848329 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; hypothetical protein complement(846104..848329) Escherichia coli S88 7130114 YP_002390627.1 CDS glnQ NC_011742.1 848446 849168 R similar to ATP-binding component of ABC transporters; glutamine ABC transporter ATP-binding protein complement(848446..849168) Escherichia coli S88 7130115 YP_002390628.1 CDS glnP NC_011742.1 849165 849824 R similar to permease component of ABC transporters; mutations impair ability of Escherichia coli to transport and utilize glutamine; glutamine ABC transporter permease protein complement(849165..849824) Escherichia coli S88 7130013 YP_002390629.1 CDS glnH NC_011742.1 849963 850709 R similar to periplasmic-binding component of ABC transporters; glutamine ABC transporter periplasmic protein complement(849963..850709) Escherichia coli S88 7130012 YP_002390630.1 CDS dps NC_011742.1 851113 851616 R binds DNA in a non-sequence-specific manner and is abundant during stationary phase; forms a DNA-protein crystal that protects DNA from damage; required for normal starvation response and long-term stationary viability; forms a homododecameric complex and sequesters iron which provides protection against oxidative damage; DNA starvation/stationary phase protection protein Dps complement(851113..851616) Escherichia coli S88 7130009 YP_002390631.1 CDS rhtA NC_011742.1 851915 852802 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12648727, 8021175; Product type t : transporter; threonine and homoserine efflux system complement(851915..852802) Escherichia coli S88 7130237 YP_002390632.1 CDS ompX NC_011742.1 853155 853670 D OmpX; involved in cell adhesion; forms an eight-stranded antiparallel beta-barrel that protrudes from the cell surface; mutations in the gene increase cell-surface contact in fimbriated strains but decrease contact in nonfimbriated strains; outer membrane protein X 853155..853670 Escherichia coli S88 7132711 YP_002390633.1 CDS ybiP NC_011742.1 853720 855303 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16514146; Product type pe : putative enzyme; putative enzyme, UPF0141 family, inner membrane complement(853720..855303) Escherichia coli S88 7133132 YP_002390634.1 CDS ECS88_0834 NC_011742.1 855575 855703 R Evidence 6 : Doubtful CDS; hypothetical protein complement(855575..855703) Escherichia coli S88 7130116 YP_002390635.1 CDS mntR NC_011742.1 855889 856356 D Transcriptional regulator that represses the manganese transporter MntH when manganese is present; manganese transport regulator MntR 855889..856356 Escherichia coli S88 7131327 YP_002390636.1 CDS ybiR NC_011742.1 856353 857471 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 856353..857471 Escherichia coli S88 7128847 YP_002390637.1 CDS ybiS NC_011742.1 857529 858449 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 10493123, 9298646; hypothetical protein complement(857529..858449) Escherichia coli S88 7130117 YP_002390638.1 CDS ybiT NC_011742.1 858668 860260 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11916677; Product type pt : putative transporter; putative transporter fused subunits of ABC superfamily: ATP-binding components 858668..860260 Escherichia coli S88 7130118 YP_002390639.1 CDS ybiV NC_011742.1 860460 861275 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15657928; Product type e : enzyme; type II HAD phosphatase complement(860460..861275) Escherichia coli S88 7130119 YP_002390640.1 CDS ybiW NC_011742.1 861421 863853 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16218870; Product type pe : putative enzyme; putative glycyl radical cofactor protein complement(861421..863853) Escherichia coli S88 7130120 YP_002390641.1 CDS ybiY NC_011742.1 863859 864758 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15581584; Product type pe : putative enzyme; putative AdoMet-dependent glycyl radical activating enzyme complement(863859..864758) Escherichia coli S88 7130121 YP_002390642.1 CDS fsaA NC_011742.1 864889 865551 D similar to transaldolase from Escherichia coli; many organisms have multiple copies; fructose-6-phosphate aldolase 864889..865551 Escherichia coli S88 7130123 YP_002390643.1 CDS moeB NC_011742.1 865627 866376 R ATP-dependent adenylate transferase, transfers adenyl moiety to the MoeD subunit of molybdopterin synthase; molybdopterin biosynthesis protein MoeB complement(865627..866376) Escherichia coli S88 7132842 YP_002390644.1 CDS moeA NC_011742.1 866376 867611 R is involved in the formation of active molybdenum cofactor and the chelation of molybdenum; molybdopterin biosynthesis protein MoeA complement(866376..867611) Escherichia coli S88 7128862 YP_002390645.1 CDS iaaA NC_011742.1 867815 868780 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15159592, 20508248, 3045084, 7984428; Product type e : enzyme; L-asparaginase 867815..868780 Escherichia coli S88 7128861 YP_002390646.1 CDS yliA NC_011742.1 868800 870638 D with GsiBCD is involved in glutathione import; GsiA contains 2 ATP-binding domains; glutathione transporter ATP-binding protein 868800..870638 Escherichia coli S88 7131601 YP_002390647.1 CDS yliB NC_011742.1 870658 872196 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 17366475; Product type pt : putative transporter; putative peptide transporter subunit: periplasmic-binding component of ABC superfamily 870658..872196 Escherichia coli S88 7131108 YP_002390648.1 CDS yliC NC_011742.1 872214 873134 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative peptide transporter permease subunit: membrane component of ABC superfamily 872214..873134 Escherichia coli S88 7131109 YP_002390649.1 CDS yliD NC_011742.1 873137 874048 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative peptide transporter permease subunit: membrane component of ABC superfamily 873137..874048 Escherichia coli S88 7131110 YP_002390650.1 CDS yliE NC_011742.1 874225 876573 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 874225..876573 Escherichia coli S88 7131111 YP_002390651.1 CDS yliF NC_011742.1 876581 877909 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15380559; Product type pe : putative enzyme; putative diguanylate cyclase 876581..877909 Escherichia coli S88 7131112 YP_002390652.1 CDS rimO NC_011742.1 877956 879281 R catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit; ribosomal protein S12 methylthiotransferase complement(877956..879281) Escherichia coli S88 7131113 YP_002390653.1 CDS bssR NC_011742.1 879494 879877 D BssS; regulator of biofilm through signal secretion; disruption of this gene in Escherichia coli led to effects on biofilm formation, alteration in expression of a number of genes and mutations in bssS led to defects in indole transport and autoinducer-2 uptake and processing; biofilm formation regulatory protein BssR 879494..879877 Escherichia coli S88 7131114 YP_002390654.1 CDS yliI NC_011742.1 879988 881103 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16522795, 16864586; Product type e : enzyme; PQQ-dependent aldose sugar dehydrogenase precursor (asd) 879988..881103 Escherichia coli S88 7129134 YP_002390655.1 CDS yliJ NC_011742.1 881100 881726 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative glutathione S-transferase complement(881100..881726) Escherichia coli S88 7131115 YP_002390656.1 CDS dacC NC_011742.1 881973 883175 D penicillin-binding protein 6a; removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors; one of four, DD-carboxypeptidase low-molecular weight penicillin-binding proteins that remove terminal D-alanine from pentapeptide side chains; D-alanyl-D-alanine carboxypeptidase fraction C 881973..883175 Escherichia coli S88 7131116 YP_002390657.1 CDS deoR NC_011742.1 883222 883980 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89231635, 89336786, 92231401, 2994018; Product type r : regulator; DNA-binding transcriptional repressor DeoR complement(883222..883980) Escherichia coli S88 7130555 YP_002390658.1 CDS ybjG NC_011742.1 884038 884634 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15778224; Product type e : enzyme; undecaprenyl pyrophosphate phosphatase complement(884038..884634) Escherichia coli S88 7130188 YP_002390659.1 CDS cmr NC_011742.1 884919 886151 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10022825, 12578981, 14688269, 21217867, 21450803, 9079913, 9644262, 99030337, 8655497; Product type t : transporter; multidrug efflux system protein 884919..886151 Escherichia coli S88 7130127 YP_002390660.1 CDS ybjH NC_011742.1 886192 886458 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(886192..886458) Escherichia coli S88 7131935 YP_002390661.1 CDS ybjI NC_011742.1 886543 887358 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15808744; Product type pe : putative enzyme; putative phosphatase complement(886543..887358) Escherichia coli S88 7130128 YP_002390662.1 CDS ybjJ NC_011742.1 887358 888566 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter complement(887358..888566) Escherichia coli S88 7130129 YP_002390663.1 CDS ybjK NC_011742.1 888650 889186 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 888650..889186 Escherichia coli S88 7130130 YP_002390664.1 CDS ybjL NC_011742.1 889361 891046 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; hypothetical protein complement(889361..891046) Escherichia coli S88 7131328 YP_002390665.1 CDS ybjM NC_011742.1 891316 891693 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 891316..891693 Escherichia coli S88 7130132 YP_002390666.1 CDS grxA NC_011742.1 891723 891980 R functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase; also involved in reducing some disulfides in a coupled system with glutathione reductase; glutaredoxin 1 complement(891723..891980) Escherichia coli S88 7130133 YP_002390667.1 CDS ybjC NC_011742.1 892140 892427 D YbjC; located in the same operon as the nfsA gene; member of the soxRS regulon which mediates in part the increased levels of superoxide in response to oxidative stress; induced by paraquat; regulated by SoxS; unknown function; hypothetical protein 892140..892427 Escherichia coli S88 7130073 YP_002390668.1 CDS nfsA NC_011742.1 892411 893133 D NADPH-dependent; oxygen-insensitive; catalyzes the reduction of nitroaromatic compounds; nitroreductase A 892411..893133 Escherichia coli S88 7130124 YP_002390669.1 CDS rimK NC_011742.1 893194 894096 D responsible for the addition of glutamate residues to the C-terminus of ribosomal protein S6; ribosomal protein S6 modification protein 893194..894096 Escherichia coli S88 7129705 YP_002390670.1 CDS ybjN NC_011742.1 894184 894660 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 894184..894660 Escherichia coli S88 7132725 YP_002390671.1 CDS potF NC_011742.1 895010 896122 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93106992, 9651355, 9298646, 8416922; Product type t : transporter; putrescine transporter subunit: periplasmic-binding component of ABC superfamily 895010..896122 Escherichia coli S88 7130134 YP_002390672.1 CDS potG NC_011742.1 896319 897350 D part of the PotFGHI ATP-dependent putrescine transporter; putrescine transporter ATP-binding subunit 896319..897350 Escherichia coli S88 7130746 YP_002390673.1 CDS potH NC_011742.1 897360 898313 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93106992; Product type t : transporter; putrescine transporter subunit: membrane component of ABC superfamily 897360..898313 Escherichia coli S88 7130747 YP_002390674.1 CDS potI NC_011742.1 898310 899155 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93106992; Product type t : transporter; putrescine transporter subunit: membrane component of ABC superfamily 898310..899155 Escherichia coli S88 7130748 YP_002390675.1 CDS ybjO NC_011742.1 899215 899703 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 899215..899703 Escherichia coli S88 7130749 YP_002390676.1 CDS rumB NC_011742.1 899744 900871 D RNA uridine methyltransferase B; catalyzes the formation of 5-methyl-uridine at position 747 in 23S rRNA; 23S rRNA methyluridine methyltransferase 899744..900871 Escherichia coli S88 7130135 YP_002390677.1 CDS artJ NC_011742.1 900900 901631 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93273744, 9298646, 9600841, 8801422; Product type t : transporter; arginine transporter subunit ; periplasmic-binding component of ABC superfamily complement(900900..901631) Escherichia coli S88 7131311 YP_002390678.1 CDS artM NC_011742.1 901856 902524 R with ArtPQJI acts to transport arginine across the inner membrane; arginine transporter permease subunit ArtM complement(901856..902524) Escherichia coli S88 7129935 YP_002390679.1 CDS artQ NC_011742.1 902524 903240 R with ArtPMJI transports arginine across the inner membrane; arginine transporter permease subunit ArtQ complement(902524..903240) Escherichia coli S88 7129936 YP_002390680.1 CDS artI NC_011742.1 903247 903978 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93273744, 9298646, 9600841, 8801422, 9740056; Product type t : transporter; arginine transporter subunit ; periplasmic-binding component of ABC superfamily complement(903247..903978) Escherichia coli S88 7129938 YP_002390681.1 CDS artP NC_011742.1 903996 904724 R With ArtMQJI transports arginine across the inner membrane; arginine transporter ATP-binding subunit complement(903996..904724) Escherichia coli S88 7129934 YP_002390682.1 CDS ybjQ NC_011742.1 905582 905905 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 905582..905905 Escherichia coli S88 7130137 YP_002390683.1 CDS ybjR NC_011742.1 905902 906732 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative cell wall amidase and lipoprotein 905902..906732 Escherichia coli S88 7130138 YP_002390684.1 CDS ybjS NC_011742.1 906729 907742 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative NAD(P)H-binding oxidoreductase with NAD(P)-binding Rossmann-fold domain complement(906729..907742) Escherichia coli S88 7130139 YP_002390685.1 CDS ybjT NC_011742.1 907841 909271 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative NAD(P)-binding Rossmann-fold domain complement(907841..909271) Escherichia coli S88 7130140 YP_002390686.1 CDS ltaE NC_011742.1 909282 910283 R low- specificity; catalyzes the formation of acetaldehyde and glycine from L-threonine; acts on L-threonine, L-allo-threonine, L-threo-phenylserine, and L-erythro-phenylserine; L-threonine aldolase complement(909282..910283) Escherichia coli S88 7130141 YP_002390687.1 CDS poxB NC_011742.1 910320 912038 R catalyzes the formation of acetate from pyruvate; pyruvate dehydrogenase complement(910320..912038) Escherichia coli S88 7129391 YP_002390688.1 CDS hcr NC_011742.1 912171 913139 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20117674; Product type e : enzyme; HCP oxidoreductase, NADH-dependent complement(912171..913139) Escherichia coli S88 7130751 YP_002390689.1 CDS hcp NC_011742.1 913151 914803 R catalyzes the reduction of hydroxylamine to ammonia and water; hydroxylamine reductase complement(913151..914803) Escherichia coli S88 7128888 YP_002390690.1 CDS ybjE NC_011742.1 914947 915846 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter complement(914947..915846) Escherichia coli S88 7128887 YP_002390691.1 CDS ECS88_0896 NC_011742.1 915824 915973 D Evidence 6 : Doubtful CDS; hypothetical protein 915824..915973 Escherichia coli S88 7130126 YP_002390692.1 CDS aqpZ NC_011742.1 916167 916862 R porin involved in osmoregulation allowing water to move into and out of the cell in response to osmotic pressure; aquaporin Z complement(916167..916862) Escherichia coli S88 7130722 YP_002390693.1 CDS ybjD NC_011742.1 917288 918946 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative nucleoside triphosphate hydrolase domain 917288..918946 Escherichia coli S88 7133079 YP_002390694.1 CDS ybjX NC_011742.1 918943 919935 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(918943..919935) Escherichia coli S88 7130125 YP_002390695.1 CDS macA NC_011742.1 920050 921165 D confers macrolide resistance via active drug efflux; macrolide transporter subunit MacA 920050..921165 Escherichia coli S88 7130142 YP_002390696.1 CDS macB NC_011742.1 921162 923108 D with MacA is involved in the export of macrolide; macrolide transporter ATP-binding /permease protein 921162..923108 Escherichia coli S88 7129402 YP_002390697.1 CDS cspD NC_011742.1 923181 923405 R inhibits DNA replication at both initiation and elongation steps; stationary phase and starvation inducible; stationary phase/starvation inducible regulatory protein CspD complement(923181..923405) Escherichia coli S88 7129403 YP_002390698.1 CDS clpS NC_011742.1 923728 924048 D involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation; binds to the N-terminal domain of the chaperone ClpA; ATP-dependent Clp protease adaptor protein ClpS 923728..924048 Escherichia coli S88 7130496 YP_002390699.1 CDS clpA NC_011742.1 924079 926355 D ATPase and specificity subunit of the ClpA-ClpP ATP dependent serine protease; directs protease to specific substrates; ATP-dependent Clp protease ATP-binding subunit 924079..926355 Escherichia coli S88 7131931 YP_002390700.1 CDS ECS88_0905 NC_011742.1 927062 928051 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, CRISPR-associated protein 927062..928051 Escherichia coli S88 7131928 YP_002390701.1 CDS ECS88_0906 NC_011742.1 928048 931281 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative CRISPR-associated helicase 928048..931281 Escherichia coli S88 7130723 YP_002390702.1 CDS ECS88_0907 NC_011742.1 931611 932918 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein CRISPR-associated 931611..932918 Escherichia coli S88 7130724 YP_002390703.1 CDS ECS88_0910 NC_011742.1 933849 934850 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein CRISPR-associated 933849..934850 Escherichia coli S88 7130727 YP_002390704.1 CDS ECS88_0911 NC_011742.1 934819 935415 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein CRISPR-associated 934819..935415 Escherichia coli S88 7130728 YP_002390705.1 CDS infA NC_011742.1 936457 936675 R stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 complement(936457..936675) Escherichia coli S88 7132005 YP_002390706.1 CDS aat NC_011742.1 936960 937664 R leucyltransferase; phenylalanyltransferse; functions in the N-end rule pathway; transfers Leu, Phe, Met, from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys; leucyl/phenylalanyl-tRNA--protein transferase complement(936960..937664) Escherichia coli S88 7131633 YP_002390707.1 CDS cydC NC_011742.1 937706 939427 R in Escherichia coli the CydCD ABC transporter exports cysteine and glutathione into the periplasm in order to maintain redox balance; important for cytochrome bd and c; cysteine/glutathione ABC transporter membrane/ATP-binding component complement(937706..939427) Escherichia coli S88 7132023 YP_002390708.1 CDS cydD NC_011742.1 939428 941194 R in Escherichia coli the CydCD ABC transporter exports cysteine and glutathione into the periplasm in order to maintain redox balance; important for cytochrome bd and c; cysteine/glutathione ABC transporter membrane/ATP-binding component complement(939428..941194) Escherichia coli S88 7130526 YP_002390709.1 CDS trxB NC_011742.1 941317 942282 R catalyzes the transfer of electrons from NADPH to thioredoxin; FAD/NAD(P) binding; thioredoxin reductase complement(941317..942282) Escherichia coli S88 7130527 YP_002390710.1 CDS lrp NC_011742.1 942826 943320 D mediates a global response to leucine; acts as a regulator for several genes involved in the high-affinity branched-chain amino acid transport system; leucine-responsive transcriptional regulator 942826..943320 Escherichia coli S88 7130356 YP_002390711.1 CDS ftsK NC_011742.1 943455 947498 D DNA-binding membrane protein required for chromosome resolution and partitioning; DNA translocase FtsK 943455..947498 Escherichia coli S88 7129389 YP_002390712.1 CDS lolA NC_011742.1 947654 948268 D participates with LolB in the incorporation of lipoprotein into the outer membrane; outer-membrane lipoprotein carrier protein 947654..948268 Escherichia coli S88 7132851 YP_002390713.1 CDS ycaJ NC_011742.1 948279 949622 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 7567469, 7628437, 11459952, 11029431; Product type cp : cell process; recombination factor protein RarA 948279..949622 Escherichia coli S88 7129368 YP_002390714.1 CDS serS NC_011742.1 949713 951005 D 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; seryl-tRNA synthetase 949713..951005 Escherichia coli S88 7130147 YP_002390715.1 CDS dmsA NC_011742.1 951244 953688 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91008971, 92011349, 94171715, 10801884, 3062312; Product type e : enzyme; dimethyl sulfoxide reductase, anaerobic, subunit A 951244..953688 Escherichia coli S88 7130582 YP_002390716.1 CDS dmsB NC_011742.1 953699 954316 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91070067, 91355180, 92011349, 3062312; Product type e : enzyme; dimethyl sulfoxide reductase, anaerobic, subunit B 953699..954316 Escherichia coli S88 7130216 YP_002390717.1 CDS dmsC NC_011742.1 954318 955181 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91008971, 92011349, 3062312, 8429002; Product type e : enzyme; dimethyl sulfoxide reductase, anaerobic, subunit C 954318..955181 Escherichia coli S88 7130217 YP_002390718.1 CDS ycaC NC_011742.1 955217 955843 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 9782055, 3062312, 11714269; Product type pe : putative enzyme; putative hydrolase complement(955217..955843) Escherichia coli S88 7130218 YP_002390719.1 CDS ycaD NC_011742.1 956157 957305 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative MFS family transporter protein 956157..957305 Escherichia coli S88 7130144 YP_002390720.1 CDS pflA NC_011742.1 957402 958142 R activates pyruvate formate-lyase 1 under anaerobic conditions; pyruvate formate lyase-activating enzyme 1 complement(957402..958142) Escherichia coli S88 7130145 YP_002390721.1 CDS pflB NC_011742.1 958334 960616 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91064082, 92276323, 10504733, 1310545, 2651404, 3053170, 9629924; Product type e : enzyme; pyruvate formate lyase I complement(958334..960616) Escherichia coli S88 7133680 YP_002390722.1 CDS focA NC_011742.1 960671 961528 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94293770, 2651404; Product type t : transporter; formate transporter complement(960671..961528) Escherichia coli S88 7133681 YP_002390723.1 CDS ycaO NC_011742.1 961934 963694 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(961934..963694) Escherichia coli S88 7132812 YP_002390724.1 CDS ycaP NC_011742.1 963824 964516 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 963824..964516 Escherichia coli S88 7130149 YP_002390725.1 CDS serC NC_011742.1 964715 965803 D catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine; phosphoserine aminotransferase 964715..965803 Escherichia coli S88 7130150 YP_002390726.1 CDS aroA NC_011742.1 965874 967157 D catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase 965874..967157 Escherichia coli S88 7130581 YP_002390727.1 CDS ycaL NC_011742.1 967327 968091 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative lipoprotein with metallohydrolase domain 967327..968091 Escherichia coli S88 7133105 YP_002390728.1 CDS cmk NC_011742.1 968264 968947 D Catalyzes the formation of (d)CDP from ATP and (d)CMP; cytidylate kinase 968264..968947 Escherichia coli S88 7130148 YP_002390729.1 CDS rpsA NC_011742.1 969058 970731 D 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; 30S ribosomal protein S1 969058..970731 Escherichia coli S88 7131934 YP_002390730.1 CDS ihfB NC_011742.1 970891 971175 D This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control; integration host factor subunit beta 970891..971175 Escherichia coli S88 7133784 YP_002390731.1 CDS ycaI NC_011742.1 971381 973645 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 971381..973645 Escherichia coli S88 7131617 YP_002390732.1 CDS msbA NC_011742.1 973682 975430 D involved in the transport of lipid A across the inner membrane; lipid transporter ATP-binding/permease protein 973682..975430 Escherichia coli S88 7130146 YP_002390733.1 CDS lpxK NC_011742.1 975427 976413 D transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate; tetraacyldisaccharide 4'-kinase 975427..976413 Escherichia coli S88 7129613 YP_002390734.1 CDS ycaQ NC_011742.1 976450 977682 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 976450..977682 Escherichia coli S88 7129385 YP_002390735.1 CDS ycaR NC_011742.1 977734 977916 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 977734..977916 Escherichia coli S88 7130151 YP_002390736.1 CDS kdsB NC_011742.1 977913 978659 D CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS; 3-deoxy-manno-octulosonate cytidylyltransferase 977913..978659 Escherichia coli S88 7130152 YP_002390737.1 CDS ycbJ NC_011742.1 978813 979706 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 978813..979706 Escherichia coli S88 7130447 YP_002390738.1 CDS ycbC NC_011742.1 979683 980462 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(979683..980462) Escherichia coli S88 7130156 YP_002390739.1 CDS smtA NC_011742.1 980598 981383 D involved in cellular zinc and cadmium homeostasis by binding excess metal ions to its cysteine sulfurs and histidine nitrogens; expression of smtA in cyanobacteria is repressed by SmtB at low concentrations of zinc; NO elicits release of Zn ions from SmtA; putative metallothionein SmtA 980598..981383 Escherichia coli S88 7130154 YP_002390740.1 CDS mukF NC_011742.1 981380 982702 D acts with MukB and MukE to condense the chromosome and allow for segregation during cell division; condesin subunit F 981380..982702 Escherichia coli S88 7130615 YP_002390741.1 CDS mukE NC_011742.1 982710 983387 D acts with MukB and MukF to condense the chromosome and allow for segregation during cell division; condesin subunit E 982710..983387 Escherichia coli S88 7129629 YP_002390742.1 CDS mukB NC_011742.1 983387 987847 D SMC (structural maintenance of chromosomes) family of proteins; involved in chromosome condensatin and partitioning; forms a homodimer and the C-terminal is essential for DNA-binding activity while the purified N-terminal domain binds FtsZ; mutations result in cell division defects; cell division protein MukB 983387..987847 Escherichia coli S88 7129628 YP_002390743.1 CDS ycbB NC_011742.1 988108 989955 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein 988108..989955 Escherichia coli S88 7129627 YP_002390744.1 CDS ycbK NC_011742.1 990136 990684 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 990136..990684 Escherichia coli S88 7130153 YP_002390745.1 CDS ycbL NC_011742.1 990711 991358 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 14529289; Product type pe : putative enzyme; putative metal-binding hydrolase 990711..991358 Escherichia coli S88 7130157 YP_002390746.1 CDS aspC NC_011742.1 991408 992598 R catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate; aromatic amino acid aminotransferase complement(991408..992598) Escherichia coli S88 7130158 YP_002390747.1 CDS ompF NC_011742.1 992783 993871 R outer membrane porin F; 1a; Ia; b; outer membrane protein F complement(992783..993871) Escherichia coli S88 7129951 YP_002390748.1 CDS asnC NC_011742.1 994473 995873 R 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; asparaginyl-tRNA synthetase complement(994473..995873) Escherichia coli S88 7133125 YP_002390749.1 CDS pncB NC_011742.1 996042 997244 R catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase complement(996042..997244) Escherichia coli S88 7129949 YP_002390750.1 CDS pepN NC_011742.1 997510 1000122 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21101837, 86164315, 87163509, 2436977, 3018440; Product type e : enzyme; aminopeptidase N 997510..1000122 Escherichia coli S88 7133747 YP_002390751.1 CDS ssuB NC_011742.1 1000317 1001084 R part of the ABC type transport system SsuABC for aliphatic sulfonates; with SsuA being the periplasmic substrate-binding subunit, SsuB the ATP-binding subunit and SsuC the permease; aliphatic sulfonates transport ATP-binding subunit complement(1000317..1001084) Escherichia coli S88 7133673 YP_002390752.1 CDS ssuC NC_011742.1 1001081 1001872 R part of the ABC type transport system for alkanesulfonate SsuABC; SsuB the ATP-binding subunit and SsuC the permease; alkanesulfonate transporter permease subunit complement(1001081..1001872) Escherichia coli S88 7130658 YP_002390753.1 CDS ssuD NC_011742.1 1001884 1003029 R catalyzes the release of sulfite from alkanesulfonates; alkanesulfonate monooxygenase complement(1001884..1003029) Escherichia coli S88 7129678 YP_002390754.1 CDS ssuA NC_011742.1 1003026 1003985 R part of the ABC type transport system SsuABC for aliphatic sulfonates; with SsuA being the periplasmic subunit SsuB the ATP-binding subunit and SsuC the permease; alkanesulfonate transporter substrate-binding subunit complement(1003026..1003985) Escherichia coli S88 7131229 YP_002390755.1 CDS ssuE NC_011742.1 1003978 1004553 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20245523, 99410391, 99436146, 8774726; Product type e : enzyme; NAD(P)H-dependent FMN reductase complement(1003978..1004553) Escherichia coli S88 7130657 YP_002390756.1 CDS pyrD NC_011742.1 1004790 1005800 D catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; uses a flavin nucleotide as an essential cofactor; class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus, which plays a role in the membrane association of the enzyme and provides the binding site for the respiratory quinones that serve as physiological electron acceptors; dihydroorotate dehydrogenase 2 1004790..1005800 Escherichia coli S88 7131230 YP_002390757.1 CDS ycbW NC_011742.1 1005974 1006516 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1005974..1006516 Escherichia coli S88 7131765 YP_002390758.1 CDS ycbX NC_011742.1 1006513 1007622 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1327782; Product type pe : putative enzyme; putative 2Fe-2S cluster-containing protein complement(1006513..1007622) Escherichia coli S88 7130159 YP_002390759.1 CDS rlmL NC_011742.1 1007720 1009828 D catalyzes the N2-methyl guanosine modification of the G2445 residue of 23S rRNA; 23S rRNA m(2)G2445 methyltransferase 1007720..1009828 Escherichia coli S88 7130160 YP_002390760.1 CDS uup NC_011742.1 1009840 1011747 D Uup; in Escherichia coli this cytoplasmic protein was shown to contain ATPase activity; mutations in this gene affect RecA-independent excision of transposons and affects Mu bacteriophage growth; ABC transporter ATPase component 1009840..1011747 Escherichia coli S88 7130161 YP_002390761.1 CDS pqiA NC_011742.1 1011877 1013130 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95270582; Product type cp : cell process; paraquat-inducible membrane protein A 1011877..1013130 Escherichia coli S88 7132457 YP_002390762.1 CDS pqiB NC_011742.1 1013135 1014775 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95270582; Product type cp : cell process; paraquat-inducible protein B 1013135..1014775 Escherichia coli S88 7130768 YP_002390763.1 CDS ymbA NC_011742.1 1014787 1015335 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1014787..1015335 Escherichia coli S88 7130769 YP_002390764.1 CDS rmf NC_011742.1 1015591 1015758 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1101029, 90207255, 2832401, 8440252; Product type f : factor; ribosome modulation factor 1015591..1015758 Escherichia coli S88 7131118 YP_002390765.1 CDS fabA NC_011742.1 1015828 1016346 R catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP; 3-hydroxydecanoyl-(acyl carrier protein) dehydratase complement(1015828..1016346) Escherichia coli S88 7132735 YP_002390766.1 CDS ycbZ NC_011742.1 1016415 1018175 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative ATP-dependent protease complement(1016415..1018175) Escherichia coli S88 7132442 YP_002390767.1 CDS ycbG NC_011742.1 1018361 1018813 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1018361..1018813 Escherichia coli S88 7130162 YP_002390768.1 CDS ompA NC_011742.1 1018891 1019931 R OmpA is believed to be a porin, involved in diffusion of nonspecific small solutes across the outer membrane. It is the most abundant integral protein of the outer membrane of E. coli, and it is known to play a role as a phage receptor, a mediator of F-factor dependent conjugation, and in maintaining the structural shape of the outer membrane; 3a; II*; G; d; outer membrane protein A complement(1018891..1019931) Escherichia coli S88 7130155 YP_002390769.1 CDS ECS88_0979 NC_011742.1 1020085 1020303 D Evidence 6 : Doubtful CDS; hypothetical protein 1020085..1020303 Escherichia coli S88 7133123 YP_002390770.1 CDS sulA NC_011742.1 1020287 1020796 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10368140, 91072263, 93163041, 98348458, 3297925, 6253901, 6306396; Product type cp : cell process; SOS cell division inhibitor complement(1020287..1020796) Escherichia coli S88 7130417 YP_002390771.1 CDS yccR NC_011742.1 1021015 1021644 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1021015..1021644 Escherichia coli S88 7131250 YP_002390772.1 CDS yccS NC_011742.1 1021607 1023760 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(1021607..1023760) Escherichia coli S88 7130167 YP_002390773.1 CDS yccF NC_011742.1 1023779 1024225 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(1023779..1024225) Escherichia coli S88 7132691 YP_002390774.1 CDS helD NC_011742.1 1024348 1026402 D catalyzes the ATP-dependent unwinding of duplex DNA in the 3' to 5' direction with respect to the bound single strand; DNA helicase IV 1024348..1026402 Escherichia coli S88 7130164 YP_002390775.1 CDS mgsA NC_011742.1 1026434 1026892 R catalyzes the formation of methylglyoxal from glycerone phosphate; methylglyoxal synthase complement(1026434..1026892) Escherichia coli S88 7128895 YP_002390776.1 CDS yccT NC_011742.1 1026988 1027650 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1026988..1027650) Escherichia coli S88 7128829 YP_002390777.1 CDS yccU NC_011742.1 1027823 1028236 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative CoA-binding protein 1027823..1028236 Escherichia coli S88 7131419 YP_002390778.1 CDS yccV NC_011742.1 1028281 1028598 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12700277, 15569148; Product type f : factor; heat shock protein HspQ complement(1028281..1028598) Escherichia coli S88 7131420 YP_002390779.1 CDS yccW NC_011742.1 1028656 1029759 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative AdoMet-dependent methyltransferase, UPF0064 family complement(1028656..1029759) Escherichia coli S88 7131421 YP_002390780.1 CDS yccX NC_011742.1 1029712 1030218 D catalyzes the hydrolysis of acylphosphate; acylphosphatase 1029712..1030218 Escherichia coli S88 7131422 YP_002390781.1 CDS tusE NC_011742.1 1030215 1030544 R transfers sulfur from TusBCD complex to MnmA; involved in thiouridation of U34 position of some tRNAs; sulfur transfer protein TusE complement(1030215..1030544) Escherichia coli S88 7131423 YP_002390782.1 CDS yccA NC_011742.1 1030636 1031295 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 6376117; Product type m : membrane component; hypothetical protein complement(1030636..1031295) Escherichia coli S88 7130373 YP_002390783.1 CDS hyaA NC_011742.1 1032016 1033134 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 86192450, 90202716, 92215587; Product type e : enzyme; hydrogenase 1, small subunit 1032016..1033134 Escherichia coli S88 7132004 YP_002390784.1 CDS hyaB NC_011742.1 1033131 1034924 D involved in hydrogen cycling during fermentative growth; hydrogenase 1 large subunit 1033131..1034924 Escherichia coli S88 7131406 YP_002390785.1 CDS hyaC NC_011742.1 1034943 1035650 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90202716, 91310595, 92215587; Product type c : carrier; hydrogenase 1 b-type cytochrome subunit 1034943..1035650 Escherichia coli S88 7131407 YP_002390786.1 CDS hyaD NC_011742.1 1035647 1036234 D HyaD; endopeptidase involved in the cleavage of the C-terminus end of HyaB (the large subunit of hydrogenase 1); hydrogenase 1 maturation protease 1035647..1036234 Escherichia coli S88 7131408 YP_002390787.1 CDS hyaE NC_011742.1 1036231 1036629 D involved in processing hydrogenase proteins HyaA and HyaB; hydrogenase-1 operon protein HyaE 1036231..1036629 Escherichia coli S88 7131409 YP_002390788.1 CDS hyaF NC_011742.1 1036626 1037483 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90202716, 91310595, 92215587; Product type f : factor; protein involved in nickel incorporation into hydrogenase-1 proteins 1036626..1037483 Escherichia coli S88 7131410 YP_002390789.1 CDS appC NC_011742.1 1037617 1039161 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92049231, 96198179; Product type c : carrier; cytochrome bd-II oxidase, subunit I 1037617..1039161 Escherichia coli S88 7131411 YP_002390790.1 CDS appB NC_011742.1 1039173 1040309 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92049231, 96198179; Product type c : carrier; cytochrome bd-II oxidase, subunit II 1039173..1040309 Escherichia coli S88 7133077 YP_002390791.1 CDS appA NC_011742.1 1040494 1041804 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20122624, 92049231, 93054596, 10696472, 2168385, 3038201, 8387749; Product type e : enzyme; phosphoanhydride phosphorylase 1040494..1041804 Escherichia coli S88 7133076 YP_002390792.1 CDS cspH NC_011742.1 1041792 1042004 R Evidence 2b : Function of strongly homologous gene; PubMedId : 9484881, 9439003; Product type f : factor; stress protein, member of the CspA-family complement(1041792..1042004) Escherichia coli S88 7133075 YP_002390793.1 CDS ECS88_1004 NC_011742.1 1041906 1042049 D Evidence 6 : Doubtful CDS; hypothetical protein 1041906..1042049 Escherichia coli S88 7130500 YP_002390794.1 CDS cspG NC_011742.1 1042290 1042502 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9484881, 15466053, 8631696, 9439003; Product type r : regulator; cold shock protein CspG 1042290..1042502 Escherichia coli S88 7130731 YP_002390795.1 CDS gnsA NC_011742.1 1042896 1043069 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15317805, 11544213; Product type pr : putative regulator; putative regulator of phosphatidylethanolamine synthesis 1042896..1043069 Escherichia coli S88 7130499 YP_002390796.1 CDS yccM NC_011742.1 1043118 1044191 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative 4Fe-4S membrane protein complement(1043118..1044191) Escherichia coli S88 7130049 YP_002390797.1 CDS torS NC_011742.1 1044274 1047006 R Member of the two-component regulatory system torS/torR involved in the anaerobic utilization of trimethylamine-N-oxide; hybrid sensory histidine kinase TorS complement(1044274..1047006) Escherichia coli S88 7130166 YP_002390798.1 CDS torT NC_011742.1 1047089 1048117 D periplasmic sensory protein associated with the TorRS two-component regulatory system; TMAO reductase system periplasmic protein TorT 1047089..1048117 Escherichia coli S88 7133497 YP_002390799.1 CDS torR NC_011742.1 1048090 1048782 R response regulator in two-component regulatory system with TorS; involved in regulation of trimethylamine N-oxide reductase genes; DNA-binding transcriptional regulator TorR complement(1048090..1048782) Escherichia coli S88 7133498 YP_002390800.1 CDS torC NC_011742.1 1048912 1050084 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94293785, 94314186, 99340208, 11056172, 11562502; Product type c : carrier; trimethylamine N-oxide (TMAO) reductase I, cytochrome c-type subunit 1048912..1050084 Escherichia coli S88 7133496 YP_002390801.1 CDS torA NC_011742.1 1050084 1052630 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88193091, 90089471, 94293785, 8302830, 8022286; Product type e : enzyme; trimethylamine N-oxide (TMAO) reductase I, catalytic subunit 1050084..1052630 Escherichia coli S88 7133493 YP_002390802.1 CDS torD NC_011742.1 1052627 1053226 D TorD; involved in the biogenesis of torA; acts on torA before the insertion of the molybdenum cofactor and, as a result, probably favors a conformation of the apoenzyme that is competent for acquiring the cofactor; chaperone protein TorD 1052627..1053226 Escherichia coli S88 7133492 YP_002390803.1 CDS cbpM NC_011742.1 1053582 1053887 R with CpbA modulates the activity of the dnaK chaperone system; interacts with CbpA and inhibits both the DnaJ-like co-chaperone activity and the DNA binding activity of CbpA; chaperone-modulator protein CbpM complement(1053582..1053887) Escherichia coli S88 7133494 YP_002390804.1 CDS cbpA NC_011742.1 1053887 1054807 R functional analog of DnaJ; co-chaperone with DnaK, molecular chaperone in an adaptive response to environmental stresses other than heat shock; curved DNA-binding protein CbpA complement(1053887..1054807) Escherichia coli S88 7129163 YP_002390805.1 CDS agp NC_011742.1 1055342 1056583 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12455612, 90368616, 91297199, 2153660, 9298646; Product type e : enzyme; glucose-1-phosphatase/inositol phosphatase 1055342..1056583 Escherichia coli S88 7129162 YP_002390806.1 CDS yccJ NC_011742.1 1056621 1056848 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1056621..1056848) Escherichia coli S88 7133034 YP_002390807.1 CDS wrbA NC_011742.1 1056869 1057465 R stationary phase protein that binds TrpR repressor; TrpR binding protein WrbA complement(1056869..1057465) Escherichia coli S88 7130165 YP_002390808.1 CDS ECS88_1019 NC_011742.1 1057669 1057905 D Evidence 6 : Doubtful CDS; hypothetical protein 1057669..1057905 Escherichia coli S88 7132502 YP_002390809.1 CDS ECS88_1020 NC_011742.1 1057869 1058027 D Evidence 6 : Doubtful CDS; hypothetical protein 1057869..1058027 Escherichia coli S88 7130732 YP_002390810.1 CDS rutF NC_011742.1 1059337 1059831 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16540542, 10633095; Product type e : enzyme; flavin:NADH oxidoreductase subunit of alternative pyrimidine degradation pathway complement(1059337..1059831) Escherichia coli S88 7131322 YP_002390811.1 CDS rutE NC_011742.1 1059842 1060432 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16540542; Product type e : enzyme; hypothetical protein complement(1059842..1060432) Escherichia coli S88 7131320 YP_002390812.1 CDS rutD NC_011742.1 1060442 1061242 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16540542; Product type e : enzyme; enzyme of the alternative pyrimidine degradation pathway complement(1060442..1061242) Escherichia coli S88 7131319 YP_002390813.1 CDS rutC NC_011742.1 1061250 1061636 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16540542; Product type e : enzyme; enzyme of the alternative pyrimidine degradation pathway complement(1061250..1061636) Escherichia coli S88 7131318 YP_002390814.1 CDS rutB NC_011742.1 1061648 1062340 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16540542; Product type e : enzyme; enzyme of the alternative pyrimidine degradation pathway complement(1061648..1062340) Escherichia coli S88 7131317 YP_002390815.1 CDS rutA NC_011742.1 1062340 1063488 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16540542; Product type e : enzyme; monooxygenase of the alternative pyrimidine degradation pathway complement(1062340..1063488) Escherichia coli S88 7131316 YP_002390816.1 CDS rutR NC_011742.1 1063718 1064356 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16540542; Product type r : regulator; DNA-binding transcriptional regulator of the alternative pyrimidine degradation pathway 1063718..1064356 Escherichia coli S88 7131315 YP_002390817.1 CDS putA NC_011742.1 1064396 1068358 R proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichai coli this protein also self-regulates transcription via a DNA-binding domain at the N-terminus; forms dimers and is a peripherally membrane-associated protein; trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase complement(1064396..1068358) Escherichia coli S88 7131323 YP_002390818.1 CDS putP NC_011742.1 1068781 1070289 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12923181, 88213396, 91227628, 93132799, 98359785, 1400239, 1567896, 3053649, 3053687, 3302614, 3325781, 8119910; Product type t : transporter; proline:sodium symporter 1068781..1070289 Escherichia coli S88 7131758 YP_002390819.1 CDS efeU NC_011742.1 1070500 1071339 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; Product type t : transporter; ferrous iron permease 1070500..1071339 Escherichia coli S88 7131759 YP_002390820.1 CDS efeO NC_011742.1 1071397 1072524 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 17627767, 10493123; Product type t : transporter; hypothetical protein 1071397..1072524 Escherichia coli S88 7132385 YP_002390821.1 CDS efeB NC_011742.1 1072530 1073801 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 17627767, 16551627, 15375152; Product type t : transporter; iron transport heme-binding periplasmic protein 1072530..1073801 Escherichia coli S88 7132384 YP_002390822.1 CDS phoH NC_011742.1 1074292 1075215 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8444794, 2160940; Product type pe : putative enzyme; hypothetical protein 1074292..1075215 Escherichia coli S88 7132383 YP_002390823.1 CDS pgaD NC_011742.1 1075265 1075678 R in Yersinia this gene is involved in biofilm formation and hemin adsorption; in Escherichia coli it is involved in PGA biosynthesis and export; putative PGA biosynthesis protein complement(1075265..1075678) Escherichia coli S88 7133725 YP_002390824.1 CDS pgaC NC_011742.1 1075680 1077005 R predicted polysaccharide polymerase involved in biofilm formation; required for the synthesis of the beta-1,6-N-acetylglucosamine polysaccharide; PgaC; in Yersinia the HmsR protein is an inner membrane protein; N-glycosyltransferase complement(1075680..1077005) Escherichia coli S88 7133689 YP_002390825.1 CDS pgaB NC_011742.1 1076998 1079016 R in Yersinia this protein is involved in biofilm formation and hemin adsorption; related protein PgaB in Escherichia coli is an outer membrane N-deacetylase involved in poly-beta-1,6-N-acetyl-D-glucosamine (PGA) export; outer membrane N-deacetylase complement(1076998..1079016) Escherichia coli S88 7133688 YP_002390826.1 CDS ycdT NC_011742.1 1082036 1083403 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 99392474; Product type pe : putative enzyme; putative diguanylate cyclase 1082036..1083403 Escherichia coli S88 7133686 YP_002390827.1 CDS ycdW NC_011742.1 1083829 1084767 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11237876, 10493123; Product type e : enzyme; 2-ketoacid reductase 1083829..1084767 Escherichia coli S88 7132003 YP_002390828.1 CDS ycdX NC_011742.1 1084822 1085559 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12661000; Product type pe : putative enzyme; putative hydrolase 1084822..1085559 Escherichia coli S88 7131425 YP_002390829.1 CDS ycdY NC_011742.1 1085583 1086137 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1085583..1086137 Escherichia coli S88 7131426 YP_002390830.1 CDS ycdZ NC_011742.1 1086239 1086730 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1086239..1086730 Escherichia coli S88 7131427 YP_002390831.1 CDS csgG NC_011742.1 1086795 1087628 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8817489; Product type lp : lipoprotein; putative outer membrane lipoprotein involved in curli production assembly/transport complement(1086795..1087628) Escherichia coli S88 7131428 YP_002390832.1 CDS csgF NC_011742.1 1087655 1088071 R nucleator protein that participates in the polymerization of curlin (CsgA) subunits into curli (extracellular fibers from Escherichia and Salmonella spp. that are involved in the colonization of inert surfaces and biofilm formation); part of the curli secretion and assembly protein complex; curli assembly protein CsgF complement(1087655..1088071) Escherichia coli S88 7131976 YP_002390833.1 CDS csgE NC_011742.1 1088096 1088485 R chaperone-like protein that participates in the polymerization of curlin (CsgA) subunits into curli (extracellular fibers from Escherichia and Salmonella spp. that are involved in the colonization of inert surfaces and biofilm formation); part of the curli secretion and assembly protein complex; curli assembly protein CsgE complement(1088096..1088485) Escherichia coli S88 7131975 YP_002390834.1 CDS csgD NC_011742.1 1088490 1089140 R activates the csgBA and csgDEFG operons involved in biofilm formation; DNA-binding transcriptional regulator CsgD complement(1088490..1089140) Escherichia coli S88 7131974 YP_002390835.1 CDS csgB NC_011742.1 1089893 1090348 D CsgB; functions as a nucleator in the assembly of curli (coiled surface structures) on the cell surface; curlin minor subunit 1089893..1090348 Escherichia coli S88 7131973 YP_002390836.1 CDS csgA NC_011742.1 1090389 1090844 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89201357, 93023873, 1677357, 8459772, 8817489, 1357528; Product type s : structure; cryptic curlin major subunit 1090389..1090844 Escherichia coli S88 7131971 YP_002390837.1 CDS csgC NC_011742.1 1090744 1091235 D involved in autoagglutination of curliated cells; not involved in production of curli fibers; putative autoagglutination protein 1090744..1091235 Escherichia coli S88 7131970 YP_002390838.1 CDS ymdA NC_011742.1 1091356 1091667 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1091356..1091667 Escherichia coli S88 7131972 YP_002390839.1 CDS ymdB NC_011742.1 1091762 1092295 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1091762..1092295 Escherichia coli S88 7131119 YP_002390840.1 CDS ymdC NC_011742.1 1092297 1093718 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative hydrolase 1092297..1093718 Escherichia coli S88 7131120 YP_002390841.1 CDS mdoC NC_011742.1 1093726 1094883 R required for the transfer of succinyl residues to the glucan backbone; glucans biosynthesis protein complement(1093726..1094883) Escherichia coli S88 7131121 YP_002390842.1 CDS ECS88_1060 NC_011742.1 1094928 1095071 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1094928..1095071) Escherichia coli S88 7128785 YP_002390843.1 CDS ECS88_1061 NC_011742.1 1095075 1095233 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1095075..1095233) Escherichia coli S88 7130734 YP_002390844.1 CDS mdoG NC_011742.1 1095277 1096812 D involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan; glucan biosynthesis protein G 1095277..1096812 Escherichia coli S88 7130735 YP_002390845.1 CDS mdoH NC_011742.1 1096805 1099348 D necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH 1096805..1099348 Escherichia coli S88 7128787 YP_002390846.1 CDS yceK NC_011742.1 1099520 1099747 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; hypothetical protein 1099520..1099747 Escherichia coli S88 7128788 YP_002390847.1 CDS msyB NC_011742.1 1099748 1100122 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 92165719; hypothetical protein complement(1099748..1100122) Escherichia coli S88 7131437 YP_002390848.1 CDS mdtG NC_011742.1 1100205 1101431 R Confers resistance to fosfomycin and deoxycholate; drug efflux system protein MdtG complement(1100205..1101431) Escherichia coli S88 7129618 YP_002390849.1 CDS lpxL NC_011742.1 1101603 1102523 R Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA; lipid A biosynthesis lauroyl acyltransferase complement(1101603..1102523) Escherichia coli S88 7128795 YP_002390850.1 CDS yceA NC_011742.1 1102748 1103800 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 1840644; hypothetical protein 1102748..1103800 Escherichia coli S88 7129386 YP_002390851.1 CDS yceI NC_011742.1 1103842 1104417 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 15741337, 11298273, 1840644, 9298646; Product type c : carrier; hypothetical protein complement(1103842..1104417) Escherichia coli S88 7131429 YP_002390852.1 CDS yceJ NC_011742.1 1104421 1104987 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative cytochrome b561 complement(1104421..1104987) Escherichia coli S88 7131435 YP_002390853.1 CDS yceO NC_011742.1 1105248 1105388 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1105248..1105388) Escherichia coli S88 7131436 YP_002390854.1 CDS solA NC_011742.1 1105409 1106527 R catalyzes the demethylation of N-methyl-L-tryptophan forming L-tryptophan and formaldehyde; FAD-binding; can also catalyze the demethylation of other N-methyl amino acids; N-methyltryptophan oxidase complement(1105409..1106527) Escherichia coli S88 7131438 YP_002390855.1 CDS bssS NC_011742.1 1106642 1106896 R BssS; regulator of biofilm through signal secretion; disruption of this gene in Escherichia coli led to effects on biofilm formation, alteration in expression of a number of genes and mutations in bssS led to defects in indole transport and autoinducer-2 uptake and processing; biofilm formation regulatory protein BssS complement(1106642..1106896) Escherichia coli S88 7130621 YP_002390856.1 CDS dinI NC_011742.1 1107186 1107563 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11230150, 11152126; Product type f : factor; DNA damage-inducible protein I complement(1107186..1107563) Escherichia coli S88 7129135 YP_002390857.1 CDS pyrC NC_011742.1 1107505 1108551 R catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase complement(1107505..1108551) Escherichia coli S88 7130209 YP_002390858.1 CDS yceB NC_011742.1 1108657 1109217 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; hypothetical protein complement(1108657..1109217) Escherichia coli S88 7131764 YP_002390859.1 CDS grxB NC_011742.1 1109351 1109998 R cofactor involved in the reduction of disulfides; glutaredoxin 2 complement(1109351..1109998) Escherichia coli S88 7131430 YP_002390860.1 CDS mdtH NC_011742.1 1110062 1111270 R Confers resistance to norfloxacin and enoxacin; multidrug resistance protein MdtH complement(1110062..1111270) Escherichia coli S88 7130074 YP_002390861.1 CDS rimJ NC_011742.1 1111506 1112090 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88121676, 90136529, 1356970; Product type e : enzyme; ribosomal-protein-S5-alanine N-acetyltransferase 1111506..1112090 Escherichia coli S88 7128796 YP_002390862.1 CDS yceH NC_011742.1 1112101 1112748 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 1356970, 2828880; hypothetical protein 1112101..1112748 Escherichia coli S88 7132724 YP_002390863.1 CDS mviM NC_011742.1 1112750 1113673 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase with NAD(P)-binding Rossmann-fold domain 1112750..1113673 Escherichia coli S88 7131434 YP_002390864.1 CDS mviN NC_011742.1 1113783 1115318 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1113783..1115318 Escherichia coli S88 7129645 YP_002390865.1 CDS flgN NC_011742.1 1115358 1115774 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10320579; Product type f : factor; export chaperone for FlgK and FlgL complement(1115358..1115774) Escherichia coli S88 7129646 YP_002390866.1 CDS flgM NC_011742.1 1115779 1116072 R regulates the flagellar specific sigma28 transcription factor; anti-sigma28 factor FlgM complement(1115779..1116072) Escherichia coli S88 7132782 YP_002390867.1 CDS flgA NC_011742.1 1116148 1116807 R required for the assembly of the flagellar basal body P-ring; flagellar basal body P-ring biosynthesis protein FlgA complement(1116148..1116807) Escherichia coli S88 7132781 YP_002390868.1 CDS flgB NC_011742.1 1116962 1117378 D with FlgF and C makes up the proximal portion of the flagellar basal body rod; Vibrio parahaemolyticus protein is associated with the polar flagella; flagellar basal body rod protein FlgB 1116962..1117378 Escherichia coli S88 7129513 YP_002390869.1 CDS flgC NC_011742.1 1117382 1117786 D with FlgF and B makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgC 1117382..1117786 Escherichia coli S88 7129514 YP_002390870.1 CDS flgD NC_011742.1 1117798 1118493 D acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod; Yersinia, Vibrio parahaemolyticus, Bradyrhizobium and other organisms have 2 copies of some flagellar genes; in V. parahaemolyticus one set used for lateral flagella production and the other is used for the polar flagella production; flagellar basal body rod modification protein 1117798..1118493 Escherichia coli S88 7129515 YP_002390871.1 CDS flgE NC_011742.1 1118518 1119723 D the hook connects flagellar basal body to the flagellar filament; flagellar hook protein FlgE 1118518..1119723 Escherichia coli S88 7129516 YP_002390872.1 CDS flgF NC_011742.1 1119743 1120498 D FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgF 1119743..1120498 Escherichia coli S88 7133389 YP_002390873.1 CDS flgG NC_011742.1 1120670 1121452 D makes up the distal portion of the flagellar basal body rod; flagellar basal body rod protein FlgG 1120670..1121452 Escherichia coli S88 7132774 YP_002390874.1 CDS flgH NC_011742.1 1121505 1122203 D part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod; flagellar basal body L-ring protein 1121505..1122203 Escherichia coli S88 7132775 YP_002390875.1 CDS flgI NC_011742.1 1122215 1123312 D part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum; flagellar basal body P-ring protein 1122215..1123312 Escherichia coli S88 7132776 YP_002390876.1 CDS flgJ NC_011742.1 1123312 1124253 D Flagellum-specific muramidase which hydrolyzes the peptidoglycan layer to assemble the rod structure in the periplasmic space; flagellar rod assembly protein/muramidase FlgJ 1123312..1124253 Escherichia coli S88 7132777 YP_002390877.1 CDS flgK NC_011742.1 1124319 1125962 D with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook; flagellar hook-associated protein FlgK 1124319..1125962 Escherichia coli S88 7132778 YP_002390878.1 CDS flgL NC_011742.1 1125974 1126927 D with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook; Yersinia, Vibrio parahaemolyticus, Bradyrhizobium and other organisms have 2 copies of this and other flagellar genes; flagellar hook-associated protein FlgL 1125974..1126927 Escherichia coli S88 7132779 YP_002390879.1 CDS rne NC_011742.1 1127122 1130307 R bifunctional ribonuclease E/endoribonuclease/RNA-binding protein/RNA degradosome binding protein; forms part of the membrane-associated degradosome complex along with PNPase, RhlB, and enolase; ribonuclease E complement(1127122..1130307) Escherichia coli S88 7132780 YP_002390880.1 CDS rluC NC_011742.1 1130880 1131839 D catalyzes the transformation of uracil to pseudouracil at nucleotides U955, U2504, and U2580 in 23S rRNA; 23S rRNA pseudouridylate synthase C 1130880..1131839 Escherichia coli S88 7129855 YP_002390881.1 CDS yceF NC_011742.1 1131951 1132535 R Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell; Maf-like protein complement(1131951..1132535) Escherichia coli S88 7132733 YP_002390882.1 CDS yceD NC_011742.1 1132734 1133255 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 90008815, 1447160; hypothetical protein 1132734..1133255 Escherichia coli S88 7130638 YP_002390883.1 CDS rpmF NC_011742.1 1133307 1133480 D some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 1133307..1133480 Escherichia coli S88 7131431 YP_002390884.1 CDS plsX NC_011742.1 1133561 1134631 D involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY; putative glycerol-3-phosphate acyltransferase PlsX 1133561..1134631 Escherichia coli S88 7133770 YP_002390885.1 CDS fabH NC_011742.1 1134699 1135652 D FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs; 3-oxoacyl-(acyl carrier protein) synthase III 1134699..1135652 Escherichia coli S88 7133742 YP_002390886.1 CDS fabD NC_011742.1 1135668 1136597 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92052166, 92183950, 92210530, 92234941, 7700236, 7768883, 9298646; Product type e : enzyme; malonyl-CoA-[acyl-carrier-protein] transacylase 1135668..1136597 Escherichia coli S88 7129436 YP_002390887.1 CDS fabG NC_011742.1 1136610 1137344 D catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-(acyl-carrier-protein) reductase 1136610..1137344 Escherichia coli S88 7132444 YP_002390888.1 CDS acpP NC_011742.1 1137555 1137791 D carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein 1137555..1137791 Escherichia coli S88 7129435 YP_002390889.1 CDS fabF NC_011742.1 1137878 1139119 D FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP; 3-oxoacyl-(acyl carrier protein) synthase II 1137878..1139119 Escherichia coli S88 7132039 YP_002390890.1 CDS pabC NC_011742.1 1139239 1140048 D catalyzes the formation of 4-aminobenzoate and pyruvate from 4-amino-4-deoxychorismate; 4-amino-4-deoxychorismate lyase 1139239..1140048 Escherichia coli S88 7132445 YP_002390891.1 CDS yceG NC_011742.1 1140051 1141073 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; hypothetical protein 1140051..1141073 Escherichia coli S88 7133155 YP_002390892.1 CDS tmk NC_011742.1 1141063 1141704 D catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP); thymidylate kinase 1141063..1141704 Escherichia coli S88 7131433 YP_002390893.1 CDS holB NC_011742.1 1141701 1142705 D catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA; DNA polymerase III subunit delta' 1141701..1142705 Escherichia coli S88 7133480 YP_002390894.1 CDS ycfH NC_011742.1 1142716 1143513 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8505303, 8509334, 10747959; Product type pe : putative enzyme; putative metallodependent hydrolase 1142716..1143513 Escherichia coli S88 7128942 YP_002390895.1 CDS ptsG NC_011742.1 1143808 1145241 D phosphoenolpyruvate-dependent sugar phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIB is phosphorylated by IIA and then transfers the phosphoryl group to the sugar; IIC forms the translocation channel; PTS system glucose-specific transporter subunits IIBC 1143808..1145241 Escherichia coli S88 7131440 YP_002390896.1 CDS fhuE NC_011742.1 1145301 1147490 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90286919, 3032906, 10529396; Product type t : transporter; ferric-rhodotorulic acid outer membrane transporter complement(1145301..1147490) Escherichia coli S88 7132363 YP_002390897.1 CDS hinT NC_011742.1 1147824 1148183 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15703176, 10493123, 2162465; Product type e : enzyme; purine nucleoside phosphoramidase 1147824..1148183 Escherichia coli S88 7129486 YP_002390898.1 CDS ycfL NC_011742.1 1148186 1148563 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1148186..1148563 Escherichia coli S88 7128916 YP_002390899.1 CDS ycfM NC_011742.1 1148577 1149218 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative outer membrane lipoprotein 1148577..1149218 Escherichia coli S88 7131442 YP_002390900.1 CDS thiK NC_011742.1 1149199 1150023 D catalyzes the phosphorylation of thiamine to thiamine phosphate; thiamine kinase 1149199..1150023 Escherichia coli S88 7131443 YP_002390901.1 CDS nagZ NC_011742.1 1150034 1151059 D hydrolyzes the terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides; beta-hexosaminidase 1150034..1151059 Escherichia coli S88 7131444 YP_002390902.1 CDS ycfP NC_011742.1 1151082 1151624 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1151082..1151624 Escherichia coli S88 7129661 YP_002390903.1 CDS ndh NC_011742.1 1152023 1153327 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14766919, 20130027, 81256452, 92296775, 94042945, 99441207, 6265208; Product type e : enzyme; respiratory NADH dehydrogenase 2/cupric reductase 1152023..1153327 Escherichia coli S88 7131445 YP_002390904.1 CDS ycfJ NC_011742.1 1153554 1154093 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 6265208, 7984428; hypothetical protein 1153554..1154093 Escherichia coli S88 7129690 YP_002390905.1 CDS ycfQ NC_011742.1 1154155 1154787 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(1154155..1154787) Escherichia coli S88 7131441 YP_002390906.1 CDS ycfR NC_011742.1 1155028 1155285 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 14727089; hypothetical protein 1155028..1155285 Escherichia coli S88 7131446 YP_002390907.1 CDS ycfS NC_011742.1 1155367 1156329 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1155367..1156329) Escherichia coli S88 7131447 YP_002390908.1 CDS mfd NC_011742.1 1156474 1159920 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14602898, 90158497, 92107993, 8465200; Product type f : factor; transcription-repair coupling factor complement(1156474..1159920) Escherichia coli S88 7131448 YP_002390909.1 CDS ycfT NC_011742.1 1160048 1161121 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(1160048..1161121) Escherichia coli S88 7128825 YP_002390910.1 CDS lolC NC_011742.1 1161383 1162582 D part of the ATP-dependent transport system LolCDE; responsible for the localization of lipoproteins to the periplasmic surface of the outer membrane; outer membrane-specific lipoprotein transporter subunit LolC 1161383..1162582 Escherichia coli S88 7131449 YP_002390911.1 CDS lolD NC_011742.1 1162575 1163276 D outer membrane specific; part of transporter complex lolCDE involved in the translocation of mature outer membrane-directed lipoproteins, from the inner membrane to the periplasmic chaperone; lipoprotein transporter ATP-binding subunit 1162575..1163276 Escherichia coli S88 7129370 YP_002390912.1 CDS lolE NC_011742.1 1163276 1164520 D part of the ATP-dependent transport system LolCDE; responsible for the localization of lipoproteins to the periplasmic surface of the outer membrane; outer membrane-specific lipoprotein transporter subunit LolE 1163276..1164520 Escherichia coli S88 7129371 YP_002390913.1 CDS ycfX NC_011742.1 1164549 1165460 D catalyzes the formation of N-acetyl-D-glucosamine-6-phosphate from N-acetyl-D-glucosamine; N-acetyl-D-glucosamine kinase 1164549..1165460 Escherichia coli S88 7129372 YP_002390914.1 CDS cobB NC_011742.1 1165476 1166297 D Modulates the activities of several enzymes which are inactive in their acetylated form; NAD-dependent deacetylase 1165476..1166297 Escherichia coli S88 7131450 YP_002390915.1 CDS ycfZ NC_011742.1 1166435 1167325 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(1166435..1167325) Escherichia coli S88 7131941 YP_002390916.1 CDS ymfA NC_011742.1 1167220 1167681 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(1167220..1167681) Escherichia coli S88 7131451 YP_002390917.1 CDS potD NC_011742.1 1167739 1168785 R can transport spermidine and putrescine but affinity is higher for spermidine; forms a complex of PotA2BCD; PotD is a periplasmic component that binds the substrate; spermidine/putrescine ABC transporter periplasmic substrate-binding protein complement(1167739..1168785) Escherichia coli S88 7131122 YP_002390918.1 CDS potC NC_011742.1 1168782 1169576 R can transport spermidine and putrescine but affinity is higher for spermidine; forms a complex of PotA2BCD; PotC is a membrane component; spermidine/putrescine ABC transporter membrane protein complement(1168782..1169576) Escherichia coli S88 7130744 YP_002390919.1 CDS potB NC_011742.1 1169573 1170400 R can transport spermidine and putrescine but affinity is higher for spermidine; forms a complex of PotA2BCD; PotB is a membrane component; spermidine/putrescine ABC transporter membrane protein complement(1169573..1170400) Escherichia coli S88 7130743 YP_002390920.1 CDS potA NC_011742.1 1170414 1171550 R functions together with PotBCD (A2BCD) in ATP-dependent polyamine transport; PotA is the membrane-associated ATPase; putrescine/spermidine ABC transporter ATPase protein complement(1170414..1171550) Escherichia coli S88 7130742 YP_002390921.1 CDS ECS88_1141 NC_011742.1 1171529 1171780 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1171529..1171780) Escherichia coli S88 7130741 YP_002390922.1 CDS pepT NC_011742.1 1171800 1173026 D catalyzes the release of the N-terminal amino acid from a tripeptide; peptidase T 1171800..1173026 Escherichia coli S88 7130736 YP_002390923.1 CDS ycfD NC_011742.1 1173075 1174196 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1173075..1174196) Escherichia coli S88 7133676 YP_002390924.1 CDS phoQ NC_011742.1 1174272 1175732 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92105017; Product type r : regulator; sensor protein PhoQ complement(1174272..1175732) Escherichia coli S88 7131439 YP_002390925.1 CDS phoP NC_011742.1 1175732 1176403 R response regulator in two-component regulatory system with PhoQ; involved in magnesium starvation and stress; DNA-binding transcriptional regulator PhoP complement(1175732..1176403) Escherichia coli S88 7133727 YP_002390926.1 CDS purB NC_011742.1 1176572 1177942 R Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase complement(1176572..1177942) Escherichia coli S88 7133726 YP_002390927.1 CDS hflD NC_011742.1 1177946 1178587 R HflD; UPF0274; in Escherichia coli this protein is peripherally associated with the membrane and appears to act with lambda CII protein; in Haemophilus influenzae a knockout of the HI0638 gene affected paracytosis; hypothetical protein complement(1177946..1178587) Escherichia coli S88 7131745 YP_002390928.1 CDS mnmA NC_011742.1 1178623 1179729 R catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA complement(1178623..1179729) Escherichia coli S88 7128910 YP_002390929.1 CDS ymfB NC_011742.1 1179783 1180244 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15292217; Product type e : enzyme; bifunctional thiamin pyrimidine pyrophosphate hydrolase and thiamin pyrophosphate hydrolase complement(1179783..1180244) Escherichia coli S88 7130342 YP_002390930.1 CDS ymfC NC_011742.1 1180254 1180907 R catalyzes the formation of pseudouridine from uracil-2457 in 23S ribosomal RNA; 23S rRNA pseudouridine synthase E complement(1180254..1180907) Escherichia coli S88 7131123 YP_002390931.1 CDS icd NC_011742.1 1181079 1182329 D Converts isocitrate to alpha ketoglutarate; isocitrate dehydrogenase 1181079..1182329 Escherichia coli S88 7131124 YP_002390932.1 CDS int NC_011742.1 1182443 1183585 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; phage integrase complement(1182443..1183585) Escherichia coli S88 7131611 YP_002390933.1 CDS ymfG NC_011742.1 1183575 1183811 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative excisionase complement(1183575..1183811) Escherichia coli S88 7131648 YP_002390934.1 CDS ECS88_1154 NC_011742.1 1183951 1184190 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(1183951..1184190) Escherichia coli S88 7131125 YP_002390935.1 CDS ECS88_1155 NC_011742.1 1184174 1184503 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(1184174..1184503) Escherichia coli S88 7130737 YP_002390936.1 CDS ECS88_1156 NC_011742.1 1184515 1184682 D Evidence 6 : Doubtful CDS; hypothetical protein; putative exported protein 1184515..1184682 Escherichia coli S88 7130738 YP_002390937.1 CDS ECS88_1157 NC_011742.1 1184915 1185097 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(1184915..1185097) Escherichia coli S88 7130819 YP_002390938.1 CDS ECS88_1158 NC_011742.1 1185108 1185299 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(1185108..1185299) Escherichia coli S88 7131500 YP_002390939.1 CDS ECS88_1159 NC_011742.1 1185272 1185460 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(1185272..1185460) Escherichia coli S88 7131501 YP_002390940.1 CDS ECS88_1160 NC_011742.1 1185451 1186131 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; exonuclease from phage origin complement(1185451..1186131) Escherichia coli S88 7131502 YP_002390941.1 CDS ECS88_1161 NC_011742.1 1186128 1186913 R Evidence 2b : Function of strongly homologous gene; PubMedId : 6458018, 6221115; Product type h : extrachromosomal origin; Recombination protein bet from phage origin complement(1186128..1186913) Escherichia coli S88 7131503 YP_002390942.1 CDS ECS88_1162 NC_011742.1 1186919 1187215 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative host-nuclease inhibitor protein Gam of bacteriophage complement(1186919..1187215) Escherichia coli S88 7131504 YP_002390943.1 CDS ECS88_1163 NC_011742.1 1187403 1187567 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Regulatory protein CIII complement(1187403..1187567) Escherichia coli S88 7131505 YP_002390944.1 CDS ECS88_1164 NC_011742.1 1187640 1188008 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; Putative single-stranded DNA binding protein of prophage complement(1187640..1188008) Escherichia coli S88 7131506 YP_002390945.1 CDS ECS88_1165 NC_011742.1 1188191 1188391 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Restriction inhibitor protein ral (Antirestriction protein) complement(1188191..1188391) Escherichia coli S88 7131507 YP_002390947.1 CDS ECS88_1167 NC_011742.1 1188605 1189186 D Evidence 2b : Function of strongly homologous gene; PubMedId : 8335629; Product type h : extrachromosomal origin; Superinfection exclusion protein B 1188605..1189186 Escherichia coli S88 7131509 YP_002390948.1 CDS ECS88_1168 NC_011742.1 1189447 1189668 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 1189447..1189668 Escherichia coli S88 7131510 YP_002390949.1 CDS ECS88_1169 NC_011742.1 1189860 1190012 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(1189860..1190012) Escherichia coli S88 7131511 YP_002390950.1 CDS ECS88_1170 NC_011742.1 1189912 1190664 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(1189912..1190664) Escherichia coli S88 7131512 YP_002390951.1 CDS ECS88_1171 NC_011742.1 1191258 1191959 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Repressor protein CI from phage origin complement(1191258..1191959) Escherichia coli S88 7131513 YP_002390952.1 CDS ECS88_1172 NC_011742.1 1191858 1192244 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative repressor protein 1191858..1192244 Escherichia coli S88 7131514 YP_002390953.1 CDS ECS88_1173 NC_011742.1 1192386 1192682 D Evidence 2b : Function of strongly homologous gene; PubMedId : 375198; Product type h : extrachromosomal origin; Regulatory protein CII from phage origin 1192386..1192682 Escherichia coli S88 7131515 YP_002390954.1 CDS ECS88_1176 NC_011742.1 1193544 1194245 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative replication protein P of bacteriophage 1193544..1194245 Escherichia coli S88 7131518 YP_002390955.1 CDS ECS88_1177 NC_011742.1 1194242 1194532 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Ren protein from phage origin 1194242..1194532 Escherichia coli S88 7131519 YP_002390956.1 CDS ECS88_1178 NC_011742.1 1194588 1195046 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; recombination protein ninB from phage origin 1194588..1195046 Escherichia coli S88 7131520 YP_002390957.1 CDS ECS88_1179 NC_011742.1 1194983 1195570 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative DNA N-6-adenine-methyltransferase from phage origin 1194983..1195570 Escherichia coli S88 7131521 YP_002390958.1 CDS ECS88_1180 NC_011742.1 1195704 1196087 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein, putative protein ninX from phage origin 1195704..1196087 Escherichia coli S88 7131522 YP_002390959.1 CDS rusA NC_011742.1 1196294 1196656 D DLP12 prophage; Holliday junction resolvase; endodeoxyribonuclease RUS 1196294..1196656 Escherichia coli S88 7131523 YP_002390960.1 CDS ybcQ NC_011742.1 1196879 1197262 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8648624, 9278503; Product type pf : putative factor; putative antitermination protein Q homolog; DLP12 prophage 1196879..1197262 Escherichia coli S88 7131312 YP_002390961.1 CDS nmpC NC_011742.1 1197451 1198593 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative outer membrane porin complement(1197451..1198593) Escherichia coli S88 7131187 YP_002390962.1 CDS essD NC_011742.1 1199122 1199337 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2019562; Product type pe : putative enzyme; putative phage lysis protein S; DLP12 prophage 1199122..1199337 Escherichia coli S88 7129726 YP_002390963.1 CDS ybcS NC_011742.1 1199337 1199834 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 3017988; Product type pe : putative enzyme; putative lysozyme; DLP12 prophage 1199337..1199834 Escherichia coli S88 7132419 YP_002390964.1 CDS rzpD NC_011742.1 1199831 1200292 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2019562; Product type pe : putative enzyme; putative murein endopeptidase; DLP12 prophage 1199831..1200292 Escherichia coli S88 7131188 YP_002390965.1 CDS borD NC_011742.1 1200324 1200617 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 95173101; Product type pm : putative membrane component; putative lipoprotein; DLP12 prophage complement(1200324..1200617) Escherichia coli S88 7131355 YP_002390966.1 CDS ECS88_1188 NC_011742.1 1201044 1201424 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative tonB-like membrane protein encoded within prophage 1201044..1201424 Escherichia coli S88 7129132 YP_002390967.1 CDS ECS88_1189 NC_011742.1 1201631 1201813 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1201631..1201813 Escherichia coli S88 7131524 YP_002390968.1 CDS ECS88_1190 NC_011742.1 1202040 1202294 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 1202040..1202294 Escherichia coli S88 7131525 YP_002390969.1 CDS ECS88_1191 NC_011742.1 1202376 1202924 D Evidence 2b : Function of strongly homologous gene; Product type f : factor; Terminase small subunit (Gp1) 1202376..1202924 Escherichia coli S88 7131526 YP_002390970.1 CDS ECS88_1192 NC_011742.1 1202854 1204824 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Terminase large subunit (Gp2) 1202854..1204824 Escherichia coli S88 7131527 YP_002390971.1 CDS ECS88_1193 NC_011742.1 1204808 1205014 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head-stabilizing protein (Head protein gp3) 1204808..1205014 Escherichia coli S88 7131528 YP_002390972.1 CDS ECS88_1194 NC_011742.1 1204981 1206603 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Portal protein (Head protein Gp4) 1204981..1206603 Escherichia coli S88 7131529 YP_002390973.1 CDS ECS88_1195 NC_011742.1 1206593 1208098 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head-tail preconnector protein GP5 [Contains: Scaffold protein GP6 (Head protein GP6)] 1206593..1208098 Escherichia coli S88 7131530 YP_002390974.1 CDS ECS88_1196 NC_011742.1 1208135 1208482 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head decoration protein (Head protein GPshp) 1208135..1208482 Escherichia coli S88 7131531 YP_002390975.1 CDS ECS88_1197 NC_011742.1 1208540 1209568 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major head protein (Head protein gp7) 1208540..1209568 Escherichia coli S88 7131532 YP_002390976.1 CDS ECS88_1198 NC_011742.1 1209572 1209994 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1209572..1209994 Escherichia coli S88 7131533 YP_002390977.1 CDS ECS88_1199 NC_011742.1 1209951 1210340 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail attachment protein (Minor capsid protein FII) 1209951..1210340 Escherichia coli S88 7131534 YP_002390978.1 CDS ECS88_1200 NC_011742.1 1210286 1210930 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein Z (GpZ) 1210286..1210930 Escherichia coli S88 7131535 YP_002390979.1 CDS ECS88_1201 NC_011742.1 1210927 1211322 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein U 1210927..1211322 Escherichia coli S88 7131536 YP_002390980.1 CDS ECS88_1202 NC_011742.1 1211300 1212070 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major tail protein V 1211300..1212070 Escherichia coli S88 7131537 YP_002390981.1 CDS ECS88_1203 NC_011742.1 1212086 1212508 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein G 1212086..1212508 Escherichia coli S88 7131538 YP_002390982.1 CDS ECS88_1204 NC_011742.1 1212490 1212924 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein T 1212490..1212924 Escherichia coli S88 7131539 YP_002390983.1 CDS ECS88_1205 NC_011742.1 1212917 1215478 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein precursor H 1212917..1215478 Escherichia coli S88 7131540 YP_002390984.1 CDS ECS88_1206 NC_011742.1 1215475 1215804 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein M 1215475..1215804 Escherichia coli S88 7131541 YP_002390985.1 CDS ECS88_1207 NC_011742.1 1215804 1216502 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein L 1215804..1216502 Escherichia coli S88 7131542 YP_002390986.1 CDS ECS88_1208 NC_011742.1 1216508 1217251 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative tail fiber component K of prophage 1216508..1217251 Escherichia coli S88 7131543 YP_002390987.1 CDS ECS88_1209 NC_011742.1 1217149 1217820 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail assembly protein I 1217149..1217820 Escherichia coli S88 7131544 YP_002390988.1 CDS ECS88_1210 NC_011742.1 1217881 1221363 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Host specificity protein J of prophage 1217881..1221363 Escherichia coli S88 7131545 YP_002390989.1 CDS ECS88_1211 NC_011742.1 1221416 1223482 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative side tail fiber protein homolog from lambdoid prophage 1221416..1223482 Escherichia coli S88 7131546 YP_002390990.1 CDS ECS88_1212 NC_011742.1 1223479 1223757 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1223479..1223757 Escherichia coli S88 7131547 YP_002390991.1 CDS ECS88_1213 NC_011742.1 1223770 1224063 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1223770..1224063 Escherichia coli S88 7131548 YP_002390992.1 CDS sitD NC_011742.1 1224155 1225012 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12654809, 10085045; Product type m : membrane component; iron transport protein, inner membrane component complement(1224155..1225012) Escherichia coli S88 7131549 YP_002390993.1 CDS sitC NC_011742.1 1225009 1225866 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12654809, 10085045; Product type m : membrane component; iron transport protein, inner membrane component complement(1225009..1225866) Escherichia coli S88 7130603 YP_002390994.1 CDS sitB NC_011742.1 1225863 1226690 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12654809, 10085045; Product type m : membrane component; iron transport protein, ATP-binding component complement(1225863..1226690) Escherichia coli S88 7130602 YP_002390995.1 CDS sitA NC_011742.1 1226690 1227604 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12654809, 10085045; Product type t : transporter; iron transport protein, periplasmic-binding protein complement(1226690..1227604) Escherichia coli S88 7130601 YP_002390996.1 CDS ECS88_1218 NC_011742.1 1228291 1229061 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1228291..1229061 Escherichia coli S88 7130600 YP_002390997.1 CDS ECS88_1219 NC_011742.1 1229184 1229339 D Evidence 6 : Doubtful CDS; hypothetical protein 1229184..1229339 Escherichia coli S88 7131550 YP_002390998.1 CDS ycgX NC_011742.1 1229947 1230351 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1229947..1230351) Escherichia coli S88 7131612 YP_002390999.1 CDS ycgE NC_011742.1 1230572 1231303 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(1230572..1231303) Escherichia coli S88 7131462 YP_002391000.1 CDS ECS88_1223 NC_011742.1 1231213 1231365 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1231213..1231365) Escherichia coli S88 7131453 YP_002391001.1 CDS ycgF NC_011742.1 1231508 1232719 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16533062, 15453820; Product type pe : putative enzyme; putative cyclic-di-GMP phosphodiesterase; blue-light sensing protein using FAD (BLUF) complement(1231508..1232719) Escherichia coli S88 7131552 YP_002391002.1 CDS ycgZ NC_011742.1 1233033 1233269 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1233033..1233269 Escherichia coli S88 7131454 YP_002391003.1 CDS ymgA NC_011742.1 1233312 1233584 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1233312..1233584 Escherichia coli S88 7131463 YP_002391004.1 CDS ymgB NC_011742.1 1233613 1233879 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1233613..1233879 Escherichia coli S88 7131133 YP_002391005.1 CDS ymgC NC_011742.1 1233992 1234240 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1233992..1234240 Escherichia coli S88 7131134 YP_002391006.1 CDS ymgF NC_011742.1 1235563 1235781 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1235563..1235781 Escherichia coli S88 7131455 YP_002391007.1 CDS ECS88_1231 NC_011742.1 1236179 1236358 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein; putative exported protein 1236179..1236358 Escherichia coli S88 7131138 YP_002391008.1 CDS ECS88_1232 NC_011742.1 1236648 1237025 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1236648..1237025 Escherichia coli S88 7131553 YP_002391009.1 CDS ECS88_1233 NC_011742.1 1237171 1237698 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1237171..1237698 Escherichia coli S88 7131554 YP_002391010.1 CDS ymgD NC_011742.1 1237756 1238085 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1237756..1238085) Escherichia coli S88 7131555 YP_002391011.1 CDS ymgG NC_011742.1 1238095 1238370 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1238095..1238370) Escherichia coli S88 7131136 YP_002391012.1 CDS minE NC_011742.1 1239731 1239997 R works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell; cell division topological specificity factor MinE complement(1239731..1239997) Escherichia coli S88 7132074 YP_002391013.1 CDS minD NC_011742.1 1240001 1240813 R ATPase; with MinC inhibits cell division by blocking formation of the polar Z ring septums; cell division inhibitor MinD complement(1240001..1240813) Escherichia coli S88 7128838 YP_002391014.1 CDS minC NC_011742.1 1240837 1241532 R blocks the formation of polar Z-ring septums; septum formation inhibitor complement(1240837..1241532) Escherichia coli S88 7128837 YP_002391015.1 CDS ycgJ NC_011742.1 1242052 1242420 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1242052..1242420 Escherichia coli S88 7128836 YP_002391016.1 CDS ycgK NC_011742.1 1242540 1242941 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1242540..1242941) Escherichia coli S88 7131456 YP_002391017.1 CDS ycgL NC_011742.1 1243150 1243476 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1243150..1243476 Escherichia coli S88 7131457 YP_002391018.1 CDS ycgM NC_011742.1 1243548 1244207 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15551868; Product type pe : putative enzyme; hypothetical protein 1243548..1244207 Escherichia coli S88 7131458 YP_002391019.1 CDS ycgN NC_011742.1 1244299 1244745 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1244299..1244745 Escherichia coli S88 7131459 YP_002391020.1 CDS umuD NC_011742.1 1245539 1245958 D binds with UmuC protein to form functional DNA pol V (UmuD'2UmuC); involved in translesion polymerization; DNA polymerase V subunit UmuD 1245539..1245958 Escherichia coli S88 7129856 YP_002391021.1 CDS umuC NC_011742.1 1245958 1247226 D binds processed UmuD protein to form functional DNA pol V (UmuD'2UmuC); involved in translesion polymerization; DNA polymerase V subunit UmuC 1245958..1247226 Escherichia coli S88 7132447 YP_002391022.1 CDS dsbB NC_011742.1 1247271 1247801 R disulfide oxidoreductase; integral membrane protein; required for perioplasmic disulfide bond formation; oxidizes DsbA protein; disulfide bond formation protein B complement(1247271..1247801) Escherichia coli S88 7132446 YP_002391023.1 CDS nhaB NC_011742.1 1247947 1249488 R involved in regulation of intracellular pH under alkaline conditions; sodium/proton antiporter complement(1247947..1249488) Escherichia coli S88 7130240 YP_002391024.1 CDS fadR NC_011742.1 1249710 1250429 D Multifunctional regulator of fatty acid metabolism; fatty acid metabolism regulator 1249710..1250429 Escherichia coli S88 7129707 YP_002391025.1 CDS ycgB NC_011742.1 1250592 1252124 R Evidence 4 : Homologs of previously reported genes of unknown function; SpoVR family protein complement(1250592..1252124) Escherichia coli S88 7129446 YP_002391026.1 CDS dadA NC_011742.1 1252454 1253752 D catalyzes the oxidative deamination of D-amino acids; D-amino acid dehydrogenase small subunit 1252454..1253752 Escherichia coli S88 7131452 YP_002391027.1 CDS dadX NC_011742.1 1253762 1254832 D catabolic enzyme, converts L-alanine to D-alanine which is then oxidized to pyruvate by dadA; alanine racemase 1253762..1254832 Escherichia coli S88 7130557 YP_002391028.1 CDS cvrA NC_011742.1 1254889 1256625 R the Vibrio parahaemolyticus gene VP2867 was found to be a potassium/proton antiporter; can rapidly extrude potassium against a potassium gradient at alkaline pH when cloned and expressed in Escherichia coli; potassium/proton antiporter complement(1254889..1256625) Escherichia coli S88 7130558 YP_002391029.1 CDS ldcA NC_011742.1 1256720 1257634 R catalyzes the release of D-alanine from L-alanyl-D-glutamyl-meso-diaminopimelyl-D-alanine; L,D-carboxypeptidase A complement(1256720..1257634) Escherichia coli S88 7130518 YP_002391030.1 CDS emtA NC_011742.1 1257734 1258345 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 98317285; Product type e : enzyme; lytic murein endotransglycosylase E 1257734..1258345 Escherichia coli S88 7130475 YP_002391031.1 CDS ycgR NC_011742.1 1258347 1259081 R Evidence 2b : Function of strongly homologous gene; PubMedId : 11031114; Product type cp : cell process; protein involved in flagellar function complement(1258347..1259081) Escherichia coli S88 7132397 YP_002391032.1 CDS ymgE NC_011742.1 1259282 1259536 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative inner membrane protein with transglycosylase-associated domain 1259282..1259536 Escherichia coli S88 7131461 YP_002391033.1 CDS prrA NC_011742.1 1259586 1261577 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type prc : putative receptor; putative outer membrane receptor, probably tonB dependent complement(1259586..1261577) Escherichia coli S88 7131137 YP_002391034.1 CDS modD NC_011742.1 1261582 1262436 R involved in molybdenum transport; molybdenum transport protein ModD complement(1261582..1262436) Escherichia coli S88 7130799 YP_002391035.1 CDS ECS88_1261 NC_011742.1 1262433 1263245 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative SAM-dependent methyltransferase complement(1262433..1263245) Escherichia coli S88 7128858 YP_002391036.1 CDS ECS88_1262 NC_011742.1 1263255 1264151 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative ABC transporter, ATP-binding protein complement(1263255..1264151) Escherichia coli S88 7131556 YP_002391037.1 CDS ECS88_1263 NC_011742.1 1264010 1264990 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative ABC transporter permease protein complement(1264010..1264990) Escherichia coli S88 7131557 YP_002391038.1 CDS ECS88_1264 NC_011742.1 1264990 1266054 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ABC transporter periplasmic binding protein complement(1264990..1266054) Escherichia coli S88 7131558 YP_002391039.1 CDS treA NC_011742.1 1266349 1268046 R periplasmic; catalyzes the hydrolysis of trehalose to glucose which can then be imported into the cell; trehalase complement(1266349..1268046) Escherichia coli S88 7131559 YP_002391040.1 CDS dhaH NC_011742.1 1268365 1269783 R phosphotransferaese subunit; phosphorylates dihydroxyacetone along with DhaK/DhaL; dihydroxyacetone kinase subunit M complement(1268365..1269783) Escherichia coli S88 7133506 YP_002391041.1 CDS dhaL NC_011742.1 1269794 1270426 R with DhaK and DhaM catalyzes the phosphorylation of dihydroxyacetone; dihydroxyacetone kinase subunit DhaL complement(1269794..1270426) Escherichia coli S88 7130200 YP_002391042.1 CDS dhaK NC_011742.1 1270437 1271507 R with DhaL and DhaM forms dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone; DhaK is the dihydroxyacetone binding subunit of the dihydroxyacetone kinase; dihydroxyacetone kinase subunit DhaK complement(1270437..1271507) Escherichia coli S88 7130202 YP_002391043.1 CDS dhaR NC_011742.1 1271735 1273654 D Positively regulates the dhaKLM operon from a sigma-70 promoter; DNA-binding transcriptional regulator DhaR 1271735..1273654 Escherichia coli S88 7130201 YP_002391044.1 CDS ECS88_1270 NC_011742.1 1273692 1273922 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(1273692..1273922) Escherichia coli S88 7130203 YP_002391045.1 CDS ychF NC_011742.1 1274058 1275149 R 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; GTP-dependent nucleic acid-binding protein EngD complement(1274058..1275149) Escherichia coli S88 7131560 YP_002391046.1 CDS pth NC_011742.1 1275266 1275850 R Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase complement(1275266..1275850) Escherichia coli S88 7131466 YP_002391047.1 CDS ychH NC_011742.1 1276128 1276406 D YchH; transcription activated by CRP (cyclic AMP receptor protein), a global transcription factor involved in regulation of metabolism in enteric bacteria; ychH presents a class II promoter to bind CRP; unknown function; hypothetical protein 1276128..1276406 Escherichia coli S88 7130815 YP_002391048.1 CDS ychM NC_011742.1 1276461 1278140 R putative role in sulfate transport across the inner membrane; member of the SulP family of sulfate transporters; seems to mediate transport via sulfate/proton symport; putative sulfate transporter YchM complement(1276461..1278140) Escherichia coli S88 7131467 YP_002391049.1 CDS prsA NC_011742.1 1278265 1279212 R catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP; ribose-phosphate pyrophosphokinase complement(1278265..1279212) Escherichia coli S88 7131469 YP_002391050.1 CDS ipk NC_011742.1 1279363 1280214 R An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis; 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase complement(1279363..1280214) Escherichia coli S88 7130800 YP_002391051.1 CDS lolB NC_011742.1 1280214 1280837 R Incorporates lipoproteins in the outer membrane after they are released by the LolA protein; outer membrane lipoprotein LolB complement(1280214..1280837) Escherichia coli S88 7130421 YP_002391052.1 CDS hemA NC_011742.1 1281051 1282307 D catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins; glutamyl-tRNA reductase 1281051..1282307 Escherichia coli S88 7129369 YP_002391053.1 CDS prfA NC_011742.1 1282349 1283431 D 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; peptide chain release factor 1 1282349..1283431 Escherichia coli S88 7128896 YP_002391054.1 CDS prmC NC_011742.1 1283431 1284264 D HemK; PrmC; transfers a methyl group from S-adenosylmethionine to amide nitrogen of specific glutamine residues in protein chain release factors PrfA and PrfB; N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase 1283431..1284264 Escherichia coli S88 7130772 YP_002391055.1 CDS ychQ NC_011742.1 1284261 1284653 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10322010; Product type pr : putative regulator; putative transcriptional regulator 1284261..1284653 Escherichia coli S88 7130783 YP_002391056.1 CDS ychA NC_011742.1 1284657 1285466 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10322010; Product type pr : putative regulator; putative transcriptional regulator 1284657..1285466 Escherichia coli S88 7131472 YP_002391057.1 CDS kdsA NC_011742.1 1285502 1286356 D catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis; 2-dehydro-3-deoxyphosphooctonate aldolase 1285502..1286356 Escherichia coli S88 7131464 YP_002391058.1 CDS ldrB NC_011742.1 1286504 1286671 R Evidence 2b : Function of strongly homologous gene; Product type f : factor; small toxic polypeptide complement(1286504..1286671) Escherichia coli S88 7130446 YP_002391059.1 CDS chaA NC_011742.1 1287017 1288117 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93266586, 94193576, 94292460; Product type t : transporter; calcium/sodium:proton antiporter complement(1287017..1288117) Escherichia coli S88 7131800 YP_002391060.1 CDS chaB NC_011742.1 1288387 1288617 D in Escherichia coli this protein putatively regulates the sodium/proton (also pH-independent calcium/proton) antiporter chaA; has weak affinity for calcium and magnesium ions; cation transport regulator 1288387..1288617 Escherichia coli S88 7129181 YP_002391061.1 CDS chaC NC_011742.1 1288754 1289470 D Evidence 1b : Function experimentally demonstrated in the studied species; Product type r : regulator; regulatory protein for cation transport 1288754..1289470 Escherichia coli S88 7129182 YP_002391062.1 CDS ychN NC_011742.1 1289514 1289867 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1289514..1289867) Escherichia coli S88 7129183 YP_002391063.1 CDS ychP NC_011742.1 1290193 1291446 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7567469; Product type pf : putative factor; hypothetical protein 1290193..1291446 Escherichia coli S88 7131470 YP_002391064.1 CDS narL NC_011742.1 1291447 1292097 R two-component response regulator NarL; phosphorylated by NarQ; activates transcription of nitrate and nitrite reductase genes and represses transcription of fumarate reductase; transcriptional regulator NarL complement(1291447..1292097) Escherichia coli S88 7131471 YP_002391065.1 CDS narX NC_011742.1 1292090 1293886 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92276349, 92374842, 94083940, 2649492, 2657652, 2668029; Product type r : regulator; nitrate/nitrite sensor protein NarX complement(1292090..1293886) Escherichia coli S88 7129681 YP_002391066.1 CDS ECS88_1292 NC_011742.1 1293912 1294130 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1293912..1294130 Escherichia coli S88 7129687 YP_002391067.1 CDS narK NC_011742.1 1294225 1295616 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91258310, 2657652, 2668029; Product type t : transporter; nitrate/nitrite transporter 1294225..1295616 Escherichia coli S88 7131561 YP_002391068.1 CDS narG NC_011742.1 1296009 1299752 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 74167294, 89384449, 92121125, 2233673, 2668029, 2995309, 3053688, 3308846, 6094247; Product type e : enzyme; nitrate reductase 1, alpha subunit 1296009..1299752 Escherichia coli S88 7131580 YP_002391069.1 CDS narH NC_011742.1 1299749 1301287 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 74167294, 89384449, 92121125, 1321049, 2832376, 3053688, 8383531, 8388253, 8664273, 9516445; Product type c : carrier; nitrate reductase 1, beta (Fe-S) subunit 1299749..1301287 Escherichia coli S88 7129674 YP_002391070.1 CDS narJ NC_011742.1 1301284 1301994 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89384449, 92121125, 9632249, 2832376; Product type f : factor; molybdenum-cofactor-assembly chaperone subunit (delta subunit) of nitrate reductase 1 1301284..1301994 Escherichia coli S88 7129675 YP_002391071.1 CDS narI NC_011742.1 1301994 1302671 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 75114694, 89384449, 92121125, 2832376, 3053688; Product type c : carrier; nitrate reductase 1, gamma (cytochrome b(NR)) subunit 1301994..1302671 Escherichia coli S88 7129677 YP_002391072.1 CDS ECS88_1298 NC_011742.1 1302724 1303953 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative transposase complement(1302724..1303953) Escherichia coli S88 7129676 YP_002391073.1 CDS purU NC_011742.1 1304716 1305558 R produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine; formyltetrahydrofolate deformylase complement(1304716..1305558) Escherichia coli S88 7132001 YP_002391074.1 CDS ychJ NC_011742.1 1305608 1306066 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1305608..1306066) Escherichia coli S88 7131757 YP_002391075.1 CDS rssA NC_011742.1 1306140 1307084 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein 1306140..1307084 Escherichia coli S88 7131468 YP_002391076.1 CDS rssB NC_011742.1 1307176 1308189 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10339606, 12912910, 9495753; Product type r : regulator; response regulator of RpoS 1307176..1308189 Escherichia coli S88 7133819 YP_002391077.1 CDS galU NC_011742.1 1308391 1309299 D together with GalF subunit composes the UTP--glucose-1-phosphate uridylyltransferase, an enzyme that catalyzes the formation of UDP-glucose from UTP and alpha-D-glucose 1-phosphate; regulates cellular levels of UDP-glucose; UTP--glucose-1-phosphate uridylyltransferase subunit GalU 1308391..1309299 Escherichia coli S88 7133820 YP_002391078.1 CDS hns NC_011742.1 1309443 1309856 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89056689, 94335643, 95267838, 95286558, 99355427, 2404280, 11298273; Product type r : regulator; global DNA-binding transcriptional dual regulator H-NS complement(1309443..1309856) Escherichia coli S88 7132178 YP_002391079.1 CDS tdk NC_011742.1 1310460 1311077 D catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase 1310460..1311077 Escherichia coli S88 7128936 YP_002391080.1 CDS ECS88_1307 NC_011742.1 1311204 1312409 R Evidence 2b : Function of strongly homologous gene; PubMedId : 6271469; Product type pe : putative enzyme; transposase IS4 complement(1311204..1312409) Escherichia coli S88 7131280 YP_002391081.1 CDS adhE NC_011742.1 1312535 1315210 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12783863, 4301680, 89291706, 91200315; Product type e : enzyme; bifunctional acetaldehyde-CoA/alcohol dehydrogenase complement(1312535..1315210) Escherichia coli S88 7131563 YP_002391082.1 CDS ychE NC_011742.1 1315687 1316334 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 1315687..1316334 Escherichia coli S88 7132053 YP_002391083.1 CDS ECS88_1310 NC_011742.1 1316492 1316806 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1316492..1316806) Escherichia coli S88 7131465 YP_002391084.1 CDS oppA NC_011742.1 1317072 1318703 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20256410, 86111605, 90256748, 92325017, 2015910, 9298646, 9600841, 2187863, 8740179, 9740056, 10972807; Product type t : transporter; oligopeptide transporter subunit ; periplasmic-binding component of ABC superfamily 1317072..1318703 Escherichia coli S88 7131564 YP_002391085.1 CDS oppB NC_011742.1 1318789 1319709 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 86111606, 93106975, 2187863; Product type t : transporter; oligopeptide transporter permease 1318789..1319709 Escherichia coli S88 7133137 YP_002391086.1 CDS oppC NC_011742.1 1319724 1320632 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 86111606; Product type t : transporter; oligopeptide transporter subunit ; membrane component of ABC superfamily 1319724..1320632 Escherichia coli S88 7133138 YP_002391087.1 CDS oppD NC_011742.1 1320644 1321657 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 86111606; Product type t : transporter; oligopeptide transporter ATP-binding component 1320644..1321657 Escherichia coli S88 7133139 YP_002391088.1 CDS oppF NC_011742.1 1321654 1322658 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 86111606; Product type t : transporter; oligopeptide transporter subunit ; ATP-binding component of ABC superfamily 1321654..1322658 Escherichia coli S88 7133140 YP_002391089.1 CDS yciU NC_011742.1 1322711 1323040 R highly acidic protein; the structure of the Haemophilus influenzae protein shows similarity to uracil DNA glycosylase inhibitor (Ugi); binds heat-unstable protein (HU-alpha) which is a histone-like protein; dsDNA-mimic protein complement(1322711..1323040) Escherichia coli S88 7133141 YP_002391090.1 CDS cls NC_011742.1 1323075 1324535 R catalyzes the transfer of a phosphatidyl group to phosphodidylglycerol to form cardiolipin (diphosphatidylglycerol); cardiolipin synthetase complement(1323075..1324535) Escherichia coli S88 7131487 YP_002391091.1 CDS ECS88_1318 NC_011742.1 1324567 1324851 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1324567..1324851 Escherichia coli S88 7131933 YP_002391092.1 CDS kch NC_011742.1 1324906 1326159 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12220501, 12912904, 94224769, 98319474; Product type t : transporter; voltage-gated potassium channel complement(1324906..1326159) Escherichia coli S88 7131565 YP_002391093.1 CDS yciI NC_011742.1 1326459 1326755 R unknown function; YciI from Haemophilus influenzae presents crystal structure similarity to a muconolactone isomerase, but does not seem to catalyze any of the predicted reactions based on sequence and structure similarity; YciI-like protein complement(1326459..1326755) Escherichia coli S88 7130436 YP_002391094.1 CDS tonB NC_011742.1 1326979 1327695 D membrane spanning protein in TonB-ExbB-ExbD complex; transduces proton motive force of the cytoplasmic membrane to outer membrane transporters; involved in the transport of ron-siderophore complexes, vitamin B12 and colicins; transport protein TonB 1326979..1327695 Escherichia coli S88 7131480 YP_002391095.1 CDS yciA NC_011742.1 1327735 1328133 R YciA; hydrolase that catalyzes the hydrolysis of the thioester bond in palmitoyl-CoA and malonyl-CoA; member of the the acyl coenzyme A hydrolase family of proteins; acyl-CoA thioester hydrolase complement(1327735..1328133) Escherichia coli S88 7133489 YP_002391096.1 CDS yciB NC_011742.1 1328239 1328778 R Involved in cell division; probably involved in intracellular septation; intracellular septation protein A complement(1328239..1328778) Escherichia coli S88 7131473 YP_002391097.1 CDS yciC NC_011742.1 1328808 1329551 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(1328808..1329551) Escherichia coli S88 7131474 YP_002391098.1 CDS ompW NC_011742.1 1329907 1330545 D receptor for colicin S4; outer membrane protein W 1329907..1330545 Escherichia coli S88 7131475 YP_002391099.1 CDS ECS88_1327 NC_011742.1 1330591 1331721 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; phage integrase complement(1330591..1331721) Escherichia coli S88 7133131 YP_002391100.1 CDS ECS88_1328 NC_011742.1 1331699 1331947 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; phage excisionase complement(1331699..1331947) Escherichia coli S88 7131566 YP_002391101.1 CDS ECS88_1329 NC_011742.1 1332012 1334483 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative exonuclease from phage origin complement(1332012..1334483) Escherichia coli S88 7131567 YP_002391102.1 CDS ydfD NC_011742.1 1334576 1334767 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; Qin prophage complement(1334576..1334767) Escherichia coli S88 7131568 YP_002391103.1 CDS ECS88_1331 NC_011742.1 1334764 1335057 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative regulator of cell division encoded by prophage complement(1334764..1335057) Escherichia coli S88 7129329 YP_002391104.1 CDS ECS88_1332 NC_011742.1 1335302 1335517 D Evidence 6 : Doubtful CDS; hypothetical protein 1335302..1335517 Escherichia coli S88 7130204 YP_002391105.1 CDS ydfC NC_011742.1 1335518 1335739 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; Qin prophage complement(1335518..1335739) Escherichia coli S88 7131570 YP_002391106.1 CDS ydfB NC_011742.1 1335769 1335897 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; Qin prophage complement(1335769..1335897) Escherichia coli S88 7129328 YP_002391107.1 CDS ydfA NC_011742.1 1335899 1336135 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(1335899..1336135) Escherichia coli S88 7129327 YP_002391108.1 CDS ECS88_1336 NC_011742.1 1336347 1336985 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative repressor protein from phage origin complement(1336347..1336985) Escherichia coli S88 7129326 YP_002391109.1 CDS ECS88_1337 NC_011742.1 1337029 1337319 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1337029..1337319 Escherichia coli S88 7131571 YP_002391110.1 CDS ECS88_1338 NC_011742.1 1337231 1337728 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1337231..1337728 Escherichia coli S88 7131572 YP_002391111.1 CDS ECS88_1339 NC_011742.1 1337794 1338870 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1337794..1338870 Escherichia coli S88 7131573 YP_002391112.1 CDS ECS88_1340 NC_011742.1 1338911 1339333 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1338911..1339333 Escherichia coli S88 7131574 YP_002391113.1 CDS ECS88_1341 NC_011742.1 1339375 1340487 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 1339375..1340487 Escherichia coli S88 7131575 YP_002391114.1 CDS ECS88_1342 NC_011742.1 1340503 1341504 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1340503..1341504 Escherichia coli S88 7131576 YP_002391115.1 CDS ECS88_1343 NC_011742.1 1341616 1341906 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1341616..1341906 Escherichia coli S88 7131577 YP_002391116.1 CDS ydfU NC_011742.1 1342725 1343771 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; Qin prophage 1342725..1343771 Escherichia coli S88 7131578 YP_002391117.1 CDS ECS88_1346 NC_011742.1 1343777 1343977 D Evidence 6 : Doubtful CDS; hypothetical protein 1343777..1343977 Escherichia coli S88 7129340 YP_002391118.1 CDS ECS88_1347 NC_011742.1 1343784 1344158 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative crossover junction endodeoxyribonuclease rusA (Holliday junction nuclease rusA) (Holliday juction resolvase) (Gp67) 1343784..1344158 Escherichia coli S88 7131579 YP_002391119.1 CDS ECS88_1348 NC_011742.1 1344155 1344976 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative antitermination protein Q of prophage 1344155..1344976 Escherichia coli S88 7129680 YP_002391120.1 CDS ECS88_1349 NC_011742.1 1345201 1345398 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1345201..1345398 Escherichia coli S88 7129192 YP_002391121.1 CDS ECS88_1350 NC_011742.1 1345549 1346598 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative DNA adenine methyltransferase ( DNA methylase) from phage origin 1345549..1346598 Escherichia coli S88 7129193 YP_002391122.1 CDS ECS88_1353 NC_011742.1 1348264 1348584 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Lysis protein S homolog from lambdoid prophage 1348264..1348584 Escherichia coli S88 7129196 YP_002391123.1 CDS ECS88_1355 NC_011742.1 1348899 1349171 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(1348899..1349171) Escherichia coli S88 7129198 YP_002391124.1 CDS ECS88_1358 NC_011742.1 1349935 1350108 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1349935..1350108 Escherichia coli S88 7129201 YP_002391125.1 CDS rzpD NC_011742.1 1350110 1350574 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2019562; Product type pe : putative enzyme; putative murein endopeptidase; DLP12 prophage 1350110..1350574 Escherichia coli S88 7129202 YP_002391126.1 CDS ECS88_1361 NC_011742.1 1350738 1350836 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1350738..1350836) Escherichia coli S88 7131356 YP_002391127.1 CDS ECS88_1362 NC_011742.1 1350882 1351307 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(1350882..1351307) Escherichia coli S88 7129203 YP_002391128.1 CDS ynfO NC_011742.1 1351350 1351583 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; Qin prophage complement(1351350..1351583) Escherichia coli S88 7129204 YP_002391129.1 CDS ECS88_1364 NC_011742.1 1351946 1352518 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Terminase small subunit (gp1) 1351946..1352518 Escherichia coli S88 7133616 YP_002391130.1 CDS ECS88_1367 NC_011742.1 1354401 1354607 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head stabilization protein (Head protein GP3) 1354401..1354607 Escherichia coli S88 7129207 YP_002391131.1 CDS ECS88_1368 NC_011742.1 1354604 1356196 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Portal protein (Head protein GP4) 1354604..1356196 Escherichia coli S88 7129208 YP_002391132.1 CDS ECS88_1369 NC_011742.1 1356186 1357691 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head-tail preconnector protein GP5 [Contains: Scaffold protein GP6 (Head protein GP6)] 1356186..1357691 Escherichia coli S88 7129209 YP_002391133.1 CDS ECS88_1370 NC_011742.1 1357728 1358075 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head decoration protein (gpD) (Major capsid protein D) 1357728..1358075 Escherichia coli S88 7129210 YP_002391134.1 CDS ECS88_1371 NC_011742.1 1358133 1359161 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major head protein (Head protein GP7) 1358133..1359161 Escherichia coli S88 7129211 YP_002391135.1 CDS ECS88_1372 NC_011742.1 1359165 1359587 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative DNA packaging protein from phage origin 1359165..1359587 Escherichia coli S88 7129212 YP_002391136.1 CDS ECS88_1373 NC_011742.1 1359544 1359933 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail attachment protein (Minor capsid protein FII) 1359544..1359933 Escherichia coli S88 7129213 YP_002391137.1 CDS ECS88_1374 NC_011742.1 1359949 1360482 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein Z (GpZ) 1359949..1360482 Escherichia coli S88 7129214 YP_002391138.1 CDS ECS88_1375 NC_011742.1 1360479 1360874 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein U 1360479..1360874 Escherichia coli S88 7129215 YP_002391139.1 CDS ECS88_1376 NC_011742.1 1360882 1361634 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major tail protein V 1360882..1361634 Escherichia coli S88 7129216 YP_002391140.1 CDS ECS88_1377 NC_011742.1 1361648 1362079 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein G 1361648..1362079 Escherichia coli S88 7129217 YP_002391141.1 CDS ECS88_1378 NC_011742.1 1362106 1362519 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein T 1362106..1362519 Escherichia coli S88 7129218 YP_002391142.1 CDS ECS88_1379 NC_011742.1 1362500 1365073 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein precursor H 1362500..1365073 Escherichia coli S88 7129219 YP_002391143.1 CDS ECS88_1380 NC_011742.1 1365070 1365339 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein M 1365070..1365339 Escherichia coli S88 7129220 YP_002391144.1 CDS ECS88_1381 NC_011742.1 1365399 1366097 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein L 1365399..1366097 Escherichia coli S88 7129221 YP_002391145.1 CDS ECS88_1382 NC_011742.1 1366060 1366845 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative tail fiber component K of prophage 1366060..1366845 Escherichia coli S88 7129222 YP_002391146.1 CDS ECS88_1383 NC_011742.1 1366743 1367384 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail assembly protein I from putative prophage 1366743..1367384 Escherichia coli S88 7129223 YP_002391147.1 CDS ECS88_1384 NC_011742.1 1367446 1367796 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 1367446..1367796 Escherichia coli S88 7129224 YP_002391148.1 CDS ECS88_1385 NC_011742.1 1367863 1371342 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Host specificity protein J 1367863..1371342 Escherichia coli S88 7129225 YP_002391149.1 CDS ECS88_1386 NC_011742.1 1371410 1372009 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; Putative Lom-like outer membrane protein of phage origin 1371410..1372009 Escherichia coli S88 7129226 YP_002391150.1 CDS ECS88_1387 NC_011742.1 1372161 1375268 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative tail fiber protein 1372161..1375268 Escherichia coli S88 7129227 YP_002391151.1 CDS tfaQ NC_011742.1 1375268 1375852 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative tail fibre chaperone; Qin prophage 1375268..1375852 Escherichia coli S88 7129228 YP_002391152.1 CDS ybcY NC_011742.1 1375907 1376491 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative AdoMet-dependent methyltransferase; DLP12 prophage complement(1375907..1376491) Escherichia coli S88 7131288 YP_002391153.1 CDS ECS88_1390 NC_011742.1 1376632 1376901 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; Putative tail fiber assembly protein 1376632..1376901 Escherichia coli S88 7131191 YP_002391154.1 CDS ECS88_1391 NC_011742.1 1376905 1377186 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative tail component 1376905..1377186 Escherichia coli S88 7129229 YP_002391155.1 CDS yciE NC_011742.1 1377674 1378180 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 15388941, 3058546, 8455549; hypothetical protein complement(1377674..1378180) Escherichia coli S88 7129230 YP_002391156.1 CDS yciF NC_011742.1 1378226 1378726 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 3058546, 8455549; hypothetical protein complement(1378226..1378726) Escherichia coli S88 7131476 YP_002391157.1 CDS yciG NC_011742.1 1378812 1378991 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1378812..1378991) Escherichia coli S88 7131477 YP_002391158.1 CDS trpA NC_011742.1 1379372 1380178 R catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha complement(1379372..1380178) Escherichia coli S88 7131478 YP_002391159.1 CDS trpB NC_011742.1 1380178 1381371 R catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta complement(1380178..1381371) Escherichia coli S88 7130343 YP_002391160.1 CDS trpC NC_011742.1 1381383 1382741 R monomeric bifunctional protein; functions in tryptophan biosynthesis pathway; phosphoribosylanthranilate is rearranged to carboxyphenylaminodeoxyribulosephosphate which is then closed to form indole-3-glycerol phosphate; bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase complement(1381383..1382741) Escherichia coli S88 7130344 YP_002391161.1 CDS trpD NC_011742.1 1382745 1384340 R bifunctional anthranilate synthase II/anthranilate phosphoribosyltransferase; TrpD; forms a heterotetramer with Trp E and the complex catalyzes the formation of anthranilate from chorismate and glutamine; also catalyzes the formation of N-(5-phospho-D-ribosyl)-anthranilate from athranilate and 5-phospho-alpha-D-ribose 1-diphosphate; functions in tryptophan biosynthesis; bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase complement(1382745..1384340) Escherichia coli S88 7130345 YP_002391162.1 CDS trpE NC_011742.1 1384340 1385902 R with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine; anthranilate synthase component I complement(1384340..1385902) Escherichia coli S88 7130346 YP_002391163.1 CDS trpL NC_011742.1 1385994 1386038 R Evidence 1c : Function experimentally demonstrated in the studied genus; Product type l : leader peptide; trp operon leader peptide complement(1385994..1386038) Escherichia coli S88 7130347 YP_002391164.1 CDS yciV NC_011742.1 1386176 1387057 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1386176..1387057 Escherichia coli S88 7130348 YP_002391165.1 CDS yciO NC_011742.1 1387054 1387674 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1387054..1387674 Escherichia coli S88 7131488 YP_002391166.1 CDS yciQ NC_011742.1 1387702 1389597 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1387702..1389597 Escherichia coli S88 7131484 YP_002391167.1 CDS rluB NC_011742.1 1389810 1390685 D catalyzes the synthesis of pseudouridine from uracil-2605 in 23S ribosomal RNA; 23S rRNA pseudouridylate synthase B 1389810..1390685 Escherichia coli S88 7131485 YP_002391168.1 CDS btuR NC_011742.1 1390725 1391315 R catalyzes the formation of adenosylcob(III)yrinic acid a,c-diamide from cob(I)yrinic acid a,c-diamide; cob(I)yrinic acid a,c-diamide adenosyltransferase complement(1390725..1391315) Escherichia coli S88 7132732 YP_002391169.1 CDS yciK NC_011742.1 1391312 1392070 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; short chain dehydrogenase complement(1391312..1392070) Escherichia coli S88 7129141 YP_002391170.1 CDS ECS88_1406 NC_011742.1 1392114 1392278 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1392114..1392278) Escherichia coli S88 7131481 YP_002391171.1 CDS sohB NC_011742.1 1392290 1393339 D SohB; periplasmic protein; member of the peptidase S49 family; putative periplasmic protease 1392290..1393339 Escherichia coli S88 7129231 YP_002391172.1 CDS yciN NC_011742.1 1393375 1393626 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 3029379, 7567469, 9868784; hypothetical protein complement(1393375..1393626) Escherichia coli S88 7130619 YP_002391173.1 CDS ECS88_1410 NC_011742.1 1393619 1393774 D Evidence 6 : Doubtful CDS; hypothetical protein 1393619..1393774 Escherichia coli S88 7131483 YP_002391174.1 CDS ECS88_1411 NC_011742.1 1393671 1393883 D Evidence 6 : Doubtful CDS; hypothetical protein 1393671..1393883 Escherichia coli S88 7129232 YP_002391175.1 CDS topA NC_011742.1 1394006 1396603 D catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity; DNA topoisomerase I 1394006..1396603 Escherichia coli S88 7129233 YP_002391176.1 CDS cysB NC_011742.1 1396813 1397787 D LysR-type transcriptional regulator; contains helix-turn-helix (HTH) motif; in Escherichia coli this protein regulates cysteine biosynthesis by controlling expression of the cys regulon; autoregulates expression; crystal structure of Klebsiella aerogenes showed tetramer formation; transcriptional regulator CysB 1396813..1397787 Escherichia coli S88 7133490 YP_002391177.1 CDS ECS88_1414 NC_011742.1 1398082 1398246 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1398082..1398246 Escherichia coli S88 7130534 YP_002391178.1 CDS ECS88_1415 NC_011742.1 1398228 1398416 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1398228..1398416 Escherichia coli S88 7129234 YP_002391179.1 CDS acnA NC_011742.1 1398775 1401450 D Catalyzes the conversion of citrate to isocitrate; aconitate hydratase 1398775..1401450 Escherichia coli S88 7129235 YP_002391180.1 CDS ribA NC_011742.1 1401514 1402104 R catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate; GTP cyclohydrolase II complement(1401514..1402104) Escherichia coli S88 7132036 YP_002391181.1 CDS pgpB NC_011742.1 1402274 1403038 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89033893, 92104964; Product type e : enzyme; phosphatidylglycerophosphatase B 1402274..1403038 Escherichia coli S88 7132714 YP_002391182.1 CDS yciS NC_011742.1 1403187 1403495 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1403187..1403495 Escherichia coli S88 7133695 YP_002391183.1 CDS yciM NC_011742.1 1403502 1404671 D Evidence 4 : Homologs of previously reported genes of unknown function; tetratricopeptide repeat protein 1403502..1404671 Escherichia coli S88 7131486 YP_002391184.1 CDS pyrF NC_011742.1 1404863 1405600 D type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase; orotidine 5'-phosphate decarboxylase 1404863..1405600 Escherichia coli S88 7131482 YP_002391185.1 CDS yciH NC_011742.1 1405600 1405926 D involved in start site selection during the initiation of translation; translation initiation factor Sui1 1405600..1405926 Escherichia coli S88 7131767 YP_002391186.1 CDS osmB NC_011742.1 1406052 1406270 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92078100, 2644204; Product type lp : lipoprotein; lipoprotein complement(1406052..1406270) Escherichia coli S88 7131479 YP_002391187.1 CDS deoT NC_011742.1 1406539 1407288 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16451192; Product type r : regulator; DNA-binding transcriptional repressor, DeoR family complement(1406539..1407288) Escherichia coli S88 7133143 YP_002391188.1 CDS ECS88_1426 NC_011742.1 1407378 1407560 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1407378..1407560) Escherichia coli S88 7130189 YP_002391189.1 CDS gmr NC_011742.1 1407699 1409684 R c-di-GMP phosphodiesterase; probably degrades signalling molecule c-di-GMP; RNase II stability modulator complement(1407699..1409684) Escherichia coli S88 7129236 YP_002391190.1 CDS rnb NC_011742.1 1409918 1411852 R Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3' to 5' direction; exoribonuclease II complement(1409918..1411852) Escherichia coli S88 7130047 YP_002391191.1 CDS yciW NC_011742.1 1411920 1413047 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative amidase or amidotransferase complement(1411920..1413047) Escherichia coli S88 7132742 YP_002391192.1 CDS fabI NC_011742.1 1413192 1413980 R Catalyzes a key regulatory step in fatty acid biosynthesis; enoyl-(acyl carrier protein) reductase complement(1413192..1413980) Escherichia coli S88 7131489 YP_002391193.1 CDS ECS88_1431 NC_011742.1 1414437 1415024 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional repressor 1414437..1415024 Escherichia coli S88 7129437 YP_002391194.1 CDS ECS88_1432 NC_011742.1 1415140 1416294 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; Putative efflux protein, membrane fusion (MFP) family precursor 1415140..1416294 Escherichia coli S88 7129237 YP_002391195.1 CDS ECS88_1433 NC_011742.1 1416294 1419401 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; Putative efflux pump (Putative multidrug-efflux transport protein) 1416294..1419401 Escherichia coli S88 7129238 YP_002391196.1 CDS ECS88_1434 NC_011742.1 1419405 1420778 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative outer membrane channel protein of an efflux system 1419405..1420778 Escherichia coli S88 7129239 YP_002391197.1 CDS ECS88_1435 NC_011742.1 1420787 1421950 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative membrane transport protein of an efflux system 1420787..1421950 Escherichia coli S88 7129240 YP_002391198.1 CDS sapF NC_011742.1 1421998 1422804 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 2109018, 10720487, 9634580; Product type t : transporter; antimicrobial peptide transporter subunit ; ATP-binding component of ABC superfamily transporter complement(1421998..1422804) Escherichia coli S88 7129241 YP_002391199.1 CDS sapD NC_011742.1 1422806 1423798 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 2109018, 10720487, 9634580, 1987159; Product type t : transporter; antimicrobial peptide transporter subunit; ATP-binding component of ABC superfamily transporter complement(1422806..1423798) Escherichia coli S88 7131362 YP_002391200.1 CDS sapC NC_011742.1 1423798 1424688 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 2109018, 9634580; Product type t : transporter; antimicrobial peptide transporter subunit ; permease component of ABC superfamily transporter complement(1423798..1424688) Escherichia coli S88 7131361 YP_002391201.1 CDS sapB NC_011742.1 1424675 1425640 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 2109018, 9634580; Product type t : transporter; antimicrobial peptide transporter subunit ; permease component of ABC superfamily transporter complement(1424675..1425640) Escherichia coli S88 7131360 YP_002391202.1 CDS sapA NC_011742.1 1425637 1427280 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 2109018, 9634580; Product type t : transporter; antimicrobial peptide transporter subunit; periplasmic-binding component of ABC superfamily transporter complement(1425637..1427280) Escherichia coli S88 7131359 YP_002391203.1 CDS ymjA NC_011742.1 1427593 1427838 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1427593..1427838) Escherichia coli S88 7131358 YP_002391204.1 CDS pspF NC_011742.1 1428265 1429242 R transcriptional activator for pspABCE which are induced in response to phage proteins, membrane altering stresses, and impaired proton expor; phage shock protein operon transcriptional activator complement(1428265..1429242) Escherichia coli S88 7131760 YP_002391205.1 CDS pspA NC_011742.1 1429408 1430076 D involved in maintaining membrane potential under membrane stress conditions; also acts as a negative transcriptional regulator of the phage shock protein (psp) operon(pspABCDE) by regulating the transcriptional activator PspF; phage shock protein PspA 1429408..1430076 Escherichia coli S88 7130808 YP_002391206.1 CDS pspB NC_011742.1 1430130 1430354 D acts together with PspC to induce psp operon during infection with phage, exposure to ethanol or osmotic shock; forms a complex with PspA and C; PspC is required for PspAB binding; phage shock protein B 1430130..1430354 Escherichia coli S88 7130803 YP_002391207.1 CDS pspC NC_011742.1 1430354 1430713 D with PsbB forms toxin/antitoxin pair; activates the psp operon in response to phage infection, exposure to ethanol or osmotic shock; DNA-binding transcriptional activator PspC 1430354..1430713 Escherichia coli S88 7130804 YP_002391208.1 CDS pspD NC_011742.1 1430722 1430943 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91295203, 97303082; Product type ph : phenotype; peripheral inner membrane phage-shock protein 1430722..1430943 Escherichia coli S88 7130805 YP_002391209.1 CDS pspE NC_011742.1 1431018 1431332 D rhodanese; catalyzes the formation of thiocyanate from thiosulfate and hydrogen cyanide; thiosulfate:cyanide sulfurtransferase 1431018..1431332 Escherichia coli S88 7130806 YP_002391210.1 CDS ycjM NC_011742.1 1431542 1433221 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative glucosyltransferase 1431542..1433221 Escherichia coli S88 7130807 YP_002391211.1 CDS ycjN NC_011742.1 1433235 1434527 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sugar transporter subunit: periplasmic-binding component of ABC superfamily transporter 1433235..1434527 Escherichia coli S88 7131492 YP_002391212.1 CDS ycjO NC_011742.1 1434548 1435429 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sugar transporter subunit: permease component of ABC superfamily transporter 1434548..1435429 Escherichia coli S88 7131493 YP_002391213.1 CDS ycjP NC_011742.1 1435416 1436258 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sugar transporter subunit: permease component of ABC superfamily transporter 1435416..1436258 Escherichia coli S88 7131494 YP_002391214.1 CDS ycjR NC_011742.1 1437360 1438148 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative isomerase/epimerase 1437360..1438148 Escherichia coli S88 7131497 YP_002391215.1 CDS ycjS NC_011742.1 1438158 1439213 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase, NADH-binding 1438158..1439213 Escherichia coli S88 7131498 YP_002391216.1 CDS ycjT NC_011742.1 1439210 1441477 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative glycosyl hydrolase/phosphorylase 1439210..1441477 Escherichia coli S88 7131499 YP_002391217.1 CDS ycjU NC_011742.1 1441474 1442133 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11972617; Product type pe : putative enzyme; putative glucose-1-phosphate phosphodismutase, beta-phosphoglucomutase 1441474..1442133 Escherichia coli S88 7129191 YP_002391218.1 CDS ycjV NC_011742.1 1442147 1443229 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sugar transporter subunit: ATP-binding component of ABC superfamily transporter 1442147..1443229 Escherichia coli S88 7129272 YP_002391219.1 CDS ompG NC_011742.1 1443274 1444179 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20464934, 89327119, 9721282; Product type t : transporter; outer membrane porin 1443274..1444179 Escherichia coli S88 7129273 YP_002391220.1 CDS ycjW NC_011742.1 1444230 1445228 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(1444230..1445228) Escherichia coli S88 7133126 YP_002391221.1 CDS ycjX NC_011742.1 1445384 1446781 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative nucleoside triphosphate hydrolase domain 1445384..1446781 Escherichia coli S88 7129274 YP_002391222.1 CDS ycjF NC_011742.1 1446778 1447839 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 1446778..1447839 Escherichia coli S88 7129275 YP_002391223.1 CDS tyrR NC_011742.1 1447987 1449528 D regulates genes involved in the biosynthesis and transport of aromatic amino acids; DNA-binding transcriptional regulator TyrR 1447987..1449528 Escherichia coli S88 7131490 YP_002391224.1 CDS tpx NC_011742.1 1449572 1450078 R antioxidant activity; thioredoxin-dependent thiol peroxidase; forms homodimers in solution; shows substrate specificity to alkyl hydroperoxides; periplasmic protein; thiol peroxidase complement(1449572..1450078) Escherichia coli S88 7130377 YP_002391225.1 CDS ycjG NC_011742.1 1450197 1451162 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11747447, 11747448, 7499381; Product type e : enzyme; L-Ala-D/L-Glu epimerase 1450197..1451162 Escherichia coli S88 7133505 YP_002391226.1 CDS mpaA NC_011742.1 1451137 1451925 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12511517; Product type e : enzyme; murein peptide amidase A complement(1451137..1451925) Escherichia coli S88 7131491 YP_002391227.1 CDS ymjC NC_011742.1 1452156 1452794 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative NAD(P) binding enzyme complement(1452156..1452794) Escherichia coli S88 7129597 YP_002391228.1 CDS ycjY NC_011742.1 1452865 1453797 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative hydrolase complement(1452865..1453797) Escherichia coli S88 7131141 YP_002391229.1 CDS ycjZ NC_011742.1 1453923 1454822 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 17366475; Product type pr : putative regulator; putative nucleic acid-binding regulator 1453923..1454822 Escherichia coli S88 7129276 YP_002391230.1 CDS mppA NC_011742.1 1455159 1456772 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10438753, 9495761; Product type t : transporter; murein tripeptide (L-ala-gamma-D-glutamyl-meso-DAP) transporter subunit ; periplasmic-binding component of ABC superfamily 1455159..1456772 Escherichia coli S88 7129277 YP_002391231.1 CDS ynaI NC_011742.1 1456823 1457854 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(1456823..1457854) Escherichia coli S88 7129599 YP_002391232.1 CDS ynaJ NC_011742.1 1458098 1458355 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1458098..1458355 Escherichia coli S88 7131142 YP_002391233.1 CDS uspE NC_011742.1 1458405 1459355 R with UspC and UspD is involved in resistance to UV irradiation; universal stress protein UspE complement(1458405..1459355) Escherichia coli S88 7131143 YP_002391234.1 CDS fnr NC_011742.1 1459507 1460259 R Global transcription factor that controls the expression of over 100 target genes in response to anoxia; fumarate/nitrate reduction transcriptional regulator complement(1459507..1460259) Escherichia coli S88 7132454 YP_002391235.1 CDS ogt NC_011742.1 1460454 1460969 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88067749, 91161525, 94252990, 98125595, 1520330; Product type e : enzyme; O-6-alkylguanine-DNA:cysteine-protein methyltransferase complement(1460454..1460969) Escherichia coli S88 7132811 YP_002391236.1 CDS ECS88_1479 NC_011742.1 1461501 1462316 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; Putative HTH-type transcriptional regulator complement(1461501..1462316) Escherichia coli S88 7130426 YP_002391237.1 CDS ECS88_1481 NC_011742.1 1462410 1463441 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; Putative HlyD family secretion protein 1462410..1463441 Escherichia coli S88 7129243 YP_002391238.1 CDS ECS88_1482 NC_011742.1 1463438 1464952 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative drug resistance transporter EmrB/QacA subfamily 1463438..1464952 Escherichia coli S88 7129244 YP_002391239.1 CDS ydaL NC_011742.1 1465147 1465710 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1465147..1465710 Escherichia coli S88 7129245 YP_002391240.1 CDS ydaM NC_011742.1 1465731 1466963 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16045609; Product type pe : putative enzyme; putative diguanylate cyclase, GG[D/E]EF domain signalling protein complement(1465731..1466963) Escherichia coli S88 7129278 YP_002391241.1 CDS zntB NC_011742.1 1467218 1468201 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; zinc transporter 1467218..1468201 Escherichia coli S88 7129279 YP_002391242.1 CDS ECS88_1486 NC_011742.1 1468476 1468649 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 1468476..1468649 Escherichia coli S88 7129280 YP_002391243.1 CDS dbpA NC_011742.1 1468679 1470052 D exhibits an RNA-dependent ATPase activity, specifically stimulated by bacterial 23S rRNA; ATP-dependent RNA helicase DbpA 1468679..1470052 Escherichia coli S88 7129143 YP_002391244.1 CDS ydaO NC_011742.1 1470181 1471116 R TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs; C32 tRNA thiolase complement(1470181..1471116) Escherichia coli S88 7130569 YP_002391245.1 CDS uspF NC_011742.1 1473443 1473877 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12732303, 12381839, 11849540, 9298646; Product type f : factor; stress-induced protein, ATP-binding protein complement(1473443..1473877) Escherichia coli S88 7129248 YP_002391246.1 CDS ompN NC_011742.1 1474018 1475151 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9642192; Product type t : transporter; outer membrane pore protein N, non-specific complement(1474018..1475151) Escherichia coli S88 7132455 YP_002391247.1 CDS ydbK NC_011742.1 1475517 1479041 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 9025293; Product type pe : putative enzyme; putative 2-oxoacid-flavodoxin fused oxidoreductase:conserved protein; 4Fe-4S cluster binding protein complement(1475517..1479041) Escherichia coli S88 7128834 YP_002391248.1 CDS ydbJ NC_011742.1 1479315 1479581 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1479315..1479581 Escherichia coli S88 7129286 YP_002391249.1 CDS hslJ NC_011742.1 1479578 1480000 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12892888, 8349564, 9025293; Product type f : factor; heat-inducible protein complement(1479578..1480000) Escherichia coli S88 7129285 YP_002391250.1 CDS ldhA NC_011742.1 1480111 1481100 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 4297266, 89123040, 90198524, 8349564, 9025293; Product type e : enzyme; fermentative D-lactate dehydrogenase, NAD-dependent complement(1480111..1481100) Escherichia coli S88 7131393 YP_002391251.1 CDS ydbH NC_011742.1 1481308 1483947 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1481308..1483947 Escherichia coli S88 7130477 YP_002391252.1 CDS ynbE NC_011742.1 1483944 1484129 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; putative lipoprotein 1483944..1484129 Escherichia coli S88 7129284 YP_002391253.1 CDS ydbL NC_011742.1 1484137 1484463 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1484137..1484463 Escherichia coli S88 7133590 YP_002391254.1 CDS ydbA NC_011742.1 1484839 1493154 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type prc : putative receptor; putative autotransported outer membrane protein involved in cell adhesion 1484839..1493154 Escherichia coli S88 7129287 YP_002391255.1 CDS ydbC NC_011742.1 1493374 1494234 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase 1493374..1494234 Escherichia coli S88 7129282 YP_002391256.1 CDS ECS88_1502 NC_011742.1 1494279 1494503 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1494279..1494503) Escherichia coli S88 7129283 YP_002391257.1 CDS ynbA NC_011742.1 1494533 1495138 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1494533..1495138 Escherichia coli S88 7129249 YP_002391258.1 CDS ynbB NC_011742.1 1495138 1496034 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative membrane associated CTP-phosphosubstrate transferase 1495138..1496034 Escherichia coli S88 7131144 YP_002391259.1 CDS ynbC NC_011742.1 1496050 1497807 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative hydrolase 1496050..1497807 Escherichia coli S88 7131145 YP_002391260.1 CDS ynbD NC_011742.1 1497821 1499113 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative membrane associated phosphatase 1497821..1499113 Escherichia coli S88 7132939 YP_002391261.1 CDS azoR NC_011742.1 1499167 1499772 R FMN-dependent; requires NADH; catalyzes the cleavage of azo bond in aromatic azo compounds; azoreductase complement(1499167..1499772) Escherichia coli S88 7133589 YP_002391262.1 CDS hrpA NC_011742.1 1500030 1503875 D involved in the post-transcriptional processing of the daa operon mRNA, which encodes proteins involved in fimbrial biogenesis of an enteropathogenic E. coli strain; ATP-dependent RNA helicase HrpA 1500030..1503875 Escherichia coli S88 7129983 YP_002391263.1 CDS ydcF NC_011742.1 1504148 1504948 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1504148..1504948 Escherichia coli S88 7131389 YP_002391264.1 CDS aldA NC_011742.1 1505145 1506584 D NAD-linked; aldehyde dehydrogenase A 1505145..1506584 Escherichia coli S88 7129290 YP_002391265.1 CDS gapC NC_011742.1 1506626 1507627 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 9622357, 9019141, 1917845, 3780374; Product type e : enzyme; glyceraldehyde-3-phosphate dehydrogenase C complement(1506626..1507627) Escherichia coli S88 7133040 YP_002391266.1 CDS cybB NC_011742.1 1507816 1508346 D B-type di-heme cytochrome with a major alpha-absorption peak at 561 nm and a minor peak at 555 nm; cytochrome b561 1507816..1508346 Escherichia coli S88 7132180 YP_002391267.1 CDS ydcA NC_011742.1 1508591 1508764 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1508591..1508764 Escherichia coli S88 7131332 YP_002391268.1 CDS ydcI NC_011742.1 1509430 1510353 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(1509430..1510353) Escherichia coli S88 7130333 YP_002391269.1 CDS ydcJ NC_011742.1 1510570 1511913 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1510570..1511913 Escherichia coli S88 7129292 YP_002391270.1 CDS mdoD NC_011742.1 1512168 1513793 D involved in the control of the structural glucose backbone of osmoregulated periplasmic glucans; glucan biosynthesis protein D 1512168..1513793 Escherichia coli S88 7129293 YP_002391271.1 CDS ECS88_1520 NC_011742.1 1513714 1513917 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1513714..1513917) Escherichia coli S88 7128786 YP_002391272.1 CDS ydcH NC_011742.1 1513933 1514157 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1513933..1514157 Escherichia coli S88 7129250 YP_002391273.1 CDS rimL NC_011742.1 1514220 1514759 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89364711; Product type e : enzyme; ribosomal-protein-L7/L12-serine acetyltransferase 1514220..1514759 Escherichia coli S88 7129291 YP_002391274.1 CDS ydcK NC_011742.1 1514751 1515731 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative enzyme complement(1514751..1515731) Escherichia coli S88 7132726 YP_002391275.1 CDS tehA NC_011742.1 1515855 1516847 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94222856, 2060788; Product type t : transporter; potassium-tellurite ethidium and proflavin transporter 1515855..1516847 Escherichia coli S88 7129294 YP_002391276.1 CDS tehB NC_011742.1 1516844 1517437 D with TehA confers resistance to tellurite; tellurite resistance protein TehB 1516844..1517437 Escherichia coli S88 7131281 YP_002391277.1 CDS ydcL NC_011742.1 1517740 1518408 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; putative lipoprotein 1517740..1518408 Escherichia coli S88 7131282 YP_002391278.1 CDS ydcO NC_011742.1 1518443 1519615 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1885518; Product type pt : putative transporter; putative benzoate transporter complement(1518443..1519615) Escherichia coli S88 7129295 YP_002391279.1 CDS ydcN NC_011742.1 1519707 1520243 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 1519707..1520243 Escherichia coli S88 7129297 YP_002391280.1 CDS ydcP NC_011742.1 1520316 1522277 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative peptidase 1520316..1522277 Escherichia coli S88 7129296 YP_002391281.1 CDS yncJ NC_011742.1 1522369 1522599 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1522369..1522599) Escherichia coli S88 7129298 YP_002391282.1 CDS ydcR NC_011742.1 1523093 1524499 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15223311; Product type pr : putative regulator; putative DNA-binding transcriptional regulator fused with a domain with PLP-binding motif 1523093..1524499 Escherichia coli S88 7129299 YP_002391283.1 CDS ydcS NC_011742.1 1524744 1525889 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11683869; Product type pt : putative transporter; putative spermidine/putrescine transporter subunit ; periplasmic-binding component of ABC superfamily transporter 1524744..1525889 Escherichia coli S88 7129300 YP_002391284.1 CDS ydcT NC_011742.1 1525907 1526740 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative spermidine/putrescine transporter subunit ; ATP-binding component of ABC superfamily tranporter 1525907..1526740 Escherichia coli S88 7129301 YP_002391285.1 CDS ydcU NC_011742.1 1526921 1527862 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative spermidine/putrescine transporter subunit ; permease of ABC superfamily transporter 1526921..1527862 Escherichia coli S88 7129303 YP_002391286.1 CDS ydcV NC_011742.1 1527852 1528646 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative spermidine/putrescine transporter subunit; permease component of ABC superfamily 1527852..1528646 Escherichia coli S88 7129304 YP_002391287.1 CDS ydcW NC_011742.1 1528668 1530092 D catalyzes the formation of 4-aminobutanoate from 4-aminobutanal; involved in putrescine degradation; gamma-aminobutyraldehyde dehydrogenase 1528668..1530092 Escherichia coli S88 7129305 YP_002391288.1 CDS ydcX NC_011742.1 1530404 1530652 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1530404..1530652 Escherichia coli S88 7129306 YP_002391289.1 CDS ydcY NC_011742.1 1530738 1530971 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1530738..1530971 Escherichia coli S88 7129307 YP_002391290.1 CDS ydcZ NC_011742.1 1530972 1531421 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(1530972..1531421) Escherichia coli S88 7129308 YP_002391291.1 CDS yncA NC_011742.1 1531418 1531936 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative acyltransferase with acyl-CoA N-acyltransferase domain complement(1531418..1531936) Escherichia coli S88 7129309 YP_002391292.1 CDS yncD NC_011742.1 1532417 1534519 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type prc : putative receptor; putative iron outer membrane receptor complement(1532417..1534519) Escherichia coli S88 7129251 YP_002391293.1 CDS yncE NC_011742.1 1534761 1535822 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1534761..1535822 Escherichia coli S88 7133593 YP_002391294.1 CDS ansP NC_011742.1 1535935 1537434 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 76005443; Product type t : transporter; L-asparagine transporter complement(1535935..1537434) Escherichia coli S88 7133594 YP_002391295.1 CDS ECS88_1551 NC_011742.1 1538842 1539126 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, PAAR motifs 1538842..1539126 Escherichia coli S88 7133596 YP_002391296.1 CDS ECS88_1552 NC_011742.1 1539145 1541550 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative VgrG/E protein associated with Rhs elements 1539145..1541550 Escherichia coli S88 7129252 YP_002391297.1 CDS ECS88_1553 NC_011742.1 1541504 1542301 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative zinc-dependent metallopeptidase 1541504..1542301 Escherichia coli S88 7129253 YP_002391298.1 CDS ECS88_1554 NC_011742.1 1542354 1543073 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein 1542354..1543073 Escherichia coli S88 7129254 YP_002391299.1 CDS ECS88_1556 NC_011742.1 1543472 1543687 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 1543472..1543687 Escherichia coli S88 7129289 YP_002391300.1 CDS yddH NC_011742.1 1544004 1544573 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1544004..1544573) Escherichia coli S88 7129256 YP_002391301.1 CDS nhoA NC_011742.1 1544748 1545593 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20267568; Product type e : enzyme; N-hydroxyarylamine O-acetyltransferase 1544748..1545593 Escherichia coli S88 7129314 YP_002391302.1 CDS yddE NC_011742.1 1545689 1546582 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 14611652, 15103639, 2233673; hypothetical protein complement(1545689..1546582) Escherichia coli S88 7129709 YP_002391303.1 CDS narV NC_011742.1 1546662 1547342 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91042410; Product type e : enzyme; nitrate reductase 2 (NRZ), gamma subunit complement(1546662..1547342) Escherichia coli S88 7129312 YP_002391304.1 CDS narW NC_011742.1 1547339 1548034 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91042410, 92186712; Product type f : factor; nitrate reductase 2 (NRZ), delta subunit (assembly subunit) complement(1547339..1548034) Escherichia coli S88 7129685 YP_002391305.1 CDS narY NC_011742.1 1548034 1549578 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91042410; Product type c : carrier; nitrate reductase 2 (NRZ), beta subunit complement(1548034..1549578) Escherichia coli S88 7129686 YP_002391306.1 CDS narZ NC_011742.1 1549575 1553315 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91042410; Product type e : enzyme; nitrate reductase 2 (NRZ), alpha subunit complement(1549575..1553315) Escherichia coli S88 7129688 YP_002391307.1 CDS narU NC_011742.1 1553410 1554798 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95266795, 2233673; Product type t : transporter; nitrate/nitrite transporter complement(1553410..1554798) Escherichia coli S88 7129689 YP_002391308.1 CDS yddG NC_011742.1 1555071 1555895 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 12410826; Product type t : transporter; hypothetical protein complement(1555071..1555895) Escherichia coli S88 7129684 YP_002391309.1 CDS fdnG NC_011742.1 1556184 1559231 D Evidence 1c : Function experimentally demonstrated in the studied genus; Product type e : enzyme; formate dehydrogenase-N, alpha subunit, nitrate-inducible 1556184..1559231 Escherichia coli S88 7129313 YP_002391310.1 CDS fdnH NC_011742.1 1559244 1560128 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 76005553, 90375017, 92332427, 11884747, 1834669; Product type c : carrier; formate dehydrogenase-N, Fe-S (beta) subunit, nitrate-inducible 1559244..1560128 Escherichia coli S88 7129454 YP_002391311.1 CDS fdnI NC_011742.1 1560121 1560774 D nitrate-inducible, cytochrome b556(fdn) component of formate dehydrogenase; formate dehydrogenase-N subunit gamma 1560121..1560774 Escherichia coli S88 7129455 YP_002391312.1 CDS ECS88_1571 NC_011742.1 1561287 1561565 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative plasmid maintenance system killer protein complement(1561287..1561565) Escherichia coli S88 7129315 YP_002391313.1 CDS adhP NC_011742.1 1561751 1562761 R similar to zinc-dependent eukaryotic ADH enzymes and distinct from fermentative ADHs; alcohol dehydrogenase complement(1561751..1562761) Escherichia coli S88 7129257 YP_002391314.1 CDS sfcA NC_011742.1 1562895 1564592 R malic enzyme; oxaloacetate-decarboxylating; NAD-dependent; catalyzes the formation of pyruvate form malate; malate dehydrogenase complement(1562895..1564592) Escherichia coli S88 7132054 YP_002391315.1 CDS bdm NC_011742.1 1564987 1565202 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10498711, 13129944; Product type f : factor; biofilm-dependent modulation protein complement(1564987..1565202) Escherichia coli S88 7130584 YP_002391316.1 CDS osmC NC_011742.1 1565547 1565978 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14512736, 91350191, 9298646; Product type m : membrane component; osmotically inducible, stress-inducible membrane protein 1565547..1565978 Escherichia coli S88 7130001 YP_002391317.1 CDS dos NC_011742.1 1566168 1568567 R heme-regulated phosphodiesterase with phosphodiesterase activity with cAMP but not with cGMP, bis(p-nitrophenyl) phosphate or p-nitrophenyl phosphate; cAMP phosphodiesterase complement(1566168..1568567) Escherichia coli S88 7133144 YP_002391318.1 CDS yddV NC_011742.1 1568592 1568810 R Evidence 7 : Gene remnant; Product type pe : putative enzyme; putative diguanylate cyclase YddV (partial) complement(1568592..1568810) Escherichia coli S88 7130231 YP_002391319.1 CDS yddW NC_011742.1 1569134 1570453 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10960106; Product type lp : lipoprotein; putative lipoprotein complement(1569134..1570453) Escherichia coli S88 7129316 YP_002391320.1 CDS gadC NC_011742.1 1570584 1572119 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15795232, 15489450; Product type t : transporter; glutamate:gamma-aminobutyric acid antiporter complement(1570584..1572119) Escherichia coli S88 7129317 YP_002391321.1 CDS gadB NC_011742.1 1572275 1573675 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12912902, 92155241, 92394884, 99406302, 8455549; Product type e : enzyme; glutamate decarboxylase B, PLP-dependent complement(1572275..1573675) Escherichia coli S88 7132165 YP_002391322.1 CDS pqqL NC_011742.1 1574036 1576831 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1659611, 11514505; Product type pe : putative enzyme; putative membrane-associated peptidase complement(1574036..1576831) Escherichia coli S88 7132164 YP_002391323.1 CDS yddB NC_011742.1 1576876 1579248 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative porin protein complement(1576876..1579248) Escherichia coli S88 7130770 YP_002391324.1 CDS yddA NC_011742.1 1579286 1580971 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative multidrug transporter fused subunits of ABC superfamily transporter: permease component; ATP-binding component complement(1579286..1580971) Escherichia coli S88 7129311 YP_002391325.1 CDS ydeM NC_011742.1 1581262 1582419 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pr : putative regulator; hypothetical protein complement(1581262..1582419) Escherichia coli S88 7129310 YP_002391326.1 CDS ydeN NC_011742.1 1582471 1584153 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative sulfatase complement(1582471..1584153) Escherichia coli S88 7129321 YP_002391327.1 CDS ydeO NC_011742.1 1584555 1585316 R regulates the cellular response to acid resistance; transcriptional regulator YdeO complement(1584555..1585316) Escherichia coli S88 7129322 YP_002391328.1 CDS ECS88_1588 NC_011742.1 1585391 1585588 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1585391..1585588) Escherichia coli S88 7129323 YP_002391329.1 CDS ydeP NC_011742.1 1585836 1588115 R in Escherichia coli it may be involved in repression of type III secretion system (TTSS) genes of the host cell; involved with increased resistance to low pH; member of the prokaryotic molybdopterin-containing oxidoreductase family; putative oxidoreductase complement(1585836..1588115) Escherichia coli S88 7129258 YP_002391330.1 CDS ECS88_1591 NC_011742.1 1589273 1589884 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative major fimbrial subunit FmlA complement(1589273..1589884) Escherichia coli S88 7129325 YP_002391331.1 CDS ECS88_1592 NC_011742.1 1590199 1590486 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative NAD(P)-binding Rossmann-fold domain complement(1590199..1590486) Escherichia coli S88 7129259 YP_002391332.1 CDS ECS88_1593 NC_011742.1 1590596 1590853 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1590596..1590853 Escherichia coli S88 7129260 YP_002391333.1 CDS hipA NC_011742.1 1591112 1592434 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91358364, 94292428, 15576765; Product type r : regulator; regulator with hipB complement(1591112..1592434) Escherichia coli S88 7129261 YP_002391334.1 CDS hipB NC_011742.1 1592434 1592700 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91358364, 94292428, 15576765, 8021189; Product type r : regulator; DNA-binding transcriptional regulator HipB complement(1592434..1592700) Escherichia coli S88 7128917 YP_002391335.1 CDS tam NC_011742.1 1593008 1593766 D catalyzes the formation of (E)-3-(methoxycarbonyl)pent-2-enedioate and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and trans-aconitate; trans-aconitate 2-methyltransferase 1593008..1593766 Escherichia coli S88 7128918 YP_002391336.1 CDS yneE NC_011742.1 1593770 1594684 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(1593770..1594684) Escherichia coli S88 7131259 YP_002391337.1 CDS uxaB NC_011742.1 1594881 1596332 R catalyzes the formation of D-tagaturonate from D-altronate; altronate oxidoreductase complement(1594881..1596332) Escherichia coli S88 7133598 YP_002391338.1 CDS yneF NC_011742.1 1596559 1597977 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative membrane-associated diguanylate cyclase (GGDEF domain) complement(1596559..1597977) Escherichia coli S88 7132464 YP_002391339.1 CDS yneG NC_011742.1 1598116 1598475 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1598116..1598475) Escherichia coli S88 7133599 YP_002391340.1 CDS yneH NC_011742.1 1598475 1599401 R catalyzes the formation of glutamate from glutamine; glutaminase complement(1598475..1599401) Escherichia coli S88 7133600 YP_002391341.1 CDS yneI NC_011742.1 1599465 1600853 R in Escherichia coli this enzyme appears to be an NAD+/NADP+-dependent succinate semialdehyde dehydrogenase; putative succinate semialdehyde dehydrogenase complement(1599465..1600853) Escherichia coli S88 7133601 YP_002391342.1 CDS yneJ NC_011742.1 1600954 1601835 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 1600954..1601835 Escherichia coli S88 7133602 YP_002391343.1 CDS ydeA NC_011742.1 1602174 1603364 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10094697, 99369894, 8383113, 10438792; Product type t : transporter; sugar efflux transporter 1602174..1603364 Escherichia coli S88 7133603 YP_002391344.1 CDS marC NC_011742.1 1603389 1604054 R protein involved in resistance to different drugs (tetracycline, chloramphenicol, beta-lactams, and quinolones); part of the multiple antibiotic resistance (mar) locus, which is composed by the genes marC and marRAB; unknown function; multiple drug resistance protein MarC complement(1603389..1604054) Escherichia coli S88 7129318 YP_002391345.1 CDS marR NC_011742.1 1604266 1604700 D Repressor of the marRAB operon which is involved in the activation of both antibiotic resistance and oxidative stress genes; DNA-binding transcriptional repressor MarR 1604266..1604700 Escherichia coli S88 7129426 YP_002391346.1 CDS marA NC_011742.1 1604721 1605104 D transcriptional activator of genes involved in the multiple antibiotic resistance (Mar) phenotype; also activates sodA, zwf and micF; DNA-binding transcriptional activator MarA 1604721..1605104 Escherichia coli S88 7129427 YP_002391347.1 CDS marB NC_011742.1 1605136 1605354 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 8383113; hypothetical protein 1605136..1605354 Escherichia coli S88 7129424 YP_002391348.1 CDS celA NC_011742.1 1605411 1606880 R converts 6-phospho-beta-D-glucosyl-(1,4)-D-glucose to glucose and glucose 6-phosphate; required for cellobiose uptake and metabolism; 6-phospho-beta-glucosidase complement(1605411..1606880) Escherichia coli S88 7129425 YP_002391349.1 CDS ECS88_1610 NC_011742.1 1606874 1608547 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative carbohydrate-specific outer membrane porin complement(1606874..1608547) Escherichia coli S88 7129262 YP_002391350.1 CDS ECS88_1611 NC_011742.1 1608602 1608916 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphotransferase system PTS, lactose/cellobiose-specific IIA subunit complement(1608602..1608916) Escherichia coli S88 7129263 YP_002391351.1 CDS ECS88_1612 NC_011742.1 1608941 1610302 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphotransferase system IIC component complement(1608941..1610302) Escherichia coli S88 7129264 YP_002391352.1 CDS ECS88_1613 NC_011742.1 1610378 1610689 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative cellobiose-specific phosphotransferase enzyme IIB component complement(1610378..1610689) Escherichia coli S88 7129265 YP_002391353.1 CDS ECS88_1614 NC_011742.1 1610888 1611586 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator HTH family 1610888..1611586 Escherichia coli S88 7129266 YP_002391354.1 CDS eamA NC_011742.1 1611631 1612530 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20305052; Product type t : transporter; O-acetylserine/cysteine export protein complement(1611631..1612530) Escherichia coli S88 7129267 YP_002391355.1 CDS ydeE NC_011742.1 1612725 1613912 D YdeF; uncharacterized member of the major facilitator superfamily (MFS) of transporters; putative MFS-type transporter YdeE 1612725..1613912 Escherichia coli S88 7132371 YP_002391356.1 CDS ydeH NC_011742.1 1614353 1615243 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1614353..1615243) Escherichia coli S88 7129319 YP_002391357.1 CDS dcp NC_011742.1 1615751 1617796 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 216006, 8226676; Product type e : enzyme; dipeptidyl carboxypeptidase II complement(1615751..1617796) Escherichia coli S88 7129320 YP_002391358.1 CDS ydfG NC_011742.1 1617933 1618679 D NADP(+)-dependent; catalyzes the formation of 2-aminomalonate-semialdehyde from L-serine; can also use 3-hydroxybutyrate, 3-hydroxy-isobutyrate, D-threonine, L-allo-threonine,D-serine; 3-hydroxy acid dehydrogenase 1617933..1618679 Escherichia coli S88 7130572 YP_002391359.1 CDS ydfH NC_011742.1 1618768 1619454 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 1618768..1619454 Escherichia coli S88 7129330 YP_002391360.1 CDS ydfZ NC_011742.1 1619631 1619834 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12084818; Product type pc : putative carrier; putative selenium carrying protein 1619631..1619834 Escherichia coli S88 7129331 YP_002391361.1 CDS ydfI NC_011742.1 1619870 1621330 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative mannonate dehydrogenase complement(1619870..1621330) Escherichia coli S88 7129341 YP_002391362.1 CDS ynfP NC_011742.1 1621681 1621773 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1621681..1621773) Escherichia coli S88 7129333 YP_002391363.1 CDS rspB NC_011742.1 1621831 1622850 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7545940; Product type pe : putative enzyme; putative dehydrogenase complement(1621831..1622850) Escherichia coli S88 7133617 YP_002391364.1 CDS rspA NC_011742.1 1622862 1624076 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 93341455, 94310441; Product type pe : putative enzyme; putative enolase/dehydratase complement(1622862..1624076) Escherichia coli S88 7133818 YP_002391365.1 CDS ynfA NC_011742.1 1624282 1624608 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(1624282..1624608) Escherichia coli S88 7133816 YP_002391366.1 CDS ynfB NC_011742.1 1624743 1625084 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1624743..1625084 Escherichia coli S88 7133604 YP_002391367.1 CDS speG NC_011742.1 1625119 1625679 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94357898; Product type e : enzyme; spermidine N1-acetyltransferase 1625119..1625679 Escherichia coli S88 7133605 YP_002391368.1 CDS ynfC NC_011742.1 1625682 1626392 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1625682..1626392) Escherichia coli S88 7130630 YP_002391369.1 CDS ynfD NC_011742.1 1626500 1626805 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 9868784; hypothetical protein 1626500..1626805 Escherichia coli S88 7133606 YP_002391370.1 CDS ynfE NC_011742.1 1627004 1629430 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14522592; Product type e : enzyme; oxidoreductase subunit 1627004..1629430 Escherichia coli S88 7133607 YP_002391371.1 CDS ynfF NC_011742.1 1629491 1631914 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14522592; Product type e : enzyme; oxidoreductase subunit 1629491..1631914 Escherichia coli S88 7133608 YP_002391372.1 CDS ynfG NC_011742.1 1631925 1632542 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14522592; Product type c : carrier; oxidoreductase, Fe-S subunit 1631925..1632542 Escherichia coli S88 7133609 YP_002391373.1 CDS ynfH NC_011742.1 1632544 1633398 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14522592; Product type m : membrane component; oxidoreductase, membrane subunit 1632544..1633398 Escherichia coli S88 7133610 YP_002391374.1 CDS dmsD NC_011742.1 1633441 1634055 D binds to the twin-arginine signal peptides of certain proteins, including dimethylsulfoxide reductase and trimethylamine N-oxide reductase that are translocated to the cytoplasmic membrane; twin-argninine leader-binding protein DmsD 1633441..1634055 Escherichia coli S88 7133611 YP_002391375.1 CDS clcB NC_011742.1 1634253 1635434 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12384697; Product type pt : putative transporter; putative voltage-gated ClC-type chloride channel ClcB 1634253..1635434 Escherichia coli S88 7130219 YP_002391376.1 CDS ynfK NC_011742.1 1635387 1636082 R DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium; putative dithiobiotin synthetase complement(1635387..1636082) Escherichia coli S88 7131926 YP_002391377.1 CDS dgsA NC_011742.1 1636207 1637427 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10318813, 20490366, 6989798, 99340206, 99395104, 99398866, 7766024; Product type r : regulator; DNA-binding transcriptional repressor complement(1636207..1637427) Escherichia coli S88 7133612 YP_002391378.1 CDS ynfL NC_011742.1 1637562 1638455 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(1637562..1638455) Escherichia coli S88 7130198 YP_002391379.1 CDS ynfM NC_011742.1 1638562 1639815 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter; MFS type 1638562..1639815 Escherichia coli S88 7133613 YP_002391380.1 CDS asr NC_011742.1 1640240 1640548 D required for growth and survival under moderately acid conditions; acid shock protein precursor 1640240..1640548 Escherichia coli S88 7133614 YP_002391381.1 CDS ydgD NC_011742.1 1640824 1641645 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative exported metallopeptidase 1640824..1641645 Escherichia coli S88 7129953 YP_002391382.1 CDS mdtI NC_011742.1 1641684 1642013 R with MdtJ is involved in resistance to deoxycholate, nalidixic acid, fosfomycin, and SDS; multidrug efflux system protein MdtI complement(1641684..1642013) Escherichia coli S88 7129344 YP_002391383.1 CDS mdtJ NC_011742.1 1642000 1642365 R with MdtI is involved in resistance to deoxycholate , nalidixic acid, fosfomycin, and SDS; multidrug efflux system protein MdtJ complement(1642000..1642365) Escherichia coli S88 7128797 YP_002391384.1 CDS tqsA NC_011742.1 1642776 1643810 D transport of quorum-sensing signal; mutations in this gene alters the transport of the quorum-sensing signal autoinducer 2 (AI-2) which affects expression of a large number of genes; putative transport protein 1642776..1643810 Escherichia coli S88 7128798 YP_002391385.1 CDS pntB NC_011742.1 1643835 1645223 R catalyzes reversible transfer of hydride ion equivalent between NAD and NADP; membrane-bound proton pump that translocates protons from cytosolic to periplasmic side of the inner membrane; forms a tetramer composed of two alpha and 2 beta subunits; AB-stereospecific enzyme; pyridine nucleotide transhydrogenase complement(1643835..1645223) Escherichia coli S88 7129345 YP_002391386.1 CDS pntA NC_011742.1 1645234 1646766 R forms a tetramer composed of 2 alpha subunits and 2 beta subunits in the inner membrane; involved in catalyzing transfer of hydride ion equivalents between NAD and NADP; stereospecific (AB-specific); functions as a proton pump by translocating protons from cytoplasm to periplasm; NAD(P) transhydrogenase subunit alpha complement(1645234..1646766) Escherichia coli S88 7133750 YP_002391387.1 CDS ydgH NC_011742.1 1647290 1648234 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1647290..1648234 Escherichia coli S88 7133749 YP_002391388.1 CDS ydgI NC_011742.1 1648420 1649802 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1311296; Product type pt : putative transporter; putative arginine/ornithine antiporter transporter 1648420..1649802 Escherichia coli S88 7129346 YP_002391389.1 CDS folM NC_011742.1 1649839 1650561 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14617668; Product type e : enzyme; short chain dehydrogenase 1649839..1650561 Escherichia coli S88 7129347 YP_002391390.1 CDS ydgC NC_011742.1 1650558 1650893 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein associated with alginate biosynthesis complement(1650558..1650893) Escherichia coli S88 7132819 YP_002391391.1 CDS rstA NC_011742.1 1651013 1651741 D response regulator in two-component regulatory system with RstB; DNA-binding transcriptional regulator RstA 1651013..1651741 Escherichia coli S88 7129343 YP_002391392.1 CDS rstB NC_011742.1 1651745 1653046 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93086426, 1495392, 1925016, 2646639; Product type r : regulator; sensor protein RstB 1651745..1653046 Escherichia coli S88 7133821 YP_002391393.1 CDS tus NC_011742.1 1653122 1654051 D binds to DNA replication terminator sequences to prevent passage of replication forks; DNA replication terminus site-binding protein 1653122..1654051 Escherichia coli S88 7133822 YP_002391394.1 CDS fumC NC_011742.1 1654048 1655451 R class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle; fumarate hydratase complement(1654048..1655451) Escherichia coli S88 7130368 YP_002391395.1 CDS fumA NC_011742.1 1655594 1657240 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88193096, 88268900, 92011457, 3005475, 6328431, 9298646; Product type e : enzyme; fumarate hydratase (fumarase A), aerobic Class I complement(1655594..1657240) Escherichia coli S88 7132155 YP_002391396.1 CDS manA NC_011742.1 1657439 1658614 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 82100097, 6397402; Product type e : enzyme; mannose-6-phosphate isomerase 1657439..1658614 Escherichia coli S88 7132153 YP_002391397.1 CDS ydgA NC_011742.1 1658715 1660223 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1658715..1660223 Escherichia coli S88 7129419 YP_002391398.1 CDS uidC NC_011742.1 1660268 1661533 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15774881; Product type t : transporter; putative outer membrane porin protein complement(1660268..1661533) Escherichia coli S88 7129342 YP_002391399.1 CDS uidB NC_011742.1 1661572 1662945 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3534890; Product type t : transporter; glucuronide transporter complement(1661572..1662945) Escherichia coli S88 7130404 YP_002391400.1 CDS uidA NC_011742.1 1662942 1664753 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87041472, 88038341, 2103475, 8125312; Product type e : enzyme; beta-D-glucuronidase complement(1662942..1664753) Escherichia coli S88 7130403 YP_002391401.1 CDS uidR NC_011742.1 1665143 1665733 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88038341, 2823062, 3934044, 11115104; Product type r : regulator; DNA-binding transcriptional repressor complement(1665143..1665733) Escherichia coli S88 7130402 YP_002391402.1 CDS hdhA NC_011742.1 1665962 1666729 R Acts on the hydroxyl group at position 7 of the steroid frame; 7-alpha-hydroxysteroid dehydrogenase complement(1665962..1666729) Escherichia coli S88 7130405 YP_002391403.1 CDS malI NC_011742.1 1666841 1667869 R regulates malXY which are involved in maltose-glucose transport; DNA-binding transcriptional repressor MalI complement(1666841..1667869) Escherichia coli S88 7128894 YP_002391404.1 CDS malX NC_011742.1 1668044 1669636 D phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS); catalyzes the phosphorylation of maltose and glucose concomitant with their translocation across the cell membrane; component IIB catalyzes the phosphorylation of the sugar molecule; IIC forms the translocation channel and contains the substrate specific binding site; bifunctional PTS system maltose and glucose-specific transporter subunits IICB 1668044..1669636 Escherichia coli S88 7129409 YP_002391405.1 CDS malY NC_011742.1 1669646 1670818 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20164451, 7665481, 91310596; Product type e : enzyme; bifunctional beta-cystathionase, PLP-dependent and regulator of maltose regulon 1669646..1670818 Escherichia coli S88 7129416 YP_002391406.1 CDS add NC_011742.1 1670922 1671923 D catalyzes the formation of inosine from adenosine; adenosine deaminase 1670922..1671923 Escherichia coli S88 7129417 YP_002391407.1 CDS ydgJ NC_011742.1 1671959 1672999 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase complement(1671959..1672999) Escherichia coli S88 7132051 YP_002391408.1 CDS blr NC_011742.1 1673167 1673367 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20392465, 10931331; Product type m : membrane component; beta-lactam resistance membrane protein 1673167..1673367 Escherichia coli S88 7129348 YP_002391409.1 CDS ydgT NC_011742.1 1673640 1673855 D YdgT; in E. coli, when complexed with H-NS or StpA binds a 26 base-pair DNA sequence of oriC; seems to play a role in optimizing the activity of oriC; non-essential; Hha protein paralog; in an hha mutant background, cnu is overexpressed and can compensate hha-induced phenotypes; oriC-binding nucleoid-associated protein 1673640..1673855 Escherichia coli S88 7129130 YP_002391410.1 CDS ydgK NC_011742.1 1673941 1674381 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1673941..1674381 Escherichia coli S88 7129351 YP_002391411.1 CDS rsxA NC_011742.1 1674458 1675039 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10411911, 10637328, 12773378; Product type pm : putative membrane component; Na(+)-translocating NADH-quinone reductase subunit E 1674458..1675039 Escherichia coli S88 7129349 YP_002391412.1 CDS rsxB NC_011742.1 1675039 1675617 D part of membrane-bound complex thought to be involved in electron transport to nitrogen; electron transport complex protein RnfB 1675039..1675617 Escherichia coli S88 7133824 YP_002391413.1 CDS rsxC NC_011742.1 1675610 1677736 D part of membrane-bound complex thought to be involved in electron transport to nitrogen; electron transport complex protein RnfC 1675610..1677736 Escherichia coli S88 7133825 YP_002391414.1 CDS rnfD NC_011742.1 1677737 1678795 D RnfD; RsxD; required for nitrogen fixation in Rhodobacter capsulatus; part of a membrane-bound complex thought to be involved in electron transport to nitrogenase; in Escherichia coli this gene is part of a cluster controlling SoxR-mediated induction of the SoxS transcription factor in the absence of oxidizing agents; electron transport complex protein RnfD 1677737..1678795 Escherichia coli S88 7133826 YP_002391415.1 CDS rsxG NC_011742.1 1678799 1679419 D part of membrane-bound complex hought to be involved in electron transport to nitrogen; electron transport complex protein RnfG 1678799..1679419 Escherichia coli S88 7133827 YP_002391416.1 CDS rsxE NC_011742.1 1679423 1680118 D in Excherichia coli RsxABCDEG reduces SoxR which turns off induction of SoxS transcription factor in the absence of oxidizing agents; similar to the rnfABCDGE operon in Rhodobacter capsulatus involved in transferring electrons to nitrogenase; electron transport complex RsxE subunit 1679423..1680118 Escherichia coli S88 7133829 YP_002391417.1 CDS nth NC_011742.1 1680118 1680753 D DNA-(apurinic or apyrimidinic site) lyase; has apurinic or apyrimidinic endonuclease activity and DNA N-glycosylase activity; removed damaged DNA at cytosines, thymines and guanines; endonuclease III 1680118..1680753 Escherichia coli S88 7133828 YP_002391418.1 CDS tppB NC_011742.1 1681364 1682866 D mutations in this gene confer resistance to the toxic peptide alafosfalin in Salmonella typhimurium; member of proton-dependent oligopeptide transport (POT) system family; in Escherichia coli this gene is regulated by OmpR although not via osmoregulation; putative tripeptide transporter permease 1681364..1682866 Escherichia coli S88 7129749 YP_002391419.1 CDS gst NC_011742.1 1682971 1683576 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95096109, 2185038, 9680481; Product type e : enzyme; glutathionine S-transferase 1682971..1683576 Escherichia coli S88 7129350 YP_002391420.1 CDS pdxY NC_011742.1 1683620 1684483 R catalyzes the formation of pyridoxal 5'-phosphate from pyridoxal; pyridoxamine kinase complement(1683620..1684483) Escherichia coli S88 7128873 YP_002391421.1 CDS tyrS NC_011742.1 1684542 1685816 R catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr); tyrosyl-tRNA synthetase complement(1684542..1685816) Escherichia coli S88 7133186 YP_002391422.1 CDS pdxH NC_011742.1 1685945 1686601 R catalyzes the formation of pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate; pyridoxamine 5'-phosphate oxidase complement(1685945..1686601) Escherichia coli S88 7130378 YP_002391423.1 CDS ydhA NC_011742.1 1686660 1686989 R MliC; membrane-bound lysozyme inhibitor of c-type lysozyme; lysozyme inhibitor complement(1686660..1686989) Escherichia coli S88 7133183 YP_002391424.1 CDS anmK NC_011742.1 1687087 1688196 R catalyzes hydrolysis of 1,6-anhydro bond of anyhydro-N-acetylmuramic acid (anhMurNAc) and phosphorylates anhMurNAc to produce N-acetyl-muramate-6-phosphate; involved in murein recycling; anhydro-N-acetylmuramic acid kinase complement(1687087..1688196) Escherichia coli S88 7129352 YP_002391425.1 CDS slyB NC_011742.1 1688470 1688937 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8544813; Product type lp : lipoprotein; putative outer membrane lipoprotein 1688470..1688937 Escherichia coli S88 7133068 YP_002391426.1 CDS slyA NC_011742.1 1688984 1689418 R Transcription regulator that can both activate or repress expression; transcriptional regulator SlyA complement(1688984..1689418) Escherichia coli S88 7130608 YP_002391427.1 CDS ydhI NC_011742.1 1689619 1689855 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1689619..1689855 Escherichia coli S88 7130607 YP_002391428.1 CDS ydhJ NC_011742.1 1689858 1690715 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12900028; Product type e : enzyme; undecaprenyl pyrophosphate phosphatase 1689858..1690715 Escherichia coli S88 7133198 YP_002391429.1 CDS ydhK NC_011742.1 1690715 1692727 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1690715..1692727 Escherichia coli S88 7133199 YP_002391430.1 CDS sodC NC_011742.1 1692728 1693249 R SodC; copper and zinc binding; converts superoxide radicals to hydrogen peroxide and water; superoxide dismutase complement(1692728..1693249) Escherichia coli S88 7133200 YP_002391431.1 CDS ydhF NC_011742.1 1693330 1694226 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase complement(1693330..1694226) Escherichia coli S88 7130618 YP_002391432.1 CDS ydhL NC_011742.1 1694275 1694685 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1694275..1694685) Escherichia coli S88 7133197 YP_002391433.1 CDS ydhM NC_011742.1 1694701 1695216 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 1694701..1695216 Escherichia coli S88 7133201 YP_002391434.1 CDS nemA NC_011742.1 1695253 1696350 D FMN-linked; catalyzes the formation of N-ethylsuccinimide from N-ethylmaleimide; N-ethylmaleimide reductase 1695253..1696350 Escherichia coli S88 7133202 YP_002391435.1 CDS gloA NC_011742.1 1696431 1696838 D Ni-dependent; catalyzes the formation of S-lactoylglutathione from methylglyoxal and glutathione; glyoxalase I 1696431..1696838 Escherichia coli S88 7129693 YP_002391436.1 CDS rnt NC_011742.1 1696941 1697588 D Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A); ribonuclease T 1696941..1697588 Escherichia coli S88 7130015 YP_002391437.1 CDS ECS88_1702 NC_011742.1 1697681 1697824 D Evidence 7 : Gene remnant; hypothetical protein, putative fragment of lhr gene 1697681..1697824 Escherichia coli S88 7132754 YP_002391438.1 CDS ydhD NC_011742.1 1697960 1698307 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15833738, 15840565, 11950925, 12730244; Product type e : enzyme; hypothetical protein complement(1697960..1698307) Escherichia coli S88 7128949 YP_002391439.1 CDS ydhO NC_011742.1 1698642 1699457 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative exported hydrolase 1698642..1699457 Escherichia coli S88 7133196 YP_002391440.1 CDS sodB NC_011742.1 1699585 1700166 D SodB; iron binding; present under aerobic and anaerobic conditions; destroys free radicals; superoxide dismutase 1699585..1700166 Escherichia coli S88 7133203 YP_002391441.1 CDS ydhP NC_011742.1 1700312 1701481 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative efflux protein; MFS family complement(1700312..1701481) Escherichia coli S88 7130617 YP_002391442.1 CDS purR NC_011742.1 1702035 1703060 D binds to the purF operator and coregulates other genes for de novo purine nucleotide synthesis; is involved in regulation of purB, purC, purEK, purHD, purL, purMN and guaBA expression; binds hypoxanthine and guanine as inducers; DNA-binding transcriptional repressor PurR 1702035..1703060 Escherichia coli S88 7133204 YP_002391443.1 CDS ydhB NC_011742.1 1703057 1703989 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2404765; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(1703057..1703989) Escherichia coli S88 7131755 YP_002391444.1 CDS ydhC NC_011742.1 1704102 1705313 D uncharacterized member of the major facilitator superfamily (MFS); inner membrane transport protein YdhC 1704102..1705313 Escherichia coli S88 7132364 YP_002391445.1 CDS cfa NC_011742.1 1705604 1706752 D catalyzes the transfer of a methylene group from S-adenosyl-L-methionine to the cis double bond of an unsaturated fatty acid chain resulting in the replacement of the double bond with a methylene bridge; cyclopropane fatty acyl phospholipid synthase 1705604..1706752 Escherichia coli S88 7133195 YP_002391446.1 CDS ribC NC_011742.1 1706792 1707433 R catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha complement(1706792..1707433) Escherichia coli S88 7129180 YP_002391447.1 CDS mdtK NC_011742.1 1707648 1709021 D NorM; MdtK; functions as a Na(+)/drug antiporter; inactivation in Vibrio cholerae results in susceptibility to fluoroquinolones; multidrug efflux protein 1707648..1709021 Escherichia coli S88 7132716 YP_002391448.1 CDS ydhQ NC_011742.1 1709062 1710318 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1709062..1710318) Escherichia coli S88 7128799 YP_002391449.1 CDS ydhR NC_011742.1 1710892 1711197 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1710892..1711197 Escherichia coli S88 7129879 YP_002391450.1 CDS ydhS NC_011742.1 1711323 1712927 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1711323..1712927 Escherichia coli S88 7133206 YP_002391451.1 CDS ydhT NC_011742.1 1712939 1713751 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1712939..1713751) Escherichia coli S88 7133207 YP_002391452.1 CDS ydhU NC_011742.1 1713755 1714540 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative cytochrome b subunit of a reductase complement(1713755..1714540) Escherichia coli S88 7133208 YP_002391453.1 CDS ydhX NC_011742.1 1714537 1715205 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative 4Fe-4S ferridoxin-type subunit of oxidoreductase complement(1714537..1715205) Escherichia coli S88 7133209 YP_002391454.1 CDS ydhW NC_011742.1 1715269 1715916 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1715269..1715916) Escherichia coli S88 7133212 YP_002391455.1 CDS ydhV NC_011742.1 1715920 1718022 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase complement(1715920..1718022) Escherichia coli S88 7133211 YP_002391456.1 CDS ydhY NC_011742.1 1718043 1718669 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; hypothetical protein complement(1718043..1718669) Escherichia coli S88 7133210 YP_002391457.1 CDS ydhZ NC_011742.1 1719125 1719334 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1719125..1719334) Escherichia coli S88 7133213 YP_002391458.1 CDS pykF NC_011742.1 1719891 1721303 D catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate kinase 1719891..1721303 Escherichia coli S88 7133214 YP_002391459.1 CDS lpp NC_011742.1 1721614 1721850 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 334727, 338599, 322142, 353292, 391404, 4261992, 4575979, 6765942; Product type lp : lipoprotein; murein lipoprotein 1721614..1721850 Escherichia coli S88 7131762 YP_002391460.1 CDS ynhG NC_011742.1 1721913 1722917 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1721913..1722917) Escherichia coli S88 7129377 YP_002391461.1 CDS sufE NC_011742.1 1723066 1723482 R Acts with SufS to catalyze the formation of L-alanine from L-cysteine; cysteine desufuration protein SufE complement(1723066..1723482) Escherichia coli S88 7133618 YP_002391462.1 CDS sufS NC_011742.1 1723495 1724715 R catalyzes the formation of L-alanine and selenide or sulfanylcysteine from selenocysteine or cysteine; bifunctional cysteine desulfurase/selenocysteine lyase complement(1723495..1724715) Escherichia coli S88 7131245 YP_002391463.1 CDS sufD NC_011742.1 1724712 1725983 R with SufBC activates cysteine desulfurase SufS; cysteine desulfurase activator complex subunit SufD complement(1724712..1725983) Escherichia coli S88 7131247 YP_002391464.1 CDS sufC NC_011742.1 1725958 1726704 R part of SUF system involved in inserting iron-sulfur clusters into proteins; in Escherichia coli this protein forms a complex with SufBD; the SufBCD complex stimulates the cysteine desulfurase SufS in conjunction with SufE; cysteine desulfurase ATPase component complement(1725958..1726704) Escherichia coli S88 7131244 YP_002391465.1 CDS sufB NC_011742.1 1726714 1728201 R with SufCD activates cysteine desulfurase SufS; cysteine desulfurase activator complex subunit SufB complement(1726714..1728201) Escherichia coli S88 7131243 YP_002391466.1 CDS sufA NC_011742.1 1728210 1728578 R functions as a scaffold on which iron-sulfur clusters ([2Fe-2S]; [4Fe-4S]) are assembled; forms a homodimer; similar to IscA protein; iron-sulfur cluster assembly scaffold protein complement(1728210..1728578) Escherichia coli S88 7131242 YP_002391467.1 CDS ydiH NC_011742.1 1729127 1729396 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1729127..1729396) Escherichia coli S88 7131331 YP_002391468.1 CDS ydiI NC_011742.1 1729415 1729825 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15808744; Product type pe : putative enzyme; hypothetical protein complement(1729415..1729825) Escherichia coli S88 7133220 YP_002391469.1 CDS ydiJ NC_011742.1 1729822 1732878 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11102686; Product type pe : putative enzyme; putative conserved FAD-linked oxidoreductase complement(1729822..1732878) Escherichia coli S88 7133221 YP_002391470.1 CDS ydiK NC_011742.1 1733092 1734204 D YdiK; inner membrane protein; ydiK promoter presents a PurR sequence, suggesting that its expression is purine-regulated; unknown function; putative inner membrane protein 1733092..1734204 Escherichia coli S88 7133222 YP_002391471.1 CDS ydiL NC_011742.1 1734633 1734989 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1734633..1734989 Escherichia coli S88 7133783 YP_002391472.1 CDS ydiM NC_011742.1 1735089 1736303 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter; MFS superfamily 1735089..1736303 Escherichia coli S88 7133224 YP_002391473.1 CDS ydiN NC_011742.1 1736530 1737795 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 1736530..1737795 Escherichia coli S88 7133225 YP_002391474.1 CDS ydiB NC_011742.1 1737807 1738673 D YdiB; quinate/shikimate dehydrogenase from Escherichia coli uses both NAD and NAD(P) to convert quinate and shikimate to 3-dehydroquinate and 3-dehydroshikimate; quinate/shikimate dehydrogenase 1737807..1738673 Escherichia coli S88 7133226 YP_002391475.1 CDS aroD NC_011742.1 1738704 1739462 D catalyzes the dehydration of 3-dehydroquinate to form 3-dehydroshikimate in aromatic amino acid biosynthesis; 3-dehydroquinate dehydratase 1738704..1739462 Escherichia coli S88 7133216 YP_002391476.1 CDS ydiF NC_011742.1 1739608 1741203 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16253988; Product type e : enzyme; short chain acyl-CoA transferase: fused alpha subunit ; beta subunit 1739608..1741203 Escherichia coli S88 7129924 YP_002391477.1 CDS ydiO NC_011742.1 1741217 1742368 D may play a role in electron transport between the anaerobic fatty acid oxidation pathway and the respiratory chain; putative acyl-CoA dehydrogenase 1741217..1742368 Escherichia coli S88 7133219 YP_002391478.1 CDS ydiP NC_011742.1 1742411 1743322 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(1742411..1743322) Escherichia coli S88 7133227 YP_002391479.1 CDS ECS88_1747 NC_011742.1 1743425 1743601 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1743425..1743601) Escherichia coli S88 7133228 YP_002391480.1 CDS ydiQ NC_011742.1 1743638 1744402 D YdiO, YdiQ, YdiR, YdiS, and YdiT may play a role in electron transport between the anaerobic fatty acid oxidation pathway and the respiratory chain; putative electron transfer flavoprotein YdiQ 1743638..1744402 Escherichia coli S88 7128950 YP_002391481.1 CDS ydiR NC_011742.1 1744422 1745360 D May play a role in a redox process; electron transfer flavoprotein subunit YdiR 1744422..1745360 Escherichia coli S88 7133229 YP_002391482.1 CDS ydiS NC_011742.1 1745415 1746704 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; hypothetical protein 1745415..1746704 Escherichia coli S88 7133230 YP_002391483.1 CDS ydiT NC_011742.1 1746701 1746994 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative 4Fe-4S ferredoxin-type oxidoreductase subunit 1746701..1746994 Escherichia coli S88 7133231 YP_002391484.1 CDS ydiD NC_011742.1 1746997 1748697 D acts in anaerobic beta-oxidation of fatty acids; possible ligase/synthase involved in anaerobic growth on fatty acids; short chain acyl-CoA synthetase 1746997..1748697 Escherichia coli S88 7133232 YP_002391485.1 CDS pps NC_011742.1 1748754 1751132 R catalyzes the formation of phosphoenolpyruvate from pyruvate; phosphoenolpyruvate synthase complement(1748754..1751132) Escherichia coli S88 7133217 YP_002391486.1 CDS ydiA NC_011742.1 1751465 1752298 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1751465..1752298 Escherichia coli S88 7130766 YP_002391487.1 CDS aroH NC_011742.1 1752455 1753501 D tryptophan sensitive; catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate; phospho-2-dehydro-3-deoxyheptonate aldolase 1752455..1753501 Escherichia coli S88 7133215 YP_002391488.1 CDS ydiE NC_011742.1 1753633 1753824 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 15039350; hypothetical protein 1753633..1753824 Escherichia coli S88 7129928 YP_002391489.1 CDS ydiU NC_011742.1 1753828 1755264 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1753828..1755264) Escherichia coli S88 7133218 YP_002391490.1 CDS ydiV NC_011742.1 1755327 1756040 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1755327..1756040) Escherichia coli S88 7133233 YP_002391491.1 CDS nlpC NC_011742.1 1756287 1756751 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12620121; Product type lp : lipoprotein; putative peptidase lipoprotein complement(1756287..1756751) Escherichia coli S88 7133234 YP_002391492.1 CDS btuD NC_011742.1 1756829 1757578 R ATP-binding protein that acts with the transmembrane protein BtuC and the solute binding protein BtuF to transport vitamin B12 into the cell; vitamin B12-transporter ATPase complement(1756829..1757578) Escherichia coli S88 7129722 YP_002391493.1 CDS btuE NC_011742.1 1757578 1758129 R similar to glutathione peroxidase; member of the btuCED operon which is required for vitamin B12 transport across the inner membrane; putative glutathione peroxidase complement(1757578..1758129) Escherichia coli S88 7129138 YP_002391494.1 CDS btuC NC_011742.1 1758191 1759171 R with BtuD and BtuF transports vitamin B12 into the cell; vtamin B12-transporter permease complement(1758191..1759171) Escherichia coli S88 7129139 YP_002391495.1 CDS ihfA NC_011742.1 1759272 1759571 R This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control; integration host factor subunit alpha complement(1759272..1759571) Escherichia coli S88 7129137 YP_002391496.1 CDS pheT NC_011742.1 1759576 1761963 R 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; phenylalanyl-tRNA synthetase subunit beta complement(1759576..1761963) Escherichia coli S88 7131616 YP_002391497.1 CDS pheS NC_011742.1 1761978 1762961 R 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; phenylalanyl-tRNA synthetase subunit alpha complement(1761978..1762961) Escherichia coli S88 7133706 YP_002391498.1 CDS pheM NC_011742.1 1763245 1763289 R Evidence 1c : Function experimentally demonstrated in the studied genus; Product type l : leader peptide; phenylalanyl-tRNA synthetase operon leader peptide complement(1763245..1763289) Escherichia coli S88 7133705 YP_002391499.1 CDS rplT NC_011742.1 1763412 1763768 R binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 complement(1763412..1763768) Escherichia coli S88 7133703 YP_002391500.1 CDS rpmI NC_011742.1 1763821 1764018 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93085722, 10094780, 3298224, 3542048, 6325158; Product type s : structure; 50S ribosomal protein L35 complement(1763821..1764018) Escherichia coli S88 7133759 YP_002391501.1 CDS thrS NC_011742.1 1764661 1766589 R 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; threonyl-tRNA synthetase complement(1764661..1766589) Escherichia coli S88 7131635 YP_002391502.1 CDS ECS88_1771 NC_011742.1 1767595 1768035 D hypothetical protein 1767595..1768035 Escherichia coli S88 7128951 YP_002391503.1 CDS ECS88_1773 NC_011742.1 1768202 1768420 D hypothetical protein 1768202..1768420 Escherichia coli S88 7128953 YP_002391504.1 CDS ydiY NC_011742.1 1768473 1769231 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1768473..1769231) Escherichia coli S88 7128954 YP_002391505.1 CDS pfkB NC_011742.1 1769517 1770446 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 78194149, 88292964, 6235149, 6310120; Product type e : enzyme; 6-phosphofructokinase 2 1769517..1770446 Escherichia coli S88 7133235 YP_002391506.1 CDS ydiZ NC_011742.1 1770547 1770837 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1770547..1770837 Escherichia coli S88 7133679 YP_002391507.1 CDS yniA NC_011742.1 1770943 1771803 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphotransferase/kinase 1770943..1771803 Escherichia coli S88 7133236 YP_002391508.1 CDS yniB NC_011742.1 1771844 1772380 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(1771844..1772380) Escherichia coli S88 7133619 YP_002391509.1 CDS yniC NC_011742.1 1772527 1773195 D YniC; catalyzes the dephosphorylation of 2-deoxyglucose 6-phosphate, mannose 6-phosphate and p-nitrophenyl phosphate; 2-deoxyglucose-6-phosphatase 1772527..1773195 Escherichia coli S88 7133620 YP_002391510.1 CDS ydjM NC_011742.1 1773359 1773949 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 10760155; Product type pm : putative membrane component; hypothetical protein 1773359..1773949 Escherichia coli S88 7133621 YP_002391511.1 CDS ydjN NC_011742.1 1774082 1775473 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative cation-acid symporter 1774082..1775473 Escherichia coli S88 7133246 YP_002391512.1 CDS cedA NC_011742.1 1775520 1775774 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9427399; Product type cp : cell process; cell division modulator complement(1775520..1775774) Escherichia coli S88 7133247 YP_002391513.1 CDS katE NC_011742.1 1775966 1778227 D Catalase HPII; monofunctional catalase that decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide; hydroperoxidase II 1775966..1778227 Escherichia coli S88 7129179 YP_002391514.1 CDS chbG NC_011742.1 1778273 1779031 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 20042356, 1987146, 2179047, 8121401, 9405618; hypothetical protein complement(1778273..1779031) Escherichia coli S88 7130431 YP_002391515.1 CDS chbF NC_011742.1 1779044 1780396 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20042356, 90185127, 9405618; Product type e : enzyme; cryptic phospho-beta-glucosidase, NAD(P)-binding complement(1779044..1780396) Escherichia coli S88 7129188 YP_002391516.1 CDS chbR NC_011742.1 1780500 1781342 R represses the celABCDF-ydjC operon involved in carbon uptake; DNA-binding transcriptional regulator ChbR complement(1780500..1781342) Escherichia coli S88 7129187 YP_002391517.1 CDS chbA NC_011742.1 1781350 1781700 R catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; involved N,N'-diacetylchitobiose transport; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake; PTS system N,N'-diacetylchitobiose-specific transporter subunit IIA complement(1781350..1781700) Escherichia coli S88 7129189 YP_002391518.1 CDS chbC NC_011742.1 1781751 1783109 R catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; involved in N,N'-diacetylchitobiose transport; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake; PTS system N,N'-diacetylchitobiose-specific transporter subunit IIC complement(1781751..1783109) Escherichia coli S88 7129184 YP_002391519.1 CDS chbB NC_011742.1 1783194 1783514 R catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; involved in N,N'-diacetylchitobiose transport; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake; PTS system N,N'-diacetylchitobiose-specific transporter subunit IIB complement(1783194..1783514) Escherichia coli S88 7129186 YP_002391520.1 CDS osmE NC_011742.1 1783813 1784151 R osmotically-inducible lipoprotein E; activator of ntr-like gene protein; DNA-binding transcriptional activator OsmE complement(1783813..1784151) Escherichia coli S88 7129185 YP_002391521.1 CDS nadE NC_011742.1 1784353 1785180 D catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers; NAD synthetase 1784353..1785180 Escherichia coli S88 7133145 YP_002391522.1 CDS ydjQ NC_011742.1 1785410 1786297 D 3' incision activity; acts with UvrC; nucleotide excision repair endonuclease 1785410..1786297 Escherichia coli S88 7129654 YP_002391523.1 CDS ydjR NC_011742.1 1786257 1786832 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 21862596; hypothetical protein complement(1786257..1786832) Escherichia coli S88 7133248 YP_002391524.1 CDS spy NC_011742.1 1787035 1787520 R periplasmic protein induced by stress response via Cpx and BaeSR system; similar to CpxP; periplasmic protein complement(1787035..1787520) Escherichia coli S88 7133249 YP_002391525.1 CDS astE NC_011742.1 1787850 1788818 R catalyzes the formation of succinate and glutamate from N(2)-succinylglutamate in arginine catabolism; succinylglutamate desuccinylase complement(1787850..1788818) Escherichia coli S88 7130636 YP_002391526.1 CDS astB NC_011742.1 1788811 1790154 R catalyzes the hydrolysis of 2-N-succinylarginine into 2-N-succinylornithine, ammonia and carbon dioxide in arginine degradation; succinylarginine dihydrolase complement(1788811..1790154) Escherichia coli S88 7129959 YP_002391527.1 CDS astD NC_011742.1 1790151 1791629 R a high throughput screen identified this enzyme as an aldehyde dehydrogenase with broad substrate specificity; converts succinylglutamate semialdehyde and NAD to succinylglutamate and NADH; succinylglutamic semialdehyde dehydrogenase complement(1790151..1791629) Escherichia coli S88 7129956 YP_002391528.1 CDS astA NC_011742.1 1791626 1792660 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14675764, 98361920; Product type e : enzyme; arginine succinyltransferase complement(1791626..1792660) Escherichia coli S88 7129958 YP_002391529.1 CDS astC NC_011742.1 1792657 1793877 R catalyzes the transamination of 2-N-succinylornithine and alpha-ketoglutarate into 2-N-succinylglutamate semialdehyde and glutamate; also functions as the catabolic acetylornithine aminotransferase catalyzing the formation of 2-N-acetylglutamate semialdehyde and glutamate from 2-N-acetylornithine and alpha-ketoglutarate; bifunctional succinylornithine transaminase/acetylornithine transaminase complement(1792657..1793877) Escherichia coli S88 7129955 YP_002391530.1 CDS xthA NC_011742.1 1794323 1795129 D removes the damaged DNA at cytosines and guanines by cleaving on the 3' side of the AP site by a beta-elimination reaction; exonuclease III 1794323..1795129 Escherichia coli S88 7129957 YP_002391531.1 CDS ydjX NC_011742.1 1795296 1796006 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1795296..1796006 Escherichia coli S88 7132524 YP_002391532.1 CDS ydjY NC_011742.1 1796011 1796688 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1796011..1796688 Escherichia coli S88 7133250 YP_002391533.1 CDS ydjZ NC_011742.1 1796702 1797409 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1796702..1797409 Escherichia coli S88 7133251 YP_002391534.1 CDS ynjA NC_011742.1 1797409 1797957 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1797409..1797957 Escherichia coli S88 7133252 YP_002391535.1 CDS ynjB NC_011742.1 1797967 1799133 D Evidence 4 : Homologs of previously reported genes of unknown function; putative ABC transporter solute-binding protein 1797967..1799133 Escherichia coli S88 7133622 YP_002391536.1 CDS ynjC NC_011742.1 1799151 1800641 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; fused putative transporter subunits of ABC superfamily: membrane components 1799151..1800641 Escherichia coli S88 7133623 YP_002391537.1 CDS ynjD NC_011742.1 1800641 1801294 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sulfate/thiosulfate transporter subunit: ATP-binding component of ABC superfamily transporter 1800641..1801294 Escherichia coli S88 7133624 YP_002391538.1 CDS ynjE NC_011742.1 1801361 1802668 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative exported thiosulfate sulfur transferase / thiosulfate binding protein 1801361..1802668 Escherichia coli S88 7133625 YP_002391539.1 CDS ynjF NC_011742.1 1802677 1803297 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type m : membrane component; putative phosphatidyl transferase, inner membrane protein complement(1802677..1803297) Escherichia coli S88 7133626 YP_002391540.1 CDS nudG NC_011742.1 1803384 1803791 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21101911; Product type e : enzyme; pyrimidine (deoxy)nucleoside triphosphate pyrophosphohydrolase 1803384..1803791 Escherichia coli S88 7133627 YP_002391541.1 CDS gdhA NC_011742.1 1804265 1805608 D converts 2-oxoglutarate to glutamate; in Escherichia coli this enzyme plays a role in glutamate synthesis when the cell is under energy restriction; uses NADPH; forms a homohexamer; glutamate dehydrogenase 1804265..1805608 Escherichia coli S88 7129755 YP_002391542.1 CDS topB NC_011742.1 1805685 1807640 R decatenates replicating daughter chromosomes; DNA topoisomerase III complement(1805685..1807640) Escherichia coli S88 7132202 YP_002391543.1 CDS selD NC_011742.1 1807645 1808688 R catalyzes the formation of selenophosphate from selenide and ATP; selenophosphate synthetase complement(1807645..1808688) Escherichia coli S88 7133491 YP_002391544.1 CDS ECS88_1815 NC_011742.1 1808630 1808779 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1808630..1808779) Escherichia coli S88 7131388 YP_002391545.1 CDS ydjA NC_011742.1 1808805 1809356 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein complement(1808805..1809356) Escherichia coli S88 7128955 YP_002391546.1 CDS ECS88_1817 NC_011742.1 1809410 1809574 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1809410..1809574 Escherichia coli S88 7133237 YP_002391547.1 CDS sppA NC_011742.1 1809517 1811373 D SppA; catalyzes the degradation of cleaved signal peptides; essential to maintain secretion of mature proteins across the membrane; protease 4 1809517..1811373 Escherichia coli S88 7128956 YP_002391548.1 CDS ansA NC_011742.1 1811540 1812556 D converts asparagine to aspartate and ammonia; cytoplasmic asparaginase I 1811540..1812556 Escherichia coli S88 7130633 YP_002391549.1 CDS pncA NC_011742.1 1812567 1813208 D catalyzes the formation of nicotinate from nicotinamide in NAD biosynthesis and the formation of pyrazinoate from pyrazinamide; nicotinamidase/pyrazinamidase 1812567..1813208 Escherichia coli S88 7133069 YP_002391550.1 CDS ydjE NC_011742.1 1813301 1814659 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter; MFS superfamily complement(1813301..1814659) Escherichia coli S88 7133746 YP_002391551.1 CDS ydjF NC_011742.1 1814777 1815535 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(1814777..1815535) Escherichia coli S88 7133238 YP_002391552.1 CDS ydjG NC_011742.1 1815672 1816652 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase complement(1815672..1816652) Escherichia coli S88 7133239 YP_002391553.1 CDS ydjH NC_011742.1 1816662 1817609 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative sugar kinase complement(1816662..1817609) Escherichia coli S88 7133240 YP_002391554.1 CDS ydjI NC_011742.1 1817614 1818450 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative aldolase complement(1817614..1818450) Escherichia coli S88 7133241 YP_002391555.1 CDS ydjJ NC_011742.1 1818471 1819514 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12897001; Product type pe : putative enzyme; putative iditol dehydrogenase complement(1818471..1819514) Escherichia coli S88 7133242 YP_002391556.1 CDS ydjK NC_011742.1 1819531 1820910 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter; MFS superfamily complement(1819531..1820910) Escherichia coli S88 7133243 YP_002391557.1 CDS ydjL NC_011742.1 1820937 1822013 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase, Zn-dependent and NAD(P)-binding complement(1820937..1822013) Escherichia coli S88 7133244 YP_002391558.1 CDS yeaC NC_011742.1 1822383 1822655 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1822383..1822655) Escherichia coli S88 7133245 YP_002391559.1 CDS msrB NC_011742.1 1822697 1823110 R this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress; methionine sulfoxide reductase B complement(1822697..1823110) Escherichia coli S88 7133254 YP_002391560.1 CDS gapA NC_011742.1 1823452 1824447 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 775311, 94131963, 98361923, 1862091, 2124629, 2990926, 7896119, 8636984, 9298646; Product type e : enzyme; glyceraldehyde-3-phosphate dehydrogenase A 1823452..1824447 Escherichia coli S88 7129617 YP_002391561.1 CDS yeaD NC_011742.1 1824531 1825415 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1824531..1825415 Escherichia coli S88 7132179 YP_002391562.1 CDS yeaE NC_011742.1 1825466 1826320 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase complement(1825466..1826320) Escherichia coli S88 7133255 YP_002391563.1 CDS mipA NC_011742.1 1826410 1827156 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10037771, 20267815; Product type f : factor; scaffolding protein for murein synthesizing machinery complement(1826410..1827156) Escherichia coli S88 7133256 YP_002391564.1 CDS yeaG NC_011742.1 1827592 1829526 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative nucleoside triphosphate hydrolase domain 1827592..1829526 Escherichia coli S88 7128840 YP_002391565.1 CDS yeaH NC_011742.1 1829639 1830922 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1829639..1830922 Escherichia coli S88 7133257 YP_002391566.1 CDS yeaI NC_011742.1 1831069 1832544 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative diguanylate cyclase 1831069..1832544 Escherichia coli S88 7133258 YP_002391567.1 CDS yeaK NC_011742.1 1834258 1834761 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1834258..1834761 Escherichia coli S88 7133261 YP_002391568.1 CDS ECS88_1842 NC_011742.1 1834762 1834914 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1834762..1834914) Escherichia coli S88 7133262 YP_002391569.1 CDS yeaL NC_011742.1 1835036 1835482 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1835036..1835482 Escherichia coli S88 7128957 YP_002391570.1 CDS yeaM NC_011742.1 1835439 1836260 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(1835439..1836260) Escherichia coli S88 7133263 YP_002391571.1 CDS yeaN NC_011742.1 1836357 1837538 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter; MFS superfamily 1836357..1837538 Escherichia coli S88 7133264 YP_002391572.1 CDS yeaO NC_011742.1 1837593 1837940 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1837593..1837940 Escherichia coli S88 7133265 YP_002391573.1 CDS yoaF NC_011742.1 1837962 1838216 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative outer membrane protein complement(1837962..1838216) Escherichia coli S88 7133266 YP_002391574.1 CDS yeaP NC_011742.1 1838399 1839424 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative diguanylate cyclase 1838399..1839424 Escherichia coli S88 7133632 YP_002391575.1 CDS yeaQ NC_011742.1 1839691 1839939 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(1839691..1839939) Escherichia coli S88 7133267 YP_002391576.1 CDS yoaG NC_011742.1 1840087 1840269 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1840087..1840269) Escherichia coli S88 7133268 YP_002391577.1 CDS yeaR NC_011742.1 1840273 1840632 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1840273..1840632) Escherichia coli S88 7133633 YP_002391578.1 CDS yeaS NC_011742.1 1840805 1841443 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; leucine export protein LeuE complement(1840805..1841443) Escherichia coli S88 7133269 YP_002391579.1 CDS rnd NC_011742.1 1841986 1843113 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88289400, 89053950, 93015723, 8107670; Product type e : enzyme; ribonuclease D complement(1841986..1843113) Escherichia coli S88 7133271 YP_002391580.1 CDS fadD NC_011742.1 1843183 1844868 R Activates fatty acids by binding to coenzyme A; long-chain-fatty-acid--CoA ligase complement(1843183..1844868) Escherichia coli S88 7132745 YP_002391581.1 CDS yeaY NC_011742.1 1845073 1845654 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16079137; Product type lp : lipoprotein; putative outer membrane-associated lipoprotein complement(1845073..1845654) Escherichia coli S88 7129442 YP_002391582.1 CDS yeaZ NC_011742.1 1845694 1846389 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative peptidase complement(1845694..1846389) Escherichia coli S88 7133272 YP_002391583.1 CDS yoaA NC_011742.1 1846447 1848357 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative ATP-dependent helicase complement(1846447..1848357) Escherichia coli S88 7133273 YP_002391584.1 CDS yoaB NC_011742.1 1848489 1848833 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1848489..1848833 Escherichia coli S88 7133628 YP_002391585.1 CDS yoaC NC_011742.1 1849195 1849554 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1849195..1849554 Escherichia coli S88 7133629 YP_002391586.1 CDS yoaH NC_011742.1 1849674 1849853 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1849674..1849853) Escherichia coli S88 7133630 YP_002391587.1 CDS pabB NC_011742.1 1849927 1851288 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88025006, 91067712, 91302313, 96011382, 6330050, 7896119; Product type e : enzyme; aminodeoxychorismate synthase, subunit I 1849927..1851288 Escherichia coli S88 7133634 YP_002391588.1 CDS yeaB NC_011742.1 1851292 1851870 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7567469; Product type pe : putative enzyme; hypothetical protein 1851292..1851870 Escherichia coli S88 7133154 YP_002391589.1 CDS sdaA NC_011742.1 1852054 1853418 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15155761, 89359152, 91056090, 93170282; Product type e : enzyme; L-serine deaminase I 1852054..1853418 Escherichia coli S88 7133253 YP_002391590.1 CDS adrB NC_011742.1 1853549 1855147 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16513732; Product type pe : putative enzyme; putative cyclic di-GMP phosphodiesterase 1853549..1855147 Escherichia coli S88 7131370 YP_002391591.1 CDS yoaE NC_011742.1 1855151 1856707 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative membrane protein fused with conserved domain complement(1855151..1856707) Escherichia coli S88 7132059 YP_002391592.1 CDS manX NC_011742.1 1857170 1858141 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87165962, 90036983, 8131846, 8676384, 9074635, 9298646; Product type t : transporter; fused mannose-specific PTS enzymes: IIA component ; IIB component 1857170..1858141 Escherichia coli S88 7133631 YP_002391593.1 CDS manY NC_011742.1 1858204 1859004 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10473571, 87165962, 90036983, 94086520, 97128775, 7811395, 8774730; Product type t : transporter; mannose-specific enzyme IIC component of PTS 1858204..1859004 Escherichia coli S88 7129420 YP_002391594.1 CDS manZ NC_011742.1 1859008 1859868 D hosphoenolpyruvate-dependent sugar phosphotransferase system catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IID with IIC forms the translocation channel; PTS system mannose-specific transporter subunit IID 1859008..1859868 Escherichia coli S88 7129421 YP_002391595.1 CDS yobD NC_011742.1 1859923 1860381 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 1859923..1860381 Escherichia coli S88 7129422 YP_002391596.1 CDS yebN NC_011742.1 1860810 1861376 D membrane protein YebN; hypothetical protein 1860810..1861376 Escherichia coli S88 7129858 YP_002391597.1 CDS rrmA NC_011742.1 1861373 1862182 R methylates the guanosine in position 745 of 23S rRNA; required for translation and cell growth; 23S rRNA methyltransferase A complement(1861373..1862182) Escherichia coli S88 7131824 YP_002391598.1 CDS cspC NC_011742.1 1862348 1862557 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20345064, 21101802, 94293754, 12071744, 7984109, 8022261, 9298646, 9868784, 9921691; Product type f : factor; cold shock-like protein CspC complement(1862348..1862557) Escherichia coli S88 7133806 YP_002391599.1 CDS yobF NC_011742.1 1862570 1862713 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1862570..1862713) Escherichia coli S88 7130495 YP_002391600.1 CDS yebO NC_011742.1 1863384 1863671 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1863384..1863671) Escherichia coli S88 7133638 YP_002391601.1 CDS yobG NC_011742.1 1863746 1863889 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1863746..1863889) Escherichia coli S88 7131825 YP_002391602.1 CDS yobH NC_011742.1 1864048 1864287 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1864048..1864287 Escherichia coli S88 7133639 YP_002391603.1 CDS kdgR NC_011742.1 1864431 1865222 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15659677, 4359651; Product type r : regulator; DNA-binding transcriptional repressor KdgR complement(1864431..1865222) Escherichia coli S88 7133640 YP_002391604.1 CDS yebQ NC_011742.1 1865399 1866772 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter; MFS superfamily 1865399..1866772 Escherichia coli S88 7130438 YP_002391605.1 CDS htpX NC_011742.1 1866818 1867699 R putative metalloprotease; heat shock protein HtpX complement(1866818..1867699) Escherichia coli S88 7131826 YP_002391606.1 CDS prc NC_011742.1 1867891 1869939 R Involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3; carboxy-terminal protease complement(1867891..1869939) Escherichia coli S88 7131400 YP_002391607.1 CDS proQ NC_011742.1 1869959 1870657 R affects solute and DNA transport through an unknown mechanism; putative solute/DNA competence effector complement(1869959..1870657) Escherichia coli S88 7130771 YP_002391608.1 CDS yebR NC_011742.1 1870754 1871305 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1870754..1871305) Escherichia coli S88 7130788 YP_002391609.1 CDS yebS NC_011742.1 1871381 1872664 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1871381..1872664 Escherichia coli S88 7131827 YP_002391610.1 CDS yebT NC_011742.1 1872633 1875266 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1872633..1875266 Escherichia coli S88 7131828 YP_002391611.1 CDS yebU NC_011742.1 1875346 1876785 D in Escherichia coli this enzyme specifically methylates C1407 of the 16S rRNA; rRNA (cytosine-C(5)-)-methyltransferase RsmF 1875346..1876785 Escherichia coli S88 7131829 YP_002391612.1 CDS yebV NC_011742.1 1876903 1877139 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1876903..1877139 Escherichia coli S88 7131830 YP_002391613.1 CDS yebW NC_011742.1 1877160 1877435 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1877160..1877435 Escherichia coli S88 7131831 YP_002391614.1 CDS pphA NC_011742.1 1877436 1878092 R Plays a key role in signaling protein misfolding via the cpxR/cpxA transducing system; modulates the phosphorylated status of many phosphoproteins; serine/threonine protein phosphatase 1 complement(1877436..1878092) Escherichia coli S88 7131832 YP_002391615.1 CDS ECS88_1892 NC_011742.1 1878317 1878469 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1878317..1878469) Escherichia coli S88 7131334 YP_002391616.1 CDS yebY NC_011742.1 1878487 1878828 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1878487..1878828) Escherichia coli S88 7128959 YP_002391617.1 CDS yebZ NC_011742.1 1878841 1879713 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(1878841..1879713) Escherichia coli S88 7131833 YP_002391618.1 CDS yobA NC_011742.1 1879717 1880091 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1879717..1880091) Escherichia coli S88 7131834 YP_002391619.1 CDS holE NC_011742.1 1880230 1880460 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15090519, 92147649, 92156151, 94131961, 1575709, 8341603, 8505306; Product type e : enzyme; DNA polymerase III subunit theta 1880230..1880460 Escherichia coli S88 7133635 YP_002391620.1 CDS yobB NC_011742.1 1880562 1881218 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1880562..1881218 Escherichia coli S88 7128945 YP_002391621.1 CDS exoX NC_011742.1 1881241 1881903 D 3'-5' exonuclease activity on single or double-strand DNA; exodeoxyribonuclease X 1881241..1881903 Escherichia coli S88 7133636 YP_002391622.1 CDS ptrB NC_011742.1 1881900 1883960 R PtrB; oligopeptidase that cleaves peptide bonds following arginine and lysine residues; protease 2 complement(1881900..1883960) Escherichia coli S88 7132439 YP_002391623.1 CDS yebE NC_011742.1 1884169 1884828 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative inner membrane protein complement(1884169..1884828) Escherichia coli S88 7130817 YP_002391624.1 CDS yebF NC_011742.1 1885155 1885523 R secreted protein; unknown function; hypothetical protein complement(1885155..1885523) Escherichia coli S88 7131820 YP_002391625.1 CDS yebG NC_011742.1 1885578 1885868 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 9368369, 99403401; Product type cp : cell process; DNA damage-inducible protein YebG complement(1885578..1885868) Escherichia coli S88 7131821 YP_002391626.1 CDS purT NC_011742.1 1886002 1887180 D non-folate utilizing enzyme, catalyzes the production of beta-formyl glycinamide ribonucleotide from formate, ATP, and beta-GAR and a side reaction producing acetyl phosphate and ADP from acetate and ATP; involved in de novo purine biosynthesis; phosphoribosylglycinamide formyltransferase 2 1886002..1887180 Escherichia coli S88 7131822 YP_002391627.1 CDS eda NC_011742.1 1887236 1887877 R catalyzes the formation of pyruvate and glyoxylate from 4-hydroxy-2-oxoglutarate; or pyruvate and D-glyceraldehyde 3-phosphate from 2-dehydro-3-deoxy-D-glyconate 6-phosphate; keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase complement(1887236..1887877) Escherichia coli S88 7131756 YP_002391628.1 CDS edd NC_011742.1 1887914 1889725 R catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate; phosphogluconate dehydratase complement(1887914..1889725) Escherichia coli S88 7132381 YP_002391629.1 CDS ECS88_1908 NC_011742.1 1889688 1889846 D hypothetical protein 1889688..1889846 Escherichia coli S88 7132382 YP_002391630.1 CDS zwf NC_011742.1 1889960 1891435 R catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase complement(1889960..1891435) Escherichia coli S88 7128960 YP_002391631.1 CDS yebK NC_011742.1 1891773 1892642 D Represses the expression of the zwf, eda, glp and gap; DNA-binding transcriptional regulator HexR 1891773..1892642 Escherichia coli S88 7131896 YP_002391632.1 CDS pykA NC_011742.1 1892770 1894212 D catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate kinase 1892770..1894212 Escherichia coli S88 7131823 YP_002391633.1 CDS lpxM NC_011742.1 1894344 1895315 R Transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA; lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase complement(1894344..1895315) Escherichia coli S88 7131761 YP_002391634.1 CDS yebA NC_011742.1 1895434 1896756 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1732206; Product type pe : putative enzyme; hypothetical protein complement(1895434..1896756) Escherichia coli S88 7129387 YP_002391635.1 CDS znuA NC_011742.1 1896772 1897704 R involved in transport of zinc(II) with ZnuA and C; high-affinity zinc transporter periplasmic component complement(1896772..1897704) Escherichia coli S88 7133274 YP_002391636.1 CDS znuC NC_011742.1 1897783 1898538 D involved in transport of zinc(II) with ZnuA and C; high-affinity zinc transporter ATPase 1897783..1898538 Escherichia coli S88 7131888 YP_002391637.1 CDS znuB NC_011742.1 1898535 1899320 D involved in transport of zinc(II) with ZnuA and C; high-affinity zinc transporter membrane component 1898535..1899320 Escherichia coli S88 7131890 YP_002391638.1 CDS ruvB NC_011742.1 1899537 1900547 R 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; Holliday junction DNA helicase RuvB complement(1899537..1900547) Escherichia coli S88 7131889 YP_002391639.1 CDS ruvA NC_011742.1 1900556 1901167 R plays an essential role in ATP-dependent branch migration of the Holliday junction; Holliday junction DNA helicase RuvA complement(1900556..1901167) Escherichia coli S88 7131325 YP_002391640.1 CDS yebB NC_011742.1 1901443 1902045 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1901443..1902045 Escherichia coli S88 7131324 YP_002391641.1 CDS ruvC NC_011742.1 1902047 1902568 R endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity; Holliday junction resolvase complement(1902047..1902568) Escherichia coli S88 7133275 YP_002391642.1 CDS yebC NC_011742.1 1902603 1903343 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1902603..1903343) Escherichia coli S88 7131326 YP_002391643.1 CDS ntpA NC_011742.1 1903372 1903815 R converts dATP to dAMP and pyrophosphate; dATP pyrophosphohydrolase complement(1903372..1903815) Escherichia coli S88 7132062 YP_002391644.1 CDS aspS NC_011742.1 1903817 1905589 R 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; aspartyl-tRNA synthetase complement(1903817..1905589) Escherichia coli S88 7129750 YP_002391645.1 CDS yecD NC_011742.1 1905899 1906465 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein 1905899..1906465 Escherichia coli S88 7129952 YP_002391646.1 CDS yecE NC_011742.1 1906462 1907280 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 2129559, 7984428; hypothetical protein 1906462..1907280 Escherichia coli S88 7131837 YP_002391647.1 CDS yecN NC_011742.1 1907333 1907728 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 1907333..1907728 Escherichia coli S88 7131838 YP_002391648.1 CDS yecO NC_011742.1 1907769 1908512 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 11746687; Product type e : enzyme; AdoMet-dependent methyltransferase 1907769..1908512 Escherichia coli S88 7131845 YP_002391649.1 CDS yecP NC_011742.1 1908509 1909480 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1908509..1909480 Escherichia coli S88 7131846 YP_002391650.1 CDS torZ NC_011742.1 1909645 1912074 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 97077292, 11004177; Product type e : enzyme; trimethylamine N-oxide reductase system III, catalytic subunit complement(1909645..1912074) Escherichia coli S88 7131847 YP_002391651.1 CDS torY NC_011742.1 1912099 1913199 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20461225, 8919859; Product type c : carrier; TMAO reductase III (TorYZ), cytochrome c-type subunit complement(1912099..1913199) Escherichia coli S88 7133500 YP_002391652.1 CDS cutC NC_011742.1 1913587 1914333 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95362641, 7635807; Product type t : transporter; copper homeostasis protein CutC complement(1913587..1914333) Escherichia coli S88 7133499 YP_002391653.1 CDS yecM NC_011742.1 1914347 1914913 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12660999; Product type pe : putative enzyme; hypothetical protein complement(1914347..1914913) Escherichia coli S88 7130516 YP_002391654.1 CDS argS NC_011742.1 1915129 1916862 D 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; arginyl-tRNA synthetase 1915129..1916862 Escherichia coli S88 7131844 YP_002391655.1 CDS flhE NC_011742.1 1916915 1917307 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 8002587, 1482109, 89181349; hypothetical protein complement(1916915..1917307) Escherichia coli S88 7133102 YP_002391656.1 CDS flhA NC_011742.1 1917307 1919385 R membrane protein involved in the flagellar export apparatus; flagellar biosynthesis protein FlhA complement(1917307..1919385) Escherichia coli S88 7132787 YP_002391657.1 CDS flhB NC_011742.1 1919378 1920526 R membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; flagellar biosynthesis protein FlhB complement(1919378..1920526) Escherichia coli S88 7132783 YP_002391658.1 CDS cheZ NC_011742.1 1920735 1921379 R cytosolic phosphatase which functions in the chemotaxis signal transduction complex by controlling the level of phosphorylated CheY through dephosphorylation; chemotaxis regulator CheZ complement(1920735..1921379) Escherichia coli S88 7132784 YP_002391659.1 CDS cheY NC_011742.1 1921390 1921779 R chemotaxis regulator that, when phosphorylated, interacts with the flagellar motor causing the flagella to spin clockwise which causes the cell to tumble; chemotaxis regulatory protein CheY complement(1921390..1921779) Escherichia coli S88 7131902 YP_002391660.1 CDS cheB NC_011742.1 1921794 1922843 R regulates chemotaxis by demethylation of methyl-accepting chemotaxis proteins; chemotaxis-specific methylesterase complement(1921794..1922843) Escherichia coli S88 7131901 YP_002391661.1 CDS cheR NC_011742.1 1922846 1923706 R methylates the MCP; chemotaxis methyltransferase CheR complement(1922846..1923706) Escherichia coli S88 7131898 YP_002391662.1 CDS tar NC_011742.1 1923997 1925658 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90094243, 92165727, 6305515, 9315712; Product type r : regulator; methyl-accepting chemotaxis protein II complement(1923997..1925658) Escherichia coli S88 7131899 YP_002391663.1 CDS cheW NC_011742.1 1925803 1926306 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91126073, 91296802, 91317710, 2002011, 3510184; Product type r : regulator; purine-binding chemotaxis protein complement(1925803..1926306) Escherichia coli S88 7129145 YP_002391664.1 CDS cheA NC_011742.1 1926327 1928291 R chemotactic sensory histidine kinase in two-component regulatory system with CheB and CheY; sensory histidine kinase/signal sensing protein; CheA is the histidine kinase component; chemotaxis protein CheA complement(1926327..1928291) Escherichia coli S88 7131900 YP_002391665.1 CDS motB NC_011742.1 1928296 1929222 R 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; flagellar motor protein MotB complement(1928296..1929222) Escherichia coli S88 7129190 YP_002391666.1 CDS motA NC_011742.1 1929219 1930106 R With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine; flagellar motor protein MotA complement(1929219..1930106) Escherichia coli S88 7128784 YP_002391667.1 CDS flhC NC_011742.1 1930233 1930811 R With FlhD is involved in the activation of class 2 flagellar genes and as well as a number of other genetic systems; transcriptional activator FlhC complement(1930233..1930811) Escherichia coli S88 7128865 YP_002391668.1 CDS flhD NC_011742.1 1930814 1931173 R with FlhC is involved in the activation of class 2 flagellar genes and is involved in the regulation of a number of other genetic systems; transcriptional activator FlhD complement(1930814..1931173) Escherichia coli S88 7132785 YP_002391669.1 CDS yecG NC_011742.1 1931944 1932372 D ppGpp-dependent; membrane-associated, stress protein produced under conditions of nutrient deprivation, osmotic shock and oxidative stress; universal stress protein UspC 1931944..1932372 Escherichia coli S88 7132786 YP_002391670.1 CDS otsA NC_011742.1 1932379 1933803 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92078100, 92121128, 93302496, 8045430; Product type e : enzyme; trehalose-6-phosphate synthase complement(1932379..1933803) Escherichia coli S88 7131840 YP_002391671.1 CDS otsB NC_011742.1 1933778 1934578 R biosynthetic; catalyzes the formation of trehalose and phosphate from trehalose-6-phosphate; expression is increased under osmotic stress and induced during the transition to stationary phase and by decreased temperature; trehalose-6-phosphate phosphatase complement(1933778..1934578) Escherichia coli S88 7133147 YP_002391672.1 CDS araH NC_011742.1 1934745 1935734 R Part of the ABC transporter complex AraFGH involved in the high affinity transport of arabinose; L-arabinose transporter permease protein complement(1934745..1935734) Escherichia coli S88 7133148 YP_002391673.1 CDS araG NC_011742.1 1935746 1937260 R Part of the ABC transporter complex AraFGH involved in the high affinity transport of arabinose; L-arabinose transporter ATP-binding protein complement(1935746..1937260) Escherichia coli S88 7133087 YP_002391674.1 CDS araF NC_011742.1 1937330 1938319 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89255061, 90375534, 2445996, 326784, 326785, 6885805, 7031057, 9298646; Product type t : transporter; L-arabinose transporter subunit ; periplasmic-binding component of ABC superfamily complement(1937330..1938319) Escherichia coli S88 7133086 YP_002391675.1 CDS yecI NC_011742.1 1939116 1939619 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative ferritin-like protein 1939116..1939619 Escherichia coli S88 7133085 YP_002391676.1 CDS yecJ NC_011742.1 1939697 1939948 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1939697..1939948) Escherichia coli S88 7131842 YP_002391677.1 CDS ECS88_1959 NC_011742.1 1940060 1940206 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1940060..1940206 Escherichia coli S88 7130427 YP_002391678.1 CDS yecR NC_011742.1 1940413 1940736 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1940413..1940736 Escherichia coli S88 7128961 YP_002391679.1 CDS ftn NC_011742.1 1940908 1941405 D cytoplasmic iron storage protein; ferritin 1940908..1941405 Escherichia coli S88 7131848 YP_002391680.1 CDS yecH NC_011742.1 1941443 1941682 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1941443..1941682) Escherichia coli S88 7132845 YP_002391681.1 CDS tyrP NC_011742.1 1941873 1943084 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89008121, 2022620; Product type t : transporter; tyrosine transporter 1941873..1943084 Escherichia coli S88 7131841 YP_002391682.1 CDS yecA NC_011742.1 1943135 1943800 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1943135..1943800) Escherichia coli S88 7130376 YP_002391683.1 CDS pgsA NC_011742.1 1944450 1944998 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 381294, 7007311, 94253011, 1323047, 3003065, 8917447; Product type e : enzyme; phosphatidylglycerophosphate synthetase complement(1944450..1944998) Escherichia coli S88 7131997 YP_002391684.1 CDS uvrC NC_011742.1 1945055 1946887 R 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; excinuclease ABC subunit C complement(1945055..1946887) Escherichia coli S88 7133696 YP_002391685.1 CDS uvrY NC_011742.1 1946884 1947540 R in Escherichia coli the protein UvrY is part of a two-component system along with BarA that is needed for efficient switching between glycolytic and gluconeogenic carbon sources possibly by regulating the Csr system; in Salmonella SirA and BarA regulate virulence gene expression also via the Csr system; response regulator complement(1946884..1947540) Escherichia coli S88 7132460 YP_002391686.1 CDS yecF NC_011742.1 1947999 1948223 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 3515318, 7567469; hypothetical protein 1947999..1948223 Escherichia coli S88 7132462 YP_002391687.1 CDS sdiA NC_011742.1 1948291 1949013 R regulates genes involved in cell division; DNA-binding transcriptional activator SdiA complement(1948291..1949013) Escherichia coli S88 7131839 YP_002391688.1 CDS yecC NC_011742.1 1949243 1949995 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative amino-acid ABC transporter ATP-binding protein YecC complement(1949243..1949995) Escherichia coli S88 7131377 YP_002391689.1 CDS yecS NC_011742.1 1949992 1950660 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter subunit: permease component of ABC superfamily transporter complement(1949992..1950660) Escherichia coli S88 7131836 YP_002391690.1 CDS yedO NC_011742.1 1950675 1951661 R catalyzes the formation of pyruvate from D-cysteine; D-cysteine desulfhydrase complement(1950675..1951661) Escherichia coli S88 7131849 YP_002391691.1 CDS fliY NC_011742.1 1951766 1952566 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96125225, 8450713, 8774726, 9298646, 9740056; Product type t : transporter; cystine transporter subunit complement(1951766..1952566) Escherichia coli S88 7131857 YP_002391692.1 CDS fliZ NC_011742.1 1952654 1953205 R expression activator of the class 2 type of flagellar operons, essential to achieve maximal cell motility; activator of type 1 fimbrial gene expression; cell density-responsive regulator; FliZ in Salmonella typhimurium induces HilA, an activator of invasion genes necessary to achieve full virulence; flagella biosynthesis protein FliZ complement(1952654..1953205) Escherichia coli S88 7132807 YP_002391693.1 CDS fliA NC_011742.1 1953251 1953970 R sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor directs late flagellar biosynthesis genes; flagellar biosynthesis sigma factor complement(1953251..1953970) Escherichia coli S88 7132808 YP_002391694.1 CDS FliC NC_011742.1 1954290 1956047 R structural flagella protein; individual Salmonella serotypes usually alternate between the production of 2 antigenic forms of flagella, termed phase 1 and phase 2, each specified by separate structural genes; flagellin complement(1954290..1956047) Escherichia coli S88 7132788 YP_002391695.1 CDS fliD NC_011742.1 1956313 1957719 D involved in flagellin assembly; flagellar capping protein 1956313..1957719 Escherichia coli S88 7132789 YP_002391696.1 CDS fliS NC_011742.1 1957744 1958154 D flagellin specific chaperone; flagellar protein FliS 1957744..1958154 Escherichia coli S88 7132790 YP_002391697.1 CDS fliT NC_011742.1 1958154 1958519 D binds flagellar cap subunits (FliD) and seems to prevents their oligomerization prior to its translocation through the flagellum-specific type III export pathway; acts as a repressor of flagellar class 2 operons by preventing FlhD2C2 to bind the promoter and inhibiting the FlhD2C2-dependent transcription; member of the type III cytoplasmic chaperone family; flagellar biosynthesis protein FliT 1958154..1958519 Escherichia coli S88 7132805 YP_002391698.1 CDS amyA NC_011742.1 1958597 1960084 D converts 1,4-alpha-D-glucans to maltodextrin; cytoplasmic alpha-amylase 1958597..1960084 Escherichia coli S88 7132806 YP_002391699.1 CDS yedD NC_011742.1 1960118 1960531 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1960118..1960531) Escherichia coli S88 7133067 YP_002391700.1 CDS yedE NC_011742.1 1960718 1961923 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; putative inner membrane protein 1960718..1961923 Escherichia coli S88 7131851 YP_002391701.1 CDS yedF NC_011742.1 1961920 1962153 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1961920..1962153 Escherichia coli S88 7131852 YP_002391702.1 CDS yedK NC_011742.1 1962262 1962930 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1962262..1962930 Escherichia coli S88 7131853 YP_002391703.1 CDS nmpC NC_011742.1 1963443 1964525 D Evidence 2b : Function of strongly homologous gene; PubMedId : 3017988, 8057841; Product type m : membrane component; outer membrane porin; DLP12 prophage 1963443..1964525 Escherichia coli S88 7131856 YP_002391704.1 CDS ybcM NC_011742.1 1965027 1965824 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12270809; Product type pr : putative regulator; putative DNA-binding transcriptional regulator; DLP12 prophage complement(1965027..1965824) Escherichia coli S88 7129727 YP_002391705.1 CDS ybcL NC_011742.1 1965834 1966385 R DLP12 prophage; similar to PEBP/RK1P protein family in eukaryotes that inhibits MEK phosphorylation by Raf-1; crystal structure suggests similar properties but exact function is unknown; putative kinase inhibitor complement(1965834..1966385) Escherichia coli S88 7131186 YP_002391706.1 CDS emrE NC_011742.1 1966554 1967066 R member of the small MDR (multidrug resistance) family of transporters; in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin; proton-dependent secondary transporter which exchanges protons for compound translocation; multidrug efflux protein complement(1966554..1967066) Escherichia coli S88 7131185 YP_002391707.1 CDS fliE NC_011742.1 1967231 1967545 R forms a junction between the M-ring and FlgB during flagella biosynthesis; flagellar hook-basal body protein FliE complement(1967231..1967545) Escherichia coli S88 7132394 YP_002391708.1 CDS fliF NC_011742.1 1967760 1969418 D 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; flagellar MS-ring protein 1967760..1969418 Escherichia coli S88 7132791 YP_002391709.1 CDS fliG NC_011742.1 1969411 1970406 D One of three proteins involved in switching the direction of the flagellar rotation; flagellar motor switch protein G 1969411..1970406 Escherichia coli S88 7132792 YP_002391710.1 CDS fliH NC_011742.1 1970399 1971085 D binds to and inhibits the function of flagella specific ATPase FliI; flagellar assembly protein H 1970399..1971085 Escherichia coli S88 7132793 YP_002391711.1 CDS fliI NC_011742.1 1971085 1972458 D involved in type III protein export during flagellum assembly; flagellum-specific ATP synthase 1971085..1972458 Escherichia coli S88 7132794 YP_002391712.1 CDS fliJ NC_011742.1 1972477 1972920 D rod/hook and filament chaperone; flagellar biosynthesis chaperone 1972477..1972920 Escherichia coli S88 7132795 YP_002391713.1 CDS fliK NC_011742.1 1972917 1974044 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1482109, 8631687; Product type s : structure; flagellar hook-length control protein 1972917..1974044 Escherichia coli S88 7132796 YP_002391714.1 CDS fliL NC_011742.1 1974149 1974613 D interacts with cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring; flagellar basal body-associated protein FliL 1974149..1974613 Escherichia coli S88 7132797 YP_002391715.1 CDS fliM NC_011742.1 1974618 1975622 D with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation; flagellar motor switch protein FliM 1974618..1975622 Escherichia coli S88 7132798 YP_002391716.1 CDS fliN NC_011742.1 1975619 1976032 D One of three proteins involved in switching the direction of the flagellar rotation; flagellar motor switch protein FliN 1975619..1976032 Escherichia coli S88 7132799 YP_002391717.1 CDS fliO NC_011742.1 1976035 1976400 D with FlhA, FlhB, FliP, FliQ and FliR is one of the membrane components of the flagellar export apparatus; flagellar biosynthesis protein FliO 1976035..1976400 Escherichia coli S88 7132800 YP_002391718.1 CDS fliP NC_011742.1 1976400 1977137 D FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliP 1976400..1977137 Escherichia coli S88 7132801 YP_002391719.1 CDS fliQ NC_011742.1 1977147 1977416 D with proteins FliP and FliR forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliQ 1977147..1977416 Escherichia coli S88 7132802 YP_002391720.1 CDS fliR NC_011742.1 1977425 1978210 D FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliR 1977425..1978210 Escherichia coli S88 7132803 YP_002391721.1 CDS rcsA NC_011742.1 1978495 1979118 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14514676, 14766922, 20167175, 90130299, 91154130, 92048476, 9882673, 7534408; Product type r : regulator; DNA-binding transcriptional activator, co-regulator with RcsB 1978495..1979118 Escherichia coli S88 7132804 YP_002391722.1 CDS dsrB NC_011742.1 1979162 1979350 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 96324407, 7534408; hypothetical protein complement(1979162..1979350) Escherichia coli S88 7131794 YP_002391723.1 CDS yodD NC_011742.1 1979513 1979740 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1979513..1979740 Escherichia coli S88 7129763 YP_002391724.1 CDS yedP NC_011742.1 1980038 1980853 D catalyzes the hydrolysis of mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate; mannosyl-3-phosphoglycerate phosphatase 1980038..1980853 Escherichia coli S88 7130246 YP_002391725.1 CDS yedQ NC_011742.1 1980850 1982544 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16530465; Product type pe : putative enzyme; putative diguanylate cyclase complement(1980850..1982544) Escherichia coli S88 7131858 YP_002391726.1 CDS ECS88_2010 NC_011742.1 1982465 1982653 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(1982465..1982653) Escherichia coli S88 7131859 YP_002391727.1 CDS yedI NC_011742.1 1982976 1983893 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(1982976..1983893) Escherichia coli S88 7128962 YP_002391728.1 CDS yedA NC_011742.1 1984066 1984986 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 1984066..1984986 Escherichia coli S88 7131854 YP_002391729.1 CDS vsr NC_011742.1 1984975 1985445 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90330522, 92049708, 94049122, 10360178, 10612397, 10871403, 2527357; Product type e : enzyme; DNA mismatch endonuclease of very short patch repair complement(1984975..1985445) Escherichia coli S88 7131850 YP_002391730.1 CDS dcm NC_011742.1 1985426 1986844 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90280700, 91285397, 93367813, 2198248, 2527357; Product type e : enzyme; DNA cytosine methylase complement(1985426..1986844) Escherichia coli S88 7132474 YP_002391731.1 CDS yedJ NC_011742.1 1986911 1987606 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7567469; Product type pe : putative enzyme; hypothetical protein complement(1986911..1987606) Escherichia coli S88 7130571 YP_002391732.1 CDS yedR NC_011742.1 1987646 1988011 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(1987646..1988011) Escherichia coli S88 7131855 YP_002391733.1 CDS ECS88_2017 NC_011742.1 1988547 1989692 D Evidence 2b : Function of strongly homologous gene; Product type pm : putative membrane component; outer membrane protein F precursor (Porin ompF) 1988547..1989692 Escherichia coli S88 7133812 YP_002391734.1 CDS hchA NC_011742.1 1990288 1991139 D Hsp31 stabilizes early unfolding protein intermediates under severe heat stress; chaperone protein HchA 1990288..1991139 Escherichia coli S88 7128963 YP_002391735.1 CDS yedV NC_011742.1 1991246 1992604 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15522865; Product type rc : receptor; sensory kinase in two-component regulatory system with YedW complement(1991246..1992604) Escherichia coli S88 7128886 YP_002391736.1 CDS yedW NC_011742.1 1992604 1993275 R induced by CusR in the presence of copper; YedW induces the expression of the upstream gene yedV (encoding a sensor kinase) as well as yedW; yedVW is one of four copper regulons found in E. coli; part of the copper homeostasis mechanism; confers resistance to copper and several drugs when induced; transcriptional regulatory protein YedW complement(1992604..1993275) Escherichia coli S88 7132941 YP_002391737.1 CDS yedX NC_011742.1 1993408 1993821 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1993408..1993821 Escherichia coli S88 7132942 YP_002391738.1 CDS yedY NC_011742.1 1993930 1994934 D in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase; sulfite oxidase activity not demonstrated; requires inner membrane anchor protein YedZ; putative sulfite oxidase subunit YedY 1993930..1994934 Escherichia coli S88 7132943 YP_002391739.1 CDS yedZ NC_011742.1 1994935 1995570 D in Escherichia coli this inner membrane protein was found to anchor the periplasmic catalytic oxidoreductase YedY; sulfite oxidase activity not demonstrated; contains heme; putative sulfite oxidase subunit YedZ 1994935..1995570 Escherichia coli S88 7132944 YP_002391740.1 CDS yodA NC_011742.1 1995827 1996477 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 12077457, 12480884, 12909634, 9579078; hypothetical protein 1995827..1996477 Escherichia coli S88 7132945 YP_002391741.1 CDS yeeI NC_011742.1 1997330 1998127 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 1997330..1998127 Escherichia coli S88 7131996 YP_002391742.1 CDS ECS88_2030 NC_011742.1 1998438 1998665 R Evidence 6 : Doubtful CDS; hypothetical protein complement(1998438..1998665) Escherichia coli S88 7129880 YP_002391743.1 CDS irp NC_011742.1 1999921 2001225 R catalyzes the conversion of chorismate to salicylate in the biosynthesis of the siderophore yersiniabactin; salicylate synthase Irp9 complement(1999921..2001225) Escherichia coli S88 7131649 YP_002391744.1 CDS irp NC_011742.1 2001253 2002656 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; yersiniabactin-iron transporter permease YbtX complement(2001253..2002656) Escherichia coli S88 7131655 YP_002391745.1 CDS irp NC_011742.1 2002526 2004355 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 10231486, 11320115; Product type t : transporter; permease and ATP-binding protein of yersiniabactin-iron ABC transporter YbtQ complement(2002526..2004355) Escherichia coli S88 7131656 YP_002391746.1 CDS irp NC_011742.1 2004315 2006117 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 10231486, 11320115; Product type t : transporter; permease and ATP-binding protein of yersiniabactin-iron ABC transporter YbtP complement(2004315..2006117) Escherichia coli S88 7131657 YP_002391747.1 CDS ybtA NC_011742.1 2006284 2007243 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 8930916; Product type r : regulator; AraC family transcriptional regulator 2006284..2007243 Escherichia coli S88 7131658 YP_002391748.1 CDS irp NC_011742.1 2007416 2013541 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 15719346, 15582399, 8366034, 11927258, 9709002; Product type e : enzyme; High-molecular-weight nonribosomal peptide/polyketide synthetase 2 (HMWP2) 2007416..2013541 Escherichia coli S88 7130143 YP_002391749.1 CDS irp NC_011742.1 2013629 2023120 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 15719346, 15582399, 11927258; Product type e : enzyme; High-molecular-weight nonribosomal peptide/polyketide synthetase 1 (HMWP1) 2013629..2023120 Escherichia coli S88 7131659 YP_002391750.1 CDS irp NC_011742.1 2023057 2024217 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 11927258; Product type e : enzyme; Thiazolinyl-S-HMWP1 reductase YbtU 2023057..2024217 Escherichia coli S88 7131660 YP_002391751.1 CDS irp NC_011742.1 2024214 2025017 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative thioesterase YbtT 2024214..2025017 Escherichia coli S88 7131661 YP_002391752.1 CDS irp NC_011742.1 2025021 2026598 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 9818149, 11927258, 9709002; Product type e : enzyme; salicyl-AMP ligase YbtE 2025021..2026598 Escherichia coli S88 7131662 YP_002391753.1 CDS fyuA NC_011742.1 2026729 2028750 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 7896707, 7984105; Product type rc : receptor; Yersiniabactin/pesticin outer membrane receptor (IRPC) 2026729..2028750 Escherichia coli S88 7130331 YP_002391754.1 CDS ECS88_2047 NC_011742.1 2032369 2033484 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2032369..2033484) Escherichia coli S88 7132953 YP_002391755.1 CDS shiA NC_011742.1 2033736 2035052 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 5332864, 9524262; Product type t : transporter; shikimate transporter 2033736..2035052 Escherichia coli S88 7128965 YP_002391756.1 CDS amn NC_011742.1 2035154 2036608 D Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile; AMP nucleosidase 2035154..2036608 Escherichia coli S88 7130599 YP_002391757.1 CDS yeeN NC_011742.1 2036951 2037667 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2036951..2037667 Escherichia coli S88 7133060 YP_002391758.1 CDS yeeO NC_011742.1 2038297 2039937 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16042411; Product type pt : putative transporter; hypothetical protein complement(2038297..2039937) Escherichia coli S88 7131995 YP_002391759.1 CDS cbl NC_011742.1 2040058 2041008 R LysR-type transcriptional regulator similar to CysB; contains helix-turn-helix (HTH) motif; in Escherichia coli this protein regulates two operons consisting of ABC transporters that are part of the cys regulon; regulated by CysB; transcriptional regulator Cbl complement(2040058..2041008) Escherichia coli S88 7129881 YP_002391760.1 CDS nac NC_011742.1 2041110 2042027 R Transcriptional activator for the hut, put and ure operons and repressor for the gdh and gltB operons in response to nitrogen limitation; nitrogen assimilation transcriptional regulator complement(2041110..2042027) Escherichia coli S88 7129161 YP_002391761.1 CDS erfK NC_011742.1 2042484 2043416 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 9298646; hypothetical protein complement(2042484..2043416) Escherichia coli S88 7129882 YP_002391762.1 CDS cobT NC_011742.1 2043481 2044560 R catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase complement(2043481..2044560) Escherichia coli S88 7132417 YP_002391763.1 CDS cobS NC_011742.1 2044572 2045315 R catalyzes the formation of adenosylcobalamin from Ado-cobinamide-GDP and alpha-ribazole; cobalamin synthase complement(2044572..2045315) Escherichia coli S88 7131943 YP_002391764.1 CDS cobU NC_011742.1 2045312 2045857 R catalyzes ATP-dependent phosphorylation of adenosylcobinamide to form adenosylcobinamide phosphate and the addition of guanosine monophosphate to adenosylcobinamide phosphate to form adenosylcobinamide-GDP; adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase complement(2045312..2045857) Escherichia coli S88 7131942 YP_002391765.1 CDS ECS88_2061 NC_011742.1 2046322 2046486 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2046322..2046486) Escherichia coli S88 7128966 YP_002391766.1 CDS ECS88_2063 NC_011742.1 2047732 2047848 R Evidence 7 : Gene remnant; Product type pe : putative enzyme; transposase, IS3 family complement(2047732..2047848) Escherichia coli S88 7128967 YP_002391767.1 CDS ECS88_2064 NC_011742.1 2048202 2048345 R Evidence 7 : Gene remnant; hypothetical protein complement(2048202..2048345) Escherichia coli S88 7128968 YP_002391768.1 CDS ECS88_2065 NC_011742.1 2048392 2048544 D Evidence 6 : Doubtful CDS; hypothetical protein 2048392..2048544 Escherichia coli S88 7128969 YP_002391769.1 CDS ECS88_2066 NC_011742.1 2048651 2048767 D Evidence 6 : Doubtful CDS; hypothetical protein 2048651..2048767 Escherichia coli S88 7128970 YP_002391770.1 CDS ECS88_2067 NC_011742.1 2048963 2050177 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative carbohydrate kinase 2048963..2050177 Escherichia coli S88 7128971 YP_002391771.1 CDS ECS88_2068 NC_011742.1 2050191 2050949 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2050191..2050949 Escherichia coli S88 7128972 YP_002391772.1 CDS ECS88_2069 NC_011742.1 2051006 2051971 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2051006..2051971 Escherichia coli S88 7128973 YP_002391773.1 CDS ECS88_2070 NC_011742.1 2051974 2053008 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphotriesterase-related protein 2051974..2053008 Escherichia coli S88 7128974 YP_002391774.1 CDS ECS88_2074 NC_011742.1 2055323 2055820 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2055323..2055820) Escherichia coli S88 7128978 YP_002391775.1 CDS ECS88_2075 NC_011742.1 2055721 2056128 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2055721..2056128) Escherichia coli S88 7128979 YP_002391776.1 CDS ECS88_2076 NC_011742.1 2056382 2056987 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2056382..2056987) Escherichia coli S88 7128980 YP_002391777.1 CDS ECS88_2079 NC_011742.1 2057746 2059359 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative transposase ORF1, IS66 family complement(2057746..2059359) Escherichia coli S88 7128981 YP_002391778.1 CDS ECS88_2080 NC_011742.1 2059390 2059740 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative transposase ORF2, IS66 family complement(2059390..2059740) Escherichia coli S88 7128982 YP_002391779.1 CDS ECS88_2081 NC_011742.1 2059737 2060162 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative transposase OrfA from plasmid origin complement(2059737..2060162) Escherichia coli S88 7128983 YP_002391780.1 CDS ECS88_2082 NC_011742.1 2060817 2061224 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; putative InterPro motifs Prophage CP4-57 regulatory protein (AlpA) 2060817..2061224 Escherichia coli S88 7128984 YP_002391781.1 CDS ECS88_2083 NC_011742.1 2061303 2061920 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2061303..2061920 Escherichia coli S88 7128985 YP_002391782.1 CDS ECS88_2085 NC_011742.1 2062348 2062608 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 2062348..2062608 Escherichia coli S88 7128986 YP_002391784.1 CDS ECS88_2087 NC_011742.1 2062879 2064447 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative transposase ORF 1, IS66 family complement(2062879..2064447) Escherichia coli S88 7128988 YP_002391785.1 CDS ECS88_2088 NC_011742.1 2064463 2064810 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative transposase ORF 2, IS66 family complement(2064463..2064810) Escherichia coli S88 7128989 YP_002391787.1 CDS ECS88_2090 NC_011742.1 2066746 2067909 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2066746..2067909 Escherichia coli S88 7128991 YP_002391788.1 CDS ECS88_2091 NC_011742.1 2067954 2068865 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative GTP-binding domain 2067954..2068865 Escherichia coli S88 7128992 YP_002391789.1 CDS ECS88_2092 NC_011742.1 2069083 2071479 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2069083..2071479 Escherichia coli S88 7128993 YP_002391790.1 CDS ECS88_2093 NC_011742.1 2071476 2072381 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2071476..2072381 Escherichia coli S88 7128994 YP_002391791.1 CDS ECS88_2094 NC_011742.1 2072378 2073448 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2072378..2073448 Escherichia coli S88 7128995 YP_002391792.1 CDS ECS88_2095 NC_011742.1 2073476 2074267 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein 2073476..2074267 Escherichia coli S88 7128996 YP_002391793.1 CDS ECS88_2096 NC_011742.1 2074283 2074693 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2074283..2074693 Escherichia coli S88 7128997 YP_002391794.1 CDS ECS88_2097 NC_011742.1 2074914 2075735 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2074914..2075735 Escherichia coli S88 7128998 YP_002391795.1 CDS ECS88_2098 NC_011742.1 2075817 2076296 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7519596; Product type h : extrachromosomal origin; putative antirestriction protein of plasmid origin 2075817..2076296 Escherichia coli S88 7128999 YP_002391796.1 CDS yeeS NC_011742.1 2076342 2076788 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11053371; Product type pf : putative factor; putative DNA repair protein; CP4-44 prophage 2076342..2076788 Escherichia coli S88 7129000 YP_002391797.1 CDS yeeT NC_011742.1 2076851 2077072 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CP4-44 prophage 2076851..2077072 Escherichia coli S88 7132956 YP_002391798.1 CDS yeeU NC_011742.1 2077146 2077514 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14594833; Product type h : extrachromosomal origin; antitoxin of the YeeV-YeeU toxin-antitoxin system; CP4-44 prophage 2077146..2077514 Escherichia coli S88 7132960 YP_002391799.1 CDS yeeW NC_011742.1 2077973 2078167 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CP4-44 prophage 2077973..2078167 Escherichia coli S88 7132968 YP_002391800.1 CDS yoeF NC_011742.1 2078608 2078964 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2078608..2078964 Escherichia coli S88 7132971 YP_002391801.1 CDS yeeX NC_011742.1 2079065 2079460 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2079065..2079460) Escherichia coli S88 7133644 YP_002391802.1 CDS yeeA NC_011742.1 2079566 2080624 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(2079566..2080624) Escherichia coli S88 7132974 YP_002391803.1 CDS sbmC NC_011742.1 2080823 2081296 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11850398, 9442027, 8709849; Product type r : regulator; DNA gyrase inhibitor complement(2080823..2081296) Escherichia coli S88 7132946 YP_002391804.1 CDS dacD NC_011742.1 2081415 2082581 R removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors; penicillin-binding protein 6B; one of four, DD-carboxypeptidase low-molecular weight penicillin-binding proteins that remove terminal D-alanine from pentapeptide side chains; D-alanyl-D-alanine carboxypeptidase complement(2081415..2082581) Escherichia coli S88 7131368 YP_002391805.1 CDS sbcB NC_011742.1 2082790 2084217 D Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates; exonuclease I 2082790..2084217 Escherichia coli S88 7130556 YP_002391806.1 CDS yeeD NC_011742.1 2084260 2084487 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2084260..2084487) Escherichia coli S88 7131364 YP_002391807.1 CDS yeeE NC_011742.1 2084501 2085559 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(2084501..2085559) Escherichia coli S88 7132947 YP_002391808.1 CDS yeeF NC_011742.1 2085738 2087096 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative amino-acid/amine transporter complement(2085738..2087096) Escherichia coli S88 7132948 YP_002391809.1 CDS yeeY NC_011742.1 2087363 2088292 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(2087363..2088292) Escherichia coli S88 7132949 YP_002391810.1 CDS yeeZ NC_011742.1 2088338 2089162 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative epimerase, with NAD(P)-binding Rossmann-fold domain complement(2088338..2089162) Escherichia coli S88 7132975 YP_002391811.1 CDS yoeB NC_011742.1 2089245 2089499 R Evidence 1b : Function experimentally demonstrated in the studied species; Product type f : factor; toxin of the YoeB-YefM toxin-antitoxin system complement(2089245..2089499) Escherichia coli S88 7132976 YP_002391812.1 CDS yefM NC_011742.1 2089496 2089747 R Antitoxin that counteracts the effect of the YoeB toxin; antitoxin YefM complement(2089496..2089747) Escherichia coli S88 7133643 YP_002391813.1 CDS hisL NC_011742.1 2090031 2090081 D Evidence 1c : Function experimentally demonstrated in the studied genus; Product type l : leader peptide; his operon leader peptide 2090031..2090081 Escherichia coli S88 7132977 YP_002391814.1 CDS hisG NC_011742.1 2090227 2091126 D long form of enzyme; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms active dimers and inactive hexamers which is dependent on concentration of substrates and inhibitors; ATP phosphoribosyltransferase 2090227..2091126 Escherichia coli S88 7128928 YP_002391815.1 CDS hisD NC_011742.1 2091132 2092436 D catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 2091132..2092436 Escherichia coli S88 7128924 YP_002391816.1 CDS hisC NC_011742.1 2092433 2093503 D catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase 2092433..2093503 Escherichia coli S88 7128922 YP_002391817.1 CDS hisB NC_011742.1 2093503 2094570 D catalyzes the formation of 3-(imidazol-4-yl)-2-oxopropyl phosphate from D-ethythro-1-(imidazol-4-yl)glycerol 3-phosphate and histidinol from histidinol phosphate; imidazole glycerol-phosphate dehydratase/histidinol phosphatase 2093503..2094570 Escherichia coli S88 7128921 YP_002391818.1 CDS hisH NC_011742.1 2094570 2095160 D with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide; imidazole glycerol phosphate synthase subunit HisH 2094570..2095160 Escherichia coli S88 7128920 YP_002391819.1 CDS hisA NC_011742.1 2095160 2095897 D catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide; 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 2095160..2095897 Escherichia coli S88 7128925 YP_002391820.1 CDS hisF NC_011742.1 2095879 2096655 D catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase; imidazole glycerol phosphate synthase subunit HisF 2095879..2096655 Escherichia coli S88 7128919 YP_002391821.1 CDS hisI NC_011742.1 2096649 2097260 D catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribosyl)-ATP and the subsequent formation of 1-(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide from 1-(5-phosphoribosyl)-AMP in histidine biosynthesis; bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein 2096649..2097260 Escherichia coli S88 7128923 YP_002391822.1 CDS cld NC_011742.1 2097432 2098409 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 98241528; Product type r : regulator; regulator of length of O-antigen component of lipopolysaccharide chains complement(2097432..2098409) Escherichia coli S88 7128926 YP_002391823.1 CDS ugd NC_011742.1 2098556 2099722 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9150218, 96326333; Product type e : enzyme; UDP-glucose 6-dehydrogenase complement(2098556..2099722) Escherichia coli S88 7131927 YP_002391824.1 CDS gnd NC_011742.1 2099971 2101377 R catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate; 6-phosphogluconate dehydrogenase complement(2099971..2101377) Escherichia coli S88 7130392 YP_002391825.1 CDS rmlA NC_011742.1 2101558 2102424 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 12171937, 14670712; Product type e : enzyme; glucose-1-phosphate thymidylyltransferase complement(2101558..2102424) Escherichia coli S88 7130048 YP_002391826.1 CDS wbvC NC_011742.1 2102569 2103099 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative O-acetyltransferase complement(2102569..2103099) Escherichia coli S88 7132736 YP_002391827.1 CDS wzy NC_011742.1 2103065 2104156 R Evidence 1a : Function experimentally demonstrated in the studied strain; PubMedId : 14670712; Product type e : enzyme; O-antigen polymerase complement(2103065..2104156) Escherichia coli S88 7132490 YP_002391828.1 CDS wbvB NC_011742.1 2104149 2105126 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15695667; Product type pe : putative enzyme; putative glycosyl transferase complement(2104149..2105126) Escherichia coli S88 7132509 YP_002391829.1 CDS wzx NC_011742.1 2105113 2106375 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15695667, 14670712; Product type pt : putative transporter; putative O antigen flippase complement(2105113..2106375) Escherichia coli S88 7132489 YP_002391830.1 CDS wbvA NC_011742.1 2106362 2107360 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2106362..2107360) Escherichia coli S88 7132506 YP_002391831.1 CDS tll NC_011742.1 2107362 2108177 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 14670712; Product type pe : putative enzyme; putative dTDP-6-deoxy-D-xylo-4-hexulose reductase complement(2107362..2108177) Escherichia coli S88 7132488 YP_002391832.1 CDS rmlC NC_011742.1 2108240 2108782 R Evidence 2b : Function of strongly homologous gene; PubMedId : 10074083, 14670712; Product type e : enzyme; dTDP-6-deoxy-D-glucose-3,5 epimerase complement(2108240..2108782) Escherichia coli S88 7133479 YP_002391833.1 CDS rmlB NC_011742.1 2108854 2109936 R NAD(P) binding; catalyzes the formation of dTDP-4-dehydro-6-deoxy-D-glucose from dTDP-glucose; dTDP-glucose 4,6 dehydratase complement(2108854..2109936) Escherichia coli S88 7132738 YP_002391834.1 CDS galF NC_011742.1 2110308 2111201 R together with GalU subunit composes the UTP--glucose-1-phosphate uridylyltransferase, an enzyme that catalyzes the formation of UDP-glucose from UTP and alpha-D-glucose 1-phosphate; regulates cellular levels of UDP-glucose; UTP--glucose-1-phosphate uridylyltransferase subunit GalF complement(2110308..2111201) Escherichia coli S88 7132737 YP_002391835.1 CDS wcaM NC_011742.1 2111376 2112770 R WcaM from Salmonella enterica is essential for biofilm formation on HEp-2 cells and chicken intestinal tissue but not on a plastic surface; may be involved in the biosynthesis of colanic acid; putative colanic acid biosynthesis protein complement(2111376..2112770) Escherichia coli S88 7132171 YP_002391836.1 CDS wcaL NC_011742.1 2112781 2114001 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 96326333; Product type pe : putative enzyme; putative glycosyl transferase complement(2112781..2114001) Escherichia coli S88 7132501 YP_002391837.1 CDS wcaK NC_011742.1 2113998 2115278 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 96326333, 8759852, 11004393; Product type pe : putative enzyme; putative pyruvyl transferase complement(2113998..2115278) Escherichia coli S88 7132500 YP_002391838.1 CDS wzxC NC_011742.1 2115554 2117032 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96326333, 8759852; Product type pt : putative transporter; colanic acid exporter complement(2115554..2117032) Escherichia coli S88 7132499 YP_002391839.1 CDS wcaJ NC_011742.1 2117034 2118428 R WcaJ; glucose-1-phosphate transferase responsible for the addition of the first glucose-1-phosphate from UDP-glucose to the lipid carrier undecaprenyl phosphate in the biosynthesis of colanic acid; putative UDP-glucose lipid carrier transferase complement(2117034..2118428) Escherichia coli S88 7132507 YP_002391840.1 CDS cpsG NC_011742.1 2118483 2119853 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93106949, 96326333, 7815923, 8759852; Product type e : enzyme; phosphomannomutase complement(2118483..2119853) Escherichia coli S88 7132498 YP_002391841.1 CDS cpsB NC_011742.1 2120046 2121482 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 82100097, 85006781, 92048476, 93122523, 96326333, 7815923, 8759852; Product type e : enzyme; mannose-1-phosphate guanyltransferase complement(2120046..2121482) Escherichia coli S88 7131954 YP_002391842.1 CDS wcaI NC_011742.1 2121485 2122708 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15670885, 96326333; Product type pe : putative enzyme; putative glycosyl transferase complement(2121485..2122708) Escherichia coli S88 7131953 YP_002391843.1 CDS nudD NC_011742.1 2122705 2123184 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96326333, 10913267, 7592609, 7815923, 8759852; Product type e : enzyme; GDP-mannose mannosyl hydrolase complement(2122705..2123184) Escherichia coli S88 7132497 YP_002391844.1 CDS fcl NC_011742.1 2123187 2124152 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96326333, 98132401, 9862812, 7815923, 8759852, 9473059; Product type e : enzyme; bifunctional GDP-fucose synthetase: GDP-4-dehydro-6-deoxy-D-mannose epimerase and GDP-4-dehydro-6-L-deoxygalactose reductase complement(2123187..2124152) Escherichia coli S88 7129752 YP_002391845.1 CDS gmd NC_011742.1 2124155 2125276 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20139699, 97400210, 10673432, 7815923, 8759852, 9257704, 14299611; Product type e : enzyme; GDP-D-mannose dehydratase, NAD(P)-binding complement(2124155..2125276) Escherichia coli S88 7129450 YP_002391846.1 CDS wcaF NC_011742.1 2125303 2125851 R acetyltransferase believed to catalyze the addition of the acetyl group that is attached through an O linkage to the first fucosyl residue of the colanic acid repetitive unit (E unit); putative colanic acid biosynthesis acetyltransferase WcaF complement(2125303..2125851) Escherichia coli S88 7130044 YP_002391847.1 CDS wcaE NC_011742.1 2125867 2126613 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11371548, 96326333, 8759852; Product type pe : putative enzyme; putative glycosyl transferase complement(2125867..2126613) Escherichia coli S88 7132496 YP_002391848.1 CDS wcaD NC_011742.1 2126694 2127914 R essential for colanic acid biosynthesis; colanic acid is an exopolysaccharide produced under stress conditions that confers acid and heat tolerance; putative colanic acid biosynthesis protein complement(2126694..2127914) Escherichia coli S88 7132495 YP_002391849.1 CDS wcaC NC_011742.1 2127889 2129106 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 96326333; Product type pe : putative enzyme; putative glycosyl transferase complement(2127889..2129106) Escherichia coli S88 7132494 YP_002391850.1 CDS wcaB NC_011742.1 2129103 2129591 R acetyltransferase believed to catalyze the addition of the acetyl group that is attached through an O linkage to the first fucosyl residue of the colanic acid repetitive unit (E unit); wcaB is induced in sessile bacteria and by osmotic shock, and repressed when grown in rich medium; putative colanic acid biosynthesis acetyltransferase WcaB complement(2129103..2129591) Escherichia coli S88 7132493 YP_002391851.1 CDS wcaA NC_011742.1 2129594 2130433 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 96326333; Product type pe : putative enzyme; putative glycosyl transferase complement(2129594..2130433) Escherichia coli S88 7132492 YP_002391852.1 CDS wzc NC_011742.1 2130562 2132724 R Wzc; catalyzes the autophosphorylation on tyrosine residues which downregulates the biosynthesis of colonic acid (an extracellular polysaccharide); tyrosine kinase complement(2130562..2132724) Escherichia coli S88 7132491 YP_002391853.1 CDS wzb NC_011742.1 2132727 2133170 R Wzb shows phosphatase activity towards the autophosphorylated Wzc protein, which induces colanic acid biosynthesis; catalyzes the phosphorylation of UDP-glucose dehydrogenase, an enzyme involved in colanic acid biosynthesis; tyrosine phosphatase complement(2132727..2133170) Escherichia coli S88 7132505 YP_002391854.1 CDS wza NC_011742.1 2133176 2134315 R Evidence 2b : Function of strongly homologous gene; PubMedId : 15090537, 96326333, 8759852, 8763957; Product type lp : lipoprotein; lipoprotein required for capsular polysaccharide translocation through the outer membrane complement(2133176..2134315) Escherichia coli S88 7132504 YP_002391855.1 CDS yegH NC_011742.1 2134974 2136557 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; fused putative membrane protein ; putative membrane protein 2134974..2136557 Escherichia coli S88 7132503 YP_002391856.1 CDS ECS88_2161 NC_011742.1 2136632 2136970 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2136632..2136970 Escherichia coli S88 7132980 YP_002391857.1 CDS ECS88_2162 NC_011742.1 2136942 2137250 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2136942..2137250 Escherichia coli S88 7129001 YP_002391858.1 CDS asmA NC_011742.1 2137303 2139156 R YegA; inner membrane protein involved in the assembly of outer membrane proteins (OMPs); asmA-null mutants show low lipopolysaccharide (LPS) levels, suggesting a role in LPS biogenesis and/or in restricting outer membrane fluidity, resulting on altered assembly of OMPs; putative assembly protein complement(2137303..2139156) Escherichia coli S88 7129002 YP_002391859.1 CDS dcd NC_011742.1 2139178 2139759 R Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis; deoxycytidine triphosphate deaminase complement(2139178..2139759) Escherichia coli S88 7129945 YP_002391860.1 CDS udk NC_011742.1 2139851 2140492 R functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor; uridine kinase complement(2139851..2140492) Escherichia coli S88 7130570 YP_002391861.1 CDS yegE NC_011742.1 2140810 2144127 D contains a MASE1 (Membrane-Associated Sensor) domain; potentially involved in signal transduction; putative sensor protein 2140810..2144127 Escherichia coli S88 7130390 YP_002391862.1 CDS alkA NC_011742.1 2144238 2145086 R inducible, catalyzes the hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine and 7-methyladenine; 3-methyl-adenine DNA glycosylase II complement(2144238..2145086) Escherichia coli S88 7132979 YP_002391863.1 CDS yegD NC_011742.1 2145220 2146572 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 6094528, 7940673, 7984428; Product type pf : putative factor; putative chaperone 2145220..2146572 Escherichia coli S88 7133042 YP_002391864.1 CDS yegI NC_011742.1 2146585 2148534 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2146585..2148534) Escherichia coli S88 7132978 YP_002391865.1 CDS yegK NC_011742.1 2148522 2149283 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2148522..2149283) Escherichia coli S88 7132981 YP_002391866.1 CDS yegL NC_011742.1 2149280 2149939 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2149280..2149939) Escherichia coli S88 7132982 YP_002391867.1 CDS mdtA NC_011742.1 2150820 2152067 D Part of a tripartite efflux system composed of MdtA, MdtB and MdtC which confers resistance against novobiocin and deoxycholate; multidrug efflux system subunit MdtA 2150820..2152067 Escherichia coli S88 7131336 YP_002391868.1 CDS mdtB NC_011742.1 2152067 2155189 D Part of a tripartite efflux system composed of MdtA, MdtB and MdtC which confers resistance against novobiocin and deoxycholate; multidrug efflux system subunit MdtB 2152067..2155189 Escherichia coli S88 7128789 YP_002391869.1 CDS mdtC NC_011742.1 2155190 2158267 D Part of a tripartite efflux system composed of MdtA, MdtB and MdtC; confers resistance against novobiocin and deoxycholate; multidrug efflux system subunit MdtC 2155190..2158267 Escherichia coli S88 7128790 YP_002391870.1 CDS mdtD NC_011742.1 2158268 2159683 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12107134, 21450803, 8282725; Product type t : transporter; multidrug efflux system protein MdtE 2158268..2159683 Escherichia coli S88 7128791 YP_002391871.1 CDS baeS NC_011742.1 2159680 2161083 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94110256, 8282725; Product type r : regulator; signal transduction histidine-protein kinase BaeS 2159680..2161083 Escherichia coli S88 7128792 YP_002391872.1 CDS baeR NC_011742.1 2161080 2161802 D response regulator in two-component regulatory system with BaeS; regulator of RNA synthesis, flagellar biosynthesis, chemotaxis and transport; DNA-binding transcriptional regulator BaeR 2161080..2161802 Escherichia coli S88 7129986 YP_002391873.1 CDS yegP NC_011742.1 2161982 2162314 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2161982..2162314 Escherichia coli S88 7129985 YP_002391874.1 CDS ECS88_2180 NC_011742.1 2162439 2163053 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(2162439..2163053) Escherichia coli S88 7132984 YP_002391875.1 CDS ECS88_2181 NC_011742.1 2163105 2165252 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2163105..2165252) Escherichia coli S88 7129003 YP_002391876.1 CDS ECS88_2182 NC_011742.1 2165224 2165940 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2165224..2165940) Escherichia coli S88 7129004 YP_002391877.1 CDS ECS88_2183 NC_011742.1 2165940 2167154 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2165940..2167154) Escherichia coli S88 7129005 YP_002391878.1 CDS yegQ NC_011742.1 2167642 2169003 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative peptidase 2167642..2169003 Escherichia coli S88 7129006 YP_002391879.1 CDS ogrK NC_011742.1 2169276 2169494 R in E. coli K-12 this is in prophage P2 remnant; DNA-binding transcriptional regulator complement(2169276..2169494) Escherichia coli S88 7131337 YP_002391880.1 CDS GpD NC_011742.1 2169576 2170739 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 3458177; Product type h : extrachromosomal origin; Phage late control gene D protein (GpD) complement(2169576..2170739) Escherichia coli S88 7133121 YP_002391881.1 CDS GpU NC_011742.1 2170739 2171218 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12426340; Product type h : extrachromosomal origin; tail assembly protein (GpU) complement(2170739..2171218) Escherichia coli S88 7130058 YP_002391882.1 CDS GpT NC_011742.1 2171233 2173680 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; tail fiber protein T (tape measure) (GpT) complement(2171233..2173680) Escherichia coli S88 7130067 YP_002391883.1 CDS GpE NC_011742.1 2173825 2174100 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; tail protein E (GpE) complement(2173825..2174100) Escherichia coli S88 7130066 YP_002391884.1 CDS ECS88_2190 NC_011742.1 2174157 2174675 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major tail tube protein (Protein FII) complement(2174157..2174675) Escherichia coli S88 7130059 YP_002391885.1 CDS ECS88_2191 NC_011742.1 2174688 2175878 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major tail sheath protein (Protein FI) complement(2174688..2175878) Escherichia coli S88 7129007 YP_002391886.1 CDS ECS88_2192 NC_011742.1 2176197 2176586 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin; putative membrane protein 2176197..2176586 Escherichia coli S88 7129008 YP_002391887.1 CDS ECS88_2193 NC_011742.1 2176609 2177295 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; site-specific recombinase, phage integrase family complement(2176609..2177295) Escherichia coli S88 7129009 YP_002391888.1 CDS ECS88_2194 NC_011742.1 2177300 2178142 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(2177300..2178142) Escherichia coli S88 7129010 YP_002391889.1 CDS ECS88_2195 NC_011742.1 2178564 2179091 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage tail fiber assembly protein (GpG) complement(2178564..2179091) Escherichia coli S88 7129011 YP_002391890.1 CDS ECS88_2196 NC_011742.1 2179095 2181830 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 9495752; Product type h : extrachromosomal origin; putative phage tail fiber protein H (GpH) complement(2179095..2181830) Escherichia coli S88 7129012 YP_002391891.1 CDS ECS88_2197 NC_011742.1 2181841 2182371 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail protein I (GpI) complement(2181841..2182371) Escherichia coli S88 7129013 YP_002391892.1 CDS ECS88_2198 NC_011742.1 2182364 2183272 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Baseplate assembly protein J (GpJ) complement(2182364..2183272) Escherichia coli S88 7129014 YP_002391893.1 CDS ECS88_2199 NC_011742.1 2183277 2183624 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Baseplate assembly protein W (GpW) complement(2183277..2183624) Escherichia coli S88 7129015 YP_002391894.1 CDS ECS88_2200 NC_011742.1 2183621 2184292 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Baseplate assembly protein V (GpV) complement(2183621..2184292) Escherichia coli S88 7129016 YP_002391895.1 CDS ECS88_2201 NC_011742.1 2184381 2185481 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein from phage origin 2184381..2185481 Escherichia coli S88 7129017 YP_002391896.1 CDS ECS88_2202 NC_011742.1 2185562 2186014 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail completion protein S (GpS) complement(2185562..2186014) Escherichia coli S88 7129018 YP_002391897.1 CDS ECS88_2203 NC_011742.1 2186007 2186474 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail completion protein R (GpR) complement(2186007..2186474) Escherichia coli S88 7129019 YP_002391898.1 CDS ECS88_2204 NC_011742.1 2186437 2186844 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative host lysis related protein from prophage complement(2186437..2186844) Escherichia coli S88 7129020 YP_002391899.1 CDS ECS88_2205 NC_011742.1 2186582 2187007 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative Protein lysB from bacteriophage P2 complement(2186582..2187007) Escherichia coli S88 7129021 YP_002391900.1 CDS ECS88_2206 NC_011742.1 2186995 2187420 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative protein lysA from Bacteriophage P2 complement(2186995..2187420) Escherichia coli S88 7129022 YP_002391901.1 CDS ECS88_2207 NC_011742.1 2187435 2187932 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative Lysozyme (Lysis protein) (Muramidase) (Endolysin) (Protein gpK) complement(2187435..2187932) Escherichia coli S88 7129023 YP_002391902.1 CDS ECS88_2208 NC_011742.1 2187932 2188213 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage lysis protein Y, holin complement(2187932..2188213) Escherichia coli S88 7129024 YP_002391903.1 CDS ECS88_2209 NC_011742.1 2188217 2188489 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail protein X (GpX) complement(2188217..2188489) Escherichia coli S88 7129025 YP_002391904.1 CDS ECS88_2210 NC_011742.1 2188420 2188989 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head completion/stabilization protein (GpL) complement(2188420..2188989) Escherichia coli S88 7129026 YP_002391905.1 CDS ECS88_2211 NC_011742.1 2189029 2189772 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Terminase, endonuclease subunit (GpM) complement(2189029..2189772) Escherichia coli S88 7129027 YP_002391906.1 CDS ECS88_2213 NC_011742.1 2190633 2192174 D Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase ORF1, IS21 family 2190633..2192174 Escherichia coli S88 7133390 YP_002391907.1 CDS ECS88_2214 NC_011742.1 2192186 2192935 D Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase ORF2, IS21 family 2192186..2192935 Escherichia coli S88 7133391 YP_002391908.1 CDS ECS88_2216 NC_011742.1 2193494 2194414 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative capsid scaffolding protein (GpO) from prophage P2 complement(2193494..2194414) Escherichia coli S88 7133393 YP_002391909.1 CDS ECS88_2217 NC_011742.1 2194492 2196294 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Terminase, ATPase subunit (GpP) 2194492..2196294 Escherichia coli S88 7133394 YP_002391910.1 CDS ECS88_2218 NC_011742.1 2196294 2197328 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative portal vertex protein (GpQ) 2196294..2197328 Escherichia coli S88 7133395 YP_002391911.1 CDS ECS88_2219 NC_011742.1 2197668 2199602 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin complement(2197668..2199602) Escherichia coli S88 7133396 YP_002391912.1 CDS ECS88_2220 NC_011742.1 2199617 2201941 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Replication gene A protein (GpA) complement(2199617..2201941) Escherichia coli S88 7133397 YP_002391913.1 CDS ECS88_2221 NC_011742.1 2201889 2202164 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 8510152; hypothetical protein complement(2201889..2202164) Escherichia coli S88 7133398 YP_002391914.1 CDS ECS88_2222 NC_011742.1 2202161 2202385 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 8510152; hypothetical protein complement(2202161..2202385) Escherichia coli S88 7133399 YP_002391915.1 CDS ECS88_2223 NC_011742.1 2202687 2202944 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 8510152; hypothetical protein complement(2202687..2202944) Escherichia coli S88 7133400 YP_002391916.1 CDS ECS88_2224 NC_011742.1 2202975 2203475 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Replication gene B protein (GpB) complement(2202975..2203475) Escherichia coli S88 7133401 YP_002391917.1 CDS ECS88_2225 NC_011742.1 2203472 2203666 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 2826134; hypothetical protein complement(2203472..2203666) Escherichia coli S88 7133402 YP_002391918.1 CDS cox NC_011742.1 2203653 2203928 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 2826134; Product type h : extrachromosomal origin; regulatory protein complement(2203653..2203928) Escherichia coli S88 7133403 YP_002391919.1 CDS ECS88_2227 NC_011742.1 2204043 2204342 D Evidence 2b : Function of strongly homologous gene; PubMedId : 3475531; Product type h : extrachromosomal origin; repressor protein C 2204043..2204342 Escherichia coli S88 7131950 YP_002391920.1 CDS yegR NC_011742.1 2205902 2206219 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2205902..2206219) Escherichia coli S88 7133406 YP_002391921.1 CDS yegS NC_011742.1 2206635 2207534 D cytosolic protein with phosphatidylglycerol kinase activity; undetermined physiological role; lipid kinase 2206635..2207534 Escherichia coli S88 7132986 YP_002391922.1 CDS gatR NC_011742.1 2207616 2208395 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 7772602; Product type r : regulator; Galactitol utilization operon repressor complement(2207616..2208395) Escherichia coli S88 7132987 YP_002391923.1 CDS gatD NC_011742.1 2208495 2209535 R Zn-dependent; NAD(P)-binding; catalyzes the formation of tagatose-6-phosphate from galactitol-1-phosphate; galactitol-1-phosphate dehydrogenase complement(2208495..2209535) Escherichia coli S88 7132190 YP_002391924.1 CDS gatC NC_011742.1 2209583 2210938 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 76024805, 77192083, 97113438, 7772602; Product type t : transporter; galactitol-specific enzyme IIC component of PTS complement(2209583..2210938) Escherichia coli S88 7132189 YP_002391925.1 CDS gatB NC_011742.1 2210942 2211226 R phosphoenolpyruvate-dependent sugar phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIB is phosphorylated by IIA and then transfers the phosphoryl group to the sugar; IIC forms the translocation channel; PTS system galactitol-specific transporter subunit IIB complement(2210942..2211226) Escherichia coli S88 7132188 YP_002391926.1 CDS gatA NC_011742.1 2211257 2211709 R phosphoenolpyruvate-dependent sugar phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIB is phosphorylated by IIA and then transfers the phosphoryl group to the sugar; IIC forms the translocation channel; PTS system galactitol-specific transporter subunit IIA complement(2211257..2211709) Escherichia coli S88 7132187 YP_002391927.1 CDS gatZ NC_011742.1 2211719 2212981 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11976750, 97113438, 7772602, 8932697; Product type e : enzyme; D-tagatose 1,6-bisphosphate aldolase 2, subunit complement(2211719..2212981) Escherichia coli S88 7132186 YP_002391928.1 CDS gatY NC_011742.1 2213010 2213864 R catalyzes the reversible reaction of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate; in enteric bacteria there are two D-tagatose 1,6-bisphosphate-specific aldolases: KbaY (also called AgaY), involved in catabolism of N-acetyl-galactosamine and D-galactosamine, and GatY which is part of the galactitol catabolism pathway; tagatose-bisphosphate aldolase complement(2213010..2213864) Escherichia coli S88 7132192 YP_002391929.1 CDS fbaB NC_011742.1 2214093 2215145 R catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate; fructose-bisphosphate aldolase complement(2214093..2215145) Escherichia coli S88 7132191 YP_002391930.1 CDS yegT NC_011742.1 2215402 2216679 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative hydrophilic substrate transporter; MFS superfamily 2215402..2216679 Escherichia coli S88 7129448 YP_002391931.1 CDS yegU NC_011742.1 2216676 2217680 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative (phospho)hydrolase 2216676..2217680 Escherichia coli S88 7132988 YP_002391932.1 CDS yegV NC_011742.1 2217677 2218642 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative kinase 2217677..2218642 Escherichia coli S88 7132989 YP_002391933.1 CDS yegW NC_011742.1 2218616 2219362 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(2218616..2219362) Escherichia coli S88 7132990 YP_002391934.1 CDS yegX NC_011742.1 2219414 2220232 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative membrane-bound hydrolase complement(2219414..2220232) Escherichia coli S88 7132991 YP_002391935.1 CDS thiD NC_011742.1 2220297 2221097 R catalyzes the formation of 4-amino-2-methyl-5-diphosphomethylpyrimidine; phosphomethylpyrimidine kinase complement(2220297..2221097) Escherichia coli S88 7132992 YP_002391936.1 CDS thiM NC_011742.1 2221094 2221882 R catalyzes the formation of 4-methyl-5-(2-phosphoethyl)-thiazole and ADP from 4-methyl-5-(2-hydroxyethyl)-thiazole and ATP; hydroxyethylthiazole kinase complement(2221094..2221882) Escherichia coli S88 7131292 YP_002391937.1 CDS yohL NC_011742.1 2222105 2222377 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2222105..2222377) Escherichia coli S88 7129859 YP_002391938.1 CDS rncA NC_011742.1 2222498 2223322 D membrane protein conferring nickel and cobalt resistance; nickel/cobalt efflux protein RcnA 2222498..2223322 Escherichia coli S88 7133651 YP_002391939.1 CDS yohN NC_011742.1 2223361 2223879 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2223361..2223879 Escherichia coli S88 7132744 YP_002391940.1 CDS yehA NC_011742.1 2223961 2224995 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative exported fimbrial-like adhesin protein complement(2223961..2224995) Escherichia coli S88 7133652 YP_002391941.1 CDS yehB NC_011742.1 2225011 2227491 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative outer membrane protein complement(2225011..2227491) Escherichia coli S88 7132993 YP_002391942.1 CDS yehC NC_011742.1 2227507 2228181 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative membrane-associated pilin chaperone complement(2227507..2228181) Escherichia coli S88 7132994 YP_002391943.1 CDS yehD NC_011742.1 2228262 2228804 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative fimbrial-like adhesin protein complement(2228262..2228804) Escherichia coli S88 7132995 YP_002391944.1 CDS yehE NC_011742.1 2229098 2229379 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2229098..2229379) Escherichia coli S88 7132996 YP_002391945.1 CDS mrp NC_011742.1 2229642 2230751 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91080852, 15601724, 2259334; Product type t : transporter; putative ATPase complement(2229642..2230751) Escherichia coli S88 7132997 YP_002391946.1 CDS metG NC_011742.1 2230883 2232916 D 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; methionyl-tRNA synthetase 2230883..2232916 Escherichia coli S88 7129612 YP_002391947.1 CDS ECS88_2257 NC_011742.1 2233057 2236845 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2156810; Product type pr : putative regulator; putative Molybdate metabolism regulator (molR) 2233057..2236845 Escherichia coli S88 7128815 YP_002391948.1 CDS yehI NC_011742.1 2236855 2240487 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2236855..2240487 Escherichia coli S88 7133407 YP_002391949.1 CDS ECS88_2260 NC_011742.1 2240570 2240740 D Evidence 6 : Doubtful CDS; hypothetical protein 2240570..2240740 Escherichia coli S88 7132998 YP_002391950.1 CDS yehL NC_011742.1 2241644 2242732 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16428726; Product type pf : putative factor; putative ABC superfamily protein 2241644..2242732 Escherichia coli S88 7133408 YP_002391951.1 CDS yehM NC_011742.1 2242739 2245015 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2242739..2245015 Escherichia coli S88 7132999 YP_002391952.1 CDS yehP NC_011742.1 2245008 2246144 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2245008..2246144 Escherichia coli S88 7133000 YP_002391953.1 CDS yehQ NC_011742.1 2246141 2248144 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2246141..2248144 Escherichia coli S88 7133001 YP_002391954.1 CDS yehR NC_011742.1 2248269 2248730 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type lp : lipoprotein; hypothetical protein 2248269..2248730 Escherichia coli S88 7133002 YP_002391955.1 CDS yehS NC_011742.1 2248771 2249241 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2248771..2249241) Escherichia coli S88 7133003 YP_002391956.1 CDS yehT NC_011742.1 2249288 2250007 R unknown function; when overproduced it confers drug-resistance; putative two-component response-regulatory protein YehT complement(2249288..2250007) Escherichia coli S88 7133004 YP_002391957.1 CDS yehU NC_011742.1 2250004 2251689 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15522865, 15322361; Product type rc : receptor; sensory kinase in two-component system with YehT complement(2250004..2251689) Escherichia coli S88 7133005 YP_002391958.1 CDS mlrA NC_011742.1 2251911 2252642 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11489123; Product type r : regulator; DNA-binding transcriptional regulator 2251911..2252642 Escherichia coli S88 7133006 YP_002391959.1 CDS yohO NC_011742.1 2252702 2252809 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2252702..2252809 Escherichia coli S88 7128841 YP_002391960.1 CDS yehW NC_011742.1 2252790 2253521 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter subunit: permease component of ABC superfamily transporter complement(2252790..2253521) Escherichia coli S88 7133653 YP_002391961.1 CDS yehX NC_011742.1 2253526 2254452 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter subunit: ATP-binding component of ABC superfamily transporter complement(2253526..2254452) Escherichia coli S88 7133007 YP_002391962.1 CDS yehY NC_011742.1 2254445 2255602 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter subunit: permease component of ABC superfamily complement(2254445..2255602) Escherichia coli S88 7133008 YP_002391963.1 CDS yehZ NC_011742.1 2255609 2256526 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15251200; Product type pt : putative transporter; putative transporter subunit: periplasmic-binding component of ABC superfamily complement(2255609..2256526) Escherichia coli S88 7133009 YP_002391964.1 CDS bglX NC_011742.1 2256716 2259013 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96303506; Product type e : enzyme; beta-D-glucoside glucohydrolase, periplasmic complement(2256716..2259013) Escherichia coli S88 7133010 YP_002391965.1 CDS dld NC_011742.1 2259209 2260924 D component of the membrane-bound D-lactate oxidase, FAD-binding, NADH independent; D-lactate dehydrogenase 2259209..2260924 Escherichia coli S88 7129119 YP_002391966.1 CDS pbpG NC_011742.1 2260963 2261895 R specifically hydrolyze the DD-diaminopimelate-alanine bonds in high-molecular-mass murein sacculi; Penicillin-binding protein 7; D-alanyl-D-alanine endopeptidase complement(2260963..2261895) Escherichia coli S88 7130215 YP_002391967.1 CDS yohC NC_011742.1 2262069 2262656 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(2262069..2262656) Escherichia coli S88 7133176 YP_002391968.1 CDS yohD NC_011742.1 2262826 2263404 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 2262826..2263404 Escherichia coli S88 7133645 YP_002391969.1 CDS yohF NC_011742.1 2263524 2264285 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; acetoin dehydrogenase complement(2263524..2264285) Escherichia coli S88 7133646 YP_002391970.1 CDS yohG NC_011742.1 2264338 2265426 R may be involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride; multidrug resistance outer membrane protein MdtQ complement(2264338..2265426) Escherichia coli S88 7133647 YP_002391971.1 CDS dusC NC_011742.1 2266468 2267418 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 22095566; Product type e : enzyme; tRNA-dihydrouridine synthase C complement(2266468..2267418) Escherichia coli S88 7133648 YP_002391972.1 CDS yohJ NC_011742.1 2267657 2268055 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 2267657..2268055 Escherichia coli S88 7132367 YP_002391973.1 CDS yohK NC_011742.1 2268052 2268747 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 2268052..2268747 Escherichia coli S88 7133649 YP_002391974.1 CDS cdd NC_011742.1 2268877 2269761 D Reclaims exogenous and endogenous cytidine and 2'-deoxycytidine molecules for UMP synthesis; cytidine deaminase 2268877..2269761 Escherichia coli S88 7133650 YP_002391975.1 CDS sanA NC_011742.1 2269911 2270630 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 96125233, 1567863, 8550448; hypothetical protein 2269911..2270630 Escherichia coli S88 7129176 YP_002391976.1 CDS yeiS NC_011742.1 2270633 2270872 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 2270633..2270872 Escherichia coli S88 7131357 YP_002391977.1 CDS yeiT NC_011742.1 2271066 2272304 D function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; putative oxidoreductase 2271066..2272304 Escherichia coli S88 7129764 YP_002391978.1 CDS yeiA NC_011742.1 2272298 2273533 D catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines; dihydropyrimidine dehydrogenase 2272298..2273533 Escherichia coli S88 7129765 YP_002391979.1 CDS mglC NC_011742.1 2273776 2274786 R ABC transporter; functions in galactose transport; part of MglA2C2B transporter complex; beta-methylgalactoside transporter inner membrane component complement(2273776..2274786) Escherichia coli S88 7133011 YP_002391980.1 CDS mglA NC_011742.1 2274802 2276322 R with MglBC transports galactose or methyl galactoside into the cell; contains 2 ATP binding domains; galactose/methyl galaxtoside transporter ATP-binding protein complement(2274802..2276322) Escherichia coli S88 7128828 YP_002391981.1 CDS mglB NC_011742.1 2276383 2277381 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87286407, 92049246, 1719366, 3057628, 3302609, 3600760, 6340108, 6885805, 7012152, 9298646; Product type t : transporter; methyl-galactoside transporter subunit ; periplasmic-binding component of ABC superfamily complement(2276383..2277381) Escherichia coli S88 7128826 YP_002391982.1 CDS galS NC_011742.1 2277661 2278701 R negative regulator of the mglBAC operon for galactose utilization; DNA-binding transcriptional regulator GalS complement(2277661..2278701) Escherichia coli S88 7128827 YP_002391983.1 CDS ECS88_2298 NC_011742.1 2278691 2278894 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2278691..2278894 Escherichia coli S88 7132176 YP_002391984.1 CDS yeiB NC_011742.1 2278843 2280000 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(2278843..2280000) Escherichia coli S88 7133409 YP_002391985.1 CDS folE NC_011742.1 2280017 2280685 R involved in the first step of tetrahydrofolate biosynthesis; catalyzes the formation of formate and 2-amino-4-hydroxy-6-(erythro-1,2, 3-trihydroxypropyl)dihydropteridine triphosphate from GTP and water; forms a homopolymer; GTP cyclohydrolase I complement(2280017..2280685) Escherichia coli S88 7133012 YP_002391986.1 CDS ECS88_2301 NC_011742.1 2280839 2281015 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2280839..2281015 Escherichia coli S88 7132817 YP_002391987.1 CDS frmC NC_011742.1 2280943 2281779 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16567800; Product type e : enzyme; S-formylglutathione hydrolase 2280943..2281779 Escherichia coli S88 7133410 YP_002391988.1 CDS cirA NC_011742.1 2281811 2283802 R Cir; FeuA; CirA; receptor protein for siderophores (colicin IA, IB and V) and microcins (E492, H47, and M); TonB-dependent; able to transport monomers, dimer, and linear trimers of 2,3-dihydorxybenzoylserine; outer membrane protein; colicin I receptor complement(2281811..2283802) Escherichia coli S88 7132831 YP_002391989.1 CDS lysP NC_011742.1 2284094 2285563 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92250419, 94252996, 1315732, 7551055; Product type t : transporter; lysine transporter complement(2284094..2285563) Escherichia coli S88 7131915 YP_002391990.1 CDS ECS88_2305 NC_011742.1 2285547 2285855 R hypothetical protein complement(2285547..2285855) Escherichia coli S88 7129395 YP_002391991.1 CDS yeiE NC_011742.1 2285768 2286649 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12400704, 1315732; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(2285768..2286649) Escherichia coli S88 7133411 YP_002391992.1 CDS yeiH NC_011742.1 2286748 2287797 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 2286748..2287797 Escherichia coli S88 7133014 YP_002391993.1 CDS nfo NC_011742.1 2287871 2288728 D 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; endonuclease IV 2287871..2288728 Escherichia coli S88 7133015 YP_002391994.1 CDS yeiI NC_011742.1 2288732 2289820 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein 2288732..2289820 Escherichia coli S88 7129702 YP_002391995.1 CDS rihB NC_011742.1 2290088 2291029 R Hydrolyzes cytidine or uridine to ribose and cytosine or uracil, respectively; ribonucleoside hydrolase 2 complement(2290088..2291029) Escherichia coli S88 7133016 YP_002391996.1 CDS yeiL NC_011742.1 2291198 2291857 D activator of nucleoside metabolism; DNA-binding transcriptional activator YeiL 2291198..2291857 Escherichia coli S88 7132721 YP_002391997.1 CDS yeiM NC_011742.1 2291924 2293174 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sodium/proton nucleoside transporter complement(2291924..2293174) Escherichia coli S88 7133017 YP_002391998.1 CDS yeiN NC_011742.1 2293268 2294206 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2293268..2294206) Escherichia coli S88 7133018 YP_002391999.1 CDS yeiC NC_011742.1 2294194 2295249 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein complement(2294194..2295249) Escherichia coli S88 7133019 YP_002392000.1 CDS fruA NC_011742.1 2295591 2297282 R phosphoenolpyruvate-dependent sugar phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIB is phosphorylated by IIA and then transfers the phosphoryl group to the sugar; IIC forms the translocation channel; PTS system fructose-specific transporter subunits IIBC complement(2295591..2297282) Escherichia coli S88 7133013 YP_002392001.1 CDS fruK NC_011742.1 2297299 2298237 R converts fructose-1-phosphate and ATP to fructose-1,6-bisphosphate and ADP; highly specific for fructose-1-phopshate; similar to PfkB; forms homodimers; 1-phosphofructokinase complement(2297299..2298237) Escherichia coli S88 7132835 YP_002392002.1 CDS fruB NC_011742.1 2298237 2299367 R phosphoenolpyruvate (PEP)-dependent, sugar transporting phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIA is phosphorylated by phospho-HP which then transfers the phosphoryl group to the IIB componentr; bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein complement(2298237..2299367) Escherichia coli S88 7132837 YP_002392003.1 CDS setB NC_011742.1 2299734 2300915 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10438463, 10209755; Product type t : transporter; lactose/glucose efflux system 2299734..2300915 Escherichia coli S88 7132836 YP_002392004.1 CDS ECS88_2319 NC_011742.1 2300912 2301298 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2300912..2301298) Escherichia coli S88 7130583 YP_002392005.1 CDS ECS88_2320 NC_011742.1 2301066 2301893 D Stimulates the peptidyltransferase activity of the 70S ribosome and enhances dipeptide synthesis with N-formylmethionyl-tRNA and puromycin in vitro, suggesting its involvement in the formation of the first peptide bond of a protein; elongation factor P 2301066..2301893 Escherichia coli S88 7133412 YP_002392006.1 CDS yeiQ NC_011742.1 2302116 2303582 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative sugar dehydrogenase, NAD-dependent 2302116..2303582 Escherichia coli S88 7133413 YP_002392007.1 CDS yeiR NC_011742.1 2303700 2304686 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative enzyme 2303700..2304686 Escherichia coli S88 7133020 YP_002392008.1 CDS yeiU NC_011742.1 2304725 2305438 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15778224; Product type e : enzyme; undecaprenyl pyrophosphate phosphatase 2304725..2305438 Escherichia coli S88 7130493 YP_002392009.1 CDS spr NC_011742.1 2305850 2306416 D by similarity, Spr seems to have peptidase activity; involved in thermoresistance; putative outer membrane lipoprotein 2305850..2306416 Escherichia coli S88 7129766 YP_002392010.1 CDS rtn NC_011742.1 2306597 2308153 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2306597..2308153 Escherichia coli S88 7130634 YP_002392011.1 CDS yejA NC_011742.1 2308235 2310049 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative oligopeptide transporter subunit ; periplasmic-binding component of ABC superfamily transporter 2308235..2310049 Escherichia coli S88 7133021 YP_002392012.1 CDS yejB NC_011742.1 2310050 2311144 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative oligopeptide transporter subunit; permease component of ABC superfamily 2310050..2311144 Escherichia coli S88 7129767 YP_002392013.1 CDS yejE NC_011742.1 2311144 2312169 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative oligopeptide transporter subunit ; permease component of ABC superfamily transporter 2311144..2312169 Escherichia coli S88 7129768 YP_002392014.1 CDS yejF NC_011742.1 2312171 2313760 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative fused oligopeptide transporter subunits of ABC superfamily: ATP-binding components 2312171..2313760 Escherichia coli S88 7129769 YP_002392015.1 CDS yejG NC_011742.1 2313764 2314108 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2313764..2314108) Escherichia coli S88 7129770 YP_002392016.1 CDS bcr NC_011742.1 2314442 2315632 R Involved in sulfonamide (sulfathiazole) and bicyclomycin resistance; bicyclomycin/multidrug efflux system complement(2314442..2315632) Escherichia coli S88 7129771 YP_002392017.1 CDS rsuA NC_011742.1 2315660 2316355 R catalyzes the synthesis pseudouridine from uracil-516 in 16S ribosomal RNA; 16S rRNA pseudouridylate synthase A complement(2315660..2316355) Escherichia coli S88 7129992 YP_002392018.1 CDS yejH NC_011742.1 2316505 2318265 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative nucleic acid ATP-dependent helicase 2316505..2318265 Escherichia coli S88 7133823 YP_002392019.1 CDS rplY NC_011742.1 2318390 2318674 D 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; 50S ribosomal protein L25 2318390..2318674 Escherichia coli S88 7129772 YP_002392020.1 CDS yejK NC_011742.1 2318813 2319820 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 99296598, 10368163; Product type f : factor; nucleoid-associated protein NdpA complement(2318813..2319820) Escherichia coli S88 7133764 YP_002392021.1 CDS yejL NC_011742.1 2320002 2320229 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2320002..2320229 Escherichia coli S88 7129773 YP_002392022.1 CDS yejM NC_011742.1 2320249 2322009 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative hydrolase, inner membrane-associated 2320249..2322009 Escherichia coli S88 7129774 YP_002392023.1 CDS narP NC_011742.1 2323379 2324026 D nitrate/nitrite response regulator NarP; NarP is phosphorylated by NarX and NarQ and can activate fdnG and nitrite or nitrate reductase systems; represses expression of other anaerobic genes; transcriptional regulator NarP 2323379..2324026 Escherichia coli S88 7133414 YP_002392024.1 CDS ccmH NC_011742.1 2324061 2325113 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10339610, 11756453, 12196152, 87260957, 91194558, 95362656, 9914305, 7635817; Product type pe : putative enzyme; heme lyase, CcmH subunit complement(2324061..2325113) Escherichia coli S88 7129682 YP_002392025.1 CDS ccmG NC_011742.1 2325110 2325667 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10339610, 12196152, 9716493, 9770295, 11256948, 11350062, 11843181, 7635817, 9537397; Product type e : enzyme; periplasmic thioredoxin of cytochrome c-type biogenesis complement(2325110..2325667) Escherichia coli S88 7129174 YP_002392026.1 CDS ccmF NC_011742.1 2325664 2327607 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10339610, 11756453, 12196152, 87260957, 8842153, 91194558, 95362656, 9716493, 7635817; Product type e : enzyme; heme lyase, CcmF subunit complement(2325664..2327607) Escherichia coli S88 7129173 YP_002392027.1 CDS ccmE NC_011742.1 2327604 2328083 R CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane; cytochrome c-type biogenesis protein CcmE complement(2327604..2328083) Escherichia coli S88 7129172 YP_002392028.1 CDS ccmD NC_011742.1 2328080 2328289 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10339610, 12196152, 95362656, 9716493, 7635817; Product type f : factor; cytochrome c biogenesis protein complement(2328080..2328289) Escherichia coli S88 7129171 YP_002392029.1 CDS ccmC NC_011742.1 2328286 2329023 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10339610, 12196152, 14532274, 21413853, 95362656, 7635817; Product type t : transporter; heme exporter subunit ; membrane component of ABC superfamily complement(2328286..2329023) Escherichia coli S88 7129170 YP_002392030.1 CDS ccmB NC_011742.1 2329065 2329727 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10339610, 12196152, 95362656, 9716493, 7635817; Product type t : transporter; heme exporter subunit ; membrane component of ABC superfamily complement(2329065..2329727) Escherichia coli S88 7129169 YP_002392031.1 CDS ccmA NC_011742.1 2329724 2330347 R ATP-binding protein; required for proper cytochrome c maturation; cytochrome c biogenesis protein CcmA complement(2329724..2330347) Escherichia coli S88 7129168 YP_002392032.1 CDS napC NC_011742.1 2330360 2330962 R with NapABDFGH functions as a nitrate reductase; NapC functions as an electron shuttle between NapAB and NapGH or quinone; cytochrome c-type protein NapC complement(2330360..2330962) Escherichia coli S88 7129167 YP_002392033.1 CDS napB NC_011742.1 2330972 2331421 R small subunit of periplasmic nitrate reductase; receives electrons from the membrane-bound NapC and passes them to NapA; citrate reductase cytochrome c-type subunit complement(2330972..2331421) Escherichia coli S88 7129669 YP_002392034.1 CDS napH NC_011742.1 2331418 2332281 R part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; quinol dehydrogenase membrane component complement(2331418..2332281) Escherichia coli S88 7129668 YP_002392035.1 CDS napG NC_011742.1 2332268 2332963 R part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; secreted by twin arginine translocation pathway; quinol dehydrogenase periplasmic component complement(2332268..2332963) Escherichia coli S88 7129673 YP_002392036.1 CDS napA NC_011742.1 2332970 2335456 R periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC; nitrate reductase catalytic subunit complement(2332970..2335456) Escherichia coli S88 7129672 YP_002392037.1 CDS napD NC_011742.1 2335453 2335716 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96228696, 99395037; Product type f : factor; assembly protein for periplasmic nitrate reductase complement(2335453..2335716) Escherichia coli S88 7129667 YP_002392038.1 CDS napF NC_011742.1 2335706 2336200 R Predicted role in electron transfer to the periplasmic nitrate reductase protein NapA.; ferredoxin-type protein complement(2335706..2336200) Escherichia coli S88 7129670 YP_002392039.1 CDS ECS88_2356 NC_011742.1 2336300 2336473 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2336300..2336473 Escherichia coli S88 7129671 YP_002392040.1 CDS eco NC_011742.1 2336608 2337096 D serine protease inhibitor, inhibits trypsin and other proteases; ecotin 2336608..2337096 Escherichia coli S88 7133415 YP_002392041.1 CDS mqo NC_011742.1 2337246 2338892 R malate dehydrogenase; catalyzes the oxidation of malate to oxaloacetate; malate:quinone oxidoreductase complement(2337246..2338892) Escherichia coli S88 7132378 YP_002392042.1 CDS yojI NC_011742.1 2339110 2340753 R efflux pump for the antibacterial peptide microcin J25; multidrug transporter membrane component/ATP-binding component complement(2339110..2340753) Escherichia coli S88 7129601 YP_002392043.1 CDS alkB NC_011742.1 2340829 2341479 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12226668, 12517444, 12862460, 14527653, 87057220, 88151899, 92017669, 3536913, 3887409, 7928996; Product type e : enzyme; oxidative demethylase of N1-methyladenine or N3-methylcytosine DNA lesions complement(2340829..2341479) Escherichia coli S88 7133654 YP_002392044.1 CDS ada NC_011742.1 2341479 2342543 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91073391, 93272965, 94252990; Product type r : regulator; fused DNA-binding transcriptional dual regulator ; O6-methylguanine-DNA methyltransferase complement(2341479..2342543) Escherichia coli S88 7133043 YP_002392045.1 CDS yojL NC_011742.1 2342617 2343672 R catalyzes the conversion of aminoimidazole ribotide to the 4-amino-5-hydroxymethyl-2-methyl pyrimidine moiety of thiamine; involved in the maintenance and/or assembly of sulfur clusters; periplasmic lipoporotein anchored to the inner membrane; part of the thiamine pyrophosphate biosynthesis pathway; thiamine biosynthesis lipoprotein ApbE complement(2342617..2343672) Escherichia coli S88 7132050 YP_002392046.1 CDS ompC NC_011742.1 2343784 2344875 R allows for ions and hydrophilic solutes to cross the outer membrane; outer membrane porin protein C complement(2343784..2344875) Escherichia coli S88 7133655 YP_002392047.1 CDS rcsD NC_011742.1 2345614 2348286 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11758943, 12864862, 21206231, 2404948, 7984428; Product type r : regulator; phosphotransfer intermediate protein in two-component regulatory system with RcsBC 2345614..2348286 Escherichia coli S88 7128835 YP_002392048.1 CDS rcsB NC_011742.1 2348303 2348953 D two-component response regulator RscB regulates the genes involved in capsule biosynthesis and cell division; probably phosphorylated by RcsC or RcsF; transcriptional regulator RcsB 2348303..2348953 Escherichia coli S88 7131797 YP_002392049.1 CDS rcsC NC_011742.1 2349153 2351954 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11758943, 12864862, 14651646, 20032358, 21450811, 88227838, 90130299, 92048476, 9209051, 2404948, 8366025; Product type r : regulator; hybrid sensory kinase in two-component regulatory system with RcsB and YojN complement(2349153..2351954) Escherichia coli S88 7131795 YP_002392050.1 CDS atoS NC_011742.1 2352169 2353995 D with AtoC is a member of a two-component regulatory system involved in the transcriptional regulation of the ato genes for acetoacetate metabolism; sensory histidine kinase AtoS 2352169..2353995 Escherichia coli S88 7131796 YP_002392051.1 CDS atoC NC_011742.1 2353992 2355377 D with AtoS is a two-component regulatory system involved in the transcriptional regulation of the ato genes for acetoacetate metabolism; acetoacetate metabolism regulatory protein AtoC 2353992..2355377 Escherichia coli S88 7129965 YP_002392052.1 CDS atoD NC_011742.1 2355573 2356235 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 73032600, 87083402; Product type c : carrier; acetyl-CoA:acetoacetyl-CoA transferase subunit alpha 2355573..2356235 Escherichia coli S88 7129962 YP_002392053.1 CDS atoA NC_011742.1 2356235 2356885 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 73032600, 87083402; Product type c : carrier; acetyl-CoA:acetoacetyl-CoA transferase, beta subunit 2356235..2356885 Escherichia coli S88 7129963 YP_002392054.1 CDS atoE NC_011742.1 2356882 2358204 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 73032600, 87083402; Product type t : transporter; short chain fatty acid transporter 2356882..2358204 Escherichia coli S88 7129960 YP_002392055.1 CDS atoB NC_011742.1 2358235 2359419 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 73032600, 87083402; Product type c : carrier; acetyl-CoA acetyltransferase 2358235..2359419 Escherichia coli S88 7129964 YP_002392056.1 CDS yfaP NC_011742.1 2359493 2360269 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2359493..2360269) Escherichia coli S88 7129961 YP_002392057.1 CDS yfaQ NC_011742.1 2360274 2361923 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2360274..2361923) Escherichia coli S88 7129781 YP_002392058.1 CDS ECS88_2376 NC_011742.1 2361924 2366543 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative large extracellular alpha-helical protein complement(2361924..2366543) Escherichia coli S88 7129782 YP_002392059.1 CDS yfaT NC_011742.1 2366462 2367085 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2366462..2367085) Escherichia coli S88 7133416 YP_002392060.1 CDS yfaA NC_011742.1 2367082 2368770 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2367082..2368770) Escherichia coli S88 7129783 YP_002392061.1 CDS gyrA NC_011742.1 2368919 2371546 R negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit A complement(2368919..2371546) Escherichia coli S88 7129776 YP_002392062.1 CDS ubiG NC_011742.1 2371693 2372415 D Involved in ubiquinone biosynthesis; 3-demethylubiquinone-9 3-methyltransferase 2371693..2372415 Escherichia coli S88 7128883 YP_002392063.1 CDS yfaL NC_011742.1 2372555 2376319 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15659678; Product type f : factor; adhesin complement(2372555..2376319) Escherichia coli S88 7130386 YP_002392064.1 CDS nrdA NC_011742.1 2376995 2379280 D Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 2376995..2379280 Escherichia coli S88 7129779 YP_002392065.1 CDS nrdB NC_011742.1 2379427 2380557 D B2 or R2 protein; type 1a enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdA; ribonucleotide-diphosphate reductase subunit beta 2379427..2380557 Escherichia coli S88 7129732 YP_002392066.1 CDS yfaE NC_011742.1 2380557 2380811 D plays a role in maintenance and possibly the biosynthesis of diferric-tyrosyl radical cofactor, essential for nucleotide reduction catalyzed by ribonucleotide reductases; 2Fe-2S ferredoxin YfaE 2380557..2380811 Escherichia coli S88 7129733 YP_002392067.1 CDS inaA NC_011742.1 2380865 2381515 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 92165728, 1537798, 6087316; hypothetical protein complement(2380865..2381515) Escherichia coli S88 7129778 YP_002392068.1 CDS glpQ NC_011742.1 2381718 2382794 R hydrolyzes deacylated phospholipids to glycerol 3-phosphate and the corresponding alcohols; periplasmic; glycerophosphodiester phosphodiesterase complement(2381718..2382794) Escherichia coli S88 7131632 YP_002392069.1 CDS glpT NC_011742.1 2382799 2384157 R catalyzes the uptake of glycerol-3-phosphate into the cell with the simultaneous export of inorganic phosphate from the cell; sn-glycerol-3-phosphate transporter complement(2382799..2384157) Escherichia coli S88 7130025 YP_002392070.1 CDS glpA NC_011742.1 2384430 2386058 D anaerobic, catalyzes the conversion of glycerol 3-phosphate to dihydroxyacetone using fumarate or nitrate as electron acceptor; sn-glycerol-3-phosphate dehydrogenase subunit A 2384430..2386058 Escherichia coli S88 7130027 YP_002392071.1 CDS glpB NC_011742.1 2386048 2387307 D sn-glycerol-3-phosphate dehydrogenase (anaerobic); catalyzes the formation of dihydroxyacetone from glycerol 3-phosphate; part of GlpABC complex; presumably this subunit is responsible for membrane interactions and contains iron-sulfur clusters; anaerobic glycerol-3-phosphate dehydrogenase subunit B 2386048..2387307 Escherichia coli S88 7130017 YP_002392072.1 CDS glpC NC_011742.1 2387304 2388494 D anaerobic; with GlpAB catalyzes the conversion of glycerol-3-phosphate to dihydroxyacetone phosphate; sn-glycerol-3-phosphate dehydrogenase subunit C 2387304..2388494 Escherichia coli S88 7130018 YP_002392073.1 CDS yfaD NC_011742.1 2388687 2389646 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2388687..2389646 Escherichia coli S88 7130019 YP_002392074.1 CDS ypaA NC_011742.1 2389659 2389844 D Evidence 7 : Gene remnant; Conserved hypothetical protein, putative transposase (fragment) 2389659..2389844 Escherichia coli S88 7129777 YP_002392075.1 CDS yfaU NC_011742.1 2389885 2390688 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12454498, 16511168, 8550403; Product type pe : putative enzyme; putative aldolase complement(2389885..2390688) Escherichia coli S88 7133656 YP_002392076.1 CDS yfaW NC_011742.1 2392052 2393269 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative epimerase/enolase/dehydratase complement(2392052..2393269) Escherichia coli S88 7129786 YP_002392077.1 CDS yfaX NC_011742.1 2393272 2394054 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(2393272..2394054) Escherichia coli S88 7129787 YP_002392078.1 CDS yfaY NC_011742.1 2394274 2395476 R Evidence 4 : Homologs of previously reported genes of unknown function; competence damage-inducible protein A complement(2394274..2395476) Escherichia coli S88 7129788 YP_002392079.1 CDS yfaZ NC_011742.1 2395576 2396118 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative outer membrane porin protein complement(2395576..2396118) Escherichia coli S88 7129789 YP_002392080.1 CDS yfaO NC_011742.1 2396397 2396822 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16430214; Product type pe : putative enzyme; putative NUDIX hydrolase 2396397..2396822 Escherichia coli S88 7129790 YP_002392081.1 CDS ais NC_011742.1 2396861 2397463 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2396861..2397463) Escherichia coli S88 7129780 YP_002392082.1 CDS yfbE NC_011742.1 2397753 2398910 D catalyzes the conversion of UDP-4-keto-arabinose to UDP-4-amino-4-deoxy-L-arabinose; UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase 2397753..2398910 Escherichia coli S88 7133038 YP_002392083.1 CDS yfbF NC_011742.1 2398914 2399882 D catalyzes the transfer of 4-deoxy-4-formamido-L-arabinose from UDP to undecaprenyl phosphate; undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase 2398914..2399882 Escherichia coli S88 7129792 YP_002392084.1 CDS yfbG NC_011742.1 2399882 2401864 D Bifunctional polymyxin resistance arnA protein; catalyzes the decarboxylation of UDP-glucuronic acid to UDP-4-keto-arabinose and the addition of a formyl group to UDP-4-amino-4-deoxy-L-arabinose to form UDP-L-4-formamido-arabinose; active in certain mutant strains; bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase 2399882..2401864 Escherichia coli S88 7129793 YP_002392085.1 CDS yfbH NC_011742.1 2401861 2402751 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2401861..2402751 Escherichia coli S88 7129794 YP_002392086.1 CDS arnT NC_011742.1 2402751 2404403 D catalyzes the addition of 4-amino-4-deoxy-L-arabinose to lipid A; 4-amino-4-deoxy-L-arabinose transferase 2402751..2404403 Escherichia coli S88 7129795 YP_002392087.1 CDS yfbW NC_011742.1 2404400 2404735 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; inner membrane protein 2404400..2404735 Escherichia coli S88 7133104 YP_002392088.1 CDS yfbJ NC_011742.1 2404453 2405121 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2404453..2405121 Escherichia coli S88 7129806 YP_002392089.1 CDS pmrD NC_011742.1 2405115 2405381 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96015440, 15569938; Product type pt : putative transporter; polymyxin resistance protein B complement(2405115..2405381) Escherichia coli S88 7129796 YP_002392090.1 CDS menE NC_011742.1 2405491 2406846 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96186953, 8626063; Product type e : enzyme; O-succinylbenzoic acid--CoA ligase complement(2405491..2406846) Escherichia coli S88 7133745 YP_002392091.1 CDS menC NC_011742.1 2406843 2407805 R catalyzes the dehydration of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid to form O-succinylbenzoate; O-succinylbenzoate synthase complement(2406843..2407805) Escherichia coli S88 7128807 YP_002392092.1 CDS menB NC_011742.1 2407805 2408662 R catalyzes the formation of 1,4-dihydroxy-2-naphthoate from O-succinylbenzoyl-CoA; naphthoate synthase complement(2407805..2408662) Escherichia coli S88 7128805 YP_002392093.1 CDS yfbB NC_011742.1 2408677 2409435 R catalyzes the hydrolysis of the thioester bond in palmitoyl-CoA; acyl-CoA thioester hydrolase YfbB complement(2408677..2409435) Escherichia coli S88 7128804 YP_002392094.1 CDS menD NC_011742.1 2409432 2411102 R SEPHCHC synthase; forms 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1- carboxylate from 2-oxoglutarate and isochorismate in menaquinone biosynthesis; 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate synthase complement(2409432..2411102) Escherichia coli S88 7129791 YP_002392095.1 CDS menF NC_011742.1 2411191 2412486 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9150206, 96140724, 2666397, 7984428, 8549818, 8764478; Product type e : enzyme; isochorismate synthase 2 complement(2411191..2412486) Escherichia coli S88 7128806 YP_002392096.1 CDS elaB NC_011742.1 2412565 2412870 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2412565..2412870) Escherichia coli S88 7128808 YP_002392097.1 CDS elaA NC_011742.1 2412925 2413386 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein complement(2412925..2413386) Escherichia coli S88 7132388 YP_002392098.1 CDS elaC NC_011742.1 2413451 2414368 D 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; ribonuclease Z 2413451..2414368 Escherichia coli S88 7132387 YP_002392099.1 CDS yfbK NC_011742.1 2414489 2416231 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2414489..2416231) Escherichia coli S88 7132389 YP_002392100.1 CDS yfbL NC_011742.1 2416369 2417340 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative membrane-associated peptidase 2416369..2417340 Escherichia coli S88 7129797 YP_002392101.1 CDS yfbM NC_011742.1 2417443 2417946 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2417443..2417946 Escherichia coli S88 7129798 YP_002392102.1 CDS nuoN NC_011742.1 2418013 2419290 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit N complement(2418013..2419290) Escherichia coli S88 7129799 YP_002392103.1 CDS nuoM NC_011742.1 2419477 2421006 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit M complement(2419477..2421006) Escherichia coli S88 7133113 YP_002392104.1 CDS nuoL NC_011742.1 2421170 2423011 R Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit L complement(2421170..2423011) Escherichia coli S88 7133112 YP_002392105.1 CDS nuoK NC_011742.1 2423008 2423310 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit K complement(2423008..2423310) Escherichia coli S88 7133111 YP_002392106.1 CDS nuoJ NC_011742.1 2423307 2423861 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit J complement(2423307..2423861) Escherichia coli S88 7133110 YP_002392107.1 CDS nuoI NC_011742.1 2423873 2424415 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I complement(2423873..2424415) Escherichia coli S88 7133109 YP_002392108.1 CDS nuoH NC_011742.1 2424430 2425407 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit H complement(2424430..2425407) Escherichia coli S88 7133108 YP_002392109.1 CDS nuoG NC_011742.1 2425404 2428136 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit G complement(2425404..2428136) Escherichia coli S88 7133107 YP_002392110.1 CDS nuoF NC_011742.1 2428183 2429520 R shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH dehydrogenase; NADH dehydrogenase I subunit F complement(2428183..2429520) Escherichia coli S88 7129109 YP_002392111.1 CDS nuoE NC_011742.1 2429517 2430017 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit E complement(2429517..2430017) Escherichia coli S88 7129761 YP_002392112.1 CDS nuoC NC_011742.1 2430020 2431822 R NuoCD; NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; subunits NuoCD, E, F, and G constitute the peripheral sector of the complex; in Escherichia coli this gene encodes a fusion protein of NuoC and NuoD that are found separate in other organisms; bifunctional NADH:ubiquinone oxidoreductase subunit C/D complement(2430020..2431822) Escherichia coli S88 7129760 YP_002392113.1 CDS nuoB NC_011742.1 2431916 2432578 R The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen; NADH dehydrogenase subunit B complement(2431916..2432578) Escherichia coli S88 7129759 YP_002392114.1 CDS nuoA NC_011742.1 2432594 2433037 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit A complement(2432594..2433037) Escherichia coli S88 7129758 YP_002392115.1 CDS lrhA NC_011742.1 2433666 2434604 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12123461, 9882671, 7565112; Product type r : regulator; DNA-binding transcriptional repressor of flagellar, motility and chemotaxis genes complement(2433666..2434604) Escherichia coli S88 7129757 YP_002392116.1 CDS yfbQ NC_011742.1 2435524 2436741 D broad specificity; family IV; in Corynebacterium glutamicum this protein can use glutamate, 2-aminobutyrate, and aspartate as amino donors and pyruvate as the acceptor; aminotransferase AlaT 2435524..2436741 Escherichia coli S88 7129388 YP_002392117.1 CDS yfbR NC_011742.1 2436825 2437424 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15489502; Product type e : enzyme; hypothetical protein 2436825..2437424 Escherichia coli S88 7129800 YP_002392118.1 CDS yfbS NC_011742.1 2437483 2439315 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter complement(2437483..2439315) Escherichia coli S88 7129801 YP_002392119.1 CDS yfbT NC_011742.1 2439402 2440052 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphatase complement(2439402..2440052) Escherichia coli S88 7129802 YP_002392120.1 CDS yfbU NC_011742.1 2440063 2440557 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2440063..2440557) Escherichia coli S88 7129803 YP_002392121.1 CDS yfbV NC_011742.1 2440640 2441095 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(2440640..2441095) Escherichia coli S88 7129804 YP_002392122.1 CDS ackA NC_011742.1 2441433 2442635 D 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; acetate kinase 2441433..2442635 Escherichia coli S88 7129805 YP_002392123.1 CDS pta NC_011742.1 2442710 2444854 D catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate; phosphate acetyltransferase 2442710..2444854 Escherichia coli S88 7132035 YP_002392124.1 CDS yfcC NC_011742.1 2445044 2446564 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pc : putative carrier; hypothetical protein 2445044..2446564 Escherichia coli S88 7130814 YP_002392125.1 CDS yfcD NC_011742.1 2446597 2447139 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16430214; Product type pe : putative enzyme; putative NUDIX hydrolase complement(2446597..2447139) Escherichia coli S88 7129808 YP_002392126.1 CDS yfcE NC_011742.1 2447197 2447751 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; phosphodiesterase complement(2447197..2447751) Escherichia coli S88 7129809 YP_002392127.1 CDS yfcF NC_011742.1 2447804 2448448 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative enzyme complement(2447804..2448448) Escherichia coli S88 7129810 YP_002392128.1 CDS yfcG NC_011742.1 2448584 2449231 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; glutathione S-transferase 2448584..2449231 Escherichia coli S88 7129811 YP_002392129.1 CDS folX NC_011742.1 2449288 2449650 D catalyzes the formation of dihydromonapterin triphosphate from dihydroneopterin triphosphate; D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase 2449288..2449650 Escherichia coli S88 7129812 YP_002392130.1 CDS yfcH NC_011742.1 2449671 2450564 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pe : putative enzyme; conserved hypothetical protein; putative NAD(P)-binding Rossmann-fold domain 2449671..2450564 Escherichia coli S88 7132821 YP_002392131.1 CDS yfcI NC_011742.1 2450612 2451502 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative transposase complement(2450612..2451502) Escherichia coli S88 7129813 YP_002392132.1 CDS hisP NC_011742.1 2451698 2452471 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10373434, 3313284, 91060556; Product type t : transporter; histidine/lysine/arginine/ornithine transporter subunit complement(2451698..2452471) Escherichia coli S88 7129814 YP_002392133.1 CDS hisM NC_011742.1 2452479 2453195 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10373434, 3313284; Product type t : transporter; histidine/lysine/arginine/ornithine transporter subunit ; membrane component of ABC superfamily complement(2452479..2453195) Escherichia coli S88 7128930 YP_002392134.1 CDS hisQ NC_011742.1 2453192 2453878 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10373434; Product type t : transporter; histidine/lysine/arginine/ornithine transporter subunit ; membrane component of ABC superfamily complement(2453192..2453878) Escherichia coli S88 7128929 YP_002392135.1 CDS hisJ NC_011742.1 2453968 2454750 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10373434, 6449635, 8161536, 9298646, 9600841, 9740056; Product type t : transporter; histidine/lysine/arginine/ornithine transporter subunit ; periplasmic-binding component of ABC superfamily complement(2453968..2454750) Escherichia coli S88 7128931 YP_002392136.1 CDS argT NC_011742.1 2454971 2455753 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 4583243, 87308226, 3040734, 9298646; Product type t : transporter; lysine/arginine/ornithine transporter subunit ; periplasmic-binding component of ABC superfamily complement(2454971..2455753) Escherichia coli S88 7128927 YP_002392137.1 CDS ubiX NC_011742.1 2456019 2456588 R catalyzes the formation of 2-octaprenylphenol from 3-octaprenyl-4-hydroxybenzoate; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase complement(2456019..2456588) Escherichia coli S88 7133103 YP_002392138.1 CDS purF NC_011742.1 2456683 2458200 R Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase complement(2456683..2458200) Escherichia coli S88 7130388 YP_002392139.1 CDS cvpA NC_011742.1 2458237 2458725 R membrane protein required for colicin V production; colicin V production protein complement(2458237..2458725) Escherichia coli S88 7131749 YP_002392140.1 CDS dedD NC_011742.1 2459257 2459919 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 3040734; hypothetical protein complement(2459257..2459919) Escherichia coli S88 7130517 YP_002392141.1 CDS folC NC_011742.1 2459909 2461177 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3040739, 91112811, 92041808, 1989505, 3040734; Product type e : enzyme; bifunctional folylpolyglutamate synthase/ dihydrofolate synthase complement(2459909..2461177) Escherichia coli S88 7130179 YP_002392142.1 CDS accD NC_011742.1 2461247 2462161 R catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits; acetyl-CoA carboxylase subunit beta complement(2461247..2462161) Escherichia coli S88 7132815 YP_002392143.1 CDS dedA NC_011742.1 2462317 2462976 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 3029016, 3040734, 7678242; Product type pm : putative membrane component; hypothetical protein complement(2462317..2462976) Escherichia coli S88 7132029 YP_002392144.1 CDS truA NC_011742.1 2463059 2463871 R mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A complement(2463059..2463871) Escherichia coli S88 7130178 YP_002392145.1 CDS usg NC_011742.1 2463871 2464884 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 92380957, 92380982, 93123150, 2681152, 2991861, 3029016; Product type pe : putative enzyme; putative semialdehyde dehydrogenase complement(2463871..2464884) Escherichia coli S88 7130351 YP_002392146.1 CDS pdxB NC_011742.1 2464950 2466086 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90036695, 91035267, 2681152, 2991861, 3029016; Product type e : enzyme; erythronate-4-phosphate dehydrogenase complement(2464950..2466086) Escherichia coli S88 7132451 YP_002392147.1 CDS flk NC_011742.1 2466185 2467180 D in Salmonella typhimurium Flk regulates flagellar biosynthesis by inhibition of the flagellar-associated type III secretion system; lowers secretion levels of the anti-sigma28 factor FlgM to the periplasm; inner membrane-anchored protein; flagella biosynthesis regulator 2466185..2467180 Escherichia coli S88 7133182 YP_002392148.1 CDS yfcJ NC_011742.1 2467177 2468355 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; hypothetical protein complement(2467177..2468355) Escherichia coli S88 7132809 YP_002392149.1 CDS fabB NC_011742.1 2468620 2469840 R FabB, beta-Ketoacyl-ACP synthase I, KASI; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP; 3-oxoacyl-(acyl carrier protein) synthase I complement(2468620..2469840) Escherichia coli S88 7129815 YP_002392150.1 CDS mnmC NC_011742.1 2469999 2472005 D catalyzes the formation of 5-methylaminomethyl-2-thiouridine in position 34 of the anticodon of tRNA molecules; 5-methylaminomethyl-2-thiouridine methyltransferase 2469999..2472005 Escherichia coli S88 7132443 YP_002392151.1 CDS yfcL NC_011742.1 2472126 2472404 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2472126..2472404) Escherichia coli S88 7130338 YP_002392152.1 CDS yfcM NC_011742.1 2472438 2472986 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2472438..2472986) Escherichia coli S88 7129816 YP_002392153.1 CDS yfcA NC_011742.1 2472986 2473795 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(2472986..2473795) Escherichia coli S88 7129817 YP_002392154.1 CDS mepA NC_011742.1 2473795 2474619 R D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm; penicillin-insensitive murein endopeptidase complement(2473795..2474619) Escherichia coli S88 7129807 YP_002392155.1 CDS aroC NC_011742.1 2474623 2475708 R catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase complement(2474623..2475708) Escherichia coli S88 7128809 YP_002392156.1 CDS prmB NC_011742.1 2475743 2476675 R involved in methylation of ribosomal protein L3; N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase complement(2475743..2476675) Escherichia coli S88 7129923 YP_002392157.1 CDS yfcN NC_011742.1 2476841 2477392 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2476841..2477392 Escherichia coli S88 7130782 YP_002392158.1 CDS ECS88_2480 NC_011742.1 2477712 2478569 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(2477712..2478569) Escherichia coli S88 7129818 YP_002392159.1 CDS yfcP NC_011742.1 2478556 2479083 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative exported fimbrial-like adhesin protein complement(2478556..2479083) Escherichia coli S88 7133424 YP_002392160.1 CDS yfcQ NC_011742.1 2479080 2479559 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative fimbrial-like adhesin exported protein complement(2479080..2479559) Escherichia coli S88 7129819 YP_002392161.1 CDS yfcR NC_011742.1 2479556 2480125 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative fimbrial-like adhesin exported protein complement(2479556..2480125) Escherichia coli S88 7129820 YP_002392162.1 CDS yfcS NC_011742.1 2480076 2480969 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative periplasmic pilus exported chaperone complement(2480076..2480969) Escherichia coli S88 7129821 YP_002392163.1 CDS yfcU NC_011742.1 2480848 2483502 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative export usher protein complement(2480848..2483502) Escherichia coli S88 7129822 YP_002392164.1 CDS ECS88_2486 NC_011742.1 2483370 2484119 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative fimbrial-like adhesin protein complement(2483370..2484119) Escherichia coli S88 7129823 YP_002392165.1 CDS sixA NC_011742.1 2484685 2485170 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10089421, 20200300, 9489669; Product type e : enzyme; phosphohistidine phosphatase complement(2484685..2485170) Escherichia coli S88 7133425 YP_002392166.1 CDS fadJ NC_011742.1 2485373 2487517 R multifunctional enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase/3-hydroxybutyryl-CoA epimerase; catalyzes the formation of an hydroxyacyl-CoA by addition of water on enoyl-CoA; exhibits 3-hydroxyacyl-CoA epimerase and 3-hydroxyacyl-CoA dehydrogenase activities: forms a heterotetramer with FadI; similar to FadA2B2 complex; involved in the anaerobic degradation of long and medium-chain fatty acids in the presence of nitrate; multifunctional fatty acid oxidation complex subunit alpha complement(2485373..2487517) Escherichia coli S88 7130604 YP_002392167.1 CDS fadI NC_011742.1 2487517 2488827 R FadI; fatty acid oxidation complex component beta; functions in a heterotetramer with FadJ; similar to FadA2B2 complex; functions in beta-oxidation of fatty acids during anaerobic growth; 3-ketoacyl-CoA thiolase complement(2487517..2488827) Escherichia coli S88 7129824 YP_002392168.1 CDS yfcZ NC_011742.1 2489008 2489292 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2489008..2489292) Escherichia coli S88 7129825 YP_002392169.1 CDS fadL NC_011742.1 2489658 2491004 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15178802, 2840553, 3286621, 91100327, 1987139, 9119048; Product type t : transporter; long-chain fatty acid outer membrane transporter 2489658..2491004 Escherichia coli S88 7129826 YP_002392170.1 CDS vacJ NC_011742.1 2491062 2491817 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8145644, 15352239; Product type lp : lipoprotein; putative lipoprotein complement(2491062..2491817) Escherichia coli S88 7129445 YP_002392171.1 CDS ECS88_2493 NC_011742.1 2491843 2492013 R Evidence 6 : Doubtful CDS; hypothetical protein complement(2491843..2492013) Escherichia coli S88 7132470 YP_002392172.1 CDS yfdC NC_011742.1 2492111 2493043 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 2492111..2493043 Escherichia coli S88 7133426 YP_002392173.1 CDS intS NC_011742.1 2493355 2494512 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative prophage CPS-53 integrase; CPS-53 (KpLE1) prophage 2493355..2494512 Escherichia coli S88 7129884 YP_002392174.1 CDS ECS88_2497 NC_011742.1 2495794 2498739 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 16689790; Product type e : enzyme; Endo-alpha-sialidase, phage head protein complement(2495794..2498739) Escherichia coli S88 7129699 YP_002392175.1 CDS ECS88_2498 NC_011742.1 2498840 2499808 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12562822; Product type h : extrachromosomal origin; Antirepressor protein ant complement(2498840..2499808) Escherichia coli S88 7133427 YP_002392176.1 CDS ECS88_2500 NC_011742.1 2500200 2500490 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage regulatory protein 2500200..2500490 Escherichia coli S88 7131363 YP_002392177.1 CDS ECS88_2501 NC_011742.1 2500490 2501026 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative Clp protease 2500490..2501026 Escherichia coli S88 7133429 YP_002392178.1 CDS ECS88_2503 NC_011742.1 2501075 2501524 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2501075..2501524) Escherichia coli S88 7133430 YP_002392179.1 CDS ECS88_2504 NC_011742.1 2501533 2502129 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(2501533..2502129) Escherichia coli S88 7133431 YP_002392180.1 CDS ECS88_2505 NC_011742.1 2502275 2502625 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein; putative membrane protein 2502275..2502625 Escherichia coli S88 7133432 YP_002392181.1 CDS ECS88_2506 NC_011742.1 2502643 2504658 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative DNA transfer protein from bacteriophage complement(2502643..2504658) Escherichia coli S88 7133433 YP_002392182.1 CDS ECS88_2507 NC_011742.1 2504655 2506106 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; DNA transfer protein complement(2504655..2506106) Escherichia coli S88 7133434 YP_002392183.1 CDS ECS88_2508 NC_011742.1 2506117 2506809 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; DNA transfer protein complement(2506117..2506809) Escherichia coli S88 7133435 YP_002392184.1 CDS ECS88_2509 NC_011742.1 2506812 2507267 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head assembly protein complement(2506812..2507267) Escherichia coli S88 7133436 YP_002392185.1 CDS ECS88_2510 NC_011742.1 2507267 2508070 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Packaged DNA stabilization protein from phage complement(2507267..2508070) Escherichia coli S88 7133437 YP_002392186.1 CDS ECS88_2511 NC_011742.1 2507968 2509386 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Packaged DNA stabilization protein from phage complement(2507968..2509386) Escherichia coli S88 7133438 YP_002392187.1 CDS ECS88_2512 NC_011742.1 2509396 2509857 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; Putative DNA stabilization protein from phage complement(2509396..2509857) Escherichia coli S88 7133439 YP_002392188.1 CDS ECS88_2513 NC_011742.1 2509838 2510065 R Evidence 6 : Doubtful CDS; hypothetical protein complement(2509838..2510065) Escherichia coli S88 7133440 YP_002392189.1 CDS ECS88_2514 NC_011742.1 2510068 2511321 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; Putative Coat protein from phage complement(2510068..2511321) Escherichia coli S88 7133441 YP_002392190.1 CDS ECS88_2515 NC_011742.1 2511340 2512233 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative bacteriophage protein complement(2511340..2512233) Escherichia coli S88 7133442 YP_002392191.1 CDS ECS88_2517 NC_011742.1 2512324 2514522 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative Bacteriophage portal protein complement(2512324..2514522) Escherichia coli S88 7133443 YP_002392192.1 CDS ECS88_2518 NC_011742.1 2514524 2515939 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Terminase large subunit complement(2514524..2515939) Escherichia coli S88 7133444 YP_002392193.1 CDS ECS88_2519 NC_011742.1 2515936 2516376 R hypothetical protein complement(2515936..2516376) Escherichia coli S88 7133445 YP_002392194.1 CDS ECS88_2520 NC_011742.1 2516379 2516621 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein complement(2516379..2516621) Escherichia coli S88 7133446 YP_002392195.1 CDS ECS88_2521 NC_011742.1 2516849 2517460 R hypothetical protein complement(2516849..2517460) Escherichia coli S88 7133447 YP_002392196.1 CDS ECS88_2522 NC_011742.1 2517597 2517749 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative bacteriophage protein (Gene 65) complement(2517597..2517749) Escherichia coli S88 7133448 YP_002392197.1 CDS ECS88_2523 NC_011742.1 2517737 2518174 R Evidence 2b : Function of strongly homologous gene; Product type e : enzyme; bacteriophage lysis protein complement(2517737..2518174) Escherichia coli S88 7133449 YP_002392198.1 CDS r NC_011742.1 2518171 2518647 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Lysozyme (Muramidase) (Endolysin) complement(2518171..2518647) Escherichia coli S88 7133450 YP_002392199.1 CDS ECS88_2525 NC_011742.1 2518631 2518954 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; lysis protein S and lysis inhibitor (holin protein) complement(2518631..2518954) Escherichia coli S88 7131778 YP_002392200.1 CDS ECS88_2526 NC_011742.1 2519551 2520069 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage antitermination protein Q complement(2519551..2520069) Escherichia coli S88 7133451 YP_002392201.1 CDS ECS88_2527 NC_011742.1 2520066 2520254 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein ninH complement(2520066..2520254) Escherichia coli S88 7133452 YP_002392202.1 CDS rusA NC_011742.1 2520251 2520613 R Evidence 2b : Function of strongly homologous gene; Product type e : enzyme; crossover junction endodeoxyribonuclease complement(2520251..2520613) Escherichia coli S88 7133453 YP_002392203.1 CDS ECS88_2529 NC_011742.1 2520610 2520900 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2520610..2520900) Escherichia coli S88 7131313 YP_002392204.1 CDS roi NC_011742.1 2520900 2521622 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; DNA-binding protein from phage origin complement(2520900..2521622) Escherichia coli S88 7133454 YP_002392205.1 CDS ninF NC_011742.1 2521615 2521791 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein from phage origin complement(2521615..2521791) Escherichia coli S88 7132757 YP_002392206.1 CDS ECS88_2532 NC_011742.1 2521784 2522245 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein ninX complement(2521784..2522245) Escherichia coli S88 7129716 YP_002392207.1 CDS ECS88_2533 NC_011742.1 2522379 2522789 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative ninB protein complement(2522379..2522789) Escherichia coli S88 7133455 YP_002392208.1 CDS ECS88_2534 NC_011742.1 2522989 2523303 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(2522989..2523303) Escherichia coli S88 7133456 YP_002392209.1 CDS ECS88_2535 NC_011742.1 2523419 2523625 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(2523419..2523625) Escherichia coli S88 7133457 YP_002392210.1 CDS ECS88_2536 NC_011742.1 2523682 2523840 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(2523682..2523840) Escherichia coli S88 7133458 YP_002392211.1 CDS ECS88_2537 NC_011742.1 2523698 2525074 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Replicative DNA helicase complement(2523698..2525074) Escherichia coli S88 7133459 YP_002392212.1 CDS ECS88_2538 NC_011742.1 2525071 2526018 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(2525071..2526018) Escherichia coli S88 7133460 YP_002392213.1 CDS ECS88_2539 NC_011742.1 2525810 2526052 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(2525810..2526052) Escherichia coli S88 7133461 YP_002392214.1 CDS ECS88_2540 NC_011742.1 2526021 2526566 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(2526021..2526566) Escherichia coli S88 7133462 YP_002392215.1 CDS cII NC_011742.1 2526316 2526696 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Regulatory protein CII complement(2526316..2526696) Escherichia coli S88 7133136 YP_002392216.1 CDS cro NC_011742.1 2526718 2526903 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Regulatory protein cro (Antirepressor) complement(2526718..2526903) Escherichia coli S88 7131912 YP_002392217.1 CDS cII NC_011742.1 2526984 2527634 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Repressor protein CII 2526984..2527634 Escherichia coli S88 7131965 YP_002392218.1 CDS N NC_011742.1 2528063 2528455 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; regulatory protein N 2528063..2528455 Escherichia coli S88 7131913 YP_002392219.1 CDS ECS88_2545 NC_011742.1 2528464 2528934 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2528464..2528934 Escherichia coli S88 7129647 YP_002392220.1 CDS ECS88_2546 NC_011742.1 2529266 2529454 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 2529266..2529454 Escherichia coli S88 7133464 YP_002392221.1 CDS ECS88_2547 NC_011742.1 2529375 2529545 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 2529375..2529545 Escherichia coli S88 7133465 YP_002392222.1 CDS erf NC_011742.1 2529526 2530161 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; DNA single-strand annealing protein; essential recombination function protein Erf 2529526..2530161 Escherichia coli S88 7133466 YP_002392223.1 CDS ECS88_2549 NC_011742.1 2530071 2530544 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 2530071..2530544 Escherichia coli S88 7132416 YP_002392224.1 CDS abc NC_011742.1 2530568 2530864 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Anti-RecBCD protein 2 2530568..2530864 Escherichia coli S88 7133467 YP_002392225.1 CDS ECS88_2551 NC_011742.1 2530941 2531408 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2530941..2531408 Escherichia coli S88 7132024 YP_002392226.1 CDS ECS88_2552 NC_011742.1 2531473 2531772 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2531473..2531772 Escherichia coli S88 7133468 YP_002392227.1 CDS ECS88_2553 NC_011742.1 2531774 2532346 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2531774..2532346 Escherichia coli S88 7133469 YP_002392228.1 CDS ECS88_2554 NC_011742.1 2532464 2532631 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2532464..2532631 Escherichia coli S88 7131979 YP_002392229.1 CDS ECS88_2555 NC_011742.1 2532624 2532908 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2532624..2532908 Escherichia coli S88 7130903 YP_002392230.1 CDS ECS88_2556 NC_011742.1 2532981 2533148 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2532981..2533148 Escherichia coli S88 7130904 YP_002392231.1 CDS torI NC_011742.1 2533206 2533406 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15197250; Product type r : regulator; response regulator inhibitor for tor operon 2533206..2533406 Escherichia coli S88 7130905 YP_002392232.1 CDS dsdC NC_011742.1 2533594 2534529 R regulates the synthesis and expression of the dsdXA operon and dadA gene; DNA-binding transcriptional regulator DsdC complement(2533594..2534529) Escherichia coli S88 7133495 YP_002392233.1 CDS dsdX NC_011742.1 2534747 2536084 D member of the Gnt family of gluconate transporters; not involved in gluconate transport; unknown function; permease DsdX 2534747..2536084 Escherichia coli S88 7130244 YP_002392234.1 CDS dsdA NC_011742.1 2536102 2537430 D catalyzes the formation of pyruvate from serine; D-serine dehydratase 2536102..2537430 Escherichia coli S88 7130245 YP_002392235.1 CDS emrY NC_011742.1 2537538 2539076 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 20378313; Product type pt : putative transporter; putative multidrug efflux system complement(2537538..2539076) Escherichia coli S88 7130243 YP_002392236.1 CDS emrK NC_011742.1 2539076 2540239 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20378313; Product type t : transporter; EmrKY-TolC multidrug resistance efflux pump, membrane fusion protein component complement(2539076..2540239) Escherichia coli S88 7132396 YP_002392237.1 CDS evgA NC_011742.1 2540655 2541269 D response regulator in two-component regulatory system with EvgS; phosphorylated EvgA activates ompC, emrKY, gadABC, hdeAB and others genes; involved in acid resistance, osmotic adaption, and drug resistance; DNA-binding transcriptional activator EvgA 2540655..2541269 Escherichia coli S88 7132395 YP_002392238.1 CDS evgS NC_011742.1 2541274 2544867 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14523115, 93173621, 9501520, 10923791, 1289796, 8125343, 9535079; Product type r : regulator; hybrid sensory histidine kinase in two-component regulatory system with EvgA 2541274..2544867 Escherichia coli S88 7132434 YP_002392239.1 CDS yfdE NC_011742.1 2544923 2546068 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein complement(2544923..2546068) Escherichia coli S88 7132435 YP_002392240.1 CDS yfdV NC_011742.1 2546142 2547086 R member of the AEC family of auxin efflux transporters; unknown function; putative transporter YfdV complement(2546142..2547086) Escherichia coli S88 7129828 YP_002392241.1 CDS oxc NC_011742.1 2547156 2548850 R catalyzes the formation of formyl-CoA from oxalyl-CoA; putative oxalyl-CoA decarboxylase complement(2547156..2548850) Escherichia coli S88 7129841 YP_002392242.1 CDS frc NC_011742.1 2548904 2550154 R catalyzes the formation of oxalyl-CoA from oxalate and Formyl-CoA; formyl-coenzyme A transferase complement(2548904..2550154) Escherichia coli S88 7133149 YP_002392243.1 CDS yfdX NC_011742.1 2550666 2551301 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 11157960; hypothetical protein complement(2550666..2551301) Escherichia coli S88 7132823 YP_002392244.1 CDS ECS88_2571 NC_011742.1 2551848 2551994 R Evidence 6 : Doubtful CDS; hypothetical protein complement(2551848..2551994) Escherichia coli S88 7129842 YP_002392245.1 CDS yfdY NC_011742.1 2551949 2552191 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 14727089; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(2551949..2552191) Escherichia coli S88 7130906 YP_002392246.1 CDS ddg NC_011742.1 2552544 2553464 D Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(palmitoleoyl)-lipid IVA in cells subjected to cold shock; lipid A biosynthesis palmitoleoyl acyltransferase 2552544..2553464 Escherichia coli S88 7133470 YP_002392247.1 CDS yfdZ NC_011742.1 2553956 2555194 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; aminotransferase complement(2553956..2555194) Escherichia coli S88 7133504 YP_002392248.1 CDS ypdA NC_011742.1 2555571 2557268 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15522865; Product type prc : putative receptor; putative sensory kinase in two-component system with YpdB 2555571..2557268 Escherichia coli S88 7133509 YP_002392249.1 CDS ypdB NC_011742.1 2557283 2558020 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15522865; Product type pr : putative regulator; putative response regulator in two-component system with YpdA 2557283..2558020 Escherichia coli S88 7133657 YP_002392250.1 CDS ypdC NC_011742.1 2558033 2558890 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding protein 2558033..2558890 Escherichia coli S88 7133658 YP_002392251.1 CDS ypdD NC_011742.1 2558893 2561388 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative fused PTS enzymes (multiphosphoryl transfer protein): Hpr component ; enzyme I component ; enzyme IIA component complement(2558893..2561388) Escherichia coli S88 7133659 YP_002392252.1 CDS ypdE NC_011742.1 2561413 2562450 R metalloprotein; exoaminopeptidase complement(2561413..2562450) Escherichia coli S88 7133660 YP_002392253.1 CDS ypdF NC_011742.1 2562450 2563535 R Xaa-Pro aminopeptidase; limited methionine aminopeptidase; aminopeptidase complement(2562450..2563535) Escherichia coli S88 7133661 YP_002392254.1 CDS ypdG NC_011742.1 2563551 2564798 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative enzyme IIC component of PTS complement(2563551..2564798) Escherichia coli S88 7133662 YP_002392255.1 CDS ypdH NC_011742.1 2564820 2565146 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative enzyme IIB component of PTS complement(2564820..2565146) Escherichia coli S88 7133663 YP_002392256.1 CDS glk NC_011742.1 2565365 2566330 R catalyzes the conversion of ATP and D-glucose to ADP and D-glucose 6-phosphate; glucokinase complement(2565365..2566330) Escherichia coli S88 7133664 YP_002392257.1 CDS yfeO NC_011742.1 2566534 2567790 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; hypothetical protein 2566534..2567790 Escherichia coli S88 7132219 YP_002392258.1 CDS ypeC NC_011742.1 2567905 2568231 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2567905..2568231 Escherichia coli S88 7133517 YP_002392259.1 CDS mntH NC_011742.1 2568372 2569610 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20177822, 20305051, 10712688, 10844693; Product type t : transporter; manganese transport protein MntH complement(2568372..2569610) Escherichia coli S88 7133666 YP_002392260.1 CDS nupC NC_011742.1 2569946 2571148 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 374403, 8022285, 7007808, 827549, 4563236, 1512211; Product type t : transporter; nucleoside (except guanosine) transporter 2569946..2571148 Escherichia coli S88 7128846 YP_002392261.1 CDS yfeA NC_011742.1 2571198 2573387 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative diguanylate cyclase complement(2571198..2573387) Escherichia coli S88 7133114 YP_002392262.1 CDS yfeC NC_011742.1 2574020 2574364 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative nucleic acid-binding transcriptional regulator 2574020..2574364 Escherichia coli S88 7131993 YP_002392263.1 CDS yfeD NC_011742.1 2574366 2574758 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative nucleic acid-binding transcriptional regulator 2574366..2574758 Escherichia coli S88 7133511 YP_002392264.1 CDS gltX NC_011742.1 2574809 2576224 R Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase complement(2574809..2576224) Escherichia coli S88 7133512 YP_002392265.1 CDS xapR NC_011742.1 2576991 2577875 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10400599, 7007808, 2201776, 7559336; Product type r : regulator; DNA-binding transcriptional activator XapR complement(2576991..2577875) Escherichia coli S88 7129889 YP_002392266.1 CDS xapB NC_011742.1 2578127 2579383 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96032385, 7559336; Product type t : transporter; xanthosine transporter complement(2578127..2579383) Escherichia coli S88 7132515 YP_002392267.1 CDS xapA NC_011742.1 2579444 2580277 R catalyzes the formation of a purine and ribose phosphate from a purine nucleoside; in E. coli this enzyme functions in xanthosine degradation; purine nucleoside phosphorylase complement(2579444..2580277) Escherichia coli S88 7132514 YP_002392268.1 CDS yfeN NC_011742.1 2580526 2581290 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; hypothetical protein 2580526..2581290 Escherichia coli S88 7132513 YP_002392269.1 CDS yfeR NC_011742.1 2581329 2582255 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(2581329..2582255) Escherichia coli S88 7133516 YP_002392270.1 CDS yfeH NC_011742.1 2582345 2583343 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative sodium/bile acid symporter family (mazG-like) 2582345..2583343 Escherichia coli S88 7133518 YP_002392271.1 CDS ECS88_2600 NC_011742.1 2583340 2583651 R Evidence 6 : Doubtful CDS; hypothetical protein complement(2583340..2583651) Escherichia coli S88 7133514 YP_002392272.1 CDS ligA NC_011742.1 2583560 2585575 R 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; NAD-dependent DNA ligase LigA complement(2583560..2585575) Escherichia coli S88 7130907 YP_002392273.1 CDS zipA NC_011742.1 2585646 2586644 R interacts with cell division protein FitsZ and may be required to anchor septal ring structure; cell division protein ZipA complement(2585646..2586644) Escherichia coli S88 7133023 YP_002392274.1 CDS cysZ NC_011742.1 2586874 2587635 D putative role in sulfur assimilation; putative sulfate transport protein CysZ 2586874..2587635 Escherichia coli S88 7131884 YP_002392275.1 CDS cysK NC_011742.1 2587820 2588791 D CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis; cysteine synthase A 2587820..2588791 Escherichia coli S88 7130550 YP_002392276.1 CDS ptsH NC_011742.1 2589175 2589432 D Evidence 1b : Function experimentally demonstrated in the studied species; Product type t : transporter; PTS system phosphohistidinoprotein-hexose phosphotransferase subunit Hpr 2589175..2589432 Escherichia coli S88 7130542 YP_002392277.1 CDS ptsI NC_011742.1 2589477 2591204 D Phosphotransferase system, enzyme I; transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein; part of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), a major carbohydrate active-transport system; phosphoenolpyruvate-protein phosphotransferase 2589477..2591204 Escherichia coli S88 7131740 YP_002392278.1 CDS crr NC_011742.1 2591245 2591754 D functions in phosphoenolpyruvate-(PEP)-dependent phosphotransferase (PTS) system; functions in the transport and phosphorylation of glucose; PTS system glucose-specific transporter subunit 2591245..2591754 Escherichia coli S88 7131741 YP_002392279.1 CDS pdxK NC_011742.1 2591797 2592648 R catalyzes the formation of pyridoxal 5'-phosphate from pyridoxal; pyridoxal kinase complement(2591797..2592648) Escherichia coli S88 7131968 YP_002392280.1 CDS yfeK NC_011742.1 2592753 2593121 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2592753..2593121 Escherichia coli S88 7133185 YP_002392281.1 CDS cysM NC_011742.1 2593124 2594035 R catalyzes the formation of cysteine from 3-O-acetyl-L-serine and hydrogen sulfide; cysteine synthase B complement(2593124..2594035) Escherichia coli S88 7133515 YP_002392282.1 CDS cysA NC_011742.1 2594170 2595267 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90202710, 90264334, 2188958, 7665461; Product type t : transporter; sulfate/thiosulfate transporter subunit complement(2594170..2595267) Escherichia coli S88 7130543 YP_002392283.1 CDS cysW NC_011742.1 2595257 2596132 R Part of the ABC transporter complex cysAWTP involved in sulfate/thiosulfate import; sulfate/thiosulfate transporter permease subunit complement(2595257..2596132) Escherichia coli S88 7130533 YP_002392284.1 CDS cysU NC_011742.1 2596132 2596965 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90264334, 2188958; Product type t : transporter; sulfate/thiosulfate transporter subunit complement(2596132..2596965) Escherichia coli S88 7130549 YP_002392285.1 CDS cysP NC_011742.1 2596965 2597981 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90264335, 2188959, 9298646; Product type t : transporter; thiosulfate transporter subunit complement(2596965..2597981) Escherichia coli S88 7130548 YP_002392286.1 CDS ucpA NC_011742.1 2598139 2598930 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 97385354, 2188959, 7984428, 9241368; Product type pe : putative enzyme; short chain dehydrogenase complement(2598139..2598930) Escherichia coli S88 7130545 YP_002392287.1 CDS murQ NC_011742.1 2599210 2600106 D catalyzes the cleavage of the lactyl ether moiety of N-acetylmuramic acid-6-phosphate (MurNAc-6-P) to form N-acetylglucosamine-6-phosphate (GlcNAc-6-P) and lactate; involved in MurNAc dissimilation pathway; N-acetylmuramic acid-6-phosphate etherase 2599210..2600106 Escherichia coli S88 7130389 YP_002392288.1 CDS murP NC_011742.1 2600110 2601534 D belongs to PEP-dependent PTS system; contains the PTS EIIBC domains; involved in uptake of exogenous N-acetylmuramic acid (MurNAc); requires crr-encoded enzyme IIA-glucose component; PTS system N-acetylmuramic acid transporter subunits EIIBC 2600110..2601534 Escherichia coli S88 7133519 YP_002392289.1 CDS yfeX NC_011742.1 2601712 2602611 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2601712..2602611) Escherichia coli S88 7129638 YP_002392290.1 CDS yfeY NC_011742.1 2602707 2603282 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 12900013, 7764507; hypothetical protein complement(2602707..2603282) Escherichia coli S88 7133520 YP_002392291.1 CDS yfeZ NC_011742.1 2603343 2603792 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(2603343..2603792) Escherichia coli S88 7133521 YP_002392292.1 CDS ypeA NC_011742.1 2603779 2604204 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative acetyltransferase complement(2603779..2604204) Escherichia coli S88 7133522 YP_002392293.1 CDS amiA NC_011742.1 2604418 2605287 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21348478, 6137479, 87242501, 1903834, 8300522; Product type e : enzyme; N-acetylmuramoyl-l-alanine amidase I 2604418..2605287 Escherichia coli S88 7133665 YP_002392294.1 CDS hemF NC_011742.1 2605291 2606190 D catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis; coproporphyrinogen III oxidase 2605291..2606190 Escherichia coli S88 7133057 YP_002392295.1 CDS yfeG NC_011742.1 2606196 2607248 R activates the transcription of the ethanolamine utilization operon; transcriptional regulator EutR complement(2606196..2607248) Escherichia coli S88 7128901 YP_002392296.1 CDS yffI NC_011742.1 2607294 2607794 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10464203; Product type ps : putative structure; putative ethanolaminosome structural protein with putative role in ethanolamine utilization complement(2607294..2607794) Escherichia coli S88 7133513 YP_002392297.1 CDS eutL NC_011742.1 2607807 2608466 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16291677, 10464203; Product type ps : putative structure; putative carboxysome-related structural protein with putative role in ethanolamine utilization complement(2607807..2608466) Escherichia coli S88 7133525 YP_002392298.1 CDS eutC NC_011742.1 2608476 2609363 R catalyzes the formation of acetaldehyde from ethanolamine; ethanolamine ammonia-lyase small subunit complement(2608476..2609363) Escherichia coli S88 7132429 YP_002392299.1 CDS eutB NC_011742.1 2609384 2610745 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3905806, 10464203; Product type e : enzyme; ethanolamine ammonia-lyase, large subunit, heavy chain complement(2609384..2610745) Escherichia coli S88 7132423 YP_002392300.1 CDS eutA NC_011742.1 2610757 2612160 R ethanolamine utilization protein EutA; reactivating factor for ethanolamine ammonia lyase complement(2610757..2612160) Escherichia coli S88 7132422 YP_002392301.1 CDS eutH NC_011742.1 2612157 2613383 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7868611, 10464203; Product type pt : putative transporter; putative ethanolamine transporter complement(2612157..2613383) Escherichia coli S88 7132421 YP_002392302.1 CDS eutG NC_011742.1 2613600 2614787 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16291677, 10464203; Product type pe : putative enzyme; putative alcohol dehydrogenase in ethanolamine utilization; ethanolaminosome complement(2613600..2614787) Escherichia coli S88 7132426 YP_002392303.1 CDS eutJ NC_011742.1 2614777 2615613 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16291677, 10464203; Product type pf : putative factor; putative chaperonin, ethanolamine utilization protein complement(2614777..2615613) Escherichia coli S88 7132425 YP_002392304.1 CDS eutE NC_011742.1 2615624 2617027 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16291677, 10464203; Product type pe : putative enzyme; putative aldehyde dehydrogenase, ethanolamine utilization protein complement(2615624..2617027) Escherichia coli S88 7132428 YP_002392305.1 CDS cchB NC_011742.1 2617039 2617326 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16291677, 10464203; Product type ps : putative structure; putative carboxysome-like ethanolaminosome structural protein, ethanolamine utilization protein complement(2617039..2617326) Escherichia coli S88 7132424 YP_002392306.1 CDS eutD NC_011742.1 2617764 2618780 R in Salmonella this enzyme is required for ethanolamine catabolism; has higher affinity for CoA than Pta; phosphotransacetylase complement(2617764..2618780) Escherichia coli S88 7132430 YP_002392307.1 CDS eutT NC_011742.1 2618777 2619580 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16291677, 10464203; Product type pe : putative enzyme; putative cobalamin adenosyltransferase in ethanolamine utilization complement(2618777..2619580) Escherichia coli S88 7132427 YP_002392308.1 CDS eutQ NC_011742.1 2619577 2620278 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 10464203; hypothetical protein complement(2619577..2620278) Escherichia coli S88 7132433 YP_002392309.1 CDS eutP NC_011742.1 2620253 2620732 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16291677, 10464203; Product type pe : putative enzyme; putative nucleoside triphosphate hydrolase domain protein complement(2620253..2620732) Escherichia coli S88 7132432 YP_002392310.1 CDS ypfE NC_011742.1 2620745 2621080 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16291677, 10464203; Product type ps : putative structure; putative carboxysome-like ethanolaminosome structural protein with putative role in ethanol utilization complement(2620745..2621080) Escherichia coli S88 7132431 YP_002392311.1 CDS maeB NC_011742.1 2621373 2623652 R NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate; malic enzyme complement(2621373..2623652) Escherichia coli S88 7133667 YP_002392312.1 CDS talA NC_011742.1 2623941 2624891 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90230300; Product type e : enzyme; transaldolase A 2623941..2624891 Escherichia coli S88 7129404 YP_002392313.1 CDS tktB NC_011742.1 2624911 2626914 D 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; transketolase 2624911..2626914 Escherichia coli S88 7131257 YP_002392314.1 CDS ypfG NC_011742.1 2626991 2628034 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2626991..2628034) Escherichia coli S88 7133477 YP_002392315.1 CDS yffH NC_011742.1 2628160 2628735 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative NUDIX hydrolase complement(2628160..2628735) Escherichia coli S88 7133668 YP_002392316.1 CDS aegA NC_011742.1 2628803 2630782 R unknown function; in E. coli the aegA gene is regulated by Fnr, NarXL, and NarQ (but not ArcA), induced under anaerobic conditions and repressed in the presence of nitrate (anaerobic); putative oxidoreductase Fe-S binding subunit complement(2628803..2630782) Escherichia coli S88 7133524 YP_002392317.1 CDS narQ NC_011742.1 2630988 2632688 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92374842, 1508040, 1528845; Product type r : regulator; nitrate/nitrite sensor protein NarQ 2630988..2632688 Escherichia coli S88 7132060 YP_002392318.1 CDS acrD NC_011742.1 2632852 2635965 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12426336, 20158894, 21450803, 79216220, 10692383, 1644752; Product type t : transporter; aminoglycoside/multidrug efflux system 2632852..2635965 Escherichia coli S88 7129683 YP_002392319.1 CDS yffB NC_011742.1 2636504 2636860 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2636504..2636860 Escherichia coli S88 7132044 YP_002392320.1 CDS dapE NC_011742.1 2636864 2637991 D dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.; succinyl-diaminopimelate desuccinylase 2636864..2637991 Escherichia coli S88 7133523 YP_002392321.1 CDS ypfN NC_011742.1 2638019 2638219 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2638019..2638219 Escherichia coli S88 7130567 YP_002392322.1 CDS ypfH NC_011742.1 2638300 2638998 R Displays esterase activity toward palmitoyl-CoA and pNP-butyrate; esterase YpfH complement(2638300..2638998) Escherichia coli S88 7132065 YP_002392323.1 CDS ypfI NC_011742.1 2639072 2641087 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative hydrolase complement(2639072..2641087) Escherichia coli S88 7131980 YP_002392324.1 CDS ypfJ NC_011742.1 2641102 2641965 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2641102..2641965) Escherichia coli S88 7132063 YP_002392325.1 CDS purC NC_011742.1 2642133 2642846 R catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase; phosphoribosylaminoimidazole-succinocarboxamide synthase complement(2642133..2642846) Escherichia coli S88 7132064 YP_002392326.1 CDS nlpB NC_011742.1 2643059 2644093 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91358331, 1885529, 2120198; Product type lp : lipoprotein; lipoprotein complement(2643059..2644093) Escherichia coli S88 7131746 YP_002392327.1 CDS dapA NC_011742.1 2644110 2644988 R catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase complement(2644110..2644988) Escherichia coli S88 7129721 YP_002392328.1 CDS gcvR NC_011742.1 2645134 2645706 D negative transcriptional regulator of the gcvTHP operon; glycine cleavage system transcriptional repressor 2645134..2645706 Escherichia coli S88 7130564 YP_002392329.1 CDS bcp NC_011742.1 2645706 2646176 D bacterioferritin comigratory protein; thiol peroxidase; thioredoxin-dependent; hydroperoxide peroxidase; in Escherichia coli this enzyme preferentially reduces linoleic acid hydroperoxide; contains an active site cysteine; thioredoxin-dependent thiol peroxidase 2645706..2646176 Escherichia coli S88 7132200 YP_002392330.1 CDS perM NC_011742.1 2646275 2647336 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative permease complement(2646275..2647336) Escherichia coli S88 7129991 YP_002392331.1 CDS yfgC NC_011742.1 2647549 2649012 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative peptidase 2647549..2649012 Escherichia coli S88 7133677 YP_002392332.1 CDS yfgD NC_011742.1 2649033 2649392 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase 2649033..2649392 Escherichia coli S88 7133528 YP_002392333.1 CDS hda NC_011742.1 2649530 2650276 R controls initiation of DNA replication by inhibiting re-initiation of replication, promotes hydrolysis of DnaA-bound ATP; DNA replication initiation factor complement(2649530..2650276) Escherichia coli S88 7133529 YP_002392334.1 CDS uraA NC_011742.1 2650326 2651615 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8332529, 7721693; Product type t : transporter; uracil transporter complement(2650326..2651615) Escherichia coli S88 7128889 YP_002392335.1 CDS upp NC_011742.1 2651701 2652327 R Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase complement(2651701..2652327) Escherichia coli S88 7132450 YP_002392336.1 CDS purM NC_011742.1 2652651 2653688 D catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis; phosphoribosylaminoimidazole synthetase 2652651..2653688 Escherichia coli S88 7132449 YP_002392337.1 CDS purN NC_011742.1 2653688 2654326 D glycinamide ribonucleotide transformylase; GAR Tfase; catalyzes the synthesis of 5'-phosphoribosylformylglycinamide from 5'-phosphoribosylglycinamide and 10-formyltetrahydrofolate; PurN requires formyl folate for the reaction unlike PurT which uses formate; phosphoribosylglycinamide formyltransferase 2653688..2654326 Escherichia coli S88 7131753 YP_002392338.1 CDS ppk NC_011742.1 2654498 2656564 D catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate; polyphosphate kinase 2654498..2656564 Escherichia coli S88 7131754 YP_002392339.1 CDS ppx NC_011742.1 2656569 2658110 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93107072, 94025037, 94165003, 8212131, 8380170; Product type e : enzyme; exopolyphosphatase 2656569..2658110 Escherichia coli S88 7130764 YP_002392340.1 CDS yfgF NC_011742.1 2658149 2660392 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(2658149..2660392) Escherichia coli S88 7130767 YP_002392341.1 CDS ECS88_2676 NC_011742.1 2660609 2660899 R Evidence 6 : Doubtful CDS; hypothetical protein complement(2660609..2660899) Escherichia coli S88 7133530 YP_002392342.1 CDS yfgH NC_011742.1 2661246 2661764 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative outer membrane lipoprotein 2661246..2661764 Escherichia coli S88 7130908 YP_002392343.1 CDS yfgI NC_011742.1 2661780 2662319 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2661780..2662319 Escherichia coli S88 7133531 YP_002392344.1 CDS guaA NC_011742.1 2662413 2663990 R contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase complement(2662413..2663990) Escherichia coli S88 7133532 YP_002392345.1 CDS guaB NC_011742.1 2664059 2665525 R catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate; inosine 5'-monophosphate dehydrogenase complement(2664059..2665525) Escherichia coli S88 7128874 YP_002392346.1 CDS xseA NC_011742.1 2665687 2667063 D bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides; exodeoxyribonuclease VII large subunit 2665687..2667063 Escherichia coli S88 7128875 YP_002392347.1 CDS ECS88_2682 NC_011742.1 2667132 2675183 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15347755, 12540539; Product type pm : putative membrane component; putative outer membrane protein; RatA precursor homolog complement(2667132..2675183) Escherichia coli S88 7132522 YP_002392348.1 CDS ECS88_2685 NC_011742.1 2676337 2678598 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8500884, 3304658, 12540539; Product type pf : putative factor; putative intimin ((attaching and effacing protein) or invasin protein (sivH-like) complement(2676337..2678598) Escherichia coli S88 7130911 YP_002392349.1 CDS ECS88_2686 NC_011742.1 2678777 2678992 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2678777..2678992) Escherichia coli S88 7130912 YP_002392350.1 CDS engA NC_011742.1 2679055 2680527 R 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; GTP-binding protein EngA complement(2679055..2680527) Escherichia coli S88 7130913 YP_002392351.1 CDS yfgL NC_011742.1 2680645 2681823 R with YaeT, YfiO, and NlpB forms a complex involved in outer membrane protein biogenesis; outer membrane protein assembly complex subunit YfgL complement(2680645..2681823) Escherichia coli S88 7130190 YP_002392352.1 CDS yfgM NC_011742.1 2681834 2682454 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2681834..2682454) Escherichia coli S88 7133533 YP_002392353.1 CDS hisS NC_011742.1 2682472 2683746 R 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; histidyl-tRNA synthetase complement(2682472..2683746) Escherichia coli S88 7133534 YP_002392354.1 CDS ispG NC_011742.1 2683857 2684975 R catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis; 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase complement(2683857..2684975) Escherichia coli S88 7129860 YP_002392355.1 CDS yfgA NC_011742.1 2685002 2686009 R Evidence 4 : Homologs of previously reported genes of unknown function; cytoskeletal protein RodZ complement(2685002..2686009) Escherichia coli S88 7130423 YP_002392356.1 CDS yfgB NC_011742.1 2686294 2687448 R 23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance; ribosomal RNA large subunit methyltransferase N complement(2686294..2687448) Escherichia coli S88 7133526 YP_002392357.1 CDS ndk NC_011742.1 2687598 2688029 R catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate; nucleoside diphosphate kinase complement(2687598..2688029) Escherichia coli S88 7133527 YP_002392358.1 CDS pbpC NC_011742.1 2688178 2690490 R penicillin-insensitive transglycosylase/transpeptidase; penicillin-binding protein 1C complement(2688178..2690490) Escherichia coli S88 7129691 YP_002392359.1 CDS yfhM NC_011742.1 2690491 2695452 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2690491..2695452) Escherichia coli S88 7133175 YP_002392360.1 CDS sseA NC_011742.1 2695659 2696504 D catalyzes the transfer of a sulfur ion to cyanide or to other thiol compounds; 3-mercaptopyruvate sulfurtransferase 2695659..2696504 Escherichia coli S88 7133543 YP_002392361.1 CDS sseB NC_011742.1 2696997 2697773 R enhances serine sensitivity caused by inhibition of homoserine dehydrogenase I; enhanced serine sensitivity protein SseB complement(2696997..2697773) Escherichia coli S88 7131338 YP_002392362.1 CDS pepB NC_011742.1 2697915 2699198 R catalyzes the removal of an N-terminal amino acid from a peptide or arylamide; aminopeptidase B complement(2697915..2699198) Escherichia coli S88 7130650 YP_002392363.1 CDS yfhJ NC_011742.1 2699257 2699457 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 10393315; Product type pf : putative factor; hypothetical protein complement(2699257..2699457) Escherichia coli S88 7133670 YP_002392364.1 CDS fdx NC_011742.1 2699469 2699804 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10393315, 20013001, 92283811, 94181532, 11551196, 1317854, 4375562, 8300516; Product type c : carrier; [2Fe-2S] ferredoxin complement(2699469..2699804) Escherichia coli S88 7133540 YP_002392365.1 CDS hscA NC_011742.1 2699806 2701656 R involved in the maturation of iron-sulfur cluster-containing proteins; chaperone protein HscA complement(2699806..2701656) Escherichia coli S88 7129461 YP_002392366.1 CDS hscB NC_011742.1 2701673 2702188 R J-type co-chaperone that regulates the ATPase and peptide-binding activity of Hsc66 chaperone; may function in biogenesis of iron-sulfur proteins; co-chaperone HscB complement(2701673..2702188) Escherichia coli S88 7131391 YP_002392367.1 CDS iscA NC_011742.1 2702284 2702607 R forms iron-sulfur clusters of ferredoxin [2FE-2S]; binds iron in the presence of the thioredoxin reductase system; forms homodimers and tetramers; similar to SufA protein; iron-sulfur cluster assembly protein complement(2702284..2702607) Escherichia coli S88 7131392 YP_002392368.1 CDS iscU NC_011742.1 2702624 2703010 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10393315, 11994302, 15153099; Product type f : factor; scaffold protein complement(2702624..2703010) Escherichia coli S88 7130413 YP_002392369.1 CDS iscS NC_011742.1 2703038 2704252 R catalyzes the removal of elemental sulfur from cysteine to produce alanine; involved in NAD biosynthesis; cysteine desulfurase complement(2703038..2704252) Escherichia coli S88 7130416 YP_002392370.1 CDS iscR NC_011742.1 2704364 2704852 R regulates the expression of the iscRSUA operon; DNA-binding transcriptional regulator IscR complement(2704364..2704852) Escherichia coli S88 7130415 YP_002392371.1 CDS yfhQ NC_011742.1 2705122 2705862 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10393315; Product type pe : putative enzyme; putative methyltransferase complement(2705122..2705862) Escherichia coli S88 7130414 YP_002392372.1 CDS suhB NC_011742.1 2705981 2706784 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6389495, 90202735, 95095968, 10747806, 2138605, 8002619; Product type e : enzyme; inositol monophosphatase 2705981..2706784 Escherichia coli S88 7133544 YP_002392373.1 CDS yfhR NC_011742.1 2706902 2707783 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative peptidase 2706902..2707783 Escherichia coli S88 7131249 YP_002392374.1 CDS csiE NC_011742.1 2707974 2709254 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95020540, 96154950; Product type cp : cell process; stationary phase inducible protein CsiE 2707974..2709254 Escherichia coli S88 7133545 YP_002392375.1 CDS hcaT NC_011742.1 2709246 2710385 R putative transporter of 3-phenylpropionate across the inner membrane; member of the major facilitator superfamily of transporters; putative 3-phenylpropionic acid transporter complement(2709246..2710385) Escherichia coli S88 7131977 YP_002392376.1 CDS yphA NC_011742.1 2710709 2711176 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 2710709..2711176 Escherichia coli S88 7128885 YP_002392377.1 CDS yphB NC_011742.1 2711336 2712208 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2711336..2712208) Escherichia coli S88 7132066 YP_002392378.1 CDS yphC NC_011742.1 2712220 2713281 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase, Zn-dependent and NAD(P)-binding complement(2712220..2713281) Escherichia coli S88 7132067 YP_002392379.1 CDS yphD NC_011742.1 2713347 2714345 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sugar transporter subunit: membrane component of ABC superfamily complement(2713347..2714345) Escherichia coli S88 7132068 YP_002392380.1 CDS yphE NC_011742.1 2714370 2715881 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; fused putative sugar transporter subunits of ABC superfamily: ATP-binding components complement(2714370..2715881) Escherichia coli S88 7132069 YP_002392381.1 CDS yphF NC_011742.1 2715904 2716887 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 9298646; Product type pt : putative transporter; putative sugar transporter subunit: periplasmic-binding component of ABC superfamily complement(2715904..2716887) Escherichia coli S88 7132070 YP_002392382.1 CDS yphG NC_011742.1 2716984 2720265 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2716984..2720265) Escherichia coli S88 7132071 YP_002392383.1 CDS yphH NC_011742.1 2720383 2721576 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 2720383..2721576 Escherichia coli S88 7132072 YP_002392384.1 CDS glyA NC_011742.1 2721640 2722893 R catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase complement(2721640..2722893) Escherichia coli S88 7132073 YP_002392385.1 CDS hmp NC_011742.1 2723222 2724412 D flavohemoprotein; catalyzes the formation of nitrate from nitric oxide; can also catalyze the reduction of dihydropteridine; nitric oxide dioxygenase 2723222..2724412 Escherichia coli S88 7130041 YP_002392386.1 CDS glnB NC_011742.1 2724457 2724795 R indirectly regulates nitrogen metabolism; at high nitrogen levels P-II prevents the phosphorylation of NR-I, the transcriptional activator of the glutamine synthetase gene (glnA); at low nitrogen levels P-II is uridylylated to form PII-UMP and interacts with an adenylyltransferase (GlnE) that activates GlnA; nitrogen regulatory protein P-II 1 complement(2724457..2724795) Escherichia coli S88 7128935 YP_002392387.1 CDS yfhA NC_011742.1 2724856 2726190 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8226691, 8412694; Product type pr : putative regulator; putative DNA-binding response regulator in two-component system complement(2724856..2726190) Escherichia coli S88 7130005 YP_002392388.1 CDS yfhG NC_011742.1 2726180 2726893 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2726180..2726893) Escherichia coli S88 7133535 YP_002392389.1 CDS yfhK NC_011742.1 2727058 2728485 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative sensory kinase in two-component system complement(2727058..2728485) Escherichia coli S88 7133538 YP_002392390.1 CDS purL NC_011742.1 2729061 2732948 R catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis; phosphoribosylformylglycinamidine synthase complement(2729061..2732948) Escherichia coli S88 7133475 YP_002392391.1 CDS yfhD NC_011742.1 2733346 2734764 D YfhD; uncharacterized member of the transglycosylase slt family; part of the rob operon, which plays a role in cellular resistance to antibiotics, bactericidal agents, and organic solvents; unknown function; putative transglycosylase 2733346..2734764 Escherichia coli S88 7131752 YP_002392392.1 CDS tadA NC_011742.1 2734761 2735297 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12110595; Product type e : enzyme; tRNA-specific adenosine deaminase complement(2734761..2735297) Escherichia coli S88 7133537 YP_002392393.1 CDS yfhB NC_011742.1 2735322 2735957 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2735322..2735957) Escherichia coli S88 7131255 YP_002392394.1 CDS yfhH NC_011742.1 2736166 2737014 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 2736166..2737014 Escherichia coli S88 7133536 YP_002392395.1 CDS yfhL NC_011742.1 2737070 2737330 D Evidence 2b : Function of strongly homologous gene; PubMedId : 8765743, 8880900; Product type c : carrier; ferredoxin (4Fe-4S cluster-containing protein) (fdx-like) 2737070..2737330 Escherichia coli S88 7133539 YP_002392396.1 CDS ECS88_2735 NC_011742.1 2737601 2737765 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2737601..2737765) Escherichia coli S88 7131339 YP_002392397.1 CDS acpS NC_011742.1 2738025 2738405 R Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids; 4'-phosphopantetheinyl transferase complement(2738025..2738405) Escherichia coli S88 7131340 YP_002392398.1 CDS pdxJ NC_011742.1 2738405 2739136 R involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase complement(2738405..2739136) Escherichia coli S88 7132040 YP_002392399.1 CDS recO NC_011742.1 2739148 2739876 R involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA; DNA repair protein RecO complement(2739148..2739876) Escherichia coli S88 7133184 YP_002392400.1 CDS era NC_011742.1 2739888 2740793 R 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; GTP-binding protein Era complement(2739888..2740793) Escherichia coli S88 7131811 YP_002392401.1 CDS rnc NC_011742.1 2740790 2741470 R 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; ribonuclease III complement(2740790..2741470) Escherichia coli S88 7132415 YP_002392402.1 CDS lepB NC_011742.1 2741737 2742711 R catalyzes the cleavage of the amino-terminal leader peptide from secretory proteins; signal peptidase I complement(2741737..2742711) Escherichia coli S88 7132743 YP_002392403.1 CDS lepA NC_011742.1 2742727 2744526 R binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA complement(2742727..2744526) Escherichia coli S88 7130483 YP_002392404.1 CDS rseC NC_011742.1 2744724 2745203 R involved in the reduction of the SoxR iron-sulfur cluster; SoxR reducing system protein RseC complement(2744724..2745203) Escherichia coli S88 7130482 YP_002392405.1 CDS rseB NC_011742.1 2745200 2746156 R periplasmic protein; interacts with the C-terminal domain of RseA and stimulates RseA binding to sigmaE via the cytoplasmic RseA N-terminal domain which then sequesters sigmaE in the membrane thereby preventing sigmaE associated with core RNAP; periplasmic negative regulator of sigmaE complement(2745200..2746156) Escherichia coli S88 7133811 YP_002392406.1 CDS rseA NC_011742.1 2746156 2746806 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9159522, 97303092, 99431977, 7768826; Product type f : factor; anti-RNA polymerase sigma factor SigE complement(2746156..2746806) Escherichia coli S88 7133810 YP_002392407.1 CDS rpoE NC_011742.1 2746839 2747414 R Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor is involved in heat shock and oxidative stress response; RNA polymerase sigma factor RpoE complement(2746839..2747414) Escherichia coli S88 7133809 YP_002392408.1 CDS nadB NC_011742.1 2747822 2749444 D catalyzes the formation of oxaloacetate from L-aspartate; L-aspartate oxidase 2747822..2749444 Escherichia coli S88 7133778 YP_002392409.1 CDS yfiC NC_011742.1 2749429 2750166 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative S-adenosyl-L-methionine-dependent methyltransferase complement(2749429..2750166) Escherichia coli S88 7129651 YP_002392410.1 CDS srmB NC_011742.1 2750298 2751632 D facilitates an early step in the assembly of the 50S subunit of the ribosome; ATP-dependent RNA helicase SrmB 2750298..2751632 Escherichia coli S88 7133548 YP_002392411.1 CDS yfiE NC_011742.1 2751665 2752546 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(2751665..2752546) Escherichia coli S88 7130646 YP_002392412.1 CDS yfiK NC_011742.1 2752649 2753236 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12562784; Product type t : transporter; neutral amino-acid efflux protein 2752649..2753236 Escherichia coli S88 7133550 YP_002392413.1 CDS yfiD NC_011742.1 2753292 2753675 R stress-induced glycyl radical protein that can replace an oxidatively damaged pyruvate formate-lyase subunit; autonomous glycyl radical cofactor GrcA complement(2753292..2753675) Escherichia coli S88 7133553 YP_002392414.1 CDS ung NC_011742.1 2753980 2754669 D 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; uracil-DNA glycosylase 2753980..2754669 Escherichia coli S88 7133549 YP_002392415.1 CDS yfiF NC_011742.1 2754717 2755754 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative methyltransferase complement(2754717..2755754) Escherichia coli S88 7132448 YP_002392416.1 CDS ECS88_2756 NC_011742.1 2755744 2755947 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative Z3866 protein complement(2755744..2755947) Escherichia coli S88 7133551 YP_002392417.1 CDS trxC NC_011742.1 2755961 2756380 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12952960, 9388228, 99175138, 10644706; Product type c : carrier; thioredoxin 2 2755961..2756380 Escherichia coli S88 7130915 YP_002392418.1 CDS yfiP NC_011742.1 2756449 2757147 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2756449..2757147 Escherichia coli S88 7130357 YP_002392419.1 CDS yfiQ NC_011742.1 2757179 2759839 D Evidence 2b : Function of strongly homologous gene; Product type e : enzyme; fused acyl-CoA synthetase: NAD(P)-binding subunit ; ATP-binding subunit 2757179..2759839 Escherichia coli S88 7133558 YP_002392420.1 CDS pssA NC_011742.1 2759953 2761308 D catalyzes de novo synthesis of phosphatidylserine from CDP-diacylglycerol and L-serine which leads eventually to the production of phosphatidylethanolamine; bounds to the ribosome; phosphatidylserine synthase 2759953..2761308 Escherichia coli S88 7133559 YP_002392421.1 CDS yfiM NC_011742.1 2761405 2761677 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2761405..2761677 Escherichia coli S88 7130809 YP_002392422.1 CDS kgtP NC_011742.1 2761674 2762972 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91219460, 1709493, 2053984, 2118499, 2190187, 8419306; Product type t : transporter; alpha-ketoglutarate transporter complement(2761674..2762972) Escherichia coli S88 7133555 YP_002392423.1 CDS ECS88_2763 NC_011742.1 2763366 2764907 D Evidence 2b : Function of strongly homologous gene; PubMedId : 7518087; Product type pe : putative enzyme; transposase for insertion sequence IS408 family (ORFA) 2763366..2764907 Escherichia coli S88 7130458 YP_002392424.1 CDS ECS88_2764 NC_011742.1 2764919 2765668 D Evidence 2b : Function of strongly homologous gene; PubMedId : 7518087; Product type e : enzyme; transposase for insertion sequence IS408 family, putative ATP-binding protein (ORFB) 2764919..2765668 Escherichia coli S88 7130916 YP_002392425.1 CDS ECS88_2768 NC_011742.1 2767111 2767833 R Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase ORF B, IS3 family, IS150 group complement(2767111..2767833) Escherichia coli S88 7130920 YP_002392426.1 CDS clpB NC_011742.1 2774042 2776615 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14550559, 14640692, 91294166, 93015925, 93388583, 99428468; Product type f : factor; protein disaggregation chaperone complement(2774042..2776615) Escherichia coli S88 7129269 YP_002392427.1 CDS yfiH NC_011742.1 2776745 2777476 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 1906060, 2066329; hypothetical protein complement(2776745..2777476) Escherichia coli S88 7131341 YP_002392428.1 CDS rluD NC_011742.1 2777473 2778453 R responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA; 23S rRNA pseudouridine synthase D complement(2777473..2778453) Escherichia coli S88 7133552 YP_002392429.1 CDS yfiO NC_011742.1 2778588 2779325 D with YaeT, NlpB and YfgL forms a complex involved in the proper assembly and/or targeting of OMPs to the outer membrane; involved in resistance to ampicillin and tetracycline; outer membrane protein assembly complex subunit YfiO 2778588..2779325 Escherichia coli S88 7132734 YP_002392430.1 CDS yfiA NC_011742.1 2779595 2779936 D associated with 30S ribosomal subunit; interferes with translation elongation; translation inhibitor protein RaiA 2779595..2779936 Escherichia coli S88 7133557 YP_002392431.1 CDS pheL NC_011742.1 2780040 2780087 D Evidence 1c : Function experimentally demonstrated in the studied genus; Product type l : leader peptide; pheA gene leader peptide 2780040..2780087 Escherichia coli S88 7133546 YP_002392432.1 CDS pheA NC_011742.1 2780186 2781346 D catalyzing the formation of prephenate from chorismate and the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis; bifunctional chorismate mutase/prephenate dehydratase 2780186..2781346 Escherichia coli S88 7133702 YP_002392433.1 CDS tyrA NC_011742.1 2781389 2782510 R catalyzes the formation of prephenate from chorismate and the formation of 4-hydroxyphenylpyruvate from prephenate in tyrosine biosynthesis; bifunctional chorismate mutase/prephenate dehydrogenase complement(2781389..2782510) Escherichia coli S88 7133701 YP_002392434.1 CDS aroF NC_011742.1 2782521 2783591 R catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, tyrosine sensitive; phospho-2-dehydro-3-deoxyheptonate aldolase complement(2782521..2783591) Escherichia coli S88 7130374 YP_002392435.1 CDS yfiL NC_011742.1 2783801 2784166 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 6396419; hypothetical protein 2783801..2784166 Escherichia coli S88 7129926 YP_002392436.1 CDS yfiR NC_011742.1 2784315 2784833 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2784315..2784833 Escherichia coli S88 7133554 YP_002392437.1 CDS yfiN NC_011742.1 2784823 2786049 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; hypothetical protein 2784823..2786049 Escherichia coli S88 7133560 YP_002392438.1 CDS yfiB NC_011742.1 2786065 2786547 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 96032391; Product type pm : putative membrane component; putative outer membrane lipoprotein 2786065..2786547 Escherichia coli S88 7133556 YP_002392439.1 CDS rplS NC_011742.1 2786624 2786971 R 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; 50S ribosomal protein L19 complement(2786624..2786971) Escherichia coli S88 7133547 YP_002392440.1 CDS trmD NC_011742.1 2787013 2787780 R methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA; tRNA (guanine-N(1)-)-methyltransferase complement(2787013..2787780) Escherichia coli S88 7133758 YP_002392441.1 CDS rimM NC_011742.1 2787811 2788359 R Essential for efficient processing of 16S rRNA; 16S rRNA-processing protein RimM complement(2787811..2788359) Escherichia coli S88 7130339 YP_002392442.1 CDS rpsP NC_011742.1 2788378 2788626 R 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; 30S ribosomal protein S16 complement(2788378..2788626) Escherichia coli S88 7132727 YP_002392443.1 CDS ffh NC_011742.1 2788763 2790124 R with 4.5S RNA forms a signal recognition particle involved in targeting and integration of inner membrane proteins; signal recognition particle protein complement(2788763..2790124) Escherichia coli S88 7133799 YP_002392444.1 CDS ypjD NC_011742.1 2790216 2791082 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 2790216..2791082 Escherichia coli S88 7129478 YP_002392445.1 CDS yfjD NC_011742.1 2791193 2792389 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 2791193..2792389 Escherichia coli S88 7132075 YP_002392446.1 CDS grpE NC_011742.1 2792444 2793037 R with DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins; may act as a thermosensor; heat shock protein GrpE complement(2792444..2793037) Escherichia coli S88 7133562 YP_002392447.1 CDS ppnK NC_011742.1 2793160 2794038 D catalyzes the phosphorylation of NAD to NADP; inorganic polyphosphate/ATP-NAD kinase 2793160..2794038 Escherichia coli S88 7130072 YP_002392448.1 CDS recN NC_011742.1 2794124 2795785 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87259985, 91355307, 95058623, 3037486; Product type cp : cell process; recombination and repair protein 2794124..2795785 Escherichia coli S88 7133561 YP_002392449.1 CDS smpA NC_011742.1 2795934 2796275 D Evidence 2b : Function of strongly homologous gene; PubMedId : 2045357; Product type lp : lipoprotein; hypothetical protein 2795934..2796275 Escherichia coli S88 7131810 YP_002392450.1 CDS yfjF NC_011742.1 2796337 2796627 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2796337..2796627) Escherichia coli S88 7130613 YP_002392451.1 CDS yfjG NC_011742.1 2796617 2797093 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2796617..2797093) Escherichia coli S88 7133563 YP_002392452.1 CDS smpB NC_011742.1 2797225 2797707 D 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; SsrA-binding protein 2797225..2797707 Escherichia coli S88 7133564 YP_002392453.1 CDS ECS88_2808 NC_011742.1 2798408 2798890 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 2798408..2798890 Escherichia coli S88 7130654 YP_002392454.1 CDS D NC_011742.1 2799204 2800304 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Late control gene D protein (GpD) complement(2799204..2800304) Escherichia coli S88 7130924 YP_002392455.1 CDS U NC_011742.1 2800301 2800786 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; bacteriophage tail protein GpU complement(2800301..2800786) Escherichia coli S88 7130552 YP_002392456.1 CDS ECS88_2811 NC_011742.1 2800783 2803860 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage tail tape measure protein complement(2800783..2803860) Escherichia coli S88 7130379 YP_002392457.1 CDS ECS88_2812 NC_011742.1 2803853 2803972 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage tail protein complement(2803853..2803972) Escherichia coli S88 7130925 YP_002392458.1 CDS ECS88_2813 NC_011742.1 2803987 2804289 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage tail protein E complement(2803987..2804289) Escherichia coli S88 7130926 YP_002392459.1 CDS fII NC_011742.1 2804344 2804859 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major tail tube protein (Protein FII) complement(2804344..2804859) Escherichia coli S88 7130927 YP_002392460.1 CDS fI NC_011742.1 2804869 2806041 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major tail sheath protein (Protein FI) complement(2804869..2806041) Escherichia coli S88 7129491 YP_002392461.1 CDS tfaE NC_011742.1 2806176 2806778 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Phage tail assembly chaperone complement(2806176..2806778) Escherichia coli S88 7129488 YP_002392462.1 CDS ECS88_2817 NC_011742.1 2806778 2808403 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative variable tail fiber protein complement(2806778..2808403) Escherichia coli S88 7131285 YP_002392463.1 CDS I NC_011742.1 2808400 2809005 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail protein I (GpI) complement(2808400..2809005) Escherichia coli S88 7130928 YP_002392464.1 CDS J NC_011742.1 2808998 2809945 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Baseplate assembly protein J (GpJ) complement(2808998..2809945) Escherichia coli S88 7131600 YP_002392465.1 CDS W NC_011742.1 2809893 2810252 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Baseplate assembly protein W (GpW) complement(2809893..2810252) Escherichia coli S88 7130430 YP_002392466.1 CDS V NC_011742.1 2810249 2810827 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Baseplate assembly protein V (GpV) complement(2810249..2810827) Escherichia coli S88 7132475 YP_002392467.1 CDS ECS88_2822 NC_011742.1 2810966 2812666 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 2810966..2812666 Escherichia coli S88 7132469 YP_002392468.1 CDS ECS88_2823 NC_011742.1 2812722 2813180 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage tail completion protein complement(2812722..2813180) Escherichia coli S88 7130929 YP_002392469.1 CDS R NC_011742.1 2813173 2813625 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail completion protein R (GpR) complement(2813173..2813625) Escherichia coli S88 7130930 YP_002392470.1 CDS ECS88_2825 NC_011742.1 2813567 2813857 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein complement(2813567..2813857) Escherichia coli S88 7131779 YP_002392471.1 CDS ECS88_2826 NC_011742.1 2813700 2814128 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative Regulatory protein complement(2813700..2814128) Escherichia coli S88 7130931 YP_002392472.1 CDS ECS88_2827 NC_011742.1 2814125 2814574 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein complement(2814125..2814574) Escherichia coli S88 7130932 YP_002392473.1 CDS R NC_011742.1 2814504 2815016 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; putative lysozyme protein R of prophage complement(2814504..2815016) Escherichia coli S88 7130933 YP_002392474.1 CDS ECS88_2829 NC_011742.1 2814997 2815212 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative secretory protein complement(2814997..2815212) Escherichia coli S88 7131780 YP_002392475.1 CDS X NC_011742.1 2815216 2815419 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Phage tail protein X (GpX) complement(2815216..2815419) Escherichia coli S88 7130934 YP_002392476.1 CDS L NC_011742.1 2815419 2815946 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Head completion/stabilization protein (GpL) complement(2815419..2815946) Escherichia coli S88 7132512 YP_002392477.1 CDS M NC_011742.1 2815979 2816629 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Terminase, endonuclease subunit (GpM) complement(2815979..2816629) Escherichia coli S88 7130469 YP_002392478.1 CDS N NC_011742.1 2816633 2817691 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; minor capsid protein H1 and H2, major capsid protein N* complement(2816633..2817691) Escherichia coli S88 7129400 YP_002392479.1 CDS O NC_011742.1 2817708 2818541 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Presumed capsid scaffolding protein (GpO) complement(2817708..2818541) Escherichia coli S88 7129648 YP_002392480.1 CDS P NC_011742.1 2818684 2820450 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Terminase, ATPase subunit (GpP) 2818684..2820450 Escherichia coli S88 7133119 YP_002392481.1 CDS ECS88_2836 NC_011742.1 2820447 2821484 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage portal protein 2820447..2821484 Escherichia coli S88 7133152 YP_002392482.1 CDS ECS88_2837 NC_011742.1 2821532 2822941 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein complement(2821532..2822941) Escherichia coli S88 7130935 YP_002392483.1 CDS ECS88_2838 NC_011742.1 2823263 2823568 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative DinI-like damage-inducible protein complement(2823263..2823568) Escherichia coli S88 7130936 YP_002392484.1 CDS ECS88_2839 NC_011742.1 2823507 2823797 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2823507..2823797) Escherichia coli S88 7130937 YP_002392485.1 CDS ECS88_2840 NC_011742.1 2823849 2824205 R Evidence 7 : Gene remnant; conserved hypothetical protein of phage origin (partial) complement(2823849..2824205) Escherichia coli S88 7130938 YP_002392486.1 CDS ECS88_2841 NC_011742.1 2824202 2826289 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative bacteriophage replication gene A protein (endonuclease) complement(2824202..2826289) Escherichia coli S88 7130939 YP_002392487.1 CDS dam NC_011742.1 2826286 2827203 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Site-specific DNA-methyltransferase (adenine-specific) complement(2826286..2827203) Escherichia coli S88 7130940 YP_002392488.1 CDS ECS88_2843 NC_011742.1 2827140 2827367 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative DksA/TraR protein family with a zinc finger complement(2827140..2827367) Escherichia coli S88 7130559 YP_002392489.1 CDS ECS88_2844 NC_011742.1 2827367 2827606 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2827367..2827606) Escherichia coli S88 7130941 YP_002392490.1 CDS ECS88_2845 NC_011742.1 2827668 2828009 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2827668..2828009) Escherichia coli S88 7130942 YP_002392491.1 CDS ECS88_2846 NC_011742.1 2828032 2828256 R Evidence 6 : Doubtful CDS; hypothetical protein complement(2828032..2828256) Escherichia coli S88 7130943 YP_002392492.1 CDS fil NC_011742.1 2828127 2828453 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein fil of phage origin complement(2828127..2828453) Escherichia coli S88 7130944 YP_002392493.1 CDS cII NC_011742.1 2828431 2828940 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; regulatory protein cII complement(2828431..2828940) Escherichia coli S88 7129492 YP_002392494.1 CDS ECS88_2849 NC_011742.1 2828973 2829215 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage regulatory protein complement(2828973..2829215) Escherichia coli S88 7131914 YP_002392495.1 CDS cI NC_011742.1 2829337 2829969 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; phage regulatory protein cI 2829337..2829969 Escherichia coli S88 7130945 YP_002392496.1 CDS int NC_011742.1 2829972 2830991 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Integrase 2829972..2830991 Escherichia coli S88 7131911 YP_002392497.1 CDS ECS88_2852 NC_011742.1 2830996 2832219 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 2830996..2832219 Escherichia coli S88 7131650 YP_002392498.1 CDS ECS88_2853 NC_011742.1 2832766 2832963 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 2832766..2832963 Escherichia coli S88 7130946 YP_002392499.1 CDS ECS88_2854 NC_011742.1 2832960 2833748 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2832960..2833748 Escherichia coli S88 7130947 YP_002392500.1 CDS ECS88_2855 NC_011742.1 2833836 2834129 R Evidence 5 : No homology to any previously reported sequences; Product type h : extrachromosomal origin; hypothetical protein complement(2833836..2834129) Escherichia coli S88 7130948 YP_002392501.1 CDS ECS88_2856 NC_011742.1 2834186 2834332 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(2834186..2834332) Escherichia coli S88 7130949 YP_002392502.1 CDS ECS88_2857 NC_011742.1 2834340 2835146 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2834340..2835146) Escherichia coli S88 7130950 YP_002392503.1 CDS ECS88_2859 NC_011742.1 2835603 2835740 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative protein from DinI-like family 2835603..2835740 Escherichia coli S88 7130951 YP_002392504.1 CDS ECS88_2860 NC_011742.1 2836105 2838054 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2836105..2838054 Escherichia coli S88 7130952 YP_002392505.1 CDS ECS88_2862 NC_011742.1 2838305 2838799 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 2838305..2838799 Escherichia coli S88 7133733 YP_002392506.1 CDS ECS88_2863 NC_011742.1 2838802 2839245 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative tail fibre assembly protein 2838802..2839245 Escherichia coli S88 7130954 YP_002392507.1 CDS tfaE NC_011742.1 2839217 2839819 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative tail fiber chaperone (assembly protein); e14 prophage complement(2839217..2839819) Escherichia coli S88 7130955 YP_002392508.1 CDS ECS88_2865 NC_011742.1 2839819 2840562 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage tail protein complement(2839819..2840562) Escherichia coli S88 7131286 YP_002392509.1 CDS ymfQ NC_011742.1 2840566 2841150 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; e14 prophage complement(2840566..2841150) Escherichia coli S88 7130956 YP_002392510.1 CDS ECS88_2867 NC_011742.1 2841141 2842199 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative baseplate J-like phage protein complement(2841141..2842199) Escherichia coli S88 7131131 YP_002392511.1 CDS ECS88_2868 NC_011742.1 2842186 2842614 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative tail protein complement(2842186..2842614) Escherichia coli S88 7130957 YP_002392512.1 CDS ECS88_2869 NC_011742.1 2842611 2843159 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative baseplate assembly phage protein complement(2842611..2843159) Escherichia coli S88 7130958 YP_002392513.1 CDS ECS88_2870 NC_011742.1 2843159 2844238 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail protein complement(2843159..2844238) Escherichia coli S88 7130959 YP_002392514.1 CDS ECS88_2871 NC_011742.1 2844235 2845605 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail/DNA circulation protein complement(2844235..2845605) Escherichia coli S88 7130960 YP_002392515.1 CDS ECS88_2872 NC_011742.1 2845624 2847459 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; phage tail tape measure protein complement(2845624..2847459) Escherichia coli S88 7130961 YP_002392516.1 CDS ECS88_2874 NC_011742.1 2847601 2847870 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2847601..2847870) Escherichia coli S88 7130962 YP_002392517.1 CDS ECS88_2875 NC_011742.1 2847870 2848226 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage tail protein complement(2847870..2848226) Escherichia coli S88 7130963 YP_002392518.1 CDS ECS88_2876 NC_011742.1 2848226 2849722 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail sheath protein complement(2848226..2849722) Escherichia coli S88 7130964 YP_002392519.1 CDS ECS88_2877 NC_011742.1 2849706 2849876 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2849706..2849876) Escherichia coli S88 7130965 YP_002392520.1 CDS ECS88_2878 NC_011742.1 2849885 2850445 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2849885..2850445) Escherichia coli S88 7130966 YP_002392521.1 CDS ECS88_2879 NC_011742.1 2850442 2850948 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2850442..2850948) Escherichia coli S88 7130967 YP_002392522.1 CDS ECS88_2880 NC_011742.1 2850923 2851333 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage head-tail adaptor complement(2850923..2851333) Escherichia coli S88 7130968 YP_002392523.1 CDS ECS88_2881 NC_011742.1 2851330 2851653 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein complement(2851330..2851653) Escherichia coli S88 7130969 YP_002392524.1 CDS ECS88_2882 NC_011742.1 2851656 2851856 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein complement(2851656..2851856) Escherichia coli S88 7130970 YP_002392525.1 CDS ECS88_2883 NC_011742.1 2851906 2853111 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative major capsid protein complement(2851906..2853111) Escherichia coli S88 7130971 YP_002392526.1 CDS ECS88_2884 NC_011742.1 2853126 2853812 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage pro-head protease complement(2853126..2853812) Escherichia coli S88 7130972 YP_002392527.1 CDS ECS88_2885 NC_011742.1 2853754 2854995 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage portal protein complement(2853754..2854995) Escherichia coli S88 7130973 YP_002392528.1 CDS ymfR NC_011742.1 2854995 2855177 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; e14 prophage complement(2854995..2855177) Escherichia coli S88 7130974 YP_002392529.1 CDS ECS88_2887 NC_011742.1 2855189 2856922 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage terminase complement(2855189..2856922) Escherichia coli S88 7131132 YP_002392530.1 CDS ECS88_2888 NC_011742.1 2856919 2857422 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage terminase, small subunit complement(2856919..2857422) Escherichia coli S88 7130975 YP_002392531.1 CDS ECS88_2889 NC_011742.1 2857539 2857889 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative endonuclease complement(2857539..2857889) Escherichia coli S88 7130976 YP_002392532.1 CDS ECS88_2890 NC_011742.1 2857929 2858432 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 2857929..2858432 Escherichia coli S88 7130977 YP_002392533.1 CDS ECS88_2891 NC_011742.1 2858539 2858790 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(2858539..2858790) Escherichia coli S88 7130978 YP_002392534.1 CDS rz NC_011742.1 2858861 2859298 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; endopeptidase; bacteriophage lysis protein complement(2858861..2859298) Escherichia coli S88 7130979 YP_002392535.1 CDS r NC_011742.1 2859295 2859771 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Lysozyme (Lysis protein) (Muramidase) (Endolysin) complement(2859295..2859771) Escherichia coli S88 7131354 YP_002392536.1 CDS ECS88_2894 NC_011742.1 2859758 2860162 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; Putative holin protein complement(2859758..2860162) Escherichia coli S88 7131781 YP_002392537.1 CDS ECS88_2895 NC_011742.1 2860215 2860550 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(2860215..2860550) Escherichia coli S88 7130980 YP_002392538.1 CDS ydfT NC_011742.1 2860736 2861488 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative antitermination protein Q; Qin prophage complement(2860736..2861488) Escherichia coli S88 7130981 YP_002392539.1 CDS ECS88_2897 NC_011742.1 2861502 2862497 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2861502..2862497) Escherichia coli S88 7129338 YP_002392540.1 CDS ECS88_2898 NC_011742.1 2862499 2863296 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative KilA protein; KilA-N domain complement(2862499..2863296) Escherichia coli S88 7130982 YP_002392541.1 CDS rusA NC_011742.1 2863316 2863705 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Crossover junction endodeoxyribonuclease complement(2863316..2863705) Escherichia coli S88 7130983 YP_002392542.1 CDS ECS88_2900 NC_011742.1 2863702 2864028 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative regulatory protein; lexA-binding domain complement(2863702..2864028) Escherichia coli S88 7131314 YP_002392543.1 CDS dam NC_011742.1 2864025 2864711 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative AdoMet-dependent methyltransferase complement(2864025..2864711) Escherichia coli S88 7132773 YP_002392544.1 CDS yfdN NC_011742.1 2864678 2865172 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage complement(2864678..2865172) Escherichia coli S88 7130560 YP_002392545.1 CDS ECS88_2903 NC_011742.1 2865169 2866110 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative phage replication protein O complement(2865169..2866110) Escherichia coli S88 7129830 YP_002392546.1 CDS ymfM NC_011742.1 2866120 2866458 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; e14 prophage complement(2866120..2866458) Escherichia coli S88 7133276 YP_002392547.1 CDS ymfL NC_011742.1 2866455 2867018 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative nucleic acid-binding protein; e14 prophage complement(2866455..2867018) Escherichia coli S88 7131130 YP_002392548.1 CDS ECS88_2907 NC_011742.1 2867050 2867553 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative DNA-binding transcriptional regulator complement(2867050..2867553) Escherichia coli S88 7131128 YP_002392549.1 CDS ymfK NC_011742.1 2867341 2868015 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12878731, 13129938, 9689094; Product type h : extrachromosomal origin; repressor protein phage e14; e14 prophage 2867341..2868015 Escherichia coli S88 7133277 YP_002392550.1 CDS ECS88_2909 NC_011742.1 2868023 2868169 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(2868023..2868169) Escherichia coli S88 7131126 YP_002392551.1 CDS ECS88_2910 NC_011742.1 2868218 2868730 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(2868218..2868730) Escherichia coli S88 7133278 YP_002392552.1 CDS ECS88_2911 NC_011742.1 2868881 2869561 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2868881..2869561 Escherichia coli S88 7133279 YP_002392553.1 CDS yfdQ NC_011742.1 2869627 2870451 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage 2869627..2870451 Escherichia coli S88 7133280 YP_002392554.1 CDS yfdR NC_011742.1 2870579 2871103 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage 2870579..2871103 Escherichia coli S88 7129833 YP_002392555.1 CDS ECS88_2915 NC_011742.1 2871188 2872078 D hypothetical protein 2871188..2872078 Escherichia coli S88 7129836 YP_002392556.1 CDS ECS88_2916 NC_011742.1 2872081 2872326 D hypothetical protein 2872081..2872326 Escherichia coli S88 7133281 YP_002392557.1 CDS ECS88_2917 NC_011742.1 2872287 2873459 D hypothetical protein 2872287..2873459 Escherichia coli S88 7133282 YP_002392558.1 CDS ECS88_2918 NC_011742.1 2873451 2874068 R hypothetical protein complement(2873451..2874068) Escherichia coli S88 7133283 YP_002392559.1 CDS ECS88_2919 NC_011742.1 2874079 2874405 R hypothetical protein complement(2874079..2874405) Escherichia coli S88 7133284 YP_002392560.1 CDS ECS88_2920 NC_011742.1 2874410 2875321 R hypothetical protein complement(2874410..2875321) Escherichia coli S88 7133285 YP_002392561.1 CDS ECS88_2921 NC_011742.1 2875287 2875550 D hypothetical protein 2875287..2875550 Escherichia coli S88 7133286 YP_002392562.1 CDS ygaT NC_011742.1 2876182 2877159 D in Escherichia coli this gene is induced by carbon starvation and depends on sigma S and cAMP-CRP; the structure of the Gab protein shows it is a member of non-heme iron (II)-dependent oxygenase superfamily which includes clavamini acid synthases; forms homotetramers in solution; hypothetical protein 2876182..2877159 Escherichia coli S88 7133287 YP_002392563.1 CDS ygaF NC_011742.1 2877179 2878447 D catalyzed the formation of 2-ketoglutarate from 2-hydroxyglutarate; hydroxyglutarate oxidase 2877179..2878447 Escherichia coli S88 7133572 YP_002392564.1 CDS gabD NC_011742.1 2878470 2879918 D catalyzes the formation of succinate from succinate semialdehyde; NADP dependent; succinate-semialdehyde dehydrogenase I 2878470..2879918 Escherichia coli S88 7133568 YP_002392565.1 CDS gabT NC_011742.1 2879932 2881212 D catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate; 4-aminobutyrate aminotransferase 2879932..2881212 Escherichia coli S88 7132160 YP_002392566.1 CDS gabP NC_011742.1 2881450 2882850 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94127927, 9685361, 8297211; Product type t : transporter; gamma-aminobutyrate transporter 2881450..2882850 Escherichia coli S88 7132162 YP_002392567.1 CDS csiR NC_011742.1 2882871 2883533 D regulator of gab gene expression; DNA-binding transcriptional regulator CsiR 2882871..2883533 Escherichia coli S88 7132161 YP_002392568.1 CDS ygaU NC_011742.1 2883534 2883983 R Evidence 4 : Homologs of previously reported genes of unknown function; LysM domain/BON superfamily protein complement(2883534..2883983) Escherichia coli S88 7131978 YP_002392569.1 CDS yqaE NC_011742.1 2884067 2884225 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(2884067..2884225) Escherichia coli S88 7133573 YP_002392570.1 CDS ygaV NC_011742.1 2884408 2884707 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 2884408..2884707 Escherichia coli S88 7132078 YP_002392571.1 CDS ygaP NC_011742.1 2884717 2885241 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pe : putative enzyme; conserved hypothetical protein; putative inner membrane protein with hydrolase activity 2884717..2885241 Escherichia coli S88 7133574 YP_002392572.1 CDS stpA NC_011742.1 2885288 2885692 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20485613, 93126121, 9643551, 98132400, 99415935, 1480493, 7961433; Product type r : regulator; DNA binding protein, nucleoid-associated complement(2885288..2885692) Escherichia coli S88 7133571 YP_002392573.1 CDS ygaW NC_011742.1 2886360 2886809 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 2886360..2886809 Escherichia coli S88 7131232 YP_002392574.1 CDS ygaC NC_011742.1 2886846 2887190 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 7961433; hypothetical protein complement(2886846..2887190) Escherichia coli S88 7133575 YP_002392575.1 CDS ygaM NC_011742.1 2887330 2887671 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2887330..2887671 Escherichia coli S88 7133566 YP_002392576.1 CDS ECS88_2937 NC_011742.1 2887728 2889062 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative fused protein: aminotransaminase/transcriptional regulator, GntR family complement(2887728..2889062) Escherichia coli S88 7133570 YP_002392577.1 CDS ECS88_2938 NC_011742.1 2889150 2889581 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2889150..2889581 Escherichia coli S88 7133288 YP_002392578.1 CDS nrdH NC_011742.1 2889790 2890035 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9218434, 11441020, 8820648; Product type pc : putative carrier; glutaredoxin-like protein 2889790..2890035 Escherichia coli S88 7133289 YP_002392579.1 CDS nrdI NC_011742.1 2890032 2890442 D in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF; ribonucleotide reductase stimulatory protein 2890032..2890442 Escherichia coli S88 7129738 YP_002392580.1 CDS nrdE NC_011742.1 2890415 2892559 D Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 2890415..2892559 Escherichia coli S88 7129739 YP_002392581.1 CDS nrdF NC_011742.1 2892569 2893528 D B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE; ribonucleotide-diphosphate reductase subunit beta 2892569..2893528 Escherichia coli S88 7129735 YP_002392582.1 CDS proV NC_011742.1 2893884 2895086 D with ProWX is involved in the high-affinity uptake of glycine betaine; glycine betaine transporter ATP-binding subunit 2893884..2895086 Escherichia coli S88 7129736 YP_002392583.1 CDS proW NC_011742.1 2895079 2896143 D with ProVX is involved in the high-affinity uptake of glycine betaine; glycine betaine transporter membrane protein 2895079..2896143 Escherichia coli S88 7130790 YP_002392584.1 CDS proX NC_011742.1 2896201 2897193 D with ProVW, part of the high-affinity transport system for the osmoprotectant glycine betaine; glycine betaine transporter periplasmic subunit 2896201..2897193 Escherichia coli S88 7130791 YP_002392585.1 CDS ECS88_2946 NC_011742.1 2897385 2898569 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16000740; Product type pt : putative transporter; putative transport protein (ousB-like) 2897385..2898569 Escherichia coli S88 7130792 YP_002392586.1 CDS ygaZ NC_011742.1 2898693 2899430 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 2898693..2899430 Escherichia coli S88 7133290 YP_002392587.1 CDS ygaH NC_011742.1 2899420 2899755 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 2899420..2899755 Escherichia coli S88 7133576 YP_002392588.1 CDS mprA NC_011742.1 2899846 2900376 D DNA-binding transcriptional repressor of microcin B17 synthesis and multidrug efflux; negative regulator of the multidrug operon emrAB; transcriptional repressor MprA 2899846..2900376 Escherichia coli S88 7133569 YP_002392589.1 CDS emrA NC_011742.1 2900503 2901675 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21450803, 93285984, 94262163, 1409590, 8203018; Product type t : transporter; multidrug efflux system 2900503..2901675 Escherichia coli S88 7129600 YP_002392590.1 CDS emrB NC_011742.1 2901692 2903230 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21450803, 93285984, 94262163, 1409590; Product type t : transporter; multidrug efflux system protein 2901692..2903230 Escherichia coli S88 7132391 YP_002392591.1 CDS ECS88_2952 NC_011742.1 2903488 2904195 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2903488..2904195 Escherichia coli S88 7132392 YP_002392592.1 CDS ECS88_2953 NC_011742.1 2904192 2905304 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative RNA related enzyme 2904192..2905304 Escherichia coli S88 7133291 YP_002392593.1 CDS luxS NC_011742.1 2905355 2905870 R catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2; S-ribosylhomocysteinase complement(2905355..2905870) Escherichia coli S88 7133292 YP_002392594.1 CDS gshA NC_011742.1 2906021 2907577 R involved in the first step of glutathione biosynthesis; glutamate--cysteine ligase complement(2906021..2907577) Escherichia coli S88 7128833 YP_002392595.1 CDS yqaA NC_011742.1 2907650 2908078 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(2907650..2908078) Escherichia coli S88 7130076 YP_002392596.1 CDS yqaB NC_011742.1 2908075 2908641 R YqaB; catalyzes the dephosphorylation of fructose 1-phosphate, 6-phosphogluconate and p-nitrophenyl phosphate (pNPP); presents beta-phosphoglucomutase activity at a lower extent; fructose-1-phosphatase complement(2908075..2908641) Escherichia coli S88 7132076 YP_002392597.1 CDS csrA NC_011742.1 2909831 2910016 R affects carbohydrate metabolism; has regulatory role in many processes; carbon storage regulator complement(2909831..2910016) Escherichia coli S88 7131986 YP_002392598.1 CDS alaS NC_011742.1 2910251 2912881 R 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; alanyl-tRNA synthetase complement(2910251..2912881) Escherichia coli S88 7130502 YP_002392599.1 CDS recX NC_011742.1 2913009 2913509 R binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities; recombination regulator RecX complement(2913009..2913509) Escherichia coli S88 7133039 YP_002392600.1 CDS recA NC_011742.1 2913578 2914639 R 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; recombinase A complement(2913578..2914639) Escherichia coli S88 7131815 YP_002392601.1 CDS ygaD NC_011742.1 2914719 2915216 R Evidence 4 : Homologs of previously reported genes of unknown function; competence damage-inducible protein A complement(2914719..2915216) Escherichia coli S88 7131803 YP_002392602.1 CDS mltB NC_011742.1 2915361 2916446 R membrane-bound lytic murein transglycosylase B; catalyzes the cleavage of the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycan; murein hydrolase B complement(2915361..2916446) Escherichia coli S88 7133567 YP_002392603.1 CDS srlA NC_011742.1 2916703 2917266 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87194727, 1334233, 3553176; Product type t : transporter; glucitol/sorbitol-specific enzyme IIC component of PTS 2916703..2917266 Escherichia coli S88 7128843 YP_002392604.1 CDS srlE NC_011742.1 2917263 2918222 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1100602, 3553176; Product type t : transporter; glucitol/sorbitol-specific enzyme IIB component of PTS 2917263..2918222 Escherichia coli S88 7130641 YP_002392605.1 CDS srlB NC_011742.1 2918233 2918604 D phosphoenolpyruvate-dependent sugar phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIB is phosphorylated by IIA and then transfers the phosphoryl group to the sugar; IIC forms the translocation channel; PTS system glucitol/sorbitol-specific transporter subunit IIA 2918233..2918604 Escherichia coli S88 7130644 YP_002392606.1 CDS srlD NC_011742.1 2918608 2919387 D catalyzes the conversion of sorbitol 6-phosphate into fructose 6-phosphate; sorbitol-6-phosphate dehydrogenase 2918608..2919387 Escherichia coli S88 7130642 YP_002392607.1 CDS gutM NC_011742.1 2919493 2919852 D regulator for glucitol utilization; DNA-binding transcriptional activator GutM 2919493..2919852 Escherichia coli S88 7130643 YP_002392608.1 CDS srlR NC_011742.1 2919919 2920692 D regulates genes involved in glucitol utilization; DNA-bindng transcriptional repressor SrlR 2919919..2920692 Escherichia coli S88 7128881 YP_002392609.1 CDS gutQ NC_011742.1 2920685 2921650 D catalyzes the conversion of D-arabinose 5-phosphate to D-ribulose-5-phosphate; D-arabinose 5-phosphate isomerase 2920685..2921650 Escherichia coli S88 7130645 YP_002392610.1 CDS norR NC_011742.1 2921647 2923161 R Required for the expression of anaerobic nitric oxide (NO) reductase; acts as a transcriptional activator for the norVW operon; anaerobic nitric oxide reductase transcription regulator complement(2921647..2923161) Escherichia coli S88 7128882 YP_002392611.1 CDS norV NC_011742.1 2923348 2924787 D detoxifies nitric oxide using NADH; anaerobic nitric oxide reductase flavorubredoxin 2923348..2924787 Escherichia coli S88 7129728 YP_002392612.1 CDS norW NC_011742.1 2924784 2925917 D catalyzes the reduction of the rubredoxin moiety of nitric oxide reductase; nitric oxide reductase 2924784..2925917 Escherichia coli S88 7129729 YP_002392613.1 CDS hypF NC_011742.1 2926141 2928393 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12377778, 92255260, 8661925; Product type e : enzyme; carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases complement(2926141..2928393) Escherichia coli S88 7129147 YP_002392614.1 CDS hydN NC_011742.1 2928546 2929073 R involved in electron transport from formate to hydrogen; electron transport protein HydN complement(2928546..2929073) Escherichia coli S88 7131598 YP_002392615.1 CDS ascG NC_011742.1 2929222 2930235 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88297127, 92334140, 1630307; Product type r : regulator; DNA-binding transcriptional repressor complement(2929222..2930235) Escherichia coli S88 7131591 YP_002392616.1 CDS ascF NC_011742.1 2930492 2931949 D phosphoenolpyruvate-dependent sugar phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIB is phosphorylated by IIA and then transfers the phosphoryl group to the sugar; IIC forms the translocation channel; PTS system cellobiose/arbutin/salicin-specific transporter subunits IIBC 2930492..2931949 Escherichia coli S88 7129941 YP_002392617.1 CDS ascB NC_011742.1 2931958 2933382 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88297127, 92334140, 1630307; Product type e : enzyme; cryptic 6-phospho-beta-glucosidase 2931958..2933382 Escherichia coli S88 7129940 YP_002392618.1 CDS ECS88_2980 NC_011742.1 2933480 2933899 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative HTH-type transcriptional regulator ygjM complement(2933480..2933899) Escherichia coli S88 7129939 YP_002392619.1 CDS ECS88_2981 NC_011742.1 2933925 2934110 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(2933925..2934110) Escherichia coli S88 7133293 YP_002392620.1 CDS hycI NC_011742.1 2934135 2934605 R involved in the C-terminal processing of the large subunit of hydrogenase 3 HycE; hydrogenase 3 maturation protease complement(2934135..2934605) Escherichia coli S88 7133294 YP_002392621.1 CDS hycH NC_011742.1 2934598 2935008 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92215587, 92326636, 1625581, 2187144, 7851435; Product type f : factor; protein required for maturation of hydrogenase 3 complement(2934598..2935008) Escherichia coli S88 7131590 YP_002392622.1 CDS hycG NC_011742.1 2935005 2935772 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90251163, 92215587, 92326636, 2187144; Product type e : enzyme; hydrogenase 3 and formate hydrogenase complex, HycG subunit complement(2935005..2935772) Escherichia coli S88 7131589 YP_002392623.1 CDS hycF NC_011742.1 2935772 2936314 R electron transfer protein for hydrogenase-3; the formate hydrogenlyase complex comprises of a formate dehydrogenase, unidentified electron carriers and hydrogenase-3; in this non-energy conserving pathway, molecular hydrogen and carbodioxide are released from formate; formate hydrogenlyase complex iron-sulfur subunit complement(2935772..2936314) Escherichia coli S88 7131588 YP_002392624.1 CDS hycE NC_011742.1 2936324 2938033 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92215587, 92326636, 94170785, 2187144, 8125094; Product type e : enzyme; hydrogenase 3, large subunit complement(2936324..2938033) Escherichia coli S88 7131587 YP_002392625.1 CDS hycD NC_011742.1 2938051 2938974 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90251163, 92215587, 92326636; Product type m : membrane component; hydrogenase 3, membrane subunit complement(2938051..2938974) Escherichia coli S88 7131586 YP_002392626.1 CDS hycC NC_011742.1 2938977 2940803 R catalyzes the oxidation of formate to carbon dioxide and molecular hydrogen; formate hydrogenlyase comprises of a formate dehydrogenase, unidentified electron carriers and a hydrogenase (subunit 3); formate hydrogenlyase subunit 3 complement(2938977..2940803) Escherichia coli S88 7131585 YP_002392627.1 CDS hycB NC_011742.1 2940800 2941411 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90251163, 92215587, 92326636, 2187144; Product type c : carrier; hydrogenase 3, Fe-S subunit complement(2940800..2941411) Escherichia coli S88 7131584 YP_002392628.1 CDS hycA NC_011742.1 2941536 2941997 R regulates several genes involved in the formate hydrogenlyase system; seems to prevent binding of FhlA transcriptional activator to the activator sequence of hyc operon; formate hydrogenlyase regulatory protein HycA complement(2941536..2941997) Escherichia coli S88 7131583 YP_002392629.1 CDS hypA NC_011742.1 2942209 2942559 D plays a role in hydrogenase nickel cofactor insertion; hydrogenase nickel incorporation protein 2942209..2942559 Escherichia coli S88 7131582 YP_002392630.1 CDS hypB NC_011742.1 2942563 2943435 D GTP hydrolase involved in nickel liganding into hydrogenases; hydrogenase nickel incorporation protein HypB 2942563..2943435 Escherichia coli S88 7131593 YP_002392631.1 CDS hypC NC_011742.1 2943426 2943698 D HypC; accessory protein necessary for maturation of the hydrogenase isoforms 1, 2 and 3; forms a complex with HypD, HypE, and HypF proteins, which is the site of ligand biosynthesis and attachment to the iron atom of the NiFe site in the hydrogenase; hydrogenase assembly chaperone 2943426..2943698 Escherichia coli S88 7131594 YP_002392632.1 CDS hypD NC_011742.1 2943698 2944819 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91194542, 92255260, 1849603; Product type f : factor; protein required for maturation of hydrogenases 2943698..2944819 Escherichia coli S88 7131595 YP_002392633.1 CDS hypE NC_011742.1 2944858 2945826 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91194542, 9485446, 1849603; Product type e : enzyme; carbamoyl phosphate phosphatase, hydrogenase 3 maturation protein 2944858..2945826 Escherichia coli S88 7131596 YP_002392634.1 CDS fhlA NC_011742.1 2945900 2947978 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20307603, 21557168, 90368529, 92140045, 94018617, 2118503, 2280686; Product type r : regulator; DNA-binding transcriptional activator 2945900..2947978 Escherichia coli S88 7131597 YP_002392635.1 CDS ECS88_2997 NC_011742.1 2947984 2948451 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; Putative molybdenum-pterin-binding-protein 2947984..2948451 Escherichia coli S88 7129481 YP_002392636.1 CDS ygbA NC_011742.1 2948490 2948834 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2948490..2948834) Escherichia coli S88 7133295 YP_002392637.1 CDS mutS NC_011742.1 2949120 2951681 D This protein performs the mismatch recognition step during the DNA repair process; DNA mismatch repair protein MutS 2949120..2951681 Escherichia coli S88 7133577 YP_002392638.1 CDS pphB NC_011742.1 2951787 2952443 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9130712; Product type e : enzyme; serine/threonine-specific protein phosphatase 2 2951787..2952443 Escherichia coli S88 7129642 YP_002392639.1 CDS ygbI NC_011742.1 2952494 2953291 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(2952494..2953291) Escherichia coli S88 7130759 YP_002392640.1 CDS ygbJ NC_011742.1 2953457 2954365 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative dehydrogenase, with NAD(P)-binding Rossmann-fold domain 2953457..2954365 Escherichia coli S88 7133579 YP_002392641.1 CDS ygbK NC_011742.1 2954362 2955624 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 11520622; hypothetical protein 2954362..2955624 Escherichia coli S88 7133580 YP_002392642.1 CDS ygbL NC_011742.1 2955621 2956259 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative aldolase 2955621..2956259 Escherichia coli S88 7133581 YP_002392643.1 CDS ygbM NC_011742.1 2956264 2957040 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2956264..2957040 Escherichia coli S88 7133582 YP_002392644.1 CDS ygbN NC_011742.1 2957129 2958493 D member of the Gnt family of gluconate transporters; not involved in gluconate transport; unknown function; inner membrane permease YgbN 2957129..2958493 Escherichia coli S88 7133583 YP_002392645.1 CDS ECS88_3008 NC_011742.1 2958636 2959679 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative exported Zn-dependent hydrolase complement(2958636..2959679) Escherichia coli S88 7133584 YP_002392646.1 CDS ECS88_3009 NC_011742.1 2959904 2960455 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 9694845; Product type pf : putative factor; putative protein with flavodoxin fold 2959904..2960455 Escherichia coli S88 7133296 YP_002392647.1 CDS rpoS NC_011742.1 2960633 2961625 R sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor controls a regulon of genes required for protection against external stresses; RNA polymerase sigma factor RpoS complement(2960633..2961625) Escherichia coli S88 7133297 YP_002392648.1 CDS nlpD NC_011742.1 2961688 2962827 R outer membrane lipoprotein involved in stationary-phase cell survival; similar to LppB virulence determinant from Haemophilus somnus; lipoprotein NlpD complement(2961688..2962827) Escherichia coli S88 7133781 YP_002392649.1 CDS pcm NC_011742.1 2962967 2963593 R catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins; protein-L-isoaspartate O-methyltransferase complement(2962967..2963593) Escherichia coli S88 7129723 YP_002392650.1 CDS surE NC_011742.1 2963587 2964348 R catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE complement(2963587..2964348) Escherichia coli S88 7133178 YP_002392651.1 CDS truD NC_011742.1 2964329 2965378 R catalyzes the modification of U13 in tRNA(Glu); tRNA pseudouridine synthase D complement(2964329..2965378) Escherichia coli S88 7131252 YP_002392652.1 CDS ispF NC_011742.1 2965375 2965854 R catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase complement(2965375..2965854) Escherichia coli S88 7130354 YP_002392653.1 CDS ispD NC_011742.1 2965854 2966564 R 4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MEP cytidylyltransferase; MCT; catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; forms homodimers; 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase complement(2965854..2966564) Escherichia coli S88 7130422 YP_002392654.1 CDS ftsB NC_011742.1 2966583 2966894 R forms a complex with FtsL and FtsQ; colocalizes to the septal region of the dividing cell; membrane protein; cell division protein FtsB complement(2966583..2966894) Escherichia coli S88 7130420 YP_002392655.1 CDS ygbE NC_011742.1 2967087 2967410 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(2967087..2967410) Escherichia coli S88 7132847 YP_002392656.1 CDS cysC NC_011742.1 2967460 2968065 R converts ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; in Escherichia coli this enzyme functions in cysteine biosynthesis; adenylylsulfate kinase complement(2967460..2968065) Escherichia coli S88 7133578 YP_002392657.1 CDS cysN NC_011742.1 2968065 2969492 R may be GTPase that regulates ATP sulfurylase activity that is involved in converting ATP and sulfate to diphosphate and adenylylsulfate; in Escherichia coli this enzyme functions in cysteine biosynthesis in the first step; forms a heterodimer with CysD; part of the GTP-binding elongation factor family CysN/NodQ; sulfate adenylyltransferase subunit 1 complement(2968065..2969492) Escherichia coli S88 7130535 YP_002392658.1 CDS cysD NC_011742.1 2969494 2970402 R with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP; sulfate adenylyltransferase subunit 2 complement(2969494..2970402) Escherichia coli S88 7130544 YP_002392659.1 CDS iap NC_011742.1 2970654 2971691 D catalyzes the sequential removal of 2 amino-terminal arginines from alkaline phosphatase isozyme 1 to form isozymes 2 and 3; alkaline phosphatase isozyme conversion aminopeptidase 2970654..2971691 Escherichia coli S88 7130536 YP_002392660.1 CDS ECS88_3025 NC_011742.1 2971816 2971968 R Evidence 1b : Function experimentally demonstrated in the studied species; Product type pm : putative membrane component; small toxic peptide complement(2971816..2971968) Escherichia coli S88 7131603 YP_002392661.1 CDS cysH NC_011742.1 2972233 2972967 R catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite; phosphoadenosine phosphosulfate reductase complement(2972233..2972967) Escherichia coli S88 7133298 YP_002392662.1 CDS cysI NC_011742.1 2973041 2974753 R hemoprotein; NADPH dependent; with the alpha subunit (a flavoprotein) catalyzes the reduction of sulfite to sulfide; sulfite reductase subunit beta complement(2973041..2974753) Escherichia coli S88 7130539 YP_002392663.1 CDS cysJ NC_011742.1 2974753 2976552 R catalyzes the reduction of sulfite to sulfide in the biosynthesis of L-cysteine from sulfate; a flavoprotein with flavin reductase activity; sulfite reductase subunit alpha complement(2974753..2976552) Escherichia coli S88 7130540 YP_002392664.1 CDS ygcM NC_011742.1 2976868 2977233 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12123838; Product type e : enzyme; 6-pyruvoyl tetrahydrobiopterin synthase (PTPS) 2976868..2977233 Escherichia coli S88 7130541 YP_002392665.1 CDS ygcN NC_011742.1 2977311 2978582 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase with FAD/NAD(P)-binding domain 2977311..2978582 Escherichia coli S88 7133588 YP_002392666.1 CDS ygcO NC_011742.1 2978573 2978833 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative 4Fe-4S cluster-containing protein 2978573..2978833 Escherichia coli S88 7132362 YP_002392667.1 CDS ygcP NC_011742.1 2978850 2979425 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative anti-terminator regulatory protein 2978850..2979425 Escherichia coli S88 7129517 YP_002392668.1 CDS ygcQ NC_011742.1 2979573 2980433 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative flavoprotein complement(2979573..2980433) Escherichia coli S88 7129518 YP_002392669.1 CDS ygcR NC_011742.1 2980430 2981209 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative flavoprotein complement(2980430..2981209) Escherichia coli S88 7129519 YP_002392670.1 CDS ygcS NC_011742.1 2981187 2982524 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter complement(2981187..2982524) Escherichia coli S88 7129520 YP_002392671.1 CDS ygcU NC_011742.1 2982618 2984072 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative FAD containing dehydrogenase complement(2982618..2984072) Escherichia coli S88 7129521 YP_002392672.1 CDS ygcW NC_011742.1 2984142 2984927 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative deoxygluconate dehydrogenase complement(2984142..2984927) Escherichia coli S88 7129522 YP_002392673.1 CDS yqcE NC_011742.1 2985245 2986522 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 2985245..2986522 Escherichia coli S88 7129523 YP_002392674.1 CDS ygcE NC_011742.1 2986549 2988027 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative kinase 2986549..2988027 Escherichia coli S88 7132081 YP_002392675.1 CDS ygcF NC_011742.1 2988501 2989172 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2988501..2989172) Escherichia coli S88 7133585 YP_002392676.1 CDS ECS88_3042 NC_011742.1 2989345 2989947 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2989345..2989947 Escherichia coli S88 7133586 YP_002392677.1 CDS ygcG NC_011742.1 2989931 2990854 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2989931..2990854 Escherichia coli S88 7133299 YP_002392678.1 CDS ECS88_3044 NC_011742.1 2990869 2992017 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2990869..2992017 Escherichia coli S88 7133587 YP_002392679.1 CDS ECS88_3046 NC_011742.1 2992011 2992916 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 2992011..2992916 Escherichia coli S88 7133300 YP_002392680.1 CDS eno NC_011742.1 2992976 2994274 R enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase complement(2992976..2994274) Escherichia coli S88 7133301 YP_002392681.1 CDS pyrG NC_011742.1 2994362 2995999 R 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; CTP synthetase complement(2994362..2995999) Escherichia coli S88 7132399 YP_002392682.1 CDS mazG NC_011742.1 2996227 2997018 R functions in degradation of stringent response intracellular messenger ppGpp; in Escherichia coli this gene is co-transcribed with the toxin/antitoxin genes mazEF; activity of MazG is inhibited by MazEF in vitro; ppGpp inhibits mazEF expression; MazG thus works in limiting the toxic activity of the MazF toxin induced during starvation; MazG also interacts with the GTPase protein Era; nucleoside triphosphate pyrophosphohydrolase complement(2996227..2997018) Escherichia coli S88 7131768 YP_002392683.1 CDS chpA NC_011742.1 2997090 2997425 R MazF; endoribonuclease; toxin of the ChpA-ChpR toxin-antitoxin system; toxin ChpA complement(2997090..2997425) Escherichia coli S88 7129428 YP_002392684.1 CDS chpR NC_011742.1 2997425 2997673 R part of the MazF-MazE toxin-antitoxin system; conteracts MazF; antitoxin MazE complement(2997425..2997673) Escherichia coli S88 7131904 YP_002392685.1 CDS relA NC_011742.1 2997751 2999985 R (p)ppGpp synthetase; catalyzes the formation of pppGpp and ppGpp from ATP and GTP or GDP; GDP/GTP pyrophosphokinase complement(2997751..2999985) Escherichia coli S88 7131905 YP_002392686.1 CDS rumA NC_011742.1 3000033 3001334 R in Escherichia coli this enzyme catalyzes the SAM-dependent methylation of U1939 in the 23S ribomal RNA; binds an iron-sulfur cluster [4Fe-4S]; 23S rRNA 5-methyluridine methyltransferase complement(3000033..3001334) Escherichia coli S88 7131816 YP_002392687.1 CDS barA NC_011742.1 3001391 3004147 D part of the two-component regulatory system with UvrY; involved in the regulation of carbon metabolism via the csrA/csrB regulatory system; hybrid sensory histidine kinase BarA 3001391..3004147 Escherichia coli S88 7131310 YP_002392688.1 CDS gudD NC_011742.1 3004378 3005718 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20233700, 9772162, 10762278, 13971911; Product type e : enzyme; (D)-glucarate dehydratase 1 complement(3004378..3005718) Escherichia coli S88 7129987 YP_002392689.1 CDS gudX NC_011742.1 3005739 3007079 R Evidence 2b : Function of strongly homologous gene; PubMedId : 9772162; Product type e : enzyme; glucarate dehydratase complement(3005739..3007079) Escherichia coli S88 7128878 YP_002392690.1 CDS gudP NC_011742.1 3007081 3008433 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10762278; Product type pt : putative transporter; putative D-glucarate transporter complement(3007081..3008433) Escherichia coli S88 7128880 YP_002392691.1 CDS yqcA NC_011742.1 3008867 3009316 R An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group; flavodoxin complement(3008867..3009316) Escherichia coli S88 7128879 YP_002392692.1 CDS truC NC_011742.1 3009334 3010116 R catalyzes formation of pseudouridine at position 65 in tRNA-Ile1 and tRNA-Asp; tRNA pseudouridine synthase C complement(3009334..3010116) Escherichia coli S88 7132079 YP_002392693.1 CDS yqcC NC_011742.1 3010116 3010445 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3010116..3010445) Escherichia coli S88 7130353 YP_002392694.1 CDS syd NC_011742.1 3011067 3011612 R putative SecY regulator that either chelates excess SecY or negatively regulates the SecYE translocase function; SecY interacting protein Syd complement(3011067..3011612) Escherichia coli S88 7130503 YP_002392695.1 CDS queF NC_011742.1 3011680 3012528 D catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in queuosine biosynthesis; 7-cyano-7-deazaguanine reductase 3011680..3012528 Escherichia coli S88 7131253 YP_002392696.1 CDS ygdH NC_011742.1 3012640 3014004 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3012640..3014004 Escherichia coli S88 7131777 YP_002392697.1 CDS sdaC NC_011742.1 3014561 3015850 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8752353, 8026499; Product type pt : putative transporter; putative serine transporter 3014561..3015850 Escherichia coli S88 7129527 YP_002392698.1 CDS sdaB NC_011742.1 3015908 3017275 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91193203, 93215657, 8385012; Product type e : enzyme; L-serine deaminase II 3015908..3017275 Escherichia coli S88 7131372 YP_002392699.1 CDS xni NC_011742.1 3017297 3018142 D has 3'-5' exonuclease activity that preferentially acts on ssDNA; also 3'-phosphodiesterase activity at sites with 3' incised apurinic/apyrimidinic sites; can remove 3' phosphoglycolate groups; exonuclease IX 3017297..3018142 Escherichia coli S88 7131371 YP_002392700.1 CDS fucO NC_011742.1 3018247 3019398 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88142551, 89291720, 2553671, 2661535, 2664711, 8385012; Product type e : enzyme; L-1,2-propanediol oxidoreductase complement(3018247..3019398) Escherichia coli S88 7132438 YP_002392701.1 CDS fucA NC_011742.1 3019423 3020070 R catalyzes the formation of glycerone phosphate and (S)-lactaldehyde from L-fuculose 1-phosphate; L-fuculose phosphate aldolase complement(3019423..3020070) Escherichia coli S88 7132149 YP_002392702.1 CDS fucP NC_011742.1 3020617 3021933 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88142551, 90036697, 2553671, 2664711, 7783647; Product type t : transporter; L-fucose transporter 3020617..3021933 Escherichia coli S88 7132146 YP_002392703.1 CDS fucI NC_011742.1 3021966 3023741 D catalyzes the conversion of the aldose L-fucose into the corresponding ketose L-fuculose; L-fucose isomerase 3021966..3023741 Escherichia coli S88 7132150 YP_002392704.1 CDS fucK NC_011742.1 3023820 3025268 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88142551, 90036697, 2664711, 13905785; Product type e : enzyme; L-fuculokinase 3023820..3025268 Escherichia coli S88 7132147 YP_002392705.1 CDS fucU NC_011742.1 3025270 3025692 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15060078, 12738765, 80049526, 2664711; Product type e : enzyme; L-fucose mutarotase 3025270..3025692 Escherichia coli S88 7132148 YP_002392706.1 CDS fucR NC_011742.1 3025750 3026481 D regulates expression of genes involved in L-fucose utilization; DNA-binding transcriptional activator FucR 3025750..3026481 Escherichia coli S88 7132152 YP_002392707.1 CDS ygdE NC_011742.1 3026525 3027625 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 21188420, 7704273; Product type pe : putative enzyme; putative RNA 2'-O-ribose methyltransferase complement(3026525..3027625) Escherichia coli S88 7132151 YP_002392708.1 CDS ygdD NC_011742.1 3027618 3028013 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 7704273; Product type pm : putative membrane component; hypothetical protein complement(3027618..3028013) Escherichia coli S88 7129526 YP_002392709.1 CDS gcvA NC_011742.1 3028032 3028949 R Glycine cleavage system transcriptional activator; activates the gcvTHP operon in the presence of glycine and represses the operon in its absence; DNA-binding transcriptional activator GcvA complement(3028032..3028949) Escherichia coli S88 7129525 YP_002392710.1 CDS ygdI NC_011742.1 3029300 3029527 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3029300..3029527) Escherichia coli S88 7132197 YP_002392711.1 CDS csdA NC_011742.1 3029719 3030924 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15148362, 9278392, 10739946, 10829016; Product type e : enzyme; cysteine sulfinate desulfinase 3029719..3030924 Escherichia coli S88 7129528 YP_002392712.1 CDS ygdK NC_011742.1 3030924 3031367 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative Fe-S metabolism protein (sufE-like) 3030924..3031367 Escherichia coli S88 7131969 YP_002392713.1 CDS ygdL NC_011742.1 3031418 3032224 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3031418..3032224) Escherichia coli S88 7129529 YP_002392714.1 CDS mltA NC_011742.1 3032301 3033398 R membrane-bound, lytic; catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine residues; murein transglycosylase A complement(3032301..3033398) Escherichia coli S88 7129530 YP_002392715.1 CDS ECS88_3083 NC_011742.1 3034518 3035039 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3034518..3035039 Escherichia coli S88 7129892 YP_002392716.1 CDS ECS88_3084 NC_011742.1 3035092 3036636 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3035092..3036636 Escherichia coli S88 7133302 YP_002392717.1 CDS ECS88_3085 NC_011742.1 3036654 3037991 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3036654..3037991 Escherichia coli S88 7133303 YP_002392718.1 CDS ECS88_3086 NC_011742.1 3037988 3038653 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative membrane associated protein 3037988..3038653 Escherichia coli S88 7133304 YP_002392719.1 CDS ECS88_3087 NC_011742.1 3038666 3040318 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3038666..3040318 Escherichia coli S88 7133305 YP_002392720.1 CDS ECS88_3088 NC_011742.1 3040376 3040867 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3040376..3040867 Escherichia coli S88 7133306 YP_002392721.1 CDS ECS88_3089 NC_011742.1 3041059 3043704 D Evidence 2b : Function of strongly homologous gene; Product type f : factor; ATPases with chaperone activity, ATP-binding subunit 3041059..3043704 Escherichia coli S88 7133307 YP_002392722.1 CDS ECS88_3090 NC_011742.1 3043716 3046196 D hypothetical protein 3043716..3046196 Escherichia coli S88 7133308 YP_002392723.1 CDS ECS88_3091 NC_011742.1 3046168 3047382 D hypothetical protein 3046168..3047382 Escherichia coli S88 7133309 YP_002392724.1 CDS ECS88_3092 NC_011742.1 3047361 3047975 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 3047361..3047975 Escherichia coli S88 7133310 YP_002392725.1 CDS ECS88_3093 NC_011742.1 3047950 3048783 D hypothetical protein 3047950..3048783 Escherichia coli S88 7133311 YP_002392726.1 CDS ECS88_3094 NC_011742.1 3048752 3049045 D hypothetical protein 3048752..3049045 Escherichia coli S88 7133312 YP_002392727.1 CDS ECS88_3096 NC_011742.1 3049660 3050907 D hypothetical protein 3049660..3050907 Escherichia coli S88 7133314 YP_002392728.1 CDS ECS88_3097 NC_011742.1 3050917 3054270 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3050917..3054270 Escherichia coli S88 7133315 YP_002392729.1 CDS ECS88_3098 NC_011742.1 3054236 3055873 D hypothetical protein 3054236..3055873 Escherichia coli S88 7133316 YP_002392730.1 CDS ECS88_3099 NC_011742.1 3055873 3057456 D hypothetical protein 3055873..3057456 Escherichia coli S88 7133317 YP_002392731.1 CDS ECS88_3100 NC_011742.1 3057444 3058085 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3057444..3058085 Escherichia coli S88 7133318 YP_002392732.1 CDS ECS88_3102 NC_011742.1 3059155 3060915 D hypothetical protein 3059155..3060915 Escherichia coli S88 7133319 YP_002392733.1 CDS ECS88_3103 NC_011742.1 3060870 3061958 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3060870..3061958 Escherichia coli S88 7133320 YP_002392734.1 CDS ECS88_3104 NC_011742.1 3061939 3062475 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3061939..3062475 Escherichia coli S88 7133321 YP_002392735.1 CDS ECS88_3105 NC_011742.1 3062479 3062907 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3062479..3062907 Escherichia coli S88 7133322 YP_002392736.1 CDS ECS88_3106 NC_011742.1 3062907 3064283 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3062907..3064283 Escherichia coli S88 7133323 YP_002392737.1 CDS ECS88_3107 NC_011742.1 3064585 3065541 R Evidence 2b : Function of strongly homologous gene; Product type e : enzyme; 2-hydroxyacid dehydrogenase complement(3064585..3065541) Escherichia coli S88 7133324 YP_002392738.1 CDS ECS88_3108 NC_011742.1 3065604 3066200 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphosugar isomerase complement(3065604..3066200) Escherichia coli S88 7133325 YP_002392739.1 CDS ECS88_3109 NC_011742.1 3066203 3067378 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative aminotransferase complement(3066203..3067378) Escherichia coli S88 7133326 YP_002392740.1 CDS ECS88_3110 NC_011742.1 3067378 3068958 R Evidence 2b : Function of strongly homologous gene; Product type t : transporter; Phosphotransferase system system, maltose and glucose-specific IIABC component complement(3067378..3068958) Escherichia coli S88 7133327 YP_002392741.1 CDS ECS88_3111 NC_011742.1 3068990 3069871 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcription antiterminator complement(3068990..3069871) Escherichia coli S88 7133328 YP_002392742.1 CDS amiC NC_011742.1 3070072 3071325 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12787347, 21348478; Product type e : enzyme; N-acetylmuramoyl-L-alanine amidase complement(3070072..3071325) Escherichia coli S88 7133329 YP_002392743.1 CDS argA NC_011742.1 3071557 3072888 D catalyzes the formation of N-acetyl-L-glutamate from L-glutamate and acetyl-CoA in arginine biosynthesis; N-acetylglutamate synthase 3071557..3072888 Escherichia coli S88 7133059 YP_002392744.1 CDS recD NC_011742.1 3072950 3074776 R helicase/nuclease; with RecBC catalyzes the exonucleolytic cleavage of DNA; RecD has 5' to 3' helicase activity; exonuclease V subunit alpha complement(3072950..3074776) Escherichia coli S88 7133091 YP_002392745.1 CDS recB NC_011742.1 3074776 3078318 R helicase/nuclease; with RecCD catalyzes the exonucleolytic cleavage of DNA; RecD has 5' to 3' helicase activity; exonuclease V subunit beta complement(3074776..3078318) Escherichia coli S88 7131806 YP_002392746.1 CDS ptr NC_011742.1 3078311 3081199 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91193232, 1570301, 3308636, 3534791, 3537960, 8099278; Product type e : enzyme; protease III complement(3078311..3081199) Escherichia coli S88 7131804 YP_002392747.1 CDS recC NC_011742.1 3081375 3084743 R catalyzes ATP-dependent exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides; component of the RecBCD (Exo V) helicase/nuclease complex that is essential for recombination; exonuclease V subunit gamma complement(3081375..3084743) Escherichia coli S88 7130816 YP_002392748.1 CDS ppdC NC_011742.1 3084756 3085079 R Evidence 2b : Function of strongly homologous gene; PubMedId : 7934814; Product type e : enzyme; hypothetical protein complement(3084756..3085079) Escherichia coli S88 7131805 YP_002392749.1 CDS ygdB NC_011742.1 3085064 3085471 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3085064..3085471) Escherichia coli S88 7130756 YP_002392750.1 CDS ppdB NC_011742.1 3085468 3086031 R Evidence 2b : Function of strongly homologous gene; PubMedId : 7934814; Product type e : enzyme; hypothetical protein complement(3085468..3086031) Escherichia coli S88 7129524 YP_002392751.1 CDS ppdA NC_011742.1 3086022 3086492 R Evidence 2b : Function of strongly homologous gene; PubMedId : 7934814; Product type e : enzyme; hypothetical protein complement(3086022..3086492) Escherichia coli S88 7130755 YP_002392752.1 CDS thyA NC_011742.1 3086677 3087471 R ThyA; catalyzes formation of dTMP and 7,8-dihydrofolate from 5,10-methylenetetrahydrofolate and dUMP; involved in deoxyribonucleotide biosynthesis; there are 2 copies in some Bacilli, one of which appears to be phage-derived; thymidylate synthase complement(3086677..3087471) Escherichia coli S88 7130754 YP_002392753.1 CDS lgt NC_011742.1 3087478 3088353 R transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase complement(3087478..3088353) Escherichia coli S88 7131308 YP_002392754.1 CDS ptsP NC_011742.1 3088504 3090750 R member of a second PTS chain involved in nitrogen metabolism; PtsP phosphorylates NPr; fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain complement(3088504..3090750) Escherichia coli S88 7130492 YP_002392755.1 CDS nudH NC_011742.1 3090763 3091293 R hydrolyzes diadenosine polyphosphate; dinucleoside polyphosphate hydrolase complement(3090763..3091293) Escherichia coli S88 7131743 YP_002392756.1 CDS mutH NC_011742.1 3091978 3092667 D MutH; Sequence-specific endonuclease that cleaves unmethylated GATC sequences during DNA repair; DNA mismatch repair protein 3091978..3092667 Escherichia coli S88 7129756 YP_002392757.1 CDS ygdQ NC_011742.1 3092736 3093449 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3092736..3093449 Escherichia coli S88 7129639 YP_002392758.1 CDS ygdR NC_011742.1 3093587 3093805 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3093587..3093805 Escherichia coli S88 7129533 YP_002392759.1 CDS tas NC_011742.1 3093913 3094953 D complements the prephenate dehydrogenase dysfunction of an Escherichia coli tyrosine auxotroph strain; member of the aldo/keto reductase 2 family; crystal structure of purified Escherichia coli protein shows bound NADPH; putative aldo-keto reductase 3093913..3094953 Escherichia coli S88 7129534 YP_002392760.1 CDS ygeD NC_011742.1 3094985 3096178 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 8300626; Product type pm : putative membrane component; lysophospholipid transporter LplT complement(3094985..3096178) Escherichia coli S88 7131261 YP_002392761.1 CDS aas NC_011742.1 3096171 3098330 R Transfers fatty acids to the 1-position via an enzyme-bound acyl-ACP intermediate in the presence of ATP and magnesium. Its physiological function is to regenerate phosphatidylethanolamine from 2-acyl-glycero-3-phosphoethanolamine (2-acyl-GPE) formed by transacylation reactions or degradation by phospholipase A1; bifunctional acyl-[acyl carrier protein] synthetase/2-acylglycerophosphoethanolamine acyltransferase complement(3096171..3098330) Escherichia coli S88 7129536 YP_002392762.1 CDS galR NC_011742.1 3098916 3099947 D controls transcription of galETKM; DNA-binding transcriptional regulator GalR 3098916..3099947 Escherichia coli S88 7133134 YP_002392763.1 CDS lysA NC_011742.1 3099954 3101216 R catalyzes the decarboxylation of diaminopimelate into lysine; pyridoxal phosphate(PLP)-binding; diaminopimelate decarboxylase complement(3099954..3101216) Escherichia coli S88 7132175 YP_002392764.1 CDS lysR NC_011742.1 3101338 3102273 D activates the transcription of the lysA gene encoding diaminopimelate decarboxylase; DNA-binding transcriptional regulator LysR 3101338..3102273 Escherichia coli S88 7129393 YP_002392765.1 CDS ygeA NC_011742.1 3102260 3102952 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15135544; Product type pe : putative enzyme; putative racemase complement(3102260..3102952) Escherichia coli S88 7129396 YP_002392766.1 CDS araE NC_011742.1 3103081 3104499 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 7030324, 90239116, 91154204, 2836407, 3543693, 6319708; Product type t : transporter; arabinose transporter complement(3103081..3104499) Escherichia coli S88 7129535 YP_002392767.1 CDS kduD NC_011742.1 3104814 3105575 R catalyzes the formation of 3-dehydro-2-deoxy-D-gluconate from 2-deoxy-D-gluconate; 2-deoxy-D-gluconate 3-dehydrogenase complement(3104814..3105575) Escherichia coli S88 7133084 YP_002392768.1 CDS kduI NC_011742.1 3105605 3106441 R 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase; catalyzes the interconversion of 4-deoxy-L-threo-5-hexosulose uronate to 3-deoxy-D-glycero-2,5-hexodiulosonate; 5-keto-4-deoxyuronate isomerase complement(3105605..3106441) Escherichia coli S88 7130451 YP_002392769.1 CDS yqeF NC_011742.1 3106728 3107909 R Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; in Rhizobia and Ralstonia is involved in PHB biosynthesis; acetyl-CoA acetyltransferase complement(3106728..3107909) Escherichia coli S88 7130452 YP_002392770.1 CDS yqeG NC_011742.1 3108164 3109393 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 3108164..3109393 Escherichia coli S88 7132085 YP_002392771.1 CDS ygeR NC_011742.1 3109862 3110617 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15150243; Product type r : regulator; Tetratricopeptide repeat transcriptional regulator complement(3109862..3110617) Escherichia coli S88 7131985 YP_002392772.1 CDS xdhA NC_011742.1 3111070 3113328 D putative molybdenum cofactor-binding protein; participates in purine salvage; xanthine dehydrogenase subunit XdhA 3111070..3113328 Escherichia coli S88 7129537 YP_002392773.1 CDS xdhB NC_011742.1 3113339 3114217 D FAD-binding subunit; with XdhA and XdhC participates in purine salvage; xanthine dehydrogenase subunit XdhB 3113339..3114217 Escherichia coli S88 7132516 YP_002392774.1 CDS xdhC NC_011742.1 3114214 3114693 D iron-sulfur-binding subunit; with XdhA and XdhB participates in purine salvage; xanthine dehydrogenase subunit XdhC 3114214..3114693 Escherichia coli S88 7132517 YP_002392775.1 CDS ygeV NC_011742.1 3114733 3116511 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(3114733..3116511) Escherichia coli S88 7132518 YP_002392776.1 CDS ygeW NC_011742.1 3116987 3118177 D Evidence 4 : Homologs of previously reported genes of unknown function; aspartate/ornithine carbamoyltransferase family protein 3116987..3118177 Escherichia coli S88 7129538 YP_002392777.1 CDS ygeX NC_011742.1 3118235 3119431 D catalyzes the formation of pyruvate from 2,3-diaminopropionate; diaminopropionate ammonia-lyase 3118235..3119431 Escherichia coli S88 7129539 YP_002392778.1 CDS ygeY NC_011742.1 3119489 3120700 D Zn-dependent extracellular dipeptidase; similar to succinyl-diaminopimelate desuccinylases; peptidase 3119489..3120700 Escherichia coli S88 7129540 YP_002392779.1 CDS hyuA NC_011742.1 3120753 3122138 D catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase 3120753..3122138 Escherichia coli S88 7129541 YP_002392780.1 CDS yqeA NC_011742.1 3122186 3123118 D catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP; carbamate kinase 3122186..3123118 Escherichia coli S88 7131599 YP_002392781.1 CDS yqeB NC_011742.1 3123159 3124784 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative NAD(P)-binding Rossman fold complement(3123159..3124784) Escherichia coli S88 7132082 YP_002392782.1 CDS yqeC NC_011742.1 3124832 3125602 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3124832..3125602) Escherichia coli S88 7132083 YP_002392783.1 CDS ygfJ NC_011742.1 3125706 3126284 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3125706..3126284 Escherichia coli S88 7132084 YP_002392784.1 CDS ygfK NC_011742.1 3126606 3129704 D with YgfM and YgfN forms a selenate reductase, which seems to catalyze the reduction of selenate to selenite; YgfK mutants are unable to reduce selenate; involved in purine salvage process; seems to act as an oxidoreductase, but sequence similarity suggests it is a dihydrothymine dehydrogenase; putative selenate reductase subunit YgfK 3126606..3129704 Escherichia coli S88 7129545 YP_002392785.1 CDS ssnA NC_011742.1 3129707 3131035 D in Escherichia coli expression is induced in response to phase-specific signals and controlled by RpoS; putative chlorohydrolase/aminohydrolase 3129707..3131035 Escherichia coli S88 7129546 YP_002392786.1 CDS ygfM NC_011742.1 3131086 3131865 D with YgfK and YgfN forms a selenate reductase, which seems to catalyze the reduction of selenate to selenite; YgfM contains a FAD domain; putative selenate reductase subunit YgfM 3131086..3131865 Escherichia coli S88 7130651 YP_002392787.1 CDS xdhD NC_011742.1 3131862 3134732 D with YgfK and YgfM forms a selenate reductase, which seems to catalyze the reduction of selenate to selenite; molybdopterin-containing enzyme; oxidase activity toward hypoxanthine and xanthine can be detected if these substrates are present at high concentration; putative selenate reductase subunit YgfN 3131862..3134732 Escherichia coli S88 7129547 YP_002392788.1 CDS ygfO NC_011742.1 3134897 3136297 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 20372655, 98213740; Product type pt : putative transporter; putative transporter 3134897..3136297 Escherichia coli S88 7132519 YP_002392789.1 CDS guaD NC_011742.1 3136312 3137631 D Catalyzes the deamination of guanine; guanine deaminase 3136312..3137631 Escherichia coli S88 7129548 YP_002392790.1 CDS ygfQ NC_011742.1 3137667 3139034 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 3137667..3139034 Escherichia coli S88 7128877 YP_002392791.1 CDS ygfS NC_011742.1 3139070 3139558 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative oxidoreductase, 4Fe-4S ferredoxin-type subunit complement(3139070..3139558) Escherichia coli S88 7129549 YP_002392792.1 CDS ygfT NC_011742.1 3139558 3141477 R unknown function; in E. coli the aegA gene is regulated by Fnr, NarXL, and NarQ (but not ArcA), induced under anaerobic conditions and repressed in the presence of nitrate (anaerobic); putative oxidoreductase Fe-S binding subunit complement(3139558..3141477) Escherichia coli S88 7129550 YP_002392793.1 CDS ECS88_3166 NC_011742.1 3141780 3141968 D Evidence 6 : Doubtful CDS; hypothetical protein 3141780..3141968 Escherichia coli S88 7129551 YP_002392794.1 CDS ygfU NC_011742.1 3141913 3143361 D Evidence 2b : Function of strongly homologous gene; PubMedId : 9098051; Product type t : transporter; transporter 3141913..3143361 Escherichia coli S88 7133330 YP_002392795.1 CDS idi NC_011742.1 3143611 3144159 D catalyzes the rearrangement of isopentenyl diphosphate to dimethylallyl phosphate; isopentenyl-diphosphate delta-isomerase 3143611..3144159 Escherichia coli S88 7129552 YP_002392796.1 CDS lysS NC_011742.1 3144202 3145719 R 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; lysyl-tRNA synthetase complement(3144202..3145719) Escherichia coli S88 7131614 YP_002392797.1 CDS prfB NC_011742.1 3145729 3146827 R 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; peptide chain release factor 2 complement(join(3145729..3146751,3146753..3146827)) Escherichia coli S88 7129397 YP_002392798.1 CDS recJ NC_011742.1 3146918 3148651 R 5'-3' single-stranded-DNA-specific exonuclease; ssDNA exonuclease RecJ complement(3146918..3148651) Escherichia coli S88 7130773 YP_002392799.1 CDS dsbC NC_011742.1 3148657 3149367 R DsbC; periplasmic protein with protein disulfide isomerase activity; this protein also shows disulfide oxidoreductase activity; thiol:disulfide interchange protein DsbC complement(3148657..3149367) Escherichia coli S88 7131809 YP_002392800.1 CDS xerD NC_011742.1 3149392 3150288 R site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; XerD specifically exchanges the bottom strands; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs; site-specific tyrosine recombinase XerD complement(3149392..3150288) Escherichia coli S88 7130241 YP_002392801.1 CDS fldB NC_011742.1 3150400 3150921 D An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic; flavodoxin FldB 3150400..3150921 Escherichia coli S88 7132521 YP_002392802.1 CDS ygfX NC_011742.1 3150961 3151368 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3150961..3151368) Escherichia coli S88 7129512 YP_002392803.1 CDS ygfY NC_011742.1 3151349 3151615 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3151349..3151615) Escherichia coli S88 7129553 YP_002392804.1 CDS ygfZ NC_011742.1 3151858 3152838 D physiological role is not clear; not essential for growth but mutants grow poorly; mutations suppress hda null mutations; may be involved in regulation of ATP-DnaA levels; may also be involved in regulation of tRNA modifications; can bind folic acid and tetrahydrofolate; forms a three domain ring-like structure with a central channel; structurally similar to DMGO protein from A. globiformis; shows sequence similarity to yeast CAF17 transcriptional regulator; putative global regulator 3151858..3152838 Escherichia coli S88 7129554 YP_002392805.1 CDS yqfA NC_011742.1 3152915 3153574 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative hemolysin, inner membrane subunit complement(3152915..3153574) Escherichia coli S88 7129555 YP_002392806.1 CDS yqfB NC_011742.1 3153738 3154049 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3153738..3154049) Escherichia coli S88 7132087 YP_002392807.1 CDS bglA NC_011742.1 3154088 3155527 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87222180, 88297127, 92334140; Product type e : enzyme; 6-phospho-beta-glucosidase A 3154088..3155527 Escherichia coli S88 7132088 YP_002392808.1 CDS gcvP NC_011742.1 3155693 3158566 R acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; glycine dehydrogenase complement(3155693..3158566) Escherichia coli S88 7129113 YP_002392809.1 CDS gcvH NC_011742.1 3158684 3159073 R part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor; glycine cleavage system protein H complement(3158684..3159073) Escherichia coli S88 7132199 YP_002392810.1 CDS gcvT NC_011742.1 3159097 3160191 R catalyzes the transfer of a methylene carbon from the methylamine-loaded GcvH protein to tetrahydrofolate, causing the release of ammonia and the generation of reduced GcvH protein; glycine cleavage system aminomethyltransferase T complement(3159097..3160191) Escherichia coli S88 7132198 YP_002392811.1 CDS visC NC_011742.1 3160639 3161841 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1339425; Product type pe : putative enzyme; hypothetical protein complement(3160639..3161841) Escherichia coli S88 7132201 YP_002392812.1 CDS ubiH NC_011742.1 3161864 3163042 R Oxygenase that introduces the hydroxyl group at carbon four of 2-octaprenyl-6-methoxyphenol resulting in the formation of 2-octaprenyl-6-methoxy-1,4-benzoquinone; 2-octaprenyl-6-methoxyphenyl hydroxylase complement(3161864..3163042) Escherichia coli S88 7132473 YP_002392813.1 CDS pepP NC_011742.1 3163039 3164364 R exopeptidase able to cleave the peptide bond of the last amino acid if linked to a proline residue; substrate can be as short as a dipeptide; proline aminopeptidase P II complement(3163039..3164364) Escherichia coli S88 7130387 YP_002392814.1 CDS ygfB NC_011742.1 3164390 3164968 R the crystal structure of Haemophilus influenzae HI0817 showed that this protein forms dimers; function unknown; hypothetical protein complement(3164390..3164968) Escherichia coli S88 7133674 YP_002392815.1 CDS zapA NC_011742.1 3165136 3165465 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 412171; Product type cp : cell process; Z-ring-associated protein 3165136..3165465 Escherichia coli S88 7129543 YP_002392816.1 CDS ygfA NC_011742.1 3165765 3166313 D ygfA expression increases five to eight fold in Escherichia coli cells growing as biofilms; unknown function; putative ligase 3165765..3166313 Escherichia coli S88 7130655 YP_002392817.1 CDS serA NC_011742.1 3166703 3167935 R catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate; D-3-phosphoglycerate dehydrogenase complement(3166703..3167935) Escherichia coli S88 7131346 YP_002392818.1 CDS rpiA NC_011742.1 3168191 3168850 R Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway; ribose-5-phosphate isomerase A complement(3168191..3168850) Escherichia coli S88 7130579 YP_002392819.1 CDS yqfE NC_011742.1 3168906 3169136 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3168906..3169136) Escherichia coli S88 7132760 YP_002392820.1 CDS argP NC_011742.1 3169277 3170170 D specific inhibitor of chromosomal initiation of replication in vitro; binds the three 13-mers in the origin (oriC) to block initiation of replication; also controls genes involved in arginine transport; chromosome replication initiation inhibitor protein 3169277..3170170 Escherichia coli S88 7132089 YP_002392821.1 CDS ygfI NC_011742.1 3171425 3172321 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(3171425..3172321) Escherichia coli S88 7131117 YP_002392822.1 CDS yggE NC_011742.1 3172479 3173219 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3172479..3173219) Escherichia coli S88 7129544 YP_002392823.1 CDS argO NC_011742.1 3173312 3173944 R Involved in the export of arginine; arginine exporter protein complement(3173312..3173944) Escherichia coli S88 7129558 YP_002392824.1 CDS mscS NC_011742.1 3174083 3174943 R participates in the regulation of osmotic pressure changes within the cel; mechanosensitive channel MscS complement(3174083..3174943) Escherichia coli S88 7133099 YP_002392825.1 CDS fbaA NC_011742.1 3175134 3176213 R catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate; fructose-bisphosphate aldolase complement(3175134..3176213) Escherichia coli S88 7129615 YP_002392826.1 CDS pgk NC_011742.1 3176428 3177591 R Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase complement(3176428..3177591) Escherichia coli S88 7129447 YP_002392827.1 CDS epd NC_011742.1 3177641 3178660 R NAD-dependent; catalyzes the formation of 4-phosphoerythronate from erythrose 4-phosphate in the biosynthesis of pyridoxine 5'-phosphate; erythrose 4-phosphate dehydrogenase complement(3177641..3178660) Escherichia coli S88 7133691 YP_002392828.1 CDS ECS88_3204 NC_011742.1 3179032 3179463 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein with PD1-like DNA-binding motif 3179032..3179463 Escherichia coli S88 7132409 YP_002392829.1 CDS ECS88_3205 NC_011742.1 3179486 3180064 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ABC-type transport system 3179486..3180064 Escherichia coli S88 7133331 YP_002392830.1 CDS ECS88_3206 NC_011742.1 3180065 3180772 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ABC-type transport system 3180065..3180772 Escherichia coli S88 7133332 YP_002392831.1 CDS ECS88_3207 NC_011742.1 3180754 3181437 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ATP-binding protein of ABC transport system 3180754..3181437 Escherichia coli S88 7133333 YP_002392832.1 CDS ECS88_3208 NC_011742.1 3181398 3182108 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ATP-binding protein of ABC transport system 3181398..3182108 Escherichia coli S88 7133334 YP_002392833.1 CDS frcK NC_011742.1 3182080 3182793 R Evidence 4 : Homologs of previously reported genes of unknown function; putative fructose transport system kinase complement(3182080..3182793) Escherichia coli S88 7133335 YP_002392834.1 CDS yggD NC_011742.1 3182790 3183299 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(3182790..3183299) Escherichia coli S88 7129556 YP_002392835.1 CDS yggP NC_011742.1 3183633 3184910 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative dehydrogenase complement(3183633..3184910) Escherichia coli S88 7129560 YP_002392836.1 CDS cmtA NC_011742.1 3184925 3186313 R Evidence 2b : Function of strongly homologous gene; PubMedId : 8353127; Product type t : transporter; fused mannitol-specific PTS enzymes: IIB component ; IIC component complement(3184925..3186313) Escherichia coli S88 7129567 YP_002392837.1 CDS cmtB NC_011742.1 3186341 3186784 R TolM; with CmtA (IIBC), CmtB possibly forms the mannitol-like permease component of the cryptic mannitol phosphotransferase system, which phosphorylates and transports various carbohydrates and polyhydric alcohols in Escherichia coli; cytoplasmic protein; putative mannitol phosphotransferase subunit EIIA complement(3186341..3186784) Escherichia coli S88 7131936 YP_002392838.1 CDS ECS88_3216 NC_011742.1 3187161 3188069 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative membrane protease 3187161..3188069 Escherichia coli S88 7131937 YP_002392839.1 CDS tktA NC_011742.1 3188289 3190280 R 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; transketolase complement(3188289..3190280) Escherichia coli S88 7133336 YP_002392840.1 CDS yggG NC_011742.1 3190558 3191316 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1310091; Product type pe : putative enzyme; putative peptidase 3190558..3191316 Escherichia coli S88 7133476 YP_002392841.1 CDS speB NC_011742.1 3191520 3192440 R catalyzes the formation of putrescine from agmatine; agmatinase complement(3191520..3192440) Escherichia coli S88 7129561 YP_002392842.1 CDS ECS88_3220 NC_011742.1 3192576 3193307 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(3192576..3193307) Escherichia coli S88 7130625 YP_002392843.1 CDS speA NC_011742.1 3193453 3195429 R catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis; arginine decarboxylase complement(3193453..3195429) Escherichia coli S88 7133337 YP_002392844.1 CDS yqgB NC_011742.1 3195438 3195584 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3195438..3195584) Escherichia coli S88 7130624 YP_002392845.1 CDS yqgC NC_011742.1 3195705 3195920 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3195705..3195920 Escherichia coli S88 7132091 YP_002392846.1 CDS metK NC_011742.1 3196224 3197378 D catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase 3196224..3197378 Escherichia coli S88 7132092 YP_002392847.1 CDS galP NC_011742.1 3197815 3199209 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9182541; Product type t : transporter; D-galactose transporter 3197815..3199209 Escherichia coli S88 7128819 YP_002392848.1 CDS sprT NC_011742.1 3199286 3199783 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 7984428, 8113204; hypothetical protein 3199286..3199783 Escherichia coli S88 7132174 YP_002392849.1 CDS endA NC_011742.1 3199878 3200585 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 72060411, 92335461, 4955462, 7867949, 8113204; Product type e : enzyme; DNA-specific endonuclease I 3199878..3200585 Escherichia coli S88 7130635 YP_002392850.1 CDS yggJ NC_011742.1 3200665 3201396 D 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; 16S ribosomal RNA methyltransferase RsmE 3200665..3201396 Escherichia coli S88 7132398 YP_002392851.1 CDS gshB NC_011742.1 3201409 3202359 D catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione; glutathione synthetase 3201409..3202359 Escherichia coli S88 7129563 YP_002392852.1 CDS yqgE NC_011742.1 3202468 3203031 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3202468..3203031 Escherichia coli S88 7130077 YP_002392853.1 CDS yqgF NC_011742.1 3203031 3203447 D similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function; Holliday junction resolvase-like protein 3203031..3203447 Escherichia coli S88 7132093 YP_002392854.1 CDS yggR NC_011742.1 3203621 3204601 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 1676385; Product type t : transporter; transporter complement(3203621..3204601) Escherichia coli S88 7132094 YP_002392855.1 CDS yggS NC_011742.1 3204619 3205323 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative enzyme 3204619..3205323 Escherichia coli S88 7129568 YP_002392856.1 CDS yggT NC_011742.1 3205341 3205907 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3205341..3205907 Escherichia coli S88 7129569 YP_002392857.1 CDS yggU NC_011742.1 3205904 3206194 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 12975589; hypothetical protein 3205904..3206194 Escherichia coli S88 7129570 YP_002392858.1 CDS yggV NC_011742.1 3206202 3206795 D HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine; putative deoxyribonucleotide triphosphate pyrophosphatase 3206202..3206795 Escherichia coli S88 7129571 YP_002392859.1 CDS yggW NC_011742.1 3206788 3207924 D catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 3206788..3207924 Escherichia coli S88 7129572 YP_002392860.1 CDS yggM NC_011742.1 3207993 3209000 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3207993..3209000) Escherichia coli S88 7129573 YP_002392861.1 CDS ansB NC_011742.1 3209117 3210163 R catalyzes the formation of aspartate from asparagine, periplasmic; regulated by cyclic AMP receptor protein (CRP) and also induced by anaerobiosis; L-asparaginase II complement(3209117..3210163) Escherichia coli S88 7129565 YP_002392862.1 CDS yggN NC_011742.1 3210339 3211058 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 11274153; hypothetical protein complement(3210339..3211058) Escherichia coli S88 7133070 YP_002392863.1 CDS yggL NC_011742.1 3211242 3211568 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3211242..3211568) Escherichia coli S88 7129566 YP_002392864.1 CDS trmB NC_011742.1 3211568 3212287 R tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine; tRNA (guanine-N(7)-)-methyltransferase complement(3211568..3212287) Escherichia coli S88 7129564 YP_002392865.1 CDS mutY NC_011742.1 3212448 3213500 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14730969, 20187555, 20316830, 20580749, 21438845, 90046892, 92409600, 9801309, 2001994, 2197596, 9846876; Product type e : enzyme; adenine DNA glycosylase 3212448..3213500 Escherichia coli S88 7129562 YP_002392866.1 CDS yggX NC_011742.1 3213528 3213803 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14594836, 10493123, 9298646, 9868784; Product type f : factor; hypothetical protein 3213528..3213803 Escherichia coli S88 7129644 YP_002392867.1 CDS mltC NC_011742.1 3213868 3214947 D Murein hydrolase C; membrane-bound; lytic; catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine residues; murein transglycosylase C 3213868..3214947 Escherichia coli S88 7129574 YP_002392868.1 CDS nupG NC_011742.1 3215149 3216405 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88029453, 90323001, 3311747; Product type t : transporter; nucleoside transporter 3215149..3216405 Escherichia coli S88 7128844 YP_002392869.1 CDS speC NC_011742.1 3216454 3218589 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87222180, 87260820; Product type e : enzyme; ornithine decarboxylase complement(3216454..3218589) Escherichia coli S88 7133115 YP_002392870.1 CDS yqgA NC_011742.1 3218988 3219695 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3218988..3219695 Escherichia coli S88 7130626 YP_002392871.1 CDS int NC_011742.1 3220074 3221336 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Prophage integrase 3220074..3221336 Escherichia coli S88 7129893 YP_002392872.1 CDS ECS88_3251 NC_011742.1 3221776 3225303 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; Putative superfamily I DNA helicase 3221776..3225303 Escherichia coli S88 7131651 YP_002392873.1 CDS ECS88_3253 NC_011742.1 3226497 3228038 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11094055; Product type pe : putative enzyme; Putative transposase for ISEc12, catalytic region (orf1) 3226497..3228038 Escherichia coli S88 7133339 YP_002392874.1 CDS ECS88_3254 NC_011742.1 3228050 3228799 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11094055; Product type pe : putative enzyme; putative transposase iISEc12, ATP-binding protein (orf2) 3228050..3228799 Escherichia coli S88 7133340 YP_002392875.1 CDS tia NC_011742.1 3229672 3230427 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8675335, 16369033; Product type f : factor; Tia invasion determinant complement(3229672..3230427) Escherichia coli S88 7133342 YP_002392876.1 CDS papG NC_011742.1 3230778 3231788 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1357526, 2895103, 11440716; Product type s : structure; Fimbrial PapG protein (P pilus class II adhesin) (PapGII) complement(3230778..3231788) Escherichia coli S88 7133471 YP_002392877.1 CDS papF NC_011742.1 3231832 3232362 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2869489, 2895103, 1357526, 8096174, 10049807; Product type s : structure; Fimbrial adapter PapF precursor complement(3231832..3232362) Escherichia coli S88 7133168 YP_002392878.1 CDS papE NC_011742.1 3232407 3232946 R Evidence 2b : Function of strongly homologous gene; PubMedId : 2869489, 2895103, 1357526, 10049807; Product type s : structure; Fimbrial tip protein PapE complement(3232407..3232946) Escherichia coli S88 7133167 YP_002392879.1 CDS papK NC_011742.1 3232955 3233494 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1357526, 8096174, 10049807, 10446050; Product type s : structure; Fimbrial adapter PapK precursor complement(3232955..3233494) Escherichia coli S88 7133166 YP_002392880.1 CDS papJ NC_011742.1 3233501 3234082 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1975085, 1357526; Product type f : factor; Protein PapJ precursor, P pilus assembly complement(3233501..3234082) Escherichia coli S88 7133172 YP_002392881.1 CDS papD NC_011742.1 3234119 3234853 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1357526, 10049807, 2478891, 10446050; Product type f : factor; Chaperone protein PapD precursor complement(3234119..3234853) Escherichia coli S88 7133171 YP_002392882.1 CDS papC NC_011742.1 3234924 3237455 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2897064, 1357526, 12399496, 2572580, 7909802, 9501230; Product type f : factor; Outer membrane usher protein PapC precursor complement(3234924..3237455) Escherichia coli S88 7133165 YP_002392883.1 CDS papH NC_011742.1 3237493 3238080 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2882856, 1357526, 2897064; Product type s : structure; minor pilin protein PapH complement(3237493..3238080) Escherichia coli S88 7133164 YP_002392884.1 CDS papA NC_011742.1 3238143 3238724 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6140260, 1357526, 10049807; Product type s : structure; major pilin protein PapA complement(3238143..3238724) Escherichia coli S88 7133169 YP_002392885.1 CDS papB NC_011742.1 3238898 3239212 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2656260, 2868893; Product type r : regulator; pap operon regulatory protein PapB complement(3238898..3239212) Escherichia coli S88 7133162 YP_002392886.1 CDS papI NC_011742.1 3239644 3239877 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2868893, 1357526; Product type r : regulator; pap operon regulatory protein PapI 3239644..3239877 Escherichia coli S88 7133163 YP_002392887.1 CDS ECS88_3268 NC_011742.1 3240072 3240335 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(3240072..3240335) Escherichia coli S88 7133170 YP_002392888.1 CDS ECS88_3269 NC_011742.1 3240220 3240456 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative phage regulatory protein complement(3240220..3240456) Escherichia coli S88 7133343 YP_002392889.1 CDS ECS88_3270 NC_011742.1 3240525 3241130 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3240525..3241130) Escherichia coli S88 7133344 YP_002392890.1 CDS ECS88_3271 NC_011742.1 3241358 3241924 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3241358..3241924) Escherichia coli S88 7133345 YP_002392891.1 CDS ECS88_3272 NC_011742.1 3242019 3242174 D Evidence 6 : Doubtful CDS; hypothetical protein 3242019..3242174 Escherichia coli S88 7133346 YP_002392892.1 CDS pgtP NC_011742.1 3243921 3245285 R Evidence 2b : Function of strongly homologous gene; Product type t : transporter; Phosphoglycerate transporter protein complement(3243921..3245285) Escherichia coli S88 7131645 YP_002392893.1 CDS pgtC NC_011742.1 3245594 3246901 D Evidence 2b : Function of strongly homologous gene; PubMedId : 2842312; Product type r : regulator; Phosphoglycerate transport regulatory protein 3245594..3246901 Escherichia coli S88 7133700 YP_002392894.1 CDS pgtB NC_011742.1 3246898 3248907 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 2842311, 2842312; Product type t : transporter; Phosphoglycerate transport system sensor protein 3246898..3248907 Escherichia coli S88 7133699 YP_002392895.1 CDS pgtA NC_011742.1 3248888 3250144 D Evidence 2b : Function of strongly homologous gene; PubMedId : 3023201; Product type r : regulator; Phosphoglycerate transport system transcriptional regulatory protein 3248888..3250144 Escherichia coli S88 7133698 YP_002392896.1 CDS ECS88_3281 NC_011742.1 3250353 3250628 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 3250353..3250628 Escherichia coli S88 7133697 YP_002392897.1 CDS ECS88_3282 NC_011742.1 3250685 3250834 D Evidence 6 : Doubtful CDS; hypothetical protein 3250685..3250834 Escherichia coli S88 7133350 YP_002392898.1 CDS ECS88_3283 NC_011742.1 3250737 3251060 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3250737..3251060) Escherichia coli S88 7133351 YP_002392899.1 CDS ECS88_3284 NC_011742.1 3251125 3251769 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3251125..3251769) Escherichia coli S88 7133352 YP_002392900.1 CDS ECS88_3285 NC_011742.1 3251790 3252098 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative transcriptional regulator complement(3251790..3252098) Escherichia coli S88 7133353 YP_002392901.1 CDS ibrA NC_011742.1 3252768 3254000 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12057959; Product type r : regulator; immunoglobulin-binding regulator complement(3252768..3254000) Escherichia coli S88 7131610 YP_002392902.1 CDS ECS88_3289 NC_011742.1 3254136 3254789 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(3254136..3254789) Escherichia coli S88 7131607 YP_002392903.1 CDS ECS88_3290 NC_011742.1 3254974 3256434 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2695400; Product type pf : putative factor; putative overcoming lysogenization defect protein (old-like) complement(3254974..3256434) Escherichia coli S88 7133355 YP_002392904.1 CDS ECS88_3291 NC_011742.1 3256593 3257480 R Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase ORF B, IS629 complement(3256593..3257480) Escherichia coli S88 7133356 YP_002392905.1 CDS ECS88_3292 NC_011742.1 3257480 3257806 R Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase ORF A, IS629 complement(3257480..3257806) Escherichia coli S88 7133357 YP_002392906.1 CDS ireA NC_011742.1 3259200 3261248 R iron-responsive element (ireA); ireA gene is located on pathogenicity island I (PAI I); outer membrane protein; putative iron-regulated outer membrane virulence protein complement(3259200..3261248) Escherichia coli S88 7133360 YP_002392907.1 CDS ECS88_3296 NC_011742.1 3261724 3261942 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3261724..3261942) Escherichia coli S88 7131654 YP_002392908.1 CDS ECS88_3297 NC_011742.1 3262030 3262770 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3262030..3262770) Escherichia coli S88 7133361 YP_002392909.1 CDS ECS88_3298 NC_011742.1 3262875 3263123 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3262875..3263123 Escherichia coli S88 7133362 YP_002392910.1 CDS ECS88_3299 NC_011742.1 3263129 3263365 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3263129..3263365) Escherichia coli S88 7133363 YP_002392911.1 CDS ECS88_3300 NC_011742.1 3263635 3263778 D Evidence 6 : Doubtful CDS; hypothetical protein 3263635..3263778 Escherichia coli S88 7133364 YP_002392912.1 CDS ECS88_3301 NC_011742.1 3263903 3264076 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(3263903..3264076) Escherichia coli S88 7133365 YP_002392913.1 CDS ECS88_3302 NC_011742.1 3264375 3265250 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3264375..3265250 Escherichia coli S88 7133366 YP_002392914.1 CDS ECS88_3303 NC_011742.1 3265247 3266200 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3265247..3266200) Escherichia coli S88 7133367 YP_002392915.1 CDS ECS88_3304 NC_011742.1 3266303 3267187 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative GTP-binding protein 3266303..3267187 Escherichia coli S88 7133368 YP_002392916.1 CDS yfjR NC_011742.1 3267390 3268070 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative HTH-type transcriptional regulator 3267390..3268070 Escherichia coli S88 7133369 YP_002392917.1 CDS ECS88_3307 NC_011742.1 3268113 3268895 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein 3268113..3268895 Escherichia coli S88 7133565 YP_002392918.1 CDS ECS88_3308 NC_011742.1 3268901 3269134 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3268901..3269134 Escherichia coli S88 7133370 YP_002392919.1 CDS ECS88_3309 NC_011742.1 3269224 3270042 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3269224..3270042 Escherichia coli S88 7133371 YP_002392920.1 CDS ECS88_3311 NC_011742.1 3270133 3270618 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7519596; Product type pf : putative factor; putative antirestriction protein (klcA-like) 3270133..3270618 Escherichia coli S88 7133372 YP_002392921.1 CDS yeeS NC_011742.1 3270663 3271109 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11053371; Product type pf : putative factor; putative DNA repair protein; CP4-44 prophage 3270663..3271109 Escherichia coli S88 7133373 YP_002392922.1 CDS yeeT NC_011742.1 3271178 3271399 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CP4-44 prophage 3271178..3271399 Escherichia coli S88 7132957 YP_002392923.1 CDS yeeU NC_011742.1 3271478 3271855 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14594833; Product type h : extrachromosomal origin; antitoxin of the YeeV-YeeU toxin-antitoxin system; CP4-44 prophage 3271478..3271855 Escherichia coli S88 7132961 YP_002392924.1 CDS yeeV NC_011742.1 3271788 3272279 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14594833; Product type f : factor; toxin of the YeeV-YeeU toxin-antitoxin system 3271788..3272279 Escherichia coli S88 7132965 YP_002392925.1 CDS yeeW NC_011742.1 3272276 3272764 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3272276..3272764 Escherichia coli S88 7132969 YP_002392926.1 CDS ECS88_3317 NC_011742.1 3272731 3272973 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3272731..3272973 Escherichia coli S88 7132972 YP_002392927.1 CDS ECS88_3318 NC_011742.1 3273058 3273903 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 9987116; hypothetical protein 3273058..3273903 Escherichia coli S88 7133374 YP_002392928.1 CDS ECS88_3319 NC_011742.1 3273974 3275509 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative EAL domain 3273974..3275509 Escherichia coli S88 7133375 YP_002392929.1 CDS kpsF NC_011742.1 3276850 3277869 D Evidence 2b : Function of strongly homologous gene; PubMedId : 8253690; Product type e : enzyme; Polysialic acid capsule expression protein 3276850..3277869 Escherichia coli S88 7133377 YP_002392930.1 CDS kpsE NC_011742.1 3277941 3279089 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8253690; Product type t : transporter; Capsule polysaccharide export inner-membrane protein 3277941..3279089 Escherichia coli S88 7130462 YP_002392931.1 CDS kpsD NC_011742.1 3279110 3280789 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8021185; Product type t : transporter; Polysialic acid transport protein precursor 3279110..3280789 Escherichia coli S88 7130461 YP_002392932.1 CDS kpsU NC_011742.1 3280799 3281539 D CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS; 3-deoxy-manno-octulosonate cytidylyltransferase 3280799..3281539 Escherichia coli S88 7130460 YP_002392933.1 CDS kpsC NC_011742.1 3281536 3283563 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 8397187, 8326861; Product type t : transporter; Capsule polysaccharide export protein 3281536..3283563 Escherichia coli S88 7130466 YP_002392934.1 CDS kpsS NC_011742.1 3283598 3284803 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 8397187, 8326861; Product type t : transporter; Capsule polysaccharide export protein 3283598..3284803 Escherichia coli S88 7130459 YP_002392935.1 CDS neuE NC_011742.1 3286172 3287407 R Evidence 2b : Function of strongly homologous gene; PubMedId : 16484189, 1735705; Product type e : enzyme; polysialic acid biosynthesis protein complement(3286172..3287407) Escherichia coli S88 7130464 YP_002392936.1 CDS neuC NC_011742.1 3287313 3288488 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14729696, 1729218; Product type e : enzyme; UDP-N-acetylglucosamine 2-epimerase complement(3287313..3288488) Escherichia coli S88 7129698 YP_002392937.1 CDS neuA NC_011742.1 3288485 3289741 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2549035; Product type e : enzyme; N-acylneuraminate cytidylyltransferase complement(3288485..3289741) Escherichia coli S88 7129696 YP_002392938.1 CDS neuB NC_011742.1 3289741 3290781 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 7814319; Product type e : enzyme; N-acylneuraminate-9-phosphate synthase complement(3289741..3290781) Escherichia coli S88 7129694 YP_002392939.1 CDS neuD NC_011742.1 3290778 3291401 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10930752, 7814319; Product type e : enzyme; NeuD protein involved in sialic acid synthesis complement(3290778..3291401) Escherichia coli S88 7129695 YP_002392940.1 CDS kpsT NC_011742.1 3291451 3292110 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1856162, 8051103, 2082146; Product type t : transporter; Polysialic acid transport ATP-binding protein complement(3291451..3292110) Escherichia coli S88 7129697 YP_002392941.1 CDS kpsM NC_011742.1 3292107 3292943 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1856162, 7715449; Product type t : transporter; Polysialic acid transport protein complement(3292107..3292943) Escherichia coli S88 7130465 YP_002392942.1 CDS yghD NC_011742.1 3293941 3294477 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative general secretion pathway protein YghD complement(3293941..3294477) Escherichia coli S88 7130463 YP_002392943.1 CDS yghE NC_011742.1 3294479 3295657 R similar to general secretory pathway protein L; GspL-like protein complement(3294479..3295657) Escherichia coli S88 7129577 YP_002392944.1 CDS ECS88_3337 NC_011742.1 3295654 3296631 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative type II secretion protein (GspK-like) complement(3295654..3296631) Escherichia coli S88 7129578 YP_002392945.1 CDS ECS88_3338 NC_011742.1 3296628 3297233 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(3296628..3297233) Escherichia coli S88 7133378 YP_002392946.1 CDS ECS88_3339 NC_011742.1 3297230 3297601 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative type II secretion protein (GspI-like) complement(3297230..3297601) Escherichia coli S88 7133379 YP_002392947.1 CDS ECS88_3340 NC_011742.1 3297598 3298161 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(3297598..3298161) Escherichia coli S88 7133380 YP_002392948.1 CDS ECS88_3341 NC_011742.1 3298165 3298647 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative general secretion pathway protein G precursor (epsG-like) complement(3298165..3298647) Escherichia coli S88 7133381 YP_002392949.1 CDS epsF NC_011742.1 3298637 3299860 R Evidence 2b : Function of strongly homologous gene; Product type t : transporter; General secretion pathway protein F complement(3298637..3299860) Escherichia coli S88 7133382 YP_002392950.1 CDS epsE NC_011742.1 3299860 3301353 R Evidence 2b : Function of strongly homologous gene; Product type t : transporter; general secretion pathway protein E complement(3299860..3301353) Escherichia coli S88 7132412 YP_002392951.1 CDS epsD NC_011742.1 3301353 3303413 R Evidence 2b : Function of strongly homologous gene; Product type t : transporter; general secretion pathway protein D precursor complement(3301353..3303413) Escherichia coli S88 7132411 YP_002392952.1 CDS yghF NC_011742.1 3303443 3304273 R part of the general (type II) secretion pathway (GSP), a signal sequence-dependent process responsible for protein export; involved in trans-location of exoproteins from the cytoplasm to the periplasm; putative type II secretion protein GspC complement(3303443..3304273) Escherichia coli S88 7132410 YP_002392953.1 CDS yghG NC_011742.1 3304420 3304830 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3304420..3304830) Escherichia coli S88 7129579 YP_002392954.1 CDS pppA NC_011742.1 3304896 3305705 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 98175453; Product type e : enzyme; bifunctional prepilin leader peptidase and methylase complement(3304896..3305705) Escherichia coli S88 7129580 YP_002392955.1 CDS yghJ NC_011742.1 3305869 3310449 R Evidence 2b : Function of strongly homologous gene; PubMedId : 1644747; Product type lp : lipoprotein; inner membrane lipoprotein complement(3305869..3310449) Escherichia coli S88 7130765 YP_002392956.1 CDS yghK NC_011742.1 3310915 3312597 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11785976, 21178909, 11283302; Product type t : transporter; glycolate transporter complement(3310915..3312597) Escherichia coli S88 7129581 YP_002392957.1 CDS glcB NC_011742.1 3312953 3315124 R catalyzes the formation of malate from glyoxylate and acetyl-CoA; malate synthase G complement(3312953..3315124) Escherichia coli S88 7129142 YP_002392958.1 CDS glcG NC_011742.1 3315146 3315550 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3315146..3315550) Escherichia coli S88 7132206 YP_002392959.1 CDS glcF NC_011742.1 3315555 3316778 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96178972, 8606183; Product type c : carrier; glycolate oxidase iron-sulfur subunit complement(3315555..3316778) Escherichia coli S88 7132211 YP_002392960.1 CDS glcE NC_011742.1 3316789 3317841 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96178972, 8606183; Product type e : enzyme; glycolate oxidase FAD binding subunit complement(3316789..3317841) Escherichia coli S88 7132210 YP_002392961.1 CDS glcD NC_011742.1 3317841 3319340 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96178972, 8606183; Product type e : enzyme; glycolate oxidase subunit GlcD complement(3317841..3319340) Escherichia coli S88 7132209 YP_002392962.1 CDS glcC NC_011742.1 3319591 3320355 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96178972, 9880556, 8606183; Product type r : regulator; DNA-binding transcriptional regulator GlcC 3319591..3320355 Escherichia coli S88 7132208 YP_002392963.1 CDS yghO NC_011742.1 3320362 3321504 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(3320362..3321504) Escherichia coli S88 7132207 YP_002392964.1 CDS ECS88_3358 NC_011742.1 3323386 3324510 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative epimerase 3323386..3324510 Escherichia coli S88 7133383 YP_002392965.1 CDS ECS88_3359 NC_011742.1 3324542 3324790 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3324542..3324790 Escherichia coli S88 7133384 YP_002392966.1 CDS ECS88_3360 NC_011742.1 3324790 3325962 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; Putative 8-amino-7-oxononanoate synthase 3324790..3325962 Escherichia coli S88 7133385 YP_002392967.1 CDS ECS88_3361 NC_011742.1 3325997 3327157 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3325997..3327157) Escherichia coli S88 7133386 YP_002392968.1 CDS ECS88_3362 NC_011742.1 3327073 3328143 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3327073..3328143) Escherichia coli S88 7129353 YP_002392969.1 CDS ECS88_3363 NC_011742.1 3328174 3328734 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; Putative transcriptional regulator complement(3328174..3328734) Escherichia coli S88 7133022 YP_002392970.1 CDS ECS88_3364 NC_011742.1 3328734 3329570 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3328734..3329570) Escherichia coli S88 7132856 YP_002392971.1 CDS ECS88_3365 NC_011742.1 3329570 3330919 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative membrane protein, conserved protein complement(3329570..3330919) Escherichia coli S88 7132857 YP_002392972.1 CDS yghR NC_011742.1 3330965 3331723 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative nucleoside triphosphate hydrolase domain complement(3330965..3331723) Escherichia coli S88 7132858 YP_002392973.1 CDS yghS NC_011742.1 3331755 3332468 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative nucleoside triphosphate hydrolase domain complement(3331755..3332468) Escherichia coli S88 7129584 YP_002392974.1 CDS yghT NC_011742.1 3332643 3333335 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative nucleoside triphosphate hydrolase domain 3332643..3333335 Escherichia coli S88 7129585 YP_002392975.1 CDS pitB NC_011742.1 3333384 3334883 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21336523, 21382172, 7775463; Product type t : transporter; phosphate transporter complement(3333384..3334883) Escherichia coli S88 7129586 YP_002392976.1 CDS gss NC_011742.1 3335175 3337034 R catalyzes the formation of glutathionylspermidine from glutathione and spermidine; also catalyzes the reverse reaction; bifunctional glutathionylspermidine amidase/glutathionylspermidine synthetase complement(3335175..3337034) Escherichia coli S88 7133737 YP_002392977.1 CDS yghU NC_011742.1 3337239 3338105 D YghU; B2989; one of eight putative glutathione transferase proteins from E. coli; putative glutathione S-transferase YghU 3337239..3338105 Escherichia coli S88 7128872 YP_002392978.1 CDS hybG NC_011742.1 3338238 3338486 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92215587, 94292472, 8021226; Product type pf : putative factor; hydrogenase 2 accessory protein HypG complement(3338238..3338486) Escherichia coli S88 7129587 YP_002392979.1 CDS hybF NC_011742.1 3338499 3338840 R plays a role in hydrogenase nickel cofactor insertion; hydrogenase nickel incorporation protein HybF complement(3338499..3338840) Escherichia coli S88 7131418 YP_002392980.1 CDS hybE NC_011742.1 3338833 3339321 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94292472, 8021226; Product type f : factor; hydrogenase 2-specific chaperone complement(3338833..3339321) Escherichia coli S88 7131417 YP_002392981.1 CDS hybD NC_011742.1 3339314 3339808 R protease responsible for the cleavage of a 15 amino acid peptide from the C-terminal end of the large subunit of hydrogenase 2 (HybC); hydrogenase 2 maturation endopeptidase complement(3339314..3339808) Escherichia coli S88 7131416 YP_002392982.1 CDS hybC NC_011742.1 3339808 3341511 R involved in hydrogen uptake; hydrogenase 2 large subunit complement(3339808..3341511) Escherichia coli S88 7131415 YP_002392983.1 CDS hybB NC_011742.1 3341508 3342686 R HybB; cytochrome b subunit of the hydrogenase 2 enzyme, composed of HybA, B, C, and O subunits; putative hydrogenase 2 b cytochrome subunit complement(3341508..3342686) Escherichia coli S88 7131414 YP_002392984.1 CDS hybA NC_011742.1 3342676 3343662 R Fe-S ferrodoxin type component; participates in the periplasmic electron-transferring activity of hydrogenase 2; hydrogenase 2 protein HybA complement(3342676..3343662) Escherichia coli S88 7131413 YP_002392985.1 CDS hybO NC_011742.1 3343665 3344783 R involved in hydrogen uptake; hydrogenase 2 small subunit complement(3343665..3344783) Escherichia coli S88 7131412 YP_002392986.1 CDS ECS88_3380 NC_011742.1 3344790 3344975 R Evidence 6 : Doubtful CDS; hypothetical protein complement(3344790..3344975) Escherichia coli S88 7132280 YP_002392987.1 CDS yghW NC_011742.1 3344972 3345259 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3344972..3345259) Escherichia coli S88 7132859 YP_002392988.1 CDS ECS88_3382 NC_011742.1 3345378 3346304 R Evidence 4 : Homologs of previously reported genes of unknown function; putative enzyme complement(3345378..3346304) Escherichia coli S88 7129588 YP_002392989.1 CDS yghZ NC_011742.1 3346422 3347462 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12583903; Product type e : enzyme; aldo-keto reductase 3346422..3347462 Escherichia coli S88 7132860 YP_002392990.1 CDS yqhA NC_011742.1 3347502 3347996 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(3347502..3347996) Escherichia coli S88 7129589 YP_002392991.1 CDS yghA NC_011742.1 3348187 3349071 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; oxidoreductase 3348187..3349071 Escherichia coli S88 7132095 YP_002392992.1 CDS exbD NC_011742.1 3349110 3349535 R membrane spanning protein in TonB-ExbB-ExbD complex; involved in the tonB-independent energy-dependent transport iron-siderophore complexes and vitamin B12 into the cell; biopolymer transport protein ExbD complement(3349110..3349535) Escherichia coli S88 7129575 YP_002392993.1 CDS exbB NC_011742.1 3349542 3350276 R membrane spanning protein in TonB-ExbB-ExbD complex; involved in the tonB-independent energy-dependent transport iron-siderophore complexes and vitamin B12 into the cell; biopolymer transport protein ExbB complement(3349542..3350276) Escherichia coli S88 7132437 YP_002392994.1 CDS metC NC_011742.1 3350528 3351715 D catalyzes the formation of L-homocysteine from cystathionine; cystathionine beta-lyase 3350528..3351715 Escherichia coli S88 7132436 YP_002392995.1 CDS yghB NC_011742.1 3351855 3352514 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3351855..3352514 Escherichia coli S88 7128812 YP_002392996.1 CDS yqhC NC_011742.1 3352554 3353510 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(3352554..3353510) Escherichia coli S88 7129576 YP_002392997.1 CDS yqhD NC_011742.1 3353647 3354810 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15327949; Product type e : enzyme; alcohol dehydrogenase, NAD(P)-dependent 3353647..3354810 Escherichia coli S88 7132096 YP_002392998.1 CDS dkgA NC_011742.1 3354915 3355742 D methylglyoxal reductase/#-keto ester reductase; catalyzes the reduction of 2,5-diketo-D-gluconic acid to 2-keto-L-gulonic acid; also catalyzes the reduction of methylglyoxal, ethyl-2-methylacetoacetate and ethyl-acetoacetate; 2,5-diketo-D-gluconate reductase A 3354915..3355742 Escherichia coli S88 7132097 YP_002392999.1 CDS yqhG NC_011742.1 3355942 3356868 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3355942..3356868 Escherichia coli S88 7130212 YP_002393000.1 CDS yqhH NC_011742.1 3356919 3357176 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; putative outer membrane lipoprotein 3356919..3357176 Escherichia coli S88 7132098 YP_002393001.1 CDS ygiQ NC_011742.1 3357218 3359437 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3357218..3359437) Escherichia coli S88 7132099 YP_002393002.1 CDS ECS88_3397 NC_011742.1 3359689 3360438 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative regulator 3359689..3360438 Escherichia coli S88 7132224 YP_002393003.1 CDS ECS88_3398 NC_011742.1 3360725 3362233 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative Fructuronate reductase 3360725..3362233 Escherichia coli S88 7132861 YP_002393004.1 CDS ECS88_3399 NC_011742.1 3362230 3363246 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative L-threonine 3-dehydrogenase 3362230..3363246 Escherichia coli S88 7132862 YP_002393005.1 CDS ECS88_3400 NC_011742.1 3363257 3364267 D Evidence 2b : Function of strongly homologous gene; Product type e : enzyme; Ureidoglycolate dehydrogenase 3363257..3364267 Escherichia coli S88 7132863 YP_002393006.1 CDS ECS88_3401 NC_011742.1 3364340 3365323 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative c4-dicarboxylate transport system binding protein; putative secreted protein 3364340..3365323 Escherichia coli S88 7132864 YP_002393007.1 CDS ECS88_3402 NC_011742.1 3365365 3365847 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative membrane protein; putative TRAP-type C4-dicarboxylate transport system, small permease component 3365365..3365847 Escherichia coli S88 7132865 YP_002393008.1 CDS ygiK NC_011742.1 3365816 3367162 D Evidence 2b : Function of strongly homologous gene; Product type t : transporter; c4-dicarboxylate permease 3365816..3367162 Escherichia coli S88 7132866 YP_002393009.1 CDS sufI NC_011742.1 3367233 3368645 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88314889, 1557036, 9298646; Product type r : regulator; repressor protein for FtsI complement(3367233..3368645) Escherichia coli S88 7129594 YP_002393010.1 CDS plsC NC_011742.1 3368720 3369457 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92212294, 1557036; Product type e : enzyme; 1-acyl-sn-glycerol-3-phosphate acyltransferase complement(3368720..3369457) Escherichia coli S88 7131246 YP_002393011.1 CDS parC NC_011742.1 3369692 3371950 R decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit A complement(3369692..3371950) Escherichia coli S88 7133741 YP_002393012.1 CDS ygiS NC_011742.1 3372088 3373695 R YgiS; uncharacterized periplasmic protein that seems to be part of a binding-protein-dependent transport system; putative binding protein complement(3372088..3373695) Escherichia coli S88 7133173 YP_002393013.1 CDS ygiV NC_011742.1 3373804 3374286 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator complement(3373804..3374286) Escherichia coli S88 7132225 YP_002393014.1 CDS ygiW NC_011742.1 3374339 3374731 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 9298646; hypothetical protein complement(3374339..3374731) Escherichia coli S88 7132226 YP_002393015.1 CDS qseB NC_011742.1 3374883 3375542 D response regulator in two-component regulatory system with QseC; regulates FlhCD which is the master regulator for flagella and motility genes; DNA-binding transcriptional regulator QseB 3374883..3375542 Escherichia coli S88 7132227 YP_002393016.1 CDS qseC NC_011742.1 3375539 3376888 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21927389; Product type r : regulator; sensor protein QseC 3375539..3376888 Escherichia coli S88 7131773 YP_002393017.1 CDS ygiZ NC_011742.1 3376934 3377266 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(3376934..3377266) Escherichia coli S88 7131774 YP_002393018.1 CDS ECS88_3414 NC_011742.1 3377273 3378010 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3377273..3378010) Escherichia coli S88 7132228 YP_002393019.1 CDS ECS88_3415 NC_011742.1 3377986 3378465 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3377986..3378465) Escherichia coli S88 7132867 YP_002393020.1 CDS mdaB NC_011742.1 3378715 3379296 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96004656, 96217538; Product type c : carrier; NADPH quinone reductase 3378715..3379296 Escherichia coli S88 7132868 YP_002393021.1 CDS ygiN NC_011742.1 3379327 3379641 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10493123, 9298646, 9600841, 9868784; Product type e : enzyme; quinol monooxygenase 3379327..3379641 Escherichia coli S88 7129430 YP_002393022.1 CDS ECS88_3418 NC_011742.1 3379686 3380573 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative bifunctional protein: transcriptional regulator and sugar phosphate isomerase complement(3379686..3380573) Escherichia coli S88 7129596 YP_002393023.1 CDS ECS88_3419 NC_011742.1 3380570 3381580 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative iron compound-binding protein of ABC transporter family complement(3380570..3381580) Escherichia coli S88 7132869 YP_002393024.1 CDS ECS88_3420 NC_011742.1 3381528 3382577 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative iron compound permease protein of ABC transporter family complement(3381528..3382577) Escherichia coli S88 7132870 YP_002393025.1 CDS ECS88_3421 NC_011742.1 3382574 3383557 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative iron compound permease protein of ABC transporter family complement(3382574..3383557) Escherichia coli S88 7132871 YP_002393026.1 CDS ECS88_3422 NC_011742.1 3383554 3384363 R Evidence 2b : Function of strongly homologous gene; Product type t : transporter; ferric enterobactin transport ATP-binding protein (fepC-like) complement(3383554..3384363) Escherichia coli S88 7132872 YP_002393027.1 CDS ECS88_3423 NC_011742.1 3384737 3386878 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type prc : putative receptor; putative iron compound receptor 3384737..3386878 Escherichia coli S88 7132873 YP_002393028.1 CDS parE NC_011742.1 3386942 3388834 R decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit B complement(3386942..3388834) Escherichia coli S88 7132874 YP_002393029.1 CDS yqiA NC_011742.1 3388863 3389444 R Displays esterase activity toward palmitoyl-CoA and pNP-butyrate; esterase YqiA complement(3388863..3389444) Escherichia coli S88 7133174 YP_002393030.1 CDS cpdA NC_011742.1 3389444 3390271 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96411758; Product type e : enzyme; cyclic 3',5'-adenosine monophosphate phosphodiesterase complement(3389444..3390271) Escherichia coli S88 7132100 YP_002393031.1 CDS yqiB NC_011742.1 3390296 3390718 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein complement(3390296..3390718) Escherichia coli S88 7131951 YP_002393032.1 CDS nudF NC_011742.1 3390719 3391348 R ADP-sugar pyrophosphatase; catalyzes the formation of D-ribose 5-phosphate from ADP-ribose; can also act on ADP-mannose and ADP-glucose; ADP-ribose pyrophosphatase NudF complement(3390719..3391348) Escherichia coli S88 7132101 YP_002393033.1 CDS tolC NC_011742.1 3391553 3393034 D trimeric outer membrane protein involved in efflux of hydrophobic/amphipathic molecules; functions with a number of efflux systems in the inner membrane to transport molecules out of the cell; outer membrane channel protein 3391553..3393034 Escherichia coli S88 7129754 YP_002393034.1 CDS ygiB NC_011742.1 3393278 3393853 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 3393278..3393853 Escherichia coli S88 7133486 YP_002393035.1 CDS ygiC NC_011742.1 3393859 3395019 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative enzyme 3393859..3395019 Escherichia coli S88 7129590 YP_002393036.1 CDS assT NC_011742.1 3395504 3397300 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 8887346, 11534764; Product type e : enzyme; arylsulfate sulfotransferase 3395504..3397300 Escherichia coli S88 7129591 YP_002393037.1 CDS dsbA NC_011742.1 3397318 3397986 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 8887346, 10600454; Product type e : enzyme; Thiol:disulfide interchange protein dsbA precursor 3397318..3397986 Escherichia coli S88 7129954 YP_002393038.1 CDS ECS88_3434 NC_011742.1 3398001 3398672 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10600454; Product type pe : putative enzyme; putative disulfide oxidoreductase 3398001..3398672 Escherichia coli S88 7130238 YP_002393039.1 CDS zupT NC_011742.1 3398718 3399533 R seems to be involved in biofilm formation; in asymptomatic bacteriuria E. coli strains 83972 and VR50, the ygiD gene is upregulated during biofilm formation in urine; hypothetical protein complement(3398718..3399533) Escherichia coli S88 7132875 YP_002393040.1 CDS ygiE NC_011742.1 3399649 3400422 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11790762, 1314093; Product type t : transporter; zinc transporter ZupT 3399649..3400422 Escherichia coli S88 7131894 YP_002393041.1 CDS ECS88_3438 NC_011742.1 3400484 3400669 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3400484..3400669) Escherichia coli S88 7129592 YP_002393042.1 CDS ygiL NC_011742.1 3401225 3401788 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative fimbrial protein 3401225..3401788 Escherichia coli S88 7132876 YP_002393043.1 CDS yqiG NC_011742.1 3401875 3404397 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative outer membrane usher protein 3401875..3404397 Escherichia coli S88 7129595 YP_002393044.1 CDS yqiH NC_011742.1 3404404 3405153 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative periplasmic pilin chaperone 3404404..3405153 Escherichia coli S88 7132103 YP_002393045.1 CDS yqiI NC_011742.1 3405150 3406199 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative fimbrial adhesin 3405150..3406199 Escherichia coli S88 7132104 YP_002393046.1 CDS ribB NC_011742.1 3406253 3406906 R DHBP synthase; functions during riboflavin biosynthesis; 3,4-dihydroxy-2-butanone 4-phosphate synthase complement(3406253..3406906) Escherichia coli S88 7132105 YP_002393047.1 CDS yqiC NC_011742.1 3407220 3407579 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3407220..3407579 Escherichia coli S88 7129861 YP_002393048.1 CDS glgS NC_011742.1 3407614 3407814 R Involved in glycogen synthesis. May be involved in glycogen priming; glycogen synthesis protein GlgS complement(3407614..3407814) Escherichia coli S88 7132102 YP_002393049.1 CDS yqiJ NC_011742.1 3408084 3408713 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3408084..3408713 Escherichia coli S88 7132217 YP_002393050.1 CDS yqiK NC_011742.1 3408740 3410401 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3408740..3410401 Escherichia coli S88 7132106 YP_002393051.1 CDS rfaE NC_011742.1 3410820 3412253 R catalyzes the phosphorylation of D-glycero-D-manno-heptose 7-phosphate to form D,D-heptose-1,7-bisphosphate and catalyzes transfer of ADP to D-glycero-D-manno-heptose 1-phosphate forming ADP-D,D-heptose; bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase complement(3410820..3412253) Escherichia coli S88 7131347 YP_002393052.1 CDS glnE NC_011742.1 3412301 3415141 R catalyzes the ATP-dependent addition of AMP to a subunit of glutamine synthetase; also catalyzes the reverse reaction - deadenylation; adenylation/deadenylation of glutamine synthetase subunits is important for the regulation of this enzyme; bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase complement(3412301..3415141) Escherichia coli S88 7131818 YP_002393053.1 CDS ygiF NC_011742.1 3415164 3416465 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8412694; Product type pe : putative enzyme; putative adenylate cyclase complement(3415164..3416465) Escherichia coli S88 7130007 YP_002393054.1 CDS ECS88_3452 NC_011742.1 3416482 3416688 R Evidence 6 : Doubtful CDS; hypothetical protein complement(3416482..3416688) Escherichia coli S88 7129593 YP_002393055.1 CDS htrG NC_011742.1 3416707 3417327 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11274153; Product type pr : putative regulator; putative signal transduction protein 3416707..3417327 Escherichia coli S88 7132877 YP_002393056.1 CDS cca NC_011742.1 3417391 3418629 D catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template; phosphohydrolase activities include hydrolysis of pyrophosphate, 5'-nucleoside tri- and diphosphates, NADP, and 2'-AMP with the production of Pi, metal-dependent phosphodiesterase activity for 2',3'-cAMP, 2',3'-cGMP, and 2',3'-cCMP, and hydrolysis 2',3'-cyclic substrates with the formation of 2'-nucleotides and 3'-nucleotides; these phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases; multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase 3417391..3418629 Escherichia coli S88 7131403 YP_002393057.1 CDS bacA NC_011742.1 3418817 3419638 R BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell; undecaprenyl pyrophosphate phosphatase complement(3418817..3419638) Escherichia coli S88 7129165 YP_002393058.1 CDS folB NC_011742.1 3419729 3420097 R catalyzes the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin and can also catalyze the epimerization of carbon 2' of dihydroneopterin and dihydromonapterin; bifunctional dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase complement(3419729..3420097) Escherichia coli S88 7129984 YP_002393059.1 CDS plsY NC_011742.1 3420202 3420819 D involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX; putative glycerol-3-phosphate acyltransferase PlsY 3420202..3420819 Escherichia coli S88 7132814 YP_002393060.1 CDS ygiP NC_011742.1 3420832 3421764 R activates expression of genes required for L-tartrate-dependent anaerobic growth on glycerol; transcriptional activator TtdR complement(3420832..3421764) Escherichia coli S88 7133743 YP_002393061.1 CDS ttdA NC_011742.1 3421971 3422882 D Involved in the tartrate degradation pathway; tartrate dehydratase subunit alpha 3421971..3422882 Escherichia coli S88 7132223 YP_002393062.1 CDS ttdB NC_011742.1 3422879 3423484 D Involved in the tartrate degradation pathway; L(+)-tartrate dehydratase subunit beta 3422879..3423484 Escherichia coli S88 7130363 YP_002393063.1 CDS ygjE NC_011742.1 3423532 3424995 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative tartrate:succinate antiporter 3423532..3424995 Escherichia coli S88 7130364 YP_002393064.1 CDS gcp NC_011742.1 3425038 3426051 R 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; putative DNA-binding/iron metalloprotein/AP endonuclease complement(3425038..3426051) Escherichia coli S88 7132229 YP_002393065.1 CDS rpsU NC_011742.1 3426289 3426504 D 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; 30S ribosomal protein S21 3426289..3426504 Escherichia coli S88 7132195 YP_002393066.1 CDS dnaG NC_011742.1 3426615 3428360 D synthesizes RNA primers at the replication forks; DNA primase 3426615..3428360 Escherichia coli S88 7133804 YP_002393067.1 CDS rpoD NC_011742.1 3428555 3430396 D 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; RNA polymerase sigma factor RpoD 3428555..3430396 Escherichia coli S88 7130224 YP_002393068.1 CDS ygjF NC_011742.1 3430475 3430981 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20412902, 99453007, 6269063, 7567469, 8878487, 9489705; Product type e : enzyme; G/U mismatch-specific DNA glycosylase complement(3430475..3430981) Escherichia coli S88 7133777 YP_002393069.1 CDS yqjH NC_011742.1 3431235 3431999 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative siderophore interacting protein complement(3431235..3431999) Escherichia coli S88 7129894 YP_002393070.1 CDS yqjI NC_011742.1 3432276 3432899 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator 3432276..3432899 Escherichia coli S88 7132115 YP_002393071.1 CDS aer NC_011742.1 3433053 3434573 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20015410, 9380671, 9643537, 9190831; Product type r : regulator; fused signal transducer for aerotaxis sensory component ; methyl accepting chemotaxis component complement(3433053..3434573) Escherichia coli S88 7132116 YP_002393072.1 CDS ygjG NC_011742.1 3434964 3436370 D catalyzes the formation of 4-aminobutyraldehyde from putrescine and 2-oxoglutarate; putrescine--2-oxoglutarate aminotransferase 3434964..3436370 Escherichia coli S88 7133024 YP_002393073.1 CDS ygjH NC_011742.1 3436412 3436744 R Evidence 2b : Function of strongly homologous gene; PubMedId : 11101501; hypothetical protein complement(3436412..3436744) Escherichia coli S88 7132231 YP_002393074.1 CDS ebgR NC_011742.1 3436963 3437946 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89128452, 2515108, 3939708; Product type r : regulator; DNA-binding transcriptional repressor EbgR 3436963..3437946 Escherichia coli S88 7132232 YP_002393075.1 CDS ebgA NC_011742.1 3438130 3441222 D in Escherichia coli this is the second beta-galactosidase system; cryptic beta-D-galactosidase subunit alpha 3438130..3441222 Escherichia coli S88 7132374 YP_002393076.1 CDS ebgC NC_011742.1 3441219 3441668 D in Escherichia coli this is the second beta-galactosidase system; cryptic beta-D-galactosidase subunit beta 3441219..3441668 Escherichia coli S88 7132372 YP_002393077.1 CDS ygjI NC_011742.1 3441731 3443164 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 3441731..3443164 Escherichia coli S88 7132373 YP_002393078.1 CDS ygjJ NC_011742.1 3443298 3444368 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3443298..3444368 Escherichia coli S88 7132233 YP_002393079.1 CDS ygjK NC_011742.1 3444385 3446736 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15213393; Product type pe : putative enzyme; putative glycosyl hydrolase 3444385..3446736 Escherichia coli S88 7132234 YP_002393080.1 CDS fadH NC_011742.1 3446907 3448925 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12840019, 89380266; Product type e : enzyme; 2,4-dienoyl-CoA reductase, NADH and FMN-linked 3446907..3448925 Escherichia coli S88 7132235 YP_002393081.1 CDS ygjO NC_011742.1 3449043 3450179 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative methyltransferase small domain complement(3449043..3450179) Escherichia coli S88 7129444 YP_002393082.1 CDS ygjP NC_011742.1 3450264 3450767 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative metal dependent hydrolase 3450264..3450767 Escherichia coli S88 7132236 YP_002393083.1 CDS ygjQ NC_011742.1 3450844 3451536 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative thioredoxin-like 3450844..3451536 Escherichia coli S88 7132237 YP_002393084.1 CDS ygjR NC_011742.1 3451597 3452601 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative NAD(P)-binding dehydrogenase 3451597..3452601 Escherichia coli S88 7132238 YP_002393085.1 CDS alx NC_011742.1 3452884 3453849 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 12107143, 2108134; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein, part of terminus 3452884..3453849 Escherichia coli S88 7130639 YP_002393086.1 CDS sstT NC_011742.1 3454173 3455417 D involved in the import of serine and threonine coupled with the import of sodium; serine/threonine transporter SstT 3454173..3455417 Escherichia coli S88 7133056 YP_002393087.1 CDS ygjV NC_011742.1 3455421 3455972 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(3455421..3455972) Escherichia coli S88 7130656 YP_002393088.1 CDS uxaA NC_011742.1 3456055 3457542 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 4570160, 83114543, 3038546; Product type e : enzyme; altronate hydrolase complement(3456055..3457542) Escherichia coli S88 7132240 YP_002393089.1 CDS uxaC NC_011742.1 3457557 3458969 R catalyzes the interconversion of D-glucuronate to D-fructuronate or D-galacturonate to D-tagaturonate; functions in glucuronic and galacturonic metabolism; glucuronate isomerase complement(3457557..3458969) Escherichia coli S88 7132463 YP_002393090.1 CDS exuT NC_011742.1 3459332 3460750 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 83218546, 98190790; Product type t : transporter; hexuronate transporter 3459332..3460750 Escherichia coli S88 7132465 YP_002393091.1 CDS exuR NC_011742.1 3460880 3461656 D regulates the exuT, uxaCA and uxuRAB operons which encode genes involved in hexuronate utilization.; DNA-binding transcriptional repressor ExuR 3460880..3461656 Escherichia coli S88 7132441 YP_002393092.1 CDS yqjA NC_011742.1 3462001 3462663 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3462001..3462663 Escherichia coli S88 7132440 YP_002393093.1 CDS yqjB NC_011742.1 3462667 3463050 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 11274153; hypothetical protein 3462667..3463050 Escherichia coli S88 7132108 YP_002393094.1 CDS yqjC NC_011742.1 3463197 3463565 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3463197..3463565 Escherichia coli S88 7132109 YP_002393095.1 CDS yqjD NC_011742.1 3463603 3463908 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3463603..3463908 Escherichia coli S88 7132110 YP_002393096.1 CDS yqjE NC_011742.1 3463911 3464315 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3463911..3464315 Escherichia coli S88 7132111 YP_002393097.1 CDS yqjK NC_011742.1 3464305 3464604 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3464305..3464604 Escherichia coli S88 7132112 YP_002393098.1 CDS yqjF NC_011742.1 3464791 3465183 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative quinol oxidase subunit 3464791..3465183 Escherichia coli S88 7132117 YP_002393099.1 CDS yqjG NC_011742.1 3465253 3466239 D Evidence 2b : Function of strongly homologous gene; PubMedId : 8478329; Product type e : enzyme; S-transferase 3465253..3466239 Escherichia coli S88 7132113 YP_002393100.1 CDS yhaH NC_011742.1 3466522 3466890 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3466522..3466890 Escherichia coli S88 7132114 YP_002393101.1 CDS yhaJ NC_011742.1 3466924 3467820 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(3466924..3467820) Escherichia coli S88 7132241 YP_002393102.1 CDS yhaK NC_011742.1 3467925 3468626 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative pirin-related protein 3467925..3468626 Escherichia coli S88 7132242 YP_002393103.1 CDS yhaL NC_011742.1 3468649 3468813 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3468649..3468813 Escherichia coli S88 7132243 YP_002393104.1 CDS yhaM NC_011742.1 3468945 3470255 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3468945..3470255) Escherichia coli S88 7132244 YP_002393105.1 CDS yhaO NC_011742.1 3470283 3471551 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter complement(3470283..3471551) Escherichia coli S88 7132245 YP_002393106.1 CDS tdcG NC_011742.1 3471889 3473253 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 98143432, 9484901; Product type e : enzyme; L-serine dehydratase 3 complement(3471889..3473253) Escherichia coli S88 7132246 YP_002393107.1 CDS tdcF NC_011742.1 3473325 3473714 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12777779, 9484901; Product type e : enzyme; hypothetical protein complement(3473325..3473714) Escherichia coli S88 7131278 YP_002393108.1 CDS tdcE NC_011742.1 3473728 3476022 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 98143432, 9484901; Product type e : enzyme; pyruvate formate-lyase 4/2-ketobutyrate formate-lyase complement(3473728..3476022) Escherichia coli S88 7131277 YP_002393109.1 CDS tdcD NC_011742.1 3476056 3477276 R catalyzes the formation of propanoyl phosphate from propanoate and ATP; TdcD also has acetate kinase activities and functions in anaerobic threonine catabolism; propionate/acetate kinase complement(3476056..3477276) Escherichia coli S88 7131276 YP_002393110.1 CDS tdcC NC_011742.1 3477290 3478621 R involved in the import of threonine and serine in combination with the import of a proton; threonine/serine transporter TdcC complement(3477290..3478621) Escherichia coli S88 7131275 YP_002393111.1 CDS tdcB NC_011742.1 3478643 3479632 R catalyzes the formation of 2-oxobutanoate from L-threonine; catabolic; threonine dehydratase complement(3478643..3479632) Escherichia coli S88 7131274 YP_002393112.1 CDS tdcA NC_011742.1 3479725 3480663 R regulates the tdcABCDEFG operon which is involved in amino acid degradation; DNA-binding transcriptional activator TdcA complement(3479725..3480663) Escherichia coli S88 7131273 YP_002393113.1 CDS garK NC_011742.1 3482171 3483397 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20225875, 69151449, 9772162; Product type e : enzyme; glycerate kinase I complement(3482171..3483397) Escherichia coli S88 7132752 YP_002393114.1 CDS garR NC_011742.1 3483413 3484303 R catalyzes the reduction of tartronate semialdehyde to glycerate; tartronate semialdehyde reductase complement(3483413..3484303) Escherichia coli S88 7132182 YP_002393115.1 CDS garL NC_011742.1 3484333 3485103 R cleaves 5-dehydro-4-deoxy-glucarate and 2-dehydro-3-deoxy-D-glucarate; alpha-dehydro-beta-deoxy-D-glucarate aldolase complement(3484333..3485103) Escherichia coli S88 7132185 YP_002393116.1 CDS garP NC_011742.1 3485119 3486453 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10762278, 9772162; Product type pt : putative transporter; putative (D)-galactarate transporter complement(3485119..3486453) Escherichia coli S88 7132183 YP_002393117.1 CDS garD NC_011742.1 3486828 3488399 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20225875, 66096392, 81027430, 9772162, 10762278, 2407727; Product type e : enzyme; (D)-galactarate dehydrogenase 3486828..3488399 Escherichia coli S88 7132184 YP_002393118.1 CDS agaR NC_011742.1 3488451 3489275 R transcriptional repressor for the agaZVWA and agaSYBCDI operons; DNA-binding transcriptional regulator AgaR complement(3488451..3489275) Escherichia coli S88 7132181 YP_002393119.1 CDS kbaZ NC_011742.1 3489524 3490804 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11976750, 20392444, 10931310, 8932697; Product type e : enzyme; tagatose 6-phosphate aldolase 1, kbaZ subunit 3489524..3490804 Escherichia coli S88 7133031 YP_002393120.1 CDS agaV NC_011742.1 3490827 3491300 D catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake;involved in N-acetylgalactosamine transport; PTS system N-acetylgalactosamine-specific transporter subunit IIB 3490827..3491300 Escherichia coli S88 7130434 YP_002393121.1 CDS ECS88_3520 NC_011742.1 3491311 3492090 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative enzyme IIC component of PTS 3491311..3492090 Escherichia coli S88 7133033 YP_002393122.1 CDS ECS88_3521 NC_011742.1 3492074 3492958 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative hexose/hexosamine family PTS permease IID component 3492074..3492958 Escherichia coli S88 7132878 YP_002393123.1 CDS ECS88_3522 NC_011742.1 3492976 3493410 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphotransferase system enzyme subunit (N-acetyl-galactosamine / galactosamine PTS system enzyme IIA component) 3492976..3493410 Escherichia coli S88 7132879 YP_002393124.1 CDS agaA NC_011742.1 3493386 3494540 D Evidence 2b : Function of strongly homologous gene; Product type e : enzyme; N-acetylglucosamine-6-phosphate deacetylase (GlcNAc 6-P deacetylase) 3493386..3494540 Escherichia coli S88 7132880 YP_002393125.1 CDS agaS NC_011742.1 3494889 3496043 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9689210, 9697096, 14731281, 8932697; Product type e : enzyme; tagatose-6-phosphate ketose/aldose isomerase 3494889..3496043 Escherichia coli S88 7133026 YP_002393126.1 CDS kbaY NC_011742.1 3496056 3496916 D catalyzes the reversible reaction of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate; in enteric bacteria there are two D-tagatose 1,6-bisphosphate-specific aldolases: KbaY (also called AgaY), involved in catabolism of N-acetyl-galactosamine and D-galactosamine, and GatY which is part of the galactitol catabolism pathway; tagatose-bisphosphate aldolase 3496056..3496916 Escherichia coli S88 7133032 YP_002393127.1 CDS agaB NC_011742.1 3497083 3497559 D catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake; involved in N-acetylgalactosamine transport; PTS system N-acetylgalactosamine-specific transporter subunit IIB 3497083..3497559 Escherichia coli S88 7130433 YP_002393128.1 CDS agaC NC_011742.1 3497598 3498401 D catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane;protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake; involved in N-acetylgalactosamine transport; PTS system N-acetylgalactosamine-specific transporter subunit IIC 3497598..3498401 Escherichia coli S88 7133027 YP_002393129.1 CDS agaD NC_011742.1 3498391 3499182 D catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; involved in N-acetylgalactosamine transport; PTS system N-acetylgalactosamine-specific transporter subunit IID 3498391..3499182 Escherichia coli S88 7133028 YP_002393130.1 CDS agaI NC_011742.1 3499183 3499950 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10931310; Product type e : enzyme; galactosamine-6-phosphate isomerase 3499183..3499950 Escherichia coli S88 7133029 YP_002393131.1 CDS yraL NC_011742.1 3500000 3500863 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative methyltransferase complement(3500000..3500863) Escherichia coli S88 7133030 YP_002393132.1 CDS yraM NC_011742.1 3500928 3502964 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3500928..3502964 Escherichia coli S88 7132118 YP_002393133.1 CDS yraN NC_011742.1 3502922 3503317 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3502922..3503317 Escherichia coli S88 7132119 YP_002393134.1 CDS yraO NC_011742.1 3503337 3503927 D Required for the timely initiation of chromosomal replication via direct interactions with the dnaA initiator protein; DnaA initiator-associating protein DiaA 3503337..3503927 Escherichia coli S88 7132120 YP_002393135.1 CDS ecfH NC_011742.1 3503937 3504512 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 11274153; hypothetical protein 3503937..3504512 Escherichia coli S88 7132121 YP_002393136.1 CDS yraQ NC_011742.1 3504625 3505665 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative permease complement(3504625..3505665) Escherichia coli S88 7132375 YP_002393137.1 CDS yraR NC_011742.1 3505738 3506373 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative nucleoside-diphosphate-sugar epimerase complement(3505738..3506373) Escherichia coli S88 7132122 YP_002393138.1 CDS yhbO NC_011742.1 3506501 3507019 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative intracellular protease 3506501..3507019 Escherichia coli S88 7132123 YP_002393139.1 CDS yhbP NC_011742.1 3506999 3507442 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3506999..3507442) Escherichia coli S88 7132251 YP_002393140.1 CDS yhbQ NC_011742.1 3507493 3507795 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; GIY-YIG nuclease superfamily protein 3507493..3507795 Escherichia coli S88 7132252 YP_002393141.1 CDS yhbS NC_011742.1 3507782 3508285 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative acyltransferase with acyl-CoA N-acyltransferase domain complement(3507782..3508285) Escherichia coli S88 7132253 YP_002393142.1 CDS yhbT NC_011742.1 3508279 3508803 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative lipid carrier protein complement(3508279..3508803) Escherichia coli S88 7132254 YP_002393143.1 CDS yhbU NC_011742.1 3509012 3510007 D Evidence 2b : Function of strongly homologous gene; PubMedId : 10206698; Product type e : enzyme; peptidase (collagenase-like) 3509012..3510007 Escherichia coli S88 7132255 YP_002393144.1 CDS yhbV NC_011742.1 3510016 3510894 D Evidence 2b : Function of strongly homologous gene; PubMedId : 10206698; Product type e : enzyme; protease 3510016..3510894 Escherichia coli S88 7132256 YP_002393145.1 CDS yhbW NC_011742.1 3510975 3511982 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein 3510975..3511982 Escherichia coli S88 7132257 YP_002393146.1 CDS mtr NC_011742.1 3512100 3513344 R tryptophan transporter of high affinity; tryptophan permease complement(3512100..3513344) Escherichia coli S88 7132258 YP_002393147.1 CDS deaD NC_011742.1 3513498 3515387 R participates in the assembly of the large subunit of the ribosome; plays a key role in optimal cell growth at low temperature and is required for normal cell division; ATP-dependent RNA helicase DeaD complement(3513498..3515387) Escherichia coli S88 7129626 YP_002393148.1 CDS nlpI NC_011742.1 3515567 3516451 R lipoprotein that appears to be involved in cell division; interacts with the periplasmic protease Prc and may be activated by protease processing; lipoprotein NlpI complement(3515567..3516451) Escherichia coli S88 7130177 YP_002393149.1 CDS pnp NC_011742.1 3516560 3518764 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87083499, 91198209, 99234021, 99340204, 2432069, 3005122, 6382163, 9008164, 9298646; Product type e : enzyme; polynucleotide phosphorylase/polyadenylase complement(3516560..3518764) Escherichia coli S88 7129725 YP_002393150.1 CDS rpsO NC_011742.1 3518942 3519211 R 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; 30S ribosomal protein S15 complement(3518942..3519211) Escherichia coli S88 7130640 YP_002393151.1 CDS truB NC_011742.1 3519360 3520304 R catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; tRNA pseudouridine synthase B complement(3519360..3520304) Escherichia coli S88 7133798 YP_002393152.1 CDS rbfA NC_011742.1 3520304 3520705 R associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock; ribosome-binding factor A complement(3520304..3520705) Escherichia coli S88 7130352 YP_002393153.1 CDS infB NC_011742.1 3520869 3523541 R 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; translation initiation factor IF-2 complement(3520869..3523541) Escherichia coli S88 7131786 YP_002393154.1 CDS nusA NC_011742.1 3523566 3525053 R modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA complement(3523566..3525053) Escherichia coli S88 7131634 YP_002393155.1 CDS yhbC NC_011742.1 3525081 3525533 R in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins; hypothetical protein complement(3525081..3525533) Escherichia coli S88 7133116 YP_002393156.1 CDS argG NC_011742.1 3526164 3527507 D catalyzes the formation of arginosuccinate from citrulline and aspartate in arginine biosynthesis; argininosuccinate synthase 3526164..3527507 Escherichia coli S88 7131984 YP_002393157.1 CDS yhbX NC_011742.1 3527515 3529140 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative hydrolase, inner membrane complement(3527515..3529140) Escherichia coli S88 7133096 YP_002393158.1 CDS secG NC_011742.1 3529695 3530027 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20194819, 21125563, 9020118, 94074540, 9564033, 9644254, 9829959, 99298179, 7556084, 8034620, 8045257, 8244950, 8253068; Product type t : transporter; preprotein translocase subunit SecG complement(3529695..3530027) Escherichia coli S88 7131983 YP_002393159.1 CDS glmM NC_011742.1 3530255 3531592 R catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase complement(3530255..3531592) Escherichia coli S88 7131383 YP_002393160.1 CDS folP NC_011742.1 3531585 3532433 R catalyzes the formation of dihydropteroate from 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate and 4-aminobenzoate; dihydropteroate synthase complement(3531585..3532433) Escherichia coli S88 7132220 YP_002393161.1 CDS hflB NC_011742.1 3532523 3534457 R inner membrane metalloprotease; may be involved in degradation of aberrant cytoplasmic and membrane proteins; ATP-dependent metalloprotease complement(3532523..3534457) Escherichia coli S88 7132820 YP_002393162.1 CDS rrmJ NC_011742.1 3534557 3535186 R Specifically methylates the uridine in position 2552 of 23S rRNA in the fully assembled 50S ribosomal subunit; 23S rRNA methyltransferase J complement(3534557..3535186) Escherichia coli S88 7132849 YP_002393163.1 CDS yhbY NC_011742.1 3535312 3535605 D RNA binding protein found associated to pre-50S subunit of the ribosome; putative role in ribosome assembly; necessary for optimal growth but not cell viability; RNA-binding protein YhbY 3535312..3535605 Escherichia coli S88 7133807 YP_002393164.1 CDS greA NC_011742.1 3535761 3536237 R 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; transcription elongation factor GreA complement(3535761..3536237) Escherichia coli S88 7132260 YP_002393165.1 CDS dacB NC_011742.1 3536485 3537918 D penicillin binding protein 4; penicillin sensitive; catalyzes the formation of D-alanine from D-alanyl-D-alanine; one of four, DD-carboxypeptidase low-molecular weight penicillin-binding proteins that remove terminal D-alanine from pentapeptide side chains; D-alanyl-D-alanine carboxypeptidase/endopeptidase 3536485..3537918 Escherichia coli S88 7130068 YP_002393166.1 CDS obgE NC_011742.1 3537959 3539131 R essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE complement(3537959..3539131) Escherichia coli S88 7130554 YP_002393167.1 CDS yhbE NC_011742.1 3539147 3540112 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(3539147..3540112) Escherichia coli S88 7133120 YP_002393168.1 CDS rpmA NC_011742.1 3540239 3540496 R involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 complement(3540239..3540496) Escherichia coli S88 7132248 YP_002393169.1 CDS rplU NC_011742.1 3540517 3540828 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91088242, 94146411, 10094780, 387076, 8312607; Product type s : structure; 50S ribosomal protein L21 complement(3540517..3540828) Escherichia coli S88 7133765 YP_002393170.1 CDS ispB NC_011742.1 3541087 3542058 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94311902, 97284515, 2670911, 8037730, 8312607; Product type e : enzyme; octaprenyl diphosphate synthase 3541087..3542058 Escherichia coli S88 7133760 YP_002393171.1 CDS sfsB NC_011742.1 3542291 3542569 D activator of maltose metabolism genes; DNA-binding transcriptional regulator Nlp 3542291..3542569 Escherichia coli S88 7130419 YP_002393172.1 CDS murA NC_011742.1 3542617 3543876 R adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active; UDP-N-acetylglucosamine 1-carboxyvinyltransferase complement(3542617..3543876) Escherichia coli S88 7130586 YP_002393173.1 CDS yrbA NC_011742.1 3543931 3544185 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(3543931..3544185) Escherichia coli S88 7129630 YP_002393174.1 CDS yrbB NC_011742.1 3544345 3544638 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3544345..3544638) Escherichia coli S88 7132124 YP_002393175.1 CDS yrbC NC_011742.1 3544638 3545273 R Evidence 2b : Function of strongly homologous gene; PubMedId : 9658016; Product type t : transporter; toluene transporter subunit: membrane component of ABC superfamily complement(3544638..3545273) Escherichia coli S88 7132125 YP_002393176.1 CDS yrbD NC_011742.1 3545292 3545843 R Evidence 2b : Function of strongly homologous gene; PubMedId : 9658016; Product type t : transporter; toluene transporter subunit: membrane component of ABC superfamily complement(3545292..3545843) Escherichia coli S88 7132126 YP_002393177.1 CDS yrbE NC_011742.1 3545848 3546630 R Evidence 2b : Function of strongly homologous gene; PubMedId : 9658016; Product type t : transporter; toluene transporter subunit: membrane component of ABC superfamily complement(3545848..3546630) Escherichia coli S88 7132127 YP_002393178.1 CDS yrbF NC_011742.1 3546638 3547447 R ATP-binding subunit of a putative ABC toluene efflux transporter; putative ABC transporter ATP-binding protein YrbF complement(3546638..3547447) Escherichia coli S88 7132128 YP_002393179.1 CDS yrbG NC_011742.1 3547657 3548634 D YrbG; inner membrane protein involved in cell envelope integrity; putative sodium ion/calcium ion exchanger; in E. coli it is non essential for cell viability; member of the YRBG family of cation/Ca2+ exchangers; putative calcium/sodium:proton antiporter 3547657..3548634 Escherichia coli S88 7132129 YP_002393180.1 CDS kdsD NC_011742.1 3548648 3549634 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12805358; Product type e : enzyme; D-arabinose 5-phosphate isomerase 3548648..3549634 Escherichia coli S88 7132130 YP_002393181.1 CDS kdsC NC_011742.1 3549655 3550221 D forms homotetramers; catalyzes hydrolysis of KDO 8-P to KDO and inorganic phosphate; functions in lipopolysaccharide biosynthesis; 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase 3549655..3550221 Escherichia coli S88 7130449 YP_002393182.1 CDS yrbK NC_011742.1 3550218 3550793 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3550218..3550793 Escherichia coli S88 7130448 YP_002393183.1 CDS lptA NC_011742.1 3550762 3551319 D LptA; periplasmic binding protein part of a putative ABC superfamily of uptake transporters; interacts with LptB protein, the ATP binding component of the uptake system; lipopolysaccharide transport periplasmic protein LptA 3550762..3551319 Escherichia coli S88 7132131 YP_002393184.1 CDS lptB NC_011742.1 3551326 3552051 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7876255, 9298646, 17056748; Product type pt : putative transporter; putative ABC transporter ATP-binding protein YhbG 3551326..3552051 Escherichia coli S88 7129378 YP_002393185.1 CDS rpoN NC_011742.1 3552099 3553532 D sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma 54 factor is responsible for the expression of enzymes involved in nitrogen assimilation and metabolism; the rhizobia often have 2 copies of this sigma factor; in Rhizobium etli RpoN1 shown to be involved in the assimilation of several nitrogen and carbon sources during free-living aerobic growth and RpoN2 is involved in symbiotic nitrogen fixation; in Bradyrhizobium both RpoN1 and N2 are functional in free-living and symbiotic conditions, rpoN1 gene was regulated in response to oxygen; RNA polymerase factor sigma-54 3552099..3553532 Escherichia coli S88 7129379 YP_002393186.1 CDS yhbH NC_011742.1 3553555 3553842 D YhbH; resting ribosome-binding protein involved in ribosome stabilization and preservation in stationary phase; binds specifically 100S ribosomes (an inactive ribosome product of a 70S ribosome dimerization); seems to be involved in modulation of the sigma(54) (RpoN) activity for quorum sensing; putative sigma(54) modulation protein 3553555..3553842 Escherichia coli S88 7133780 YP_002393187.1 CDS ptsN NC_011742.1 3553960 3554451 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88212176, 90136533, 90274974, 95020584, 95181483, 7876255, 8025669, 8444818, 9636714; Product type t : transporter; PTS system transporter subunit IIA-like nitrogen-regulatory protein PtsN 3553960..3554451 Escherichia coli S88 7132249 YP_002393188.1 CDS yhbJ NC_011742.1 3554497 3555351 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3554497..3555351 Escherichia coli S88 7131742 YP_002393189.1 CDS npr NC_011742.1 3555348 3555620 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10473571, 95181483, 7876255, 8025669; Product type t : transporter; phosphohistidinoprotein-hexose phosphotransferase component of N-regulated PTS system (Npr) 3555348..3555620 Escherichia coli S88 7132250 YP_002393190.1 CDS yrbL NC_011742.1 3555834 3556466 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 89083480; hypothetical protein 3555834..3556466 Escherichia coli S88 7129731 YP_002393191.1 CDS mtgA NC_011742.1 3556463 3557191 R glycosyltransferase; polymerizes glycan strands in the peptidoglycan; monofunctional biosynthetic peptidoglycan transglycosylase complement(3556463..3557191) Escherichia coli S88 7132132 YP_002393192.1 CDS elbB NC_011742.1 3557188 3557841 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92246944, 98269038, 1575737, 9603997; Product type pe : putative enzyme; isoprenoid biosynthesis protein with amidotransferase-like domain complement(3557188..3557841) Escherichia coli S88 7129619 YP_002393193.1 CDS arcB NC_011742.1 3558071 3560407 R sensor-regulator protein which regulates the expression of many genes in response to respiratory growth conditions including anaerobic repression of the arc modulon; hybrid sensory histidine kinase in two-component regulatory system with ArcA; aerobic respiration control sensor protein ArcB complement(3558071..3560407) Escherichia coli S88 7131348 YP_002393194.1 CDS yhcC NC_011742.1 3560503 3561432 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative Fe-S oxidoreductase complement(3560503..3561432) Escherichia coli S88 7133090 YP_002393195.1 CDS gltB NC_011742.1 3562014 3566567 D catalyzes the formation of glutamate from glutamine and alpha-ketoglutarate; glutamate synthase subunit alpha 3562014..3566567 Escherichia coli S88 7132262 YP_002393196.1 CDS gltD NC_011742.1 3566580 3567998 D glutamate synthase is composed of subunits alpha and beta; beta subunit is a flavin adenine dinucleotide-NADPH dependent oxidoreductase; provides electrons to the alpha subunit, which binds L-glutamine and 2-oxoglutarate and forms L-glutamate; glutamate synthase subunit beta 3566580..3567998 Escherichia coli S88 7130030 YP_002393197.1 CDS yhcH NC_011742.1 3568066 3568530 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3568066..3568530) Escherichia coli S88 7130031 YP_002393198.1 CDS nanK NC_011742.1 3568527 3569402 R catalyzes the phosphorylation of the N-acetylmannosamine (ManNAc) liberated from N-acetyl-neuraminic acid by the nanA protein; N-acetylmannosamine kinase complement(3568527..3569402) Escherichia coli S88 7132263 YP_002393199.1 CDS nanE NC_011742.1 3569399 3570088 R Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate; N-acetylmannosamine-6-phosphate 2-epimerase complement(3569399..3570088) Escherichia coli S88 7129664 YP_002393200.1 CDS nanT NC_011742.1 3570136 3571626 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96011396, 9864311, 7592358; Product type t : transporter; putative sialic acid transporter complement(3570136..3571626) Escherichia coli S88 7129663 YP_002393201.1 CDS nanA NC_011742.1 3571735 3572628 R catalyzes the formation of pyruvate and N-acetylmannosamine from N-acetylneuraminic acid; N-acetylneuraminate lyase complement(3571735..3572628) Escherichia coli S88 7129666 YP_002393202.1 CDS nanR NC_011742.1 3572750 3573541 R Transcriptional repressor of the nan operon that encodes proteins involved in sialic acid utilization; transcriptional regulator NanR complement(3572750..3573541) Escherichia coli S88 7129662 YP_002393203.1 CDS sspB NC_011742.1 3573649 3574146 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12445774, 94293773, 1721886, 3029697, 8022275; Product type f : factor; ClpXP protease specificity-enhancing factor complement(3573649..3574146) Escherichia coli S88 7129665 YP_002393204.1 CDS sspA NC_011742.1 3574152 3574790 R transcriptional activator; required for activation of bacteriophage P1 late promoter; induced by starvation; stringent starvation protein A complement(3574152..3574790) Escherichia coli S88 7130653 YP_002393205.1 CDS rpsI NC_011742.1 3575185 3575577 R forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 complement(3575185..3575577) Escherichia coli S88 7130652 YP_002393206.1 CDS rplM NC_011742.1 3575593 3576021 R in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 complement(3575593..3576021) Escherichia coli S88 7133792 YP_002393207.1 CDS yhcM NC_011742.1 3576241 3577368 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative nucleoside triphosphate hydrolase domain complement(3576241..3577368) Escherichia coli S88 7133752 YP_002393208.1 CDS yhcB NC_011742.1 3577562 3577960 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16079137; Product type pe : putative enzyme; cytochrome d ubiquinol oxidase subunit III 3577562..3577960 Escherichia coli S88 7132264 YP_002393209.1 CDS degQ NC_011742.1 3578114 3579481 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8830688, 96165272, 8576051, 8576052, 9740056; Product type e : enzyme; serine endoprotease 3578114..3579481 Escherichia coli S88 7132261 YP_002393210.1 CDS degS NC_011742.1 3579571 3580638 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15137941, 15225661, 21352996, 96165272, 99431977, 3322223, 8576051; Product type e : enzyme; serine endoprotease 3579571..3580638 Escherichia coli S88 7130182 YP_002393211.1 CDS mdh NC_011742.1 3580701 3581639 R oxidizes malate to oxaloacetate; malate dehydrogenase complement(3580701..3581639) Escherichia coli S88 7130183 YP_002393212.1 CDS argR NC_011742.1 3582074 3582544 D regulates arginine biosynthesis when complexed with arginine by binding at site that overlap the promotors of the arginine biosynthesis genes; arginine repressor 3582074..3582544 Escherichia coli S88 7129431 YP_002393213.1 CDS yhcN NC_011742.1 3582908 3583171 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3582908..3583171 Escherichia coli S88 7133101 YP_002393214.1 CDS yhcO NC_011742.1 3583226 3583498 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative barnase inhibitor complement(3583226..3583498) Escherichia coli S88 7132265 YP_002393215.1 CDS aaeB NC_011742.1 3583590 3585557 R with AaeA forms an efflux pump whose substrates are p-hydroxybenzoic acid 6-hydroxy-2-naphthoic and 2-hydroxycinnamate; p-hydroxybenzoic acid efflux subunit AaeB complement(3583590..3585557) Escherichia coli S88 7132266 YP_002393216.1 CDS aaeA NC_011742.1 3585563 3586495 R with AaeB forms an efflux pump whose substrates are p-hydroxybenzoic acid, 6-hydroxy-2-naphthoic and 2-hydroxycinnamate; p-hydroxybenzoic acid efflux subunit AaeA complement(3585563..3586495) Escherichia coli S88 7132015 YP_002393217.1 CDS aaeX NC_011742.1 3586503 3586706 R membrane protein AaeX; the gene is a member of the aaeXAB operon; hypothetical protein complement(3586503..3586706) Escherichia coli S88 7132014 YP_002393218.1 CDS aaeR NC_011742.1 3586889 3587818 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15489430; Product type r : regulator; putative DNA-binding transcriptional regulator 3586889..3587818 Escherichia coli S88 7132017 YP_002393219.1 CDS tldD NC_011742.1 3587946 3589391 R responsible for the proteolytic maturation of the E. coli pMccB17 plasmid-encoded microcin B17, an exported protein that targets the essential topoisomerase II DNA gyrase; degrades the E. coli plasmid F-encoded CcdA; protease TldD complement(3587946..3589391) Escherichia coli S88 7132016 YP_002393220.1 CDS yhdP NC_011742.1 3589547 3593347 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 10960106; Product type pm : putative membrane component; hypothetical protein complement(3589547..3593347) Escherichia coli S88 7133478 YP_002393221.1 CDS rng NC_011742.1 3593415 3594884 R involved in the processing of the 5'end of 16S rRNA; ribonuclease G complement(3593415..3594884) Escherichia coli S88 7132272 YP_002393222.1 CDS yhdE NC_011742.1 3594874 3595467 R Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell; Maf-like protein complement(3594874..3595467) Escherichia coli S88 7132747 YP_002393223.1 CDS mreD NC_011742.1 3595476 3595964 R part of cell wall structural complex MreBCD; transmembrane component; rod shape-determining protein MreD complement(3595476..3595964) Escherichia coli S88 7132267 YP_002393224.1 CDS ECS88_3625 NC_011742.1 3595948 3596079 R Evidence 6 : Doubtful CDS; hypothetical protein complement(3595948..3596079) Escherichia coli S88 7129611 YP_002393225.1 CDS mreC NC_011742.1 3595964 3597067 R 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; rod shape-determining protein MreC complement(3595964..3597067) Escherichia coli S88 7132881 YP_002393226.1 CDS mreB NC_011742.1 3597133 3598176 R functions in MreBCD complex in some organisms; rod shape-determining protein MreB complement(3597133..3598176) Escherichia coli S88 7129610 YP_002393227.1 CDS ECS88_3628 NC_011742.1 3598284 3598472 D Evidence 6 : Doubtful CDS; hypothetical protein 3598284..3598472 Escherichia coli S88 7129609 YP_002393228.1 CDS csrD NC_011742.1 3598481 3600421 R regulates the degradation of the small RNAs CsrB and CsrC; may function to targate RNase E to specific RNA molecules; regulatory protein CsrD complement(3598481..3600421) Escherichia coli S88 7132882 YP_002393229.1 CDS yhdH NC_011742.1 3600573 3601547 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase, Zn-dependent and NAD(P)-binding 3600573..3601547 Escherichia coli S88 7130505 YP_002393230.1 CDS accB NC_011742.1 3602525 3602995 D composes the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase complex, the enzyme that catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, which in turn controls the rate of fatty acid metabolism; acetyl-CoA carboxylase biotin carboxyl carrier protein subunit 3602525..3602995 Escherichia coli S88 7132268 YP_002393231.1 CDS accC NC_011742.1 3603006 3604355 D an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism; acetyl-CoA carboxylase biotin carboxylase subunit 3603006..3604355 Escherichia coli S88 7132027 YP_002393232.1 CDS ECS88_3633 NC_011742.1 3604447 3605493 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3604447..3605493) Escherichia coli S88 7132028 YP_002393233.1 CDS ECS88_3634 NC_011742.1 3605490 3606452 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative carbohydrate kinase complement(3605490..3606452) Escherichia coli S88 7132883 YP_002393234.1 CDS ECS88_3635 NC_011742.1 3606474 3607463 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sugar transporter subunit: membrane component of ABC superfamily complement(3606474..3607463) Escherichia coli S88 7132884 YP_002393235.1 CDS ECS88_3636 NC_011742.1 3607464 3608993 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sugar transporter subunit: ATP-binding component of ABC superfamily complement(3607464..3608993) Escherichia coli S88 7132885 YP_002393236.1 CDS ECS88_3637 NC_011742.1 3609024 3609920 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ABC-type sugar transport system, periplasmic component complement(3609024..3609920) Escherichia coli S88 7132886 YP_002393237.1 CDS gatY NC_011742.1 3609950 3610804 R catalyzes the reversible reaction of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate; in enteric bacteria there are two D-tagatose 1,6-bisphosphate-specific aldolases: KbaY (also called AgaY), involved in catabolism of N-acetyl-galactosamine and D-galactosamine, and GatY which is part of the galactitol catabolism pathway; tagatose-bisphosphate aldolase complement(3609950..3610804) Escherichia coli S88 7132887 YP_002393238.1 CDS ECS88_3639 NC_011742.1 3611145 3611975 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DEOR-type transcriptional regulator 3611145..3611975 Escherichia coli S88 7132888 YP_002393239.1 CDS yhdT NC_011742.1 3613035 3613277 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 3613035..3613277 Escherichia coli S88 7132891 YP_002393240.1 CDS panF NC_011742.1 3613267 3614718 D 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; sodium/panthothenate symporter 3613267..3614718 Escherichia coli S88 7132273 YP_002393241.1 CDS prmA NC_011742.1 3614730 3615611 D methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype; ribosomal protein L11 methyltransferase 3614730..3615611 Escherichia coli S88 7133161 YP_002393242.1 CDS dusB NC_011742.1 3615940 3616905 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 22095566, 1459953, 1547773, 2835774, 2837762, 8226664; Product type e : enzyme; tRNA-dihydrouridine synthase B 3615940..3616905 Escherichia coli S88 7130781 YP_002393243.1 CDS fis NC_011742.1 3616931 3617227 D Stimulates excision of phage lambda; affects Mu development; acts as an activator of rRNA and iRNA transcription; DNA-binding protein Fis 3616931..3617227 Escherichia coli S88 7132366 YP_002393244.1 CDS yhdJ NC_011742.1 3617315 3618199 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 15028690, 9073062; Product type e : enzyme; putative methyltransferase 3617315..3618199 Escherichia coli S88 7129502 YP_002393245.1 CDS yhdU NC_011742.1 3618283 3618462 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 3618283..3618462 Escherichia coli S88 7132269 YP_002393246.1 CDS envR NC_011742.1 3618465 3619127 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8203018, 11257026, 8407802, 1720861; Product type r : regulator; DNA-binding transcriptional regulator EnvR complement(3618465..3619127) Escherichia coli S88 7132274 YP_002393247.1 CDS acrE NC_011742.1 3619527 3620684 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94012493, 1720861; Product type lp : lipoprotein; cytoplasmic membrane lipoprotein 3619527..3620684 Escherichia coli S88 7132407 YP_002393248.1 CDS acrF NC_011742.1 3620696 3623800 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94262163, 99449638, 1720861, 8407802; Product type t : transporter; multidrug efflux system protein 3620696..3623800 Escherichia coli S88 7132045 YP_002393249.1 CDS yhdV NC_011742.1 3624053 3624274 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative outer membrane protein 3624053..3624274 Escherichia coli S88 7132046 YP_002393250.1 CDS aapJ NC_011742.1 3624813 3625730 D Evidence 2b : Function of strongly homologous gene; PubMedId : 8898392; Product type t : transporter; amino-acid transporter subunit ; periplasmic-binding component of ABC superfamily 3624813..3625730 Escherichia coli S88 7132892 YP_002393251.1 CDS aapQ NC_011742.1 3625798 3626979 D Evidence 2b : Function of strongly homologous gene; PubMedId : 8898392; Product type t : transporter; amino-acid transporter subunit ; membrane component of ABC superfamily 3625798..3626979 Escherichia coli S88 7132018 YP_002393252.1 CDS aapM NC_011742.1 3626989 3628092 D Evidence 2b : Function of strongly homologous gene; PubMedId : 8898392; Product type t : transporter; amino-acid transporter subunit ; membrane component of ABC superfamily 3626989..3628092 Escherichia coli S88 7132021 YP_002393253.1 CDS aapP NC_011742.1 3628100 3628858 D Evidence 2b : Function of strongly homologous gene; PubMedId : 8809753, 8898392; Product type t : transporter; amino-acid transporter subunit ; ATP-binding component of ABC superfamily 3628100..3628858 Escherichia coli S88 7132019 YP_002393254.1 CDS yrdA NC_011742.1 3634415 3635296 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3634415..3635296 Escherichia coli S88 7129268 YP_002393255.1 CDS yrdB NC_011742.1 3635272 3635529 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3635272..3635529) Escherichia coli S88 7132133 YP_002393256.1 CDS aroE NC_011742.1 3635526 3636344 R AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase complement(3635526..3636344) Escherichia coli S88 7132134 YP_002393257.1 CDS yrdC NC_011742.1 3636349 3636921 R RimN; YrdC; required for maturation of 16s RNA; binds preferentially double stranded RNA; putative ribosome maturation factor complement(3636349..3636921) Escherichia coli S88 7129925 YP_002393258.1 CDS yrdD NC_011742.1 3636926 3637468 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative DNA topoisomerase complement(3636926..3637468) Escherichia coli S88 7132135 YP_002393259.1 CDS smg NC_011742.1 3637497 3637970 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 8432722; hypothetical protein complement(3637497..3637970) Escherichia coli S88 7132136 YP_002393260.1 CDS smf NC_011742.1 3637942 3639066 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 8112305, 8432722; DNA protecting protein DprA complement(3637942..3639066) Escherichia coli S88 7130612 YP_002393261.1 CDS def NC_011742.1 3639196 3639705 D cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+); peptide deformylase 3639196..3639705 Escherichia coli S88 7130611 YP_002393262.1 CDS fmt NC_011742.1 3639720 3640667 D modifies the free amino group of the aminoacyl moiety of methionyl-tRNA(fMet) which is important in translation initiation; inactivation of this gene in Escherichia coli severely impairs growth; methionyl-tRNA formyltransferase 3639720..3640667 Escherichia coli S88 7130180 YP_002393263.1 CDS rsmB NC_011742.1 3640719 3642008 D catalyzes the methylation of cytosine at position 967 (m5C967) of 16S rRNA; SAM-dependent methyltransferase; 16S rRNA methyltransferase B 3640719..3642008 Escherichia coli S88 7132810 YP_002393264.1 CDS trkA NC_011742.1 3642030 3643406 D involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain; potassium transporter peripheral membrane component 3642030..3643406 Escherichia coli S88 7133814 YP_002393265.1 CDS mscL NC_011742.1 3643536 3643949 D forms homopentamer; channel that opens in response to pressure or hypoosmotic shock; large-conductance mechanosensitive channel 3643536..3643949 Escherichia coli S88 7130334 YP_002393266.1 CDS yhdL NC_011742.1 3643946 3644164 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3643946..3644164) Escherichia coli S88 7129614 YP_002393267.1 CDS zntR NC_011742.1 3644220 3644645 R mediates expression of the zinc export protein ZntA in response to high levels of zinc; member of MerR family of transcriptional regulators; zinc-responsive transcriptional regulator complement(3644220..3644645) Escherichia coli S88 7132270 YP_002393268.1 CDS yhdN NC_011742.1 3644656 3645024 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3644656..3645024) Escherichia coli S88 7131887 YP_002393269.1 CDS rplQ NC_011742.1 3645131 3645514 R is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 complement(3645131..3645514) Escherichia coli S88 7132271 YP_002393270.1 CDS rpoA NC_011742.1 3645555 3646544 R 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; DNA-directed RNA polymerase subunit alpha complement(3645555..3646544) Escherichia coli S88 7133756 YP_002393271.1 CDS rpsD NC_011742.1 3646570 3647190 R 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; 30S ribosomal protein S4 complement(3646570..3647190) Escherichia coli S88 7133774 YP_002393272.1 CDS rpsK NC_011742.1 3647224 3647613 R 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; 30S ribosomal protein S11 complement(3647224..3647613) Escherichia coli S88 7133787 YP_002393273.1 CDS rpsM NC_011742.1 3647630 3647986 R 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; 30S ribosomal protein S13 complement(3647630..3647986) Escherichia coli S88 7133794 YP_002393274.1 CDS secY NC_011742.1 3648281 3649612 R 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; preprotein translocase subunit SecY complement(3648281..3649612) Escherichia coli S88 7133796 YP_002393275.1 CDS rplO NC_011742.1 3649620 3650054 R late assembly protein; 50S ribosomal protein L15 complement(3649620..3650054) Escherichia coli S88 7131385 YP_002393276.1 CDS rpmD NC_011742.1 3650058 3650237 R L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7; 50S ribosomal protein L30 complement(3650058..3650237) Escherichia coli S88 7133754 YP_002393277.1 CDS rpsE NC_011742.1 3650241 3650744 R 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; 30S ribosomal protein S5 complement(3650241..3650744) Escherichia coli S88 7133768 YP_002393278.1 CDS rplR NC_011742.1 3650759 3651112 R binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 complement(3650759..3651112) Escherichia coli S88 7133788 YP_002393279.1 CDS rplF NC_011742.1 3651122 3651655 R 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; 50S ribosomal protein L6 complement(3651122..3651655) Escherichia coli S88 7133757 YP_002393280.1 CDS rpsH NC_011742.1 3651668 3652060 R binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 complement(3651668..3652060) Escherichia coli S88 7132768 YP_002393281.1 CDS rpsN NC_011742.1 3652094 3652399 R located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif; 30S ribosomal protein S14 complement(3652094..3652399) Escherichia coli S88 7133791 YP_002393282.1 CDS rplE NC_011742.1 3652414 3652953 R 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; 50S ribosomal protein L5 complement(3652414..3652953) Escherichia coli S88 7133797 YP_002393283.1 CDS rplX NC_011742.1 3652968 3653282 R assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 complement(3652968..3653282) Escherichia coli S88 7132767 YP_002393284.1 CDS rplN NC_011742.1 3653293 3653664 R binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 complement(3653293..3653664) Escherichia coli S88 7133763 YP_002393285.1 CDS rpsQ NC_011742.1 3653829 3654083 R primary binding protein; helps mediate assembly; involved in translation fidelity; 30S ribosomal protein S17 complement(3653829..3654083) Escherichia coli S88 7133753 YP_002393286.1 CDS rpmC NC_011742.1 3654083 3654274 R one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29 complement(3654083..3654274) Escherichia coli S88 7133800 YP_002393287.1 CDS rplP NC_011742.1 3654274 3654684 R located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 complement(3654274..3654684) Escherichia coli S88 7133767 YP_002393288.1 CDS rpsC NC_011742.1 3654697 3655398 R 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; 30S ribosomal protein S3 complement(3654697..3655398) Escherichia coli S88 7133755 YP_002393289.1 CDS rplV NC_011742.1 3655416 3655748 R 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; 50S ribosomal protein L22 complement(3655416..3655748) Escherichia coli S88 7133786 YP_002393290.1 CDS rpsS NC_011742.1 3655763 3656041 R protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 complement(3655763..3656041) Escherichia coli S88 7133761 YP_002393291.1 CDS rplB NC_011742.1 3656058 3656879 R 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; 50S ribosomal protein L2 complement(3656058..3656879) Escherichia coli S88 7133802 YP_002393292.1 CDS rplW NC_011742.1 3656897 3657199 R binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 complement(3656897..3657199) Escherichia coli S88 7132764 YP_002393293.1 CDS rplD NC_011742.1 3657196 3657801 R L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA; 50S ribosomal protein L4 complement(3657196..3657801) Escherichia coli S88 7133762 YP_002393294.1 CDS rplC NC_011742.1 3657812 3658441 R 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; 50S ribosomal protein L3 complement(3657812..3658441) Escherichia coli S88 7132766 YP_002393295.1 CDS rpsJ NC_011742.1 3658474 3658785 R 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; 30S ribosomal protein S10 complement(3658474..3658785) Escherichia coli S88 7132765 YP_002393296.1 CDS pioO NC_011742.1 3659023 3659442 R calcium-binding protein that may be required for the initiation of chromosome replication; chromosome replication protein PioO complement(3659023..3659442) Escherichia coli S88 7133793 YP_002393297.1 CDS gspA NC_011742.1 3659444 3660913 R Evidence 2b : Function of strongly homologous gene; PubMedId : 96256608; Product type t : transporter; general secretory pathway component, cryptic complement(3659444..3660913) Escherichia coli S88 7133735 YP_002393298.1 CDS gspC NC_011742.1 3661093 3661908 D Evidence 2b : Function of strongly homologous gene; PubMedId : 96256608; Product type t : transporter; general secretory pathway component, cryptic 3661093..3661908 Escherichia coli S88 7130079 YP_002393299.1 CDS gspD NC_011742.1 3661892 3663844 D Evidence 2b : Function of strongly homologous gene; PubMedId : 96256608; Product type t : transporter; general secretory pathway component, cryptic 3661892..3663844 Escherichia coli S88 7130080 YP_002393300.1 CDS gspE NC_011742.1 3663854 3665335 D Evidence 2b : Function of strongly homologous gene; PubMedId : 96256608; Product type t : transporter; general secretory pathway component, cryptic 3663854..3665335 Escherichia coli S88 7130081 YP_002393301.1 CDS gspF NC_011742.1 3665332 3666528 D Evidence 2b : Function of strongly homologous gene; PubMedId : 96256608, 7896718; Product type t : transporter; general secretory pathway component, cryptic 3665332..3666528 Escherichia coli S88 7130082 YP_002393302.1 CDS gspG NC_011742.1 3666538 3666975 D Evidence 2b : Function of strongly homologous gene; PubMedId : 95204361, 96256608; Product type t : transporter; pseudopilin, cryptic, general secretion pathway 3666538..3666975 Escherichia coli S88 7130083 YP_002393303.1 CDS gspH NC_011742.1 3666983 3667492 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 96256608; Product type pt : putative transporter; putative general secretory pathway component, cryptic 3666983..3667492 Escherichia coli S88 7130084 YP_002393304.1 CDS gspI NC_011742.1 3667489 3667884 D Evidence 2b : Function of strongly homologous gene; PubMedId : 96256608, 1588814; Product type t : transporter; general secretory pathway component, cryptic 3667489..3667884 Escherichia coli S88 7130085 YP_002393305.1 CDS gspJ NC_011742.1 3667877 3668464 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 96256608; Product type pt : putative transporter; putative general secretory pathway component, cryptic 3667877..3668464 Escherichia coli S88 7128866 YP_002393306.1 CDS gspK NC_011742.1 3668457 3669440 D Evidence 2b : Function of strongly homologous gene; PubMedId : 96256608; Product type t : transporter; general secretory pathway component, cryptic 3668457..3669440 Escherichia coli S88 7128867 YP_002393307.1 CDS gspL NC_011742.1 3669455 3670618 D Evidence 2b : Function of strongly homologous gene; PubMedId : 96256608; Product type t : transporter; general secretory pathway component, cryptic 3669455..3670618 Escherichia coli S88 7128868 YP_002393308.1 CDS gspM NC_011742.1 3670615 3671076 D Evidence 2b : Function of strongly homologous gene; PubMedId : 96099298, 96256608, 7959070; Product type t : transporter; general secretory pathway component, cryptic 3670615..3671076 Escherichia coli S88 7128869 YP_002393309.1 CDS gspO NC_011742.1 3671076 3671753 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95047556, 96256608, 98175453, 1676385, 2661540, 7959070; Product type e : enzyme; bifunctional prepilin leader peptidase and methylase 3671076..3671753 Escherichia coli S88 7128870 YP_002393310.1 CDS bfr NC_011742.1 3671782 3672258 R iron storage protein; bacterioferritin complement(3671782..3672258) Escherichia coli S88 7128871 YP_002393311.1 CDS bfd NC_011742.1 3672330 3672524 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8954950, 9889981, 2661540, 8639572; Product type c : carrier; bacterioferritin-associated ferredoxin complement(3672330..3672524) Escherichia coli S88 7129112 YP_002393312.1 CDS chiA NC_011742.1 3672693 3675395 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10760150, 10419961, 2661540; Product type e : enzyme; periplasmic endochitinase complement(3672693..3675395) Escherichia coli S88 7129111 YP_002393313.1 CDS tufA NC_011742.1 3675687 3676871 R 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; elongation factor Tu complement(3675687..3676871) Escherichia coli S88 7131903 YP_002393314.1 CDS fusA NC_011742.1 3676942 3679056 R EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G complement(3676942..3679056) Escherichia coli S88 7130366 YP_002393315.1 CDS rpsG NC_011742.1 3679153 3679623 R binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 complement(3679153..3679623) Escherichia coli S88 7132157 YP_002393316.1 CDS rpsL NC_011742.1 3679720 3680094 R 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; 30S ribosomal protein S12 complement(3679720..3680094) Escherichia coli S88 7133790 YP_002393317.1 CDS tusB NC_011742.1 3680220 3680507 R in Escherichai coli the heterohexameric TusBCD complex is involved in sulfur related that results in thiouridation to U34 position in some tRNAs; sulfur transfer complex subunit TusB complement(3680220..3680507) Escherichia coli S88 7133795 YP_002393318.1 CDS tusC NC_011742.1 3680514 3680873 R in Escherichai coli the heterohexameric TusBCD complex is involved in sulfur related that results in thiouridation to U34 position in some tRNAs; sulfur relay protein TusC complement(3680514..3680873) Escherichia coli S88 7130370 YP_002393319.1 CDS tusD NC_011742.1 3680873 3681259 R in Escherichai coli the heterohexameric TusBCD complex is involved in sulfur related that results in thiouridation to U34 position in some tRNAs; sulfur transfer complex subunit TusD complement(3680873..3681259) Escherichia coli S88 7130371 YP_002393320.1 CDS yheO NC_011742.1 3681259 3681981 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(3681259..3681981) Escherichia coli S88 7130372 YP_002393321.1 CDS fkpA NC_011742.1 3682148 3682960 R rotamase; FKBP-type peptidyl-prolyl cis-trans isomerase complement(3682148..3682960) Escherichia coli S88 7132276 YP_002393322.1 CDS slyX NC_011742.1 3683181 3683399 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3683181..3683399 Escherichia coli S88 7129509 YP_002393323.1 CDS slyD NC_011742.1 3683448 3684038 R rotamase; FKBP-type peptidyl-prolyl cis-trans isomerase complement(3683448..3684038) Escherichia coli S88 7130610 YP_002393324.1 CDS yheV NC_011742.1 3684133 3684333 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3684133..3684333) Escherichia coli S88 7130609 YP_002393325.1 CDS kefB NC_011742.1 3684343 3686148 R involved in potassium efflux; glutathione-regulated potassium-efflux system protein KefB complement(3684343..3686148) Escherichia coli S88 7132281 YP_002393326.1 CDS kefG NC_011742.1 3686148 3686702 R required for KefB activity; glutathione-regulated potassium-efflux system ancillary protein KefG complement(3686148..3686702) Escherichia coli S88 7130454 YP_002393327.1 CDS yheS NC_011742.1 3686830 3688743 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ABC transporter ATP-binding protein 3686830..3688743 Escherichia coli S88 7130457 YP_002393328.1 CDS yheT NC_011742.1 3688743 3689765 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 9889164; Product type pe : putative enzyme; putative hydrolase 3688743..3689765 Escherichia coli S88 7132277 YP_002393329.1 CDS yheU NC_011742.1 3689759 3689977 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3689759..3689977 Escherichia coli S88 7132278 YP_002393330.1 CDS prkB NC_011742.1 3690031 3690900 D Evidence 2b : Function of strongly homologous gene; PubMedId : 2559876; Product type e : enzyme; phosphoribulokinase 3690031..3690900 Escherichia coli S88 7129679 YP_002393331.1 CDS yhfA NC_011742.1 3690955 3691359 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3690955..3691359) Escherichia coli S88 7130779 YP_002393332.1 CDS ECS88_3747 NC_011742.1 3691439 3691654 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 3691439..3691654 Escherichia coli S88 7131967 YP_002393333.1 CDS crp NC_011742.1 3691661 3692293 D complexes with cyclic AMP and binds to specific DNA sites near the promoter to regulate the transcription of several catabolite-sensitive operons; cAMP-regulatory protein 3691661..3692293 Escherichia coli S88 7132893 YP_002393334.1 CDS yhfK NC_011742.1 3692332 3694434 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3692332..3694434 Escherichia coli S88 7131966 YP_002393335.1 CDS argD NC_011742.1 3694501 3695721 R DapATase; bifunctional enzyme that functions in arginine and lysine biosynthetic pathways; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine or N-succinyl-2-L-amino-6-oxoheptanedioate from 2-oxoglutarate and N-succinyl-L-2,6-diaminoheptanedioate; bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein complement(3694501..3695721) Escherichia coli S88 7132284 YP_002393336.1 CDS pabA NC_011742.1 3695807 3696370 R aminodeoxychorismate synthase subunit PabA; with PabB catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine in para-aminobenzoate synthesis; PabA provides the glutamine amidotransferase activity; para-aminobenzoate synthase component II complement(3695807..3696370) Escherichia coli S88 7133094 YP_002393337.1 CDS fic NC_011742.1 3696402 3697004 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92021789, 94095125, 2007139, 2403545, 2546924, 7549107; Product type cp : cell process; cell filamentation protein Fic complement(3696402..3697004) Escherichia coli S88 7133153 YP_002393338.1 CDS yhfG NC_011742.1 3696994 3697161 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3696994..3697161) Escherichia coli S88 7129489 YP_002393339.1 CDS ppiA NC_011742.1 3697266 3697838 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90272647, 91175755, 1606970, 2001362, 2007139, 2190212, 2403545, 2546924, 8130188, 8180197; Product type e : enzyme; peptidyl-prolyl cis-trans isomerase A (rotamase A) complement(3697266..3697838) Escherichia coli S88 7132283 YP_002393340.1 CDS tsgA NC_011742.1 3698108 3699289 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 20509826; Product type pt : putative transporter; hypothetical protein 3698108..3699289 Escherichia coli S88 7130760 YP_002393341.1 CDS nirB NC_011742.1 3699551 3702094 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93062014, 2200672, 2445993, 2543955; Product type e : enzyme; nitrite reductase, large subunit, NAD(P) H-binding 3699551..3702094 Escherichia coli S88 7130359 YP_002393342.1 CDS nirD NC_011742.1 3702091 3702417 D involved in reducing nitrite to ammonium to detoxify nitrite accumulation in anaerobic nitrate-respiring cells and regenerate NAD+; bounds to NirB, the cytoplasmic subunit, whose expression is induced at high nitrate concentrations; nitrite reductase small subunit 3702091..3702417 Escherichia coli S88 7129717 YP_002393343.1 CDS nirC NC_011742.1 3702543 3703349 D member of the FNT family of formate and nitrite transporters; nitrite transporter NirC 3702543..3703349 Escherichia coli S88 7129719 YP_002393344.1 CDS cysG NC_011742.1 3703368 3704741 D multifunction enzyme consisting of uroporphyrin-III C-methyltransferase, precorrin-2 dehydrogenase and sirohydrochlorin ferrochelatase; catalyzes the methylation of uroporphyrinogen III to form precorrin-2, then catalyzes formation of sirohydrochlorin from precorrin-2 and finally catalyzed the formation of siroheme from sirohydrochlorin; siroheme synthase 3703368..3704741 Escherichia coli S88 7129718 YP_002393345.1 CDS yhfL NC_011742.1 3704993 3705160 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative secreted peptide 3704993..3705160 Escherichia coli S88 7130538 YP_002393346.1 CDS yhfS NC_011742.1 3705268 3706353 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3705268..3706353) Escherichia coli S88 7132285 YP_002393347.1 CDS yhfT NC_011742.1 3706365 3707669 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(3706365..3707669) Escherichia coli S88 7132286 YP_002393348.1 CDS yhfU NC_011742.1 3707681 3708034 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3707681..3708034) Escherichia coli S88 7132287 YP_002393349.1 CDS php NC_011742.1 3708045 3708923 R phosphotriesterase homology protein; PhP; YhfV; member of a family of proteins related to phosphotriesterase (PTE); putative hydrolase complement(3708045..3708923) Escherichia coli S88 7132288 YP_002393350.1 CDS yhfW NC_011742.1 3708920 3710146 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative mutase complement(3708920..3710146) Escherichia coli S88 7133730 YP_002393351.1 CDS yhfX NC_011742.1 3710147 3711310 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative amino acid racemase complement(3710147..3711310) Escherichia coli S88 7132289 YP_002393352.1 CDS yhfY NC_011742.1 3711394 3711756 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3711394..3711756) Escherichia coli S88 7132290 YP_002393353.1 CDS yhfZ NC_011742.1 3711773 3712678 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3711773..3712678) Escherichia coli S88 7132291 YP_002393354.1 CDS trpS NC_011742.1 3712838 3713842 R 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; tryptophanyl-tRNA synthetase complement(3712838..3713842) Escherichia coli S88 7132292 YP_002393355.1 CDS gph NC_011742.1 3713835 3714593 R catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate; phosphoglycolate phosphatase complement(3713835..3714593) Escherichia coli S88 7130350 YP_002393356.1 CDS rpe NC_011742.1 3714586 3715263 R catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate; ribulose-phosphate 3-epimerase complement(3714586..3715263) Escherichia coli S88 7130060 YP_002393357.1 CDS dam NC_011742.1 3715281 3716117 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90136529, 92262475, 92272672, 2549371, 6300769, 7603433, 8341592; Product type e : enzyme; DNA adenine methylase complement(3715281..3716117) Escherichia coli S88 7132758 YP_002393358.1 CDS damX NC_011742.1 3716224 3717510 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3716224..3717510) Escherichia coli S88 7130561 YP_002393359.1 CDS aroB NC_011742.1 3717602 3718690 R catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase complement(3717602..3718690) Escherichia coli S88 7130562 YP_002393360.1 CDS aroK NC_011742.1 3718747 3719268 R type I enzyme similar to type II but differentially regulated; major shikimate kinase in fully repressed cells; catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis; shikimate kinase I complement(3718747..3719268) Escherichia coli S88 7131860 YP_002393361.1 CDS hofQ NC_011742.1 3719669 3720907 R outer membrane porin probably involved in uptake of extracellular double-stranded DNA; similar to outer membrane competence protein ComE from Haemophilus influenzae and outer membrane protein PilQ involved in type IV pilus production from Pseudomonas aeruginosa; outer membrane porin HofQ complement(3719669..3720907) Escherichia coli S88 7129929 YP_002393362.1 CDS yrfA NC_011742.1 3720819 3721223 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3720819..3721223) Escherichia coli S88 7128939 YP_002393363.1 CDS yrfB NC_011742.1 3721213 3721653 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(3721213..3721653) Escherichia coli S88 7132137 YP_002393364.1 CDS yrfC NC_011742.1 3721637 3722176 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative fimbrial assembly protein (pilN-like) complement(3721637..3722176) Escherichia coli S88 7132138 YP_002393365.1 CDS yrfD NC_011742.1 3722176 3722955 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative pilus assembly protein complement(3722176..3722955) Escherichia coli S88 7132139 YP_002393366.1 CDS mrcA NC_011742.1 3723075 3725627 D bifunctional murein transglycosylase/murein transpeptidase; penicillin-binding protein 1A; involved in the synthesis of cross-linked peptidoglycan from the lipid intermediates in cell wall formation; penicillin-insensitive transglycosylase catalyzes the formation of linear glycan strands and the penicillin-sensitive transpeptidase catalyzes the cross-linking of the peptide subunits; peptidoglycan synthetase 3723075..3725627 Escherichia coli S88 7132140 YP_002393367.1 CDS nudE NC_011742.1 3725793 3726353 R ADP-sugar pyrophosphatase; catalyzes the formation of D-ribose 5-phosphate from ADP-ribose; can also act on ADP-mannose and ADP-glucose; ADP-ribose diphosphatase NudE complement(3725793..3726353) Escherichia coli S88 7129605 YP_002393368.1 CDS igaA NC_011742.1 3726673 3728808 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 11553591; Product type r : regulator; intracellular growth attenuator protein 3726673..3728808 Escherichia coli S88 7129753 YP_002393369.1 CDS yrfG NC_011742.1 3728873 3729541 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative hydrolase 3728873..3729541 Escherichia coli S88 7131615 YP_002393370.1 CDS hslR NC_011742.1 3729552 3729953 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9867837, 10675343, 10675344; Product type f : factor; ribosome-associated heat shock protein Hsp15 3729552..3729953 Escherichia coli S88 7132141 YP_002393371.1 CDS hslO NC_011742.1 3729978 3730856 D becomes active under oxidative stress; four conserved cysteines bind a zinc atom when they are in the reduced state and the enzyme is inactive; oxidative stress results in oxidized cysteines, release of zinc, and binding of Hsp33 to aggregation-prone proteins; forms dimers and higher order oligomers; Hsp33-like chaperonin 3729978..3730856 Escherichia coli S88 7131395 YP_002393372.1 CDS yhgE NC_011742.1 3730919 3732643 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 20223645; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(3730919..3732643) Escherichia coli S88 7131394 YP_002393373.1 CDS ECS88_3789 NC_011742.1 3732719 3732850 R Evidence 6 : Doubtful CDS; hypothetical protein complement(3732719..3732850) Escherichia coli S88 7132294 YP_002393374.1 CDS pck NC_011742.1 3733022 3734644 D PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP; phosphoenolpyruvate carboxykinase 3733022..3734644 Escherichia coli S88 7132894 YP_002393375.1 CDS envZ NC_011742.1 3734720 3736072 R membrane-localized osmosensor; histidine kinase; in high osmolarity EnvZ autophosphorylates itself and transfers phosphoryl group to OmpR; osmolarity sensor protein complement(3734720..3736072) Escherichia coli S88 7133177 YP_002393376.1 CDS ompR NC_011742.1 3736069 3736788 R part of two-component system EnvZ/OmpR; regulates transcription of outer membrane porin genes ompC/F; under high osmolarity EnvZ functions as kinase/phosphotransferase and phosphorylates OmpR; the result is increased expression of ompC and repression of ompF; also functions in regulation of other genes; forms dimers upon phosphorylation; osmolarity response regulator complement(3736069..3736788) Escherichia coli S88 7132408 YP_002393377.1 CDS greB NC_011742.1 3737016 3737492 D 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; transcription elongation factor GreB 3737016..3737492 Escherichia coli S88 7133128 YP_002393378.1 CDS yhgF NC_011742.1 3737589 3739910 D Evidence 2b : Function of strongly homologous gene; PubMedId : 8755871; Product type f : factor; transcriptional accessory protein 3737589..3739910 Escherichia coli S88 7130069 YP_002393379.1 CDS feoA NC_011742.1 3740350 3740577 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94012482, 8407793; Product type t : transporter; ferrous iron transport protein A 3740350..3740577 Escherichia coli S88 7132295 YP_002393380.1 CDS feoB NC_011742.1 3740594 3742915 D cytoplasmic membrane ferrous uptake system permease; mutations disrupt the ability of Escherichia coli to take up ferrous iron; GTP-binding protein which requires GTP for efficient iron(II) uptake; ferrous iron transport protein B 3740594..3742915 Escherichia coli S88 7129469 YP_002393381.1 CDS yhgG NC_011742.1 3742926 3743162 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 3742926..3743162 Escherichia coli S88 7129470 YP_002393382.1 CDS yhgA NC_011742.1 3743365 3744258 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2678009; Product type ph : phenotype; hypothetical protein 3743365..3744258 Escherichia coli S88 7132296 YP_002393383.1 CDS bioH NC_011742.1 3744478 3745248 R Shows carboxylesterase activity with a preference for short chain fatty acid esters; involved in pimeloyl-CoA synthesis; carboxylesterase BioH complement(3744478..3745248) Escherichia coli S88 7132293 YP_002393384.1 CDS gntX NC_011742.1 3745286 3745969 D involved in high-affinity gluconate transport; gluconate periplasmic binding protein 3745286..3745969 Escherichia coli S88 7129125 YP_002393385.1 CDS gntY NC_011742.1 3746028 3746603 D cytoplasmic protein that may be involved in the utilization of double-stranded DNA as a carbon source; putative DNA uptake protein 3746028..3746603 Escherichia coli S88 7130055 YP_002393386.1 CDS gntT NC_011742.1 3746964 3748280 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 172599, 4574689, 4582156, 93139975, 97141270, 98019089, 2845225, 3040894, 7984428, 9045817; Product type t : transporter; gluconate transporter, high-affinity GNT I system 3746964..3748280 Escherichia coli S88 7130056 YP_002393387.1 CDS malQ NC_011742.1 3748325 3750409 R amylomaltase; acts to release glucose from maltodextrins; 4-alpha-glucanotransferase complement(3748325..3750409) Escherichia coli S88 7130053 YP_002393388.1 CDS malP NC_011742.1 3750419 3752812 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89033892, 10220320, 10469642, 2845225, 3037809, 3155826, 6283313, 6339728, 6986282, 9009262; Product type e : enzyme; maltodextrin phosphorylase complement(3750419..3752812) Escherichia coli S88 7129413 YP_002393389.1 CDS malT NC_011742.1 3753435 3756140 D Positively regulates the transcription of the maltose regulon whose gene products are responsible for uptake and catabolism of malto-oligosaccharides; transcriptional regulator MalT 3753435..3756140 Escherichia coli S88 7129412 YP_002393390.1 CDS rtcA NC_011742.1 3756183 3757199 R catalyzes the conversion of terminal3'-phosphate of RNA to the 2',3'-cyclicphosphodiester; RNA 3'-terminal-phosphate cyclase complement(3756183..3757199) Escherichia coli S88 7129415 YP_002393391.1 CDS rtcB NC_011742.1 3757203 3758429 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 9738023; hypothetical protein complement(3757203..3758429) Escherichia coli S88 7133830 YP_002393392.1 CDS glpR NC_011742.1 3760197 3760955 R represses the glpD, glpFK, glpTQ, and glpACB operons involved in glycerol-3-phosphate metabolism; DNA-binding transcriptional repressor GlpR complement(3760197..3760955) Escherichia coli S88 7133106 YP_002393393.1 CDS glpG NC_011742.1 3760972 3761802 R protease responsible for the cleavage between Ser and Asp residues of proteins in regions of high local hydrophilicity; intramembrane serine protease GlpG complement(3760972..3761802) Escherichia coli S88 7130026 YP_002393394.1 CDS glpE NC_011742.1 3761847 3762173 R belongs to rhodanese family; thiosulfate thiotransferase; in Escherichia coli this enzyme catalyzes the formation of thiocyanate from thiosulfate and cyanide with low efficiency; contains an active site cysteine; thiosulfate sulfurtransferase complement(3761847..3762173) Escherichia coli S88 7130023 YP_002393395.1 CDS glpD NC_011742.1 3762363 3763868 D in Escherichia coli this homodimeric enzyme is expressed under aerobic conditions; anaerobic expression is repressed by the arcAB system; converts sn-glycerol-3-phosphate and ubiquinone-8 to dihydroxy acetone phosphate and ubiquinol-8; associates with the cytoplasmic membrane; glycerol-3-phosphate dehydrogenase 3762363..3763868 Escherichia coli S88 7130021 YP_002393396.1 CDS ECS88_3816 NC_011742.1 3763922 3764527 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3763922..3764527) Escherichia coli S88 7130020 YP_002393397.1 CDS ECS88_3817 NC_011742.1 3764530 3765297 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3764530..3765297) Escherichia coli S88 7132895 YP_002393398.1 CDS ECS88_3818 NC_011742.1 3765300 3766010 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3765300..3766010) Escherichia coli S88 7132896 YP_002393399.1 CDS aufG NC_011742.1 3766183 3767304 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15213132; Product type ps : putative structure; putative fimbrial-like adhesin protein AufG complement(3766183..3767304) Escherichia coli S88 7132897 YP_002393400.1 CDS aufF NC_011742.1 3767319 3768119 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15213132; Product type pf : putative factor; putative fimbrial chaperone AufF complement(3767319..3768119) Escherichia coli S88 7129981 YP_002393401.1 CDS aufE NC_011742.1 3768126 3768641 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15213132; Product type ps : putative structure; putative minor fimbrial subunit AufE complement(3768126..3768641) Escherichia coli S88 7129980 YP_002393402.1 CDS aufD NC_011742.1 3768586 3769158 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative minor fimbrial subunit AufD complement(3768586..3769158) Escherichia coli S88 7129979 YP_002393403.1 CDS aufC NC_011742.1 3769149 3771743 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15213132; Product type pf : putative factor; putative outer membrane export usher protein AufC complement(3769149..3771743) Escherichia coli S88 7129978 YP_002393404.1 CDS aufB NC_011742.1 3771780 3772559 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15213132; Product type pf : putative factor; putative fimbrial chaperone AufB complement(3771780..3772559) Escherichia coli S88 7129977 YP_002393405.1 CDS aufA NC_011742.1 3772633 3773337 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15213132; Product type s : structure; Auf fimbriae major fimbrial subunit AufA complement(3772633..3773337) Escherichia coli S88 7129976 YP_002393406.1 CDS glgP NC_011742.1 3773831 3776278 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88330897, 91104907, 91236706, 2645169, 2975249, 3047129, 3097003; Product type e : enzyme; glycogen phosphorylase complement(3773831..3776278) Escherichia coli S88 7129975 YP_002393407.1 CDS glgA NC_011742.1 3776297 3777730 R catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose; glycogen synthase complement(3776297..3777730) Escherichia coli S88 7132216 YP_002393408.1 CDS glgC NC_011742.1 3777730 3779025 R catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate; glucose-1-phosphate adenylyltransferase complement(3777730..3779025) Escherichia coli S88 7132213 YP_002393409.1 CDS glgX NC_011742.1 3779043 3781016 R catalyzes the hydrolysis of the alpha-1,6-glucosidic linkages in partially depolymerized glycogen; glycogen debranching enzyme complement(3779043..3781016) Escherichia coli S88 7132215 YP_002393410.1 CDS glgB NC_011742.1 3781013 3783199 R catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain; glycogen branching enzyme complement(3781013..3783199) Escherichia coli S88 7132218 YP_002393411.1 CDS asd NC_011742.1 3783472 3784575 R catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde; aspartate-semialdehyde dehydrogenase complement(3783472..3784575) Escherichia coli S88 7132214 YP_002393412.1 CDS yhgN NC_011742.1 3784767 3785360 D YhgN; Ec0197; hydrolyzes nucleoside triphosphates with an O6 atom-containing purine base to nucleoside monophosphate and pyrophosphate; seems to play a role in the elimination of aberrant purine-derived nucleotides containing the 6-keto group; shows preference for deoxyinosine triphosphate and xanthosine triphosphate over standard nucleoside triphosphates (dATP, dCTP, dGTP, and dTTP); putative dITP- and XTP- hydrolase 3784767..3785360 Escherichia coli S88 7129942 YP_002393413.1 CDS gntU NC_011742.1 3785417 3786757 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8655507, 9119199, 9135111, 97141270; Product type t : transporter; low affinity gluconate transporter complement(3785417..3786757) Escherichia coli S88 7132297 YP_002393414.1 CDS gntK NC_011742.1 3786761 3787288 R thermoresistant; catalyzes the formation of 6-phospho-D-gluconate from gluconate; gluconate kinase 1 complement(3786761..3787288) Escherichia coli S88 7130054 YP_002393415.1 CDS gntR NC_011742.1 3787427 3788422 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 172599, 9135111, 93139975, 9537375, 8655507; Product type r : regulator; DNA-binding transcriptional repressor complement(3787427..3788422) Escherichia coli S88 7130050 YP_002393416.1 CDS yhhW NC_011742.1 3788515 3789210 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3788515..3789210) Escherichia coli S88 7130052 YP_002393417.1 CDS yhhX NC_011742.1 3789333 3790370 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10493123; Product type pe : putative enzyme; putative dehydrogenase complement(3789333..3790370) Escherichia coli S88 7132307 YP_002393418.1 CDS ECS88_3838 NC_011742.1 3790215 3790475 D Evidence 6 : Doubtful CDS; hypothetical protein 3790215..3790475 Escherichia coli S88 7132308 YP_002393419.1 CDS yhhY NC_011742.1 3790704 3791192 D YhhY; regulated by the fur regulator; unknown function; putative acetyltransferase YhhY 3790704..3791192 Escherichia coli S88 7131349 YP_002393420.1 CDS yrhA NC_011742.1 3792606 3793097 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3792606..3793097 Escherichia coli S88 7132311 YP_002393421.1 CDS yrhB NC_011742.1 3793547 3793831 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3793547..3793831 Escherichia coli S88 7132142 YP_002393422.1 CDS ggt NC_011742.1 3793869 3795602 R periplasmic enzyme; post-translationally processed into two subunits which are required for wild-type enzyme activity; cleaves the gammaglutamyl linkages of compounds such as glutathione and transfer the gammaglutamyl group to other amino acids and peptides; gamma-glutamyltranspeptidase complement(3793869..3795602) Escherichia coli S88 7130575 YP_002393423.1 CDS yhhA NC_011742.1 3795722 3796162 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3795722..3796162 Escherichia coli S88 7132203 YP_002393424.1 CDS ugpQ NC_011742.1 3796149 3796892 R hydrolyzes diesters during transport at the inner face of the cytoplasmic membrane to glycerol-3-phosphate and alcohol; induced when cells are starved for inorganic phosphate; cytoplasmic glycerophosphodiester phosphodiesterase complement(3796149..3796892) Escherichia coli S88 7132298 YP_002393425.1 CDS ugpC NC_011742.1 3796889 3797959 R part of the UgpABCE glycerol-3-phosphate uptake system; glycerol-3-phosphate transporter ATP-binding subunit complement(3796889..3797959) Escherichia coli S88 7130397 YP_002393426.1 CDS ugpE NC_011742.1 3797961 3798806 R with UgpABC is involved in uptake of glycerol-3-phosphate; glycerol-3-phosphate transporter membrane protein complement(3797961..3798806) Escherichia coli S88 7130395 YP_002393427.1 CDS ugpA NC_011742.1 3798803 3799690 R with UgpEC is involved in the uptake of glycerol-3-phosphate; glycerol-3-phosphate transporter permease complement(3798803..3799690) Escherichia coli S88 7130396 YP_002393428.1 CDS ugpB NC_011742.1 3799788 3801104 R with UgpACE is involved in the uptake of glycerol-3-phosphate; glycerol-3-phosphate transporter periplasmic binding protein complement(3799788..3801104) Escherichia coli S88 7130393 YP_002393429.1 CDS livF NC_011742.1 3801501 3802214 R with LivGHMJ and LivGHMK is part of the high-affinity branched-chain amino acid transport system; LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine, and valine; leucine/isoleucine/valine transporter ATP-binding subunit complement(3801501..3802214) Escherichia coli S88 7130394 YP_002393430.1 CDS livG NC_011742.1 3802216 3802983 R Part of the ABC transporter complexes LivFGHMJ and LivFGHMK involved in the high-affinity transport of branched-chain amino acids; LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine, and valine; leucine/isoleucine/valine transporter ATP-binding subunit complement(3802216..3802983) Escherichia coli S88 7129358 YP_002393431.1 CDS livM NC_011742.1 3802980 3804257 R Part of the ABC transporter complex LivFGHMJ and LivFGHMK involved in the high-affinity transport of branched-chain amino acids; LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine, and valine; leucine/isoleucine/valine transporter permease subunit complement(3802980..3804257) Escherichia coli S88 7129359 YP_002393432.1 CDS livH NC_011742.1 3804254 3805180 R LivHMGF is the membrane component of the LIV-I/LS branched-chain amino acid transporter; branched-chain amino acid transporter permease subunit LivH complement(3804254..3805180) Escherichia coli S88 7129363 YP_002393433.1 CDS livK NC_011742.1 3805228 3806337 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14702302, 90307651, 2195019, 2649683, 3891753, 4077929, 9298646, 9298646; Product type t : transporter; leucine transporter subunit ; periplasmic-binding component of ABC superfamily complement(3805228..3806337) Escherichia coli S88 7129360 YP_002393434.1 CDS yhhK NC_011742.1 3806761 3807144 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3806761..3807144 Escherichia coli S88 7129362 YP_002393435.1 CDS livJ NC_011742.1 3807332 3808435 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14702302, 90307651, 2195019, 2649682, 328304, 3891753, 4077929, 9298646, 10972807; Product type t : transporter; leucine/isoleucine/valine transporter subunit ; periplasmic-binding component of ABC superfamily complement(3807332..3808435) Escherichia coli S88 7132301 YP_002393436.1 CDS ECS88_3858 NC_011742.1 3809370 3809771 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative component of a paralog of phosphotransferase system, mannose/fructose-specific component IIA 3809370..3809771 Escherichia coli S88 7129361 YP_002393437.1 CDS ECS88_3859 NC_011742.1 3809778 3810263 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative component of a paralog of phosphotransferase system, mannose/fructose-specific component IIA 3809778..3810263 Escherichia coli S88 7132899 YP_002393438.1 CDS ECS88_3860 NC_011742.1 3810280 3811026 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphotransferase system enzyme IIC 3810280..3811026 Escherichia coli S88 7132900 YP_002393439.1 CDS ECS88_3861 NC_011742.1 3810947 3811873 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphotransferase system enzyme IID 3810947..3811873 Escherichia coli S88 7132901 YP_002393440.1 CDS ECS88_3862 NC_011742.1 3811845 3812795 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative Phosphoglycerate dehydrogenase 3811845..3812795 Escherichia coli S88 7132902 YP_002393441.1 CDS ECS88_3863 NC_011742.1 3812795 3813679 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative paralog of dihydrodipicolinate synthase 3812795..3813679 Escherichia coli S88 7132903 YP_002393442.1 CDS rpoH NC_011742.1 3813783 3814637 R binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters; RNA polymerase factor sigma-32 complement(3813783..3814637) Escherichia coli S88 7132904 YP_002393443.1 CDS ftsX NC_011742.1 3814882 3815940 R putative ABC transporter, membrane protein; cell division protein FtsX complement(3814882..3815940) Escherichia coli S88 7133779 YP_002393444.1 CDS ftsE NC_011742.1 3815933 3816601 R putative ATP-binding protein of an ATP-binding cassette transporter; when bound to FtsX, FtsEX localizes to the cell division site and plays a role in the assembly or stability of the septal ring under low-salt growth conditions; cell division protein FtsE complement(3815933..3816601) Escherichia coli S88 7132143 YP_002393445.1 CDS ftsY NC_011742.1 3816604 3818100 R signal recognition protein receptor; functions in the targeting and insertion of membrane proteins; cell division protein FtsY complement(3816604..3818100) Escherichia coli S88 7132848 YP_002393446.1 CDS rsmD NC_011742.1 3818250 3818846 D catalyzes the methylation of 16S rRNA at position G966; 16S rRNA m(2)G966-methyltransferase 3818250..3818846 Escherichia coli S88 7132144 YP_002393447.1 CDS ECS88_3869 NC_011742.1 3818713 3819105 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3818713..3819105 Escherichia coli S88 7132299 YP_002393448.1 CDS yhhM NC_011742.1 3819108 3819467 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3819108..3819467) Escherichia coli S88 7132905 YP_002393449.1 CDS yhhN NC_011742.1 3819608 3820234 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3819608..3820234 Escherichia coli S88 7132302 YP_002393450.1 CDS zntA NC_011742.1 3820308 3822506 D P-type ATPase involved in the export of lead, cadmium, zinc and mercury; zinc/cadmium/mercury/lead-transporting ATPase 3820308..3822506 Escherichia coli S88 7132303 YP_002393451.1 CDS tusA NC_011742.1 3822775 3823020 R TusA; transfers sulfur to TusBCD complex; involved in thiouridation of U34 position of some tRNAs; sulfur transfer protein SirA complement(3822775..3823020) Escherichia coli S88 7131886 YP_002393452.1 CDS yhhQ NC_011742.1 3823241 3823906 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 3823241..3823906 Escherichia coli S88 7130369 YP_002393453.1 CDS dcrB NC_011742.1 3823979 3824536 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12558182, 8752353; Product type t : transporter; hypothetical protein 3823979..3824536 Escherichia coli S88 7132304 YP_002393454.1 CDS yhhS NC_011742.1 3824540 3825757 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; major facilitator superfamily transporter complement(3824540..3825757) Escherichia coli S88 7130573 YP_002393455.1 CDS yhhT NC_011742.1 3825889 3826938 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3825889..3826938 Escherichia coli S88 7132305 YP_002393456.1 CDS acpT NC_011742.1 3826993 3827580 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20092861, 10625633, 8939709; Product type e : enzyme; holo-(acyl carrier protein) synthase 2 3826993..3827580 Escherichia coli S88 7132306 YP_002393457.1 CDS nikA NC_011742.1 3827691 3829265 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12960164, 7934931, 92077434, 7867647; Product type t : transporter; nickel transporter subunit ; periplasmic-binding component of ABC superfamily 3827691..3829265 Escherichia coli S88 7132041 YP_002393458.1 CDS nikB NC_011742.1 3829265 3830209 D with NikACDE is involved in nickel transport into the cell; nickel transporter permease NikB 3829265..3830209 Escherichia coli S88 7129710 YP_002393459.1 CDS nikC NC_011742.1 3830206 3831039 D with NikABDE is involved in nickel transport into the cell; nickel transporter permease NikC 3830206..3831039 Escherichia coli S88 7129711 YP_002393460.1 CDS nikD NC_011742.1 3831039 3831803 D with NikABCE is involved in nickel transport into the cell; nickel transporter ATP-binding protein NikD 3831039..3831803 Escherichia coli S88 7129712 YP_002393461.1 CDS nikE NC_011742.1 3831800 3832606 D with NikABCD is involved with nickel transport into the cell; nickel transporter ATP-binding protein NikE 3831800..3832606 Escherichia coli S88 7129713 YP_002393462.1 CDS nikR NC_011742.1 3832612 3833013 D Inhibits transcription at high concentrations of nickel; nickel responsive regulator 3832612..3833013 Escherichia coli S88 7129714 YP_002393463.1 CDS ECS88_3885 NC_011742.1 3833203 3833958 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator 3833203..3833958 Escherichia coli S88 7129715 YP_002393464.1 CDS ECS88_3886 NC_011742.1 3833983 3834456 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphotransferase system enzyme subunit IIA 3833983..3834456 Escherichia coli S88 7132906 YP_002393465.1 CDS ECS88_3887 NC_011742.1 3834453 3834734 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphotransferase system enzyme IIB 3834453..3834734 Escherichia coli S88 7132907 YP_002393466.1 CDS ECS88_3888 NC_011742.1 3834781 3836169 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative phosphotransferase system permease component IIC 3834781..3836169 Escherichia coli S88 7132908 YP_002393467.1 CDS ECS88_3889 NC_011742.1 3836162 3837670 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative carbohydrate kinase 3836162..3837670 Escherichia coli S88 7132909 YP_002393468.1 CDS ECS88_3890 NC_011742.1 3837660 3837929 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative phosphocarrier HPr protein of a carbohydrate phosphotransferase system 3837660..3837929 Escherichia coli S88 7132910 YP_002393469.1 CDS gatY NC_011742.1 3837961 3838812 D class II aldolase; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis and gluconeogenesis; putative fructose-1,6-bisphosphate aldolase 3837961..3838812 Escherichia coli S88 7132911 YP_002393470.1 CDS yhhJ NC_011742.1 3838922 3840046 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter subunit: membrane component of ABC superfamily complement(3838922..3840046) Escherichia coli S88 7132912 YP_002393471.1 CDS rbbA NC_011742.1 3840046 3842781 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20074572; Product type e : enzyme; fused ribosome-associated ATPase: ATP-binding protein ; ATP-binding protein ; putative membrane protein complement(3840046..3842781) Escherichia coli S88 7132300 YP_002393472.1 CDS yhiI NC_011742.1 3842778 3843845 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative HlyD family secretion protein complement(3842778..3843845) Escherichia coli S88 7131785 YP_002393473.1 CDS yhiM NC_011742.1 3844579 3845631 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3844579..3845631 Escherichia coli S88 7132314 YP_002393474.1 CDS yhiN NC_011742.1 3845718 3846911 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase with FAD/NAD(P)-binding domain complement(3845718..3846911) Escherichia coli S88 7132315 YP_002393475.1 CDS pitA NC_011742.1 3847143 3848642 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87014120; Product type t : transporter; phosphate transporter, low-affinity 3847143..3848642 Escherichia coli S88 7132316 YP_002393476.1 CDS yhiO NC_011742.1 3848713 3849048 R ppGpp-dependent, membrane associated, stress protein produced under conditions of nutrient deprivation, osmotic shock and oxidative stress; universal stress protein UspB complement(3848713..3849048) Escherichia coli S88 7133736 YP_002393477.1 CDS uspA NC_011742.1 3849439 3849873 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12732303, 93086426, 93308072, 94203056, 10499297, 10652104, 10931298, 11157932, 1453957, 8506346, 8932299, 9298646, 9405142; Product type f : factor; universal stress global response regulator 3849439..3849873 Escherichia coli S88 7132317 YP_002393478.1 CDS yhiP NC_011742.1 3850190 3851659 D member of the POT family of peptide transporters; probable proton-dependent peptide transporter function; inner membrane transporter YhiP 3850190..3851659 Escherichia coli S88 7132453 YP_002393479.1 CDS yhiQ NC_011742.1 3851708 3852460 R predicted SAM-dependent methyltransferase; putative methyltransferase complement(3851708..3852460) Escherichia coli S88 7132318 YP_002393480.1 CDS prlC NC_011742.1 3852468 3854510 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92394891, 1325967, 8366062; Product type e : enzyme; oligopeptidase A complement(3852468..3854510) Escherichia coli S88 7132319 YP_002393481.1 CDS yhiR NC_011742.1 3854713 3855555 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11591672; Product type pe : putative enzyme; putative DNA (exogenous) processing protein 3854713..3855555 Escherichia coli S88 7130780 YP_002393482.1 CDS gor NC_011742.1 3855627 3856979 D catalyzes the reduction of 2 glutathione to glutathione disulfide; maintains high levels of reduced glutathione in the cytosol; involved in redox regulation and oxidative defense; glutathione reductase 3855627..3856979 Escherichia coli S88 7132320 YP_002393483.1 CDS ECS88_3906 NC_011742.1 3857033 3857182 R Evidence 6 : Doubtful CDS; hypothetical protein complement(3857033..3857182) Escherichia coli S88 7130057 YP_002393484.1 CDS ECS88_3907 NC_011742.1 3857138 3857317 D Evidence 6 : Doubtful CDS; hypothetical protein 3857138..3857317 Escherichia coli S88 7132913 YP_002393485.1 CDS arsC NC_011742.1 3857650 3858075 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95355341, 7721697; Product type e : enzyme; arsenate reductase 3857650..3858075 Escherichia coli S88 7132914 YP_002393486.1 CDS slp NC_011742.1 3859259 3859825 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94293775, 8022277; Product type lp : lipoprotein; outer membrane lipoprotein 3859259..3859825 Escherichia coli S88 7132321 YP_002393487.1 CDS yhiF NC_011742.1 3859978 3860508 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8022277; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 3859978..3860508 Escherichia coli S88 7130605 YP_002393488.1 CDS chuS NC_011742.1 3860565 3861593 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16275907; Product type e : enzyme; Heme oxygenase complement(3860565..3861593) Escherichia coli S88 7132313 YP_002393489.1 CDS chuA NC_011742.1 3861642 3863624 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11179376, 7768795, 9393841, 9680204, 9157252; Product type t : transporter; outer membrane hemin receptor complement(3861642..3863624) Escherichia coli S88 7131907 YP_002393490.1 CDS chuT NC_011742.1 3864230 3865222 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7768795, 9393841, 9680204; Product type pt : putative transporter; putative periplasmic binding protein 3864230..3865222 Escherichia coli S88 7131906 YP_002393491.1 CDS ECS88_3915 NC_011742.1 3865242 3866579 D catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 3865242..3866579 Escherichia coli S88 7131908 YP_002393492.1 CDS ECS88_3916 NC_011742.1 3866592 3867086 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein (chuX protein) 3866592..3867086 Escherichia coli S88 7132915 YP_002393493.1 CDS ECS88_3917 NC_011742.1 3867086 3867709 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein (chuY) 3867086..3867709 Escherichia coli S88 7132916 YP_002393494.1 CDS chuU NC_011742.1 3867758 3868750 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative hemin transport system permease 3867758..3868750 Escherichia coli S88 7132917 YP_002393495.1 CDS hmuV NC_011742.1 3868594 3869517 D with HmuTU is involved in the transport of hemin; hemin importer ATP-binding subunit 3868594..3869517 Escherichia coli S88 7131909 YP_002393496.1 CDS yhiD NC_011742.1 3869569 3870216 R inner membrane protein involved in cell density-dependent acid resistance; part of the acid fitness island (AFI) of E. coli; putative Mg(2+) transport ATPase complement(3869569..3870216) Escherichia coli S88 7131910 YP_002393497.1 CDS hdeB NC_011742.1 3870280 3870606 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94064579, 8885264, 12071744, 8244952, 8455549, 9298646, 9868784; Product type pf : putative factor; acid-resistance protein complement(3870280..3870606) Escherichia coli S88 7132312 YP_002393498.1 CDS hdeA NC_011742.1 3870722 3871054 R inactive form; acid-resistance protein complement(3870722..3871054) Escherichia coli S88 7128891 YP_002393499.1 CDS hdeD NC_011742.1 3871309 3871881 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94064579, 8244952, 8455549; Product type pm : putative membrane component; acid-resistance membrane protein 3871309..3871881 Escherichia coli S88 7128890 YP_002393500.1 CDS gadE NC_011742.1 3872680 3873207 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12399493, 12940989, 14702398; Product type r : regulator; DNA-binding transcriptional activator 3872680..3873207 Escherichia coli S88 7128892 YP_002393501.1 CDS mdtE NC_011742.1 3873546 3874703 D with MdtF and tolC is involved in resistance to rhodamine 6G, erythromycin, doxorubicin and other compounds; multidrug efflux system protein MdtE 3873546..3874703 Escherichia coli S88 7132166 YP_002393502.1 CDS mdtF NC_011742.1 3874728 3877841 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21450803; Product type t : transporter; multidrug transporter, RpoS-dependent 3874728..3877841 Escherichia coli S88 7128793 YP_002393503.1 CDS gadW NC_011742.1 3878204 3878932 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12446650; Product type r : regulator; DNA-binding transcriptional activator complement(3878204..3878932) Escherichia coli S88 7128794 YP_002393504.1 CDS gadX NC_011742.1 3879301 3880125 R regulates genes in response to acid and/or during stationary phase; DNA-binding transcriptional regulator GadX complement(3879301..3880125) Escherichia coli S88 7132169 YP_002393505.1 CDS gadA NC_011742.1 3880493 3881893 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92155241, 92394884, 99406302, 1522060, 1740158, 7764225, 9298646; Product type e : enzyme; glutamate decarboxylase A, PLP-dependent complement(3880493..3881893) Escherichia coli S88 7132168 YP_002393506.1 CDS yhjA NC_011742.1 3882104 3883501 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8163487, 14563563; Product type e : enzyme; cytochrome C peroxidase (cpp-like) complement(3882104..3883501) Escherichia coli S88 7132163 YP_002393507.1 CDS treF NC_011742.1 3883906 3885555 D cytoplasmic; catalyzes the hydrolysis of trehalose to glucose; trehalase 3883906..3885555 Escherichia coli S88 7132322 YP_002393508.1 CDS yhjB NC_011742.1 3885606 3886208 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding response regulator in two-component regulatory system complement(3885606..3886208) Escherichia coli S88 7130330 YP_002393509.1 CDS yhjC NC_011742.1 3886656 3887627 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 3886656..3887627 Escherichia coli S88 7132323 YP_002393510.1 CDS yhjD NC_011742.1 3887676 3888689 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3887676..3888689 Escherichia coli S88 7132324 YP_002393511.1 CDS yhjE NC_011742.1 3889082 3890404 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 3889082..3890404 Escherichia coli S88 7132325 YP_002393512.1 CDS yhjG NC_011742.1 3890457 3892520 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative outer membrane biogenesis protein complement(3890457..3892520) Escherichia coli S88 7132326 YP_002393513.1 CDS yhjH NC_011742.1 3892575 3893342 R in Escherichia coli this protein is involved in flagellar function; EAL domain-containing protein complement(3892575..3893342) Escherichia coli S88 7132327 YP_002393514.1 CDS ECS88_3939 NC_011742.1 3893296 3893490 D Evidence 6 : Doubtful CDS; hypothetical protein 3893296..3893490 Escherichia coli S88 7132328 YP_002393515.1 CDS kdgK NC_011742.1 3893574 3894503 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 4359651, 13813474; Product type e : enzyme; ketodeoxygluconokinase 3893574..3894503 Escherichia coli S88 7132918 YP_002393516.1 CDS yhjJ NC_011742.1 3894599 3896095 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 9298646; Product type pe : putative enzyme; putative zinc-dependent peptidase complement(3894599..3896095) Escherichia coli S88 7130437 YP_002393517.1 CDS dctA NC_011742.1 3896315 3897601 R involved in the transport of C4-dicarboxylates across the membrane; C4-dicarboxylate transporter DctA complement(3896315..3897601) Escherichia coli S88 7132329 YP_002393518.1 CDS yhjK NC_011742.1 3897784 3899733 R HmsP in Yersinia pestis plays a role in invasion of epithelial cells; the EAL-domain portion of HmsP from Y. pestis shows phosphodiesterase activity which is required for the inhibition of biofilm formation; inner membrane protein; similar to a putative phosphodiesterase protein from E. coli; putative phosphodiesterase complement(3897784..3899733) Escherichia coli S88 7130574 YP_002393519.1 CDS bcsC NC_011742.1 3899854 3903327 R cellulose is produced by the multicellular morphotypes of E. coli and Salmonella typhimurium; the cellulose biosynthesis genes bcsA, bcsB, bcsZ and bcsC are constitutively transcribed, however, cellulose synthesis is dependent on the expression of adrA; cellulose synthase subunit BcsC complement(3899854..3903327) Escherichia coli S88 7132330 YP_002393520.1 CDS bcsZ NC_011742.1 3903309 3904415 R catalyzes the hydrolysis of 1,4-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans; endo-1,4-D-glucanase complement(3903309..3904415) Escherichia coli S88 7129996 YP_002393521.1 CDS bcsB NC_011742.1 3904422 3906761 R binds the cellulose synthase activator, bis-(3'-5') cyclic diguanylic acid (c-di-GMP); cellulose synthase regulator protein complement(3904422..3906761) Escherichia coli S88 7130000 YP_002393522.1 CDS yhjR NC_011742.1 3910150 3910338 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3910150..3910338) Escherichia coli S88 7132331 YP_002393523.1 CDS bcsE NC_011742.1 3910611 3912182 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11929533, 11260463; Product type pe : putative enzyme; putative cellulose biosynthesis protease 3910611..3912182 Escherichia coli S88 7132332 YP_002393524.1 CDS bcsF NC_011742.1 3912179 3912370 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3912179..3912370 Escherichia coli S88 7129997 YP_002393525.1 CDS bcsG NC_011742.1 3912367 3914046 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11929533, 11260463; Product type pe : putative enzyme; putative cellulose biosynthesis endoglucanase 3912367..3914046 Escherichia coli S88 7129998 YP_002393526.1 CDS ldrD NC_011742.1 3914132 3914374 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12123448; Product type f : factor; toxic polypeptide, small complement(3914132..3914374) Escherichia coli S88 7129999 YP_002393527.1 CDS ldrD NC_011742.1 3914615 3914857 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12123448; Product type f : factor; toxic polypeptide, small complement(3914615..3914857) Escherichia coli S88 7131801 YP_002393528.1 CDS ldrD NC_011742.1 3915097 3915372 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12123448; Product type f : factor; toxic polypeptide, small complement(3915097..3915372) Escherichia coli S88 7130480 YP_002393529.1 CDS ECS88_3958 NC_011742.1 3915369 3915530 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3915369..3915530) Escherichia coli S88 7131802 YP_002393530.1 CDS yhjV NC_011742.1 3915680 3916951 D Evidence 2b : Function of strongly homologous gene; PubMedId : 15901718; Product type t : transporter; transporter 3915680..3916951 Escherichia coli S88 7132919 YP_002393531.1 CDS dppF NC_011742.1 3916981 3917985 R Part of the ABC transporter complex DppABCDF involved in the transport of dipeptides; dipeptide transporter ATP-binding subunit complement(3916981..3917985) Escherichia coli S88 7132333 YP_002393532.1 CDS dppD NC_011742.1 3917982 3918965 R DppD and DppF are the ATP-binding components of the ABC dipeptide transport system DppABCDF; dipeptide transporter ATP-binding subunit complement(3917982..3918965) Escherichia coli S88 7130236 YP_002393533.1 CDS dppC NC_011742.1 3918976 3919878 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 7536291; Product type t : transporter; dipeptide transporter complement(3918976..3919878) Escherichia coli S88 7130235 YP_002393534.1 CDS dppB NC_011742.1 3919888 3920907 R transports peptides consisting of two or three amino acids; dipeptide transporter permease DppB complement(3919888..3920907) Escherichia coli S88 7130234 YP_002393535.1 CDS dppA NC_011742.1 3921058 3922665 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91100289, 92065799, 1702779, 1956284, 7536291, 8527431, 8563629, 9298646, 9600841, 9740056, 10972807; Product type t : transporter; dipeptide transporter ; periplasmic-binding component of ABC superfamily complement(3921058..3922665) Escherichia coli S88 7130233 YP_002393536.1 CDS eptB NC_011742.1 3923574 3925265 R catalyzes the addition of a phosphoethanolamine group to the outer Kdo residue of lipopolysaccharide; phosphoethanolamine transferase complement(3923574..3925265) Escherichia coli S88 7129922 YP_002393537.1 CDS yhjX NC_011742.1 3925589 3926797 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter complement(3925589..3926797) Escherichia coli S88 7132414 YP_002393538.1 CDS yhjY NC_011742.1 3927026 3927724 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3927026..3927724) Escherichia coli S88 7132334 YP_002393539.1 CDS tag NC_011742.1 3927882 3928445 D constitutive, catalyzes the hydrolysis of alkylated DNA, releasing 3-methyladenine; 3-methyl-adenine DNA glycosylase I 3927882..3928445 Escherichia coli S88 7132335 YP_002393540.1 CDS yiaC NC_011742.1 3928442 3928882 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11237876; Product type pe : putative enzyme; hypothetical protein 3928442..3928882 Escherichia coli S88 7131256 YP_002393541.1 CDS bisC NC_011742.1 3928851 3931130 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 82119950, 90202748, 2180922, 374979; Product type e : enzyme; biotin sulfoxide reductase complement(3928851..3931130) Escherichia coli S88 7132338 YP_002393542.1 CDS yiaD NC_011742.1 3931337 3931996 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative outer membrane lipoprotein 3931337..3931996 Escherichia coli S88 7129128 YP_002393543.1 CDS tiaE NC_011742.1 3932100 3933074 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15801772, 11237876, 99030322, 99357626, 9298646, 9811658; Product type e : enzyme; 2-oxo-carboxylic acid reductase (glyoxalate reductase) (2-ketoaldonate reductase) 3932100..3933074 Escherichia coli S88 7132339 YP_002393544.1 CDS yiaF NC_011742.1 3933124 3933834 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3933124..3933834) Escherichia coli S88 7133472 YP_002393545.1 CDS yiaG NC_011742.1 3934268 3934558 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator 3934268..3934558 Escherichia coli S88 7132340 YP_002393546.1 CDS cspA NC_011742.1 3934839 3935051 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20345064, 90115858, 94293754, 94293756, 99177178, 10696873, 1597410, 1961761, 2404279, 7515185, 8197194, 9405743, 9439003, 9692981; Product type f : factor; major cold shock protein 3934839..3935051 Escherichia coli S88 7132341 YP_002393547.1 CDS glyS NC_011742.1 3935714 3937783 R glycine--tRNA ligase beta chain; glyS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase subunit beta complement(3935714..3937783) Escherichia coli S88 7132772 YP_002393548.1 CDS glyQ NC_011742.1 3937793 3938704 R glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase subunit alpha complement(3937793..3938704) Escherichia coli S88 7130043 YP_002393549.1 CDS ysaB NC_011742.1 3938799 3939098 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3938799..3939098) Escherichia coli S88 7130042 YP_002393550.1 CDS yiaH NC_011742.1 3939273 3940268 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 3939273..3940268 Escherichia coli S88 7131863 YP_002393551.1 CDS yiaA NC_011742.1 3940310 3940747 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(3940310..3940747) Escherichia coli S88 7132342 YP_002393552.1 CDS yiaB NC_011742.1 3940793 3941134 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 6320721; Product type pm : putative membrane component; hypothetical protein complement(3940793..3941134) Escherichia coli S88 7132336 YP_002393553.1 CDS xylB NC_011742.1 3941303 3942757 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6330500, 92366447, 95050816, 6320721; Product type e : enzyme; xylulokinase complement(3941303..3942757) Escherichia coli S88 7132337 YP_002393554.1 CDS xylA NC_011742.1 3942829 3944151 R catalyzes the interconversion of D-xylose to D-xylulose; xylose isomerase complement(3942829..3944151) Escherichia coli S88 7132526 YP_002393555.1 CDS xylF NC_011742.1 3944517 3945509 D periplasmic substrate-binding component of the ATP-dependent xylose transport system; high affinity; D-xylose transporter subunit XylF 3944517..3945509 Escherichia coli S88 7132525 YP_002393556.1 CDS xylG NC_011742.1 3945587 3947128 D with XylFH is part of the high affinity xylose ABC transporter; xylose transporter ATP-binding subunit 3945587..3947128 Escherichia coli S88 7130820 YP_002393557.1 CDS xylH NC_011742.1 3947106 3948287 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94316500; Product type t : transporter; D-xylose transporter subunit ; membrane component of ABC superfamily 3947106..3948287 Escherichia coli S88 7130248 YP_002393558.1 CDS ECS88_3987 NC_011742.1 3948199 3948375 D Evidence 6 : Doubtful CDS; hypothetical protein 3948199..3948375 Escherichia coli S88 7130249 YP_002393559.1 CDS xylR NC_011742.1 3948365 3949516 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6330500, 94316500; Product type r : regulator; DNA-binding transcriptional activator, xylose-binding 3948365..3949516 Escherichia coli S88 7132920 YP_002393560.1 CDS bax NC_011742.1 3949640 3950464 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 1544897; hypothetical protein complement(3949640..3950464) Escherichia coli S88 7130250 YP_002393561.1 CDS malS NC_011742.1 3950784 3952814 D periplasmic enzyme that degrades maltodextrins that enter via the outer membrane porin LamB; hydrolyzes alpha-(1,4) glycosidic linkages; contains internal disulfide bonds; periplasmic alpha-amylase precursor 3950784..3952814 Escherichia coli S88 7129990 YP_002393562.1 CDS avtA NC_011742.1 3952992 3954245 D transaminase C; catalyzes transamination of alanine, valine, and 2-aminobutyrate with their respective 2-keto acids; also catalyzes terminal step in valine biosynthesis; valine--pyruvate transaminase 3952992..3954245 Escherichia coli S88 7129414 YP_002393563.1 CDS yiaI NC_011742.1 3954397 3954870 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative hydrogenase, 4Fe-4S ferredoxin-type component complement(3954397..3954870) Escherichia coli S88 7129982 YP_002393564.1 CDS yiaJ NC_011742.1 3954972 3955820 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 20372646, 9826648; Product type r : regulator; DNA-binding transcriptional repressor complement(3954972..3955820) Escherichia coli S88 7132343 YP_002393565.1 CDS yiaK NC_011742.1 3956021 3957019 D NAD(P)H-dependent; catalyzes the reduction of 2,3-diketo-L-gulonate to 3-keto-L-gulonate; 2,3-diketo-L-gulonate reductase 3956021..3957019 Escherichia coli S88 7132344 YP_002393566.1 CDS yiaL NC_011742.1 3957031 3957495 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 21617392; hypothetical protein 3957031..3957495 Escherichia coli S88 7132345 YP_002393567.1 CDS ECS88_3996 NC_011742.1 3957518 3958438 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3957518..3958438 Escherichia coli S88 7132346 YP_002393568.1 CDS yiaM NC_011742.1 3958552 3959019 D membrane-spanning protein involved in uptake of 2,3-diketo-L-gulonate; part of the tri-partite ATP-independent periplasmic transport system (TRAP) YiaMNO; 2,3-diketo-L-gulonate TRAP transporter small permease protein YiaM 3958552..3959019 Escherichia coli S88 7132921 YP_002393569.1 CDS yiaN NC_011742.1 3958824 3960299 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14668138, 21617392; Product type t : transporter; transporter 3958824..3960299 Escherichia coli S88 7132347 YP_002393570.1 CDS yiaO NC_011742.1 3960312 3961298 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14668138, 21617392; Product type t : transporter; transporter 3960312..3961298 Escherichia coli S88 7132348 YP_002393571.1 CDS lyxK NC_011742.1 3961302 3962798 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21617392, 95050816, 7961955; Product type e : enzyme; L-xylulose kinase 3961302..3962798 Escherichia coli S88 7132349 YP_002393572.1 CDS sgbH NC_011742.1 3962795 3963457 D catalyzes the formation of L-xylulose-5-phosphate from 3-keto-L-gulonate-6-phosphate; 3-keto-L-gulonate-6-phosphate decarboxylase 3962795..3963457 Escherichia coli S88 7129399 YP_002393573.1 CDS sgbU NC_011742.1 3963450 3964310 D L-xylulose 5-phosphate 3-epimerase activity not yet demonstrated; may be involved in the utilization of 2,3-diketo-L-gulonate; putative L-xylulose 5-phosphate 3-epimerase 3963450..3964310 Escherichia coli S88 7130588 YP_002393574.1 CDS sgbE NC_011742.1 3964304 3964999 D catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate in the anaerobic catabolism of L-ascorbate; links the arabinose metabolic pathway to the pentose phosphate pathway and allows the bacteria to use arabinose as an energy source; L-ribulose-5-phosphate 4-epimerase 3964304..3964999 Escherichia coli S88 7130589 YP_002393575.1 CDS aldB NC_011742.1 3965046 3966584 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95286498, 7768815; Product type e : enzyme; aldehyde dehydrogenase B complement(3965046..3966584) Escherichia coli S88 7130587 YP_002393576.1 CDS ECS88_4005 NC_011742.1 3966692 3967987 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3966692..3967987) Escherichia coli S88 7133041 YP_002393577.1 CDS yiaY NC_011742.1 3968117 3969268 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 2935393; Product type e : enzyme; putative alcohol dehydrogenase complement(3968117..3969268) Escherichia coli S88 7132922 YP_002393578.1 CDS selB NC_011742.1 3969459 3971303 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90264431, 91317715, 9315303, 94148228, 2140572, 2531290; Product type f : factor; selenocysteinyl-tRNA-specific translation factor complement(3969459..3971303) Escherichia coli S88 7132350 YP_002393579.1 CDS selA NC_011742.1 3971300 3972691 R catalyzes the formation of selenocysteinyl-tRNA(Sec) from seryl-tRNA(Sec) and L-selenophosphate in selenoprotein biosynthesis; selenocysteine synthase complement(3971300..3972691) Escherichia coli S88 7131387 YP_002393580.1 CDS yibF NC_011742.1 3972789 3973397 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8387990; Product type pe : putative enzyme; putative glutathione S-transferase complement(3972789..3973397) Escherichia coli S88 7131386 YP_002393581.1 CDS yibH NC_011742.1 3973468 3974604 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3973468..3974604) Escherichia coli S88 7132352 YP_002393582.1 CDS yibI NC_011742.1 3974607 3974969 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(3974607..3974969) Escherichia coli S88 7132353 YP_002393583.1 CDS mtlA NC_011742.1 3975505 3977418 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92052139, 92283796, 94131964, 1946374, 3135464, 3142516, 6309813, 9551558; Product type t : transporter; fused mannitol-specific PTS enzymes: IIA components ; IIB components ; IIC components 3975505..3977418 Escherichia coli S88 7132354 YP_002393584.1 CDS mtlD NC_011742.1 3977737 3978885 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90254197, 1964486, 3135464, 6384188, 8300537, 13295236; Product type e : enzyme; mannitol-1-phosphate 5-dehydrogenase 3977737..3978885 Escherichia coli S88 7129620 YP_002393585.1 CDS mtlR NC_011742.1 3978885 3979472 D Acts as a repressor of the mtlAD operon; mannitol repressor protein 3978885..3979472 Escherichia coli S88 7129621 YP_002393586.1 CDS yibT NC_011742.1 3979483 3979692 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(3979483..3979692) Escherichia coli S88 7129622 YP_002393587.1 CDS yibL NC_011742.1 3979976 3980338 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3979976..3980338 Escherichia coli S88 7132359 YP_002393588.1 CDS ECS88_4017 NC_011742.1 3980897 3981055 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein 3980897..3981055 Escherichia coli S88 7132356 YP_002393589.1 CDS ECS88_4018 NC_011742.1 3981131 3981580 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 3981131..3981580 Escherichia coli S88 7132923 YP_002393590.1 CDS ECS88_4019 NC_011742.1 3981624 3986375 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative exported adhesin 3981624..3986375 Escherichia coli S88 7132924 YP_002393591.1 CDS lldP NC_011742.1 3986785 3988440 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94012541, 11283302, 11785976, 8407843; Product type t : transporter; L-lactate permease 3986785..3988440 Escherichia coli S88 7132925 YP_002393592.1 CDS lldR NC_011742.1 3988440 3989216 D represses the lctPRD operon; DNA-binding transcriptional repressor LldR 3988440..3989216 Escherichia coli S88 7129365 YP_002393593.1 CDS lldD NC_011742.1 3989213 3990403 D flavin mononucleotide-dependent dehydrogenase; functions in aerobic respiration and also has a role in anaerobic nitrate respiration; L-lactate dehydrogenase 3989213..3990403 Escherichia coli S88 7129366 YP_002393594.1 CDS yibK NC_011742.1 3990451 3990924 D member of the SPOUT superfamily of RNA methyltransferases; no methyltransferase activity observed with certain tRNA substrates; putative tRNA/rRNA methyltransferase YibK 3990451..3990924 Escherichia coli S88 7129364 YP_002393595.1 CDS cysE NC_011742.1 3990979 3991800 R catalyzes the O-acetylation of serine; serine acetyltransferase complement(3990979..3991800) Escherichia coli S88 7132355 YP_002393596.1 CDS gpsA NC_011742.1 3991880 3992899 R catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase complement(3991880..3992899) Escherichia coli S88 7130537 YP_002393597.1 CDS secB NC_011742.1 3992899 3993366 R molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA; preprotein translocase subunit SecB complement(3992899..3993366) Escherichia coli S88 7130064 YP_002393598.1 CDS grxC NC_011742.1 3993430 3993681 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94316500, 95024051, 99175138, 11031118, 7937896, 8636094, 9973569; Product type c : carrier; glutaredoxin 3 complement(3993430..3993681) Escherichia coli S88 7131379 YP_002393599.1 CDS yibN NC_011742.1 3993822 3994253 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative rhodanese-related sulfurtransferase complement(3993822..3994253) Escherichia coli S88 7130075 YP_002393600.1 CDS gpmI NC_011742.1 3994498 3996042 D catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 3994498..3996042 Escherichia coli S88 7132357 YP_002393601.1 CDS envC NC_011742.1 3996076 3997335 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12113939, 21972773; Product type cp : cell process; hypothetical protein 3996076..3997335 Escherichia coli S88 7130062 YP_002393602.1 CDS yibQ NC_011742.1 3997339 3998298 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative polysaccharide deacetylase 3997339..3998298 Escherichia coli S88 7132406 YP_002393603.1 CDS yibD NC_011742.1 3998285 3999319 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15659689, 2647748; Product type pe : putative enzyme; putative glycosyl transferase complement(3998285..3999319) Escherichia coli S88 7132358 YP_002393604.1 CDS tdh NC_011742.1 3999558 4000583 R converts threonine and NAD to 1,2-amino-3-oxobutanoate and NADH; functions in threonine catabolism; L-threonine 3-dehydrogenase complement(3999558..4000583) Escherichia coli S88 7132351 YP_002393605.1 CDS kbl NC_011742.1 4000593 4001789 R catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine; 2-amino-3-ketobutyrate coenzyme A ligase complement(4000593..4001789) Escherichia coli S88 7131279 YP_002393606.1 CDS rfaD NC_011742.1 4002003 4002935 D catalyzes the interconversion between ADP-D-glycero-beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose; ADP-L-glycero-D-mannoheptose-6-epimerase 4002003..4002935 Escherichia coli S88 7130435 YP_002393607.1 CDS waaF NC_011742.1 4002945 4003991 D catalyzes the transfer of the second heptose to the heptosyl-KDO2 moiety of the lipopolysaccharide inner core; ADP-heptose:LPS heptosyltransferase II 4002945..4003991 Escherichia coli S88 7132477 YP_002393608.1 CDS waaC NC_011742.1 4003995 4004975 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20507564, 92250420, 93239678, 9446588, 1624462, 8478319; Product type e : enzyme; ADP-heptose:LPS heptosyl transferase I 4003995..4004975 Escherichia coli S88 7132478 YP_002393609.1 CDS waaL NC_011742.1 4005045 4006298 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92250420, 92325067, 93054344, 1624462; Product type e : enzyme; lipid A-core surface O-antigen ligase complement(4005045..4006298) Escherichia coli S88 7132476 YP_002393610.1 CDS waaV NC_011742.1 4006344 4007327 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative beta1,3-glucosyltransferase complement(4006344..4007327) Escherichia coli S88 7132480 YP_002393611.1 CDS waaW NC_011742.1 4007409 4008437 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9791168, 9756860, 9792656; Product type e : enzyme; UDP-galactose:(Galactosyl) LPS alpha1, 2-galactosyltransferase complement(4007409..4008437) Escherichia coli S88 7132485 YP_002393612.1 CDS waaY NC_011742.1 4008463 4009155 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92250420, 92325067, 9756860; Product type e : enzyme; lipopolysaccharide core biosynthesis protein complement(4008463..4009155) Escherichia coli S88 7132486 YP_002393613.1 CDS waaT NC_011742.1 4009165 4010160 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9791168, 9756860, 9792656; Product type e : enzyme; UDP-galactose:(Glucosyl) LPS alpha1, 2-galactosyltransferase complement(4009165..4010160) Escherichia coli S88 7132487 YP_002393614.1 CDS waaO NC_011742.1 4010177 4011193 R Evidence 1b : Function experimentally demonstrated in the studied species; Product type e : enzyme; UDP-glucose:(Glucosyl) LPS alpha1, 3-glucosyltransferase complement(4010177..4011193) Escherichia coli S88 7132484 YP_002393615.1 CDS waaP NC_011742.1 4011209 4012015 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21101922, 92121133, 92210496, 9756860, 1732225; Product type e : enzyme; kinase that phosphorylates core heptose of lipopolysaccharide complement(4011209..4012015) Escherichia coli S88 7132481 YP_002393616.1 CDS waaG NC_011742.1 4011999 4013123 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92121133, 92210496, 92250420, 1447141, 1732225, 7988890; Product type e : enzyme; glucosyltransferase I complement(4011999..4013123) Escherichia coli S88 7132482 YP_002393617.1 CDS waaQ NC_011742.1 4013120 4014178 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9756860, 1447141, 1732225; Product type e : enzyme; lipopolysaccharide core biosynthesis protein complement(4013120..4014178) Escherichia coli S88 7132479 YP_002393618.1 CDS kdtA NC_011742.1 4014591 4015868 D catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A; 3-deoxy-D-manno-octulosonic-acid transferase 4014591..4015868 Escherichia coli S88 7132483 YP_002393619.1 CDS coaD NC_011742.1 4015876 4016355 D Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase 4015876..4016355 Escherichia coli S88 7130450 YP_002393620.1 CDS mutM NC_011742.1 4016394 4017203 R Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases; formamidopyrimidine-DNA glycosylase complement(4016394..4017203) Escherichia coli S88 7131939 YP_002393621.1 CDS rpmG NC_011742.1 4017301 4017468 R 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; 50S ribosomal protein L33 complement(4017301..4017468) Escherichia coli S88 7129641 YP_002393622.1 CDS rpmB NC_011742.1 4017489 4017725 R required for 70S ribosome assembly; 50S ribosomal protein L28 complement(4017489..4017725) Escherichia coli S88 7133771 YP_002393623.1 CDS radC NC_011742.1 4017942 4018610 R Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase; DNA repair protein RadC complement(4017942..4018610) Escherichia coli S88 7133766 YP_002393624.1 CDS dfp NC_011742.1 4018782 4020002 D catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine; bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase 4018782..4020002 Escherichia coli S88 7130828 YP_002393625.1 CDS dut NC_011742.1 4019983 4020438 D catalyzes the formation of dUMP from dUTP; deoxyuridine 5'-triphosphate nucleotidohydrolase 4019983..4020438 Escherichia coli S88 7130191 YP_002393626.1 CDS slmA NC_011742.1 4020545 4021141 D FtsZ binding protein; synthetically lethal with a defect in the Min system; this protein is the first identified nucleoid occlusion factor which works along with the Min system to properly position the FtsZ ring assembly; nucleoid occlusion protein 4020545..4021141 Escherichia coli S88 7132368 YP_002393627.1 CDS pyrE NC_011742.1 4021178 4021819 R involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate; orotate phosphoribosyltransferase complement(4021178..4021819) Escherichia coli S88 7130365 YP_002393628.1 CDS rph NC_011742.1 4021885 4022625 R RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs; ribonuclease PH complement(4021885..4022625) Escherichia coli S88 7131766 YP_002393629.1 CDS yicC NC_011742.1 4022728 4023591 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4022728..4023591 Escherichia coli S88 7132759 YP_002393630.1 CDS dinD NC_011742.1 4023801 4024637 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 913680, 94334998, 95095962, 1925027, 2158980, 2664418, 8002613, 8057377, 8195095; Product type cp : cell process; DNA-damage-inducible protein D 4023801..4024637 Escherichia coli S88 7132360 YP_002393631.1 CDS yicG NC_011742.1 4024929 4025546 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 4024929..4025546 Escherichia coli S88 7130206 YP_002393632.1 CDS ligB NC_011742.1 4025543 4027225 R this ligase is similar to LigA but it lacks the C-terminal BRCT domain; catalyzes strand joining of nicked DNA in the presence of a divalent cation and NAD+; NAD-dependent DNA ligase LigB complement(4025543..4027225) Escherichia coli S88 7132279 YP_002393633.1 CDS gmk NC_011742.1 4027483 4028106 D Essential for recycling GMP and indirectly, cGMP; guanylate kinase 4027483..4028106 Escherichia coli S88 7129354 YP_002393634.1 CDS rpoZ NC_011742.1 4028161 4028436 D promotes RNA polymerase assembly or stability; latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits; DNA-directed RNA polymerase subunit omega 4028161..4028436 Escherichia coli S88 7130046 YP_002393635.1 CDS spoT NC_011742.1 4028455 4030563 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12224635, 89255395, 93266525, 94068533, 2005134, 2549050; Product type e : enzyme; bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase 4028455..4030563 Escherichia coli S88 7133782 YP_002393636.1 CDS trmH NC_011742.1 4030570 4031259 D specifically modifies tRNA at position G18; tRNA guanosine-2'-O-methyltransferase 4030570..4031259 Escherichia coli S88 7130632 YP_002393637.1 CDS recG NC_011742.1 4031265 4033346 D catalyzes branch migration in Holliday junction intermediates; ATP-dependent DNA helicase RecG 4031265..4033346 Escherichia coli S88 7130341 YP_002393638.1 CDS gltS NC_011742.1 4033380 4034585 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91203811, 93106943, 1544582, 2017136, 2254324; Product type t : transporter; glutamate transporter complement(4033380..4034585) Escherichia coli S88 7131808 YP_002393639.1 CDS yicE NC_011742.1 4034865 4036256 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 4034865..4036256 Escherichia coli S88 7130037 YP_002393640.1 CDS yicH NC_011742.1 4036377 4038086 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4036377..4038086 Escherichia coli S88 7132361 YP_002393641.1 CDS ECS88_4072 NC_011742.1 4038130 4038849 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative sugar related regulatory protein complement(4038130..4038849) Escherichia coli S88 7130821 YP_002393642.1 CDS ECS88_4073 NC_011742.1 4038791 4039756 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative sugar kinase/transcriptional regulator. ATPase domain complement(4038791..4039756) Escherichia coli S88 7132926 YP_002393643.1 CDS ECS88_4074 NC_011742.1 4039771 4040631 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein complement(4039771..4040631) Escherichia coli S88 7132927 YP_002393644.1 CDS ECS88_4075 NC_011742.1 4040712 4041563 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative sugar aldolase complement(4040712..4041563) Escherichia coli S88 7132928 YP_002393645.1 CDS ECS88_4076 NC_011742.1 4041575 4042666 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative phosphotransferase system, fructose-specific IIC component complement(4041575..4042666) Escherichia coli S88 7132929 YP_002393646.1 CDS ECS88_4077 NC_011742.1 4042691 4043005 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative phosphotransferase system, fructose-specific IIB subunit complement(4042691..4043005) Escherichia coli S88 7132930 YP_002393647.1 CDS ECS88_4078 NC_011742.1 4043023 4043493 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative phosphotransferase system (PTS), fructose-specific IIA component complement(4043023..4043493) Escherichia coli S88 7132931 YP_002393648.1 CDS ECS88_4079 NC_011742.1 4043520 4045073 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative PTS system transcriptional antiterminator complement(4043520..4045073) Escherichia coli S88 7132932 YP_002393649.1 CDS yicI NC_011742.1 4045368 4047686 R catalyzes the transfer of alpha-xylosyl residue from alpha-xyloside to xylose, glucose, mannose, fructose, maltose, isomaltose, nigerose, kojibiose, sucrose, and trehalose; shows higher activity against alpha-xylosyl fluoride, isoprimeverose (6-O-alpha-xylopyranosyl-glucopyranose), and alpha-xyloside in xyloglucan oligosaccharides; alpha-xylosidase YicI complement(4045368..4047686) Escherichia coli S88 7132933 YP_002393650.1 CDS yicJ NC_011742.1 4047696 4049078 R may be involved in the transport of galactosides-pentoses-hexuronides; putative transporter complement(4047696..4049078) Escherichia coli S88 7130822 YP_002393651.1 CDS ECS88_4082 NC_011742.1 4049389 4050555 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative RhuM-like cytoplasmic protein 4049389..4050555 Escherichia coli S88 7129895 YP_002393652.1 CDS ECS88_4083 NC_011742.1 4051125 4051493 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4051125..4051493 Escherichia coli S88 7132934 YP_002393653.1 CDS yicL NC_011742.1 4051790 4052713 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 4051790..4052713 Escherichia coli S88 7132935 YP_002393654.1 CDS nlpA NC_011742.1 4052717 4053535 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88298691, 89359178, 9914480, 3003106; Product type lp : lipoprotein; cytoplasmic membrane lipoprotein-28 complement(4052717..4053535) Escherichia coli S88 7130824 YP_002393655.1 CDS yicS NC_011742.1 4053688 4054050 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4053688..4054050 Escherichia coli S88 7129720 YP_002393656.1 CDS nepI NC_011742.1 4054091 4055446 R experimental results in Escherichia coli suggest that this gene encodes an inosine export protein; member of major facilitator superfamily; MFS; ribonucleoside transporter complement(4054091..4055446) Escherichia coli S88 7130829 YP_002393657.1 CDS yicN NC_011742.1 4055492 4055944 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4055492..4055944) Escherichia coli S88 7130825 YP_002393658.1 CDS yicO NC_011742.1 4055997 4057331 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative xanthine/uracil permease complement(4055997..4057331) Escherichia coli S88 7130826 YP_002393659.1 CDS ade NC_011742.1 4057506 4059272 D catalyzes the formation of hypoxanthine from adenine; in E. coli this activity has been detected in mutant strains but not in wild type; cryptic adenine deaminase 4057506..4059272 Escherichia coli S88 7130827 YP_002393660.1 CDS uhpT NC_011742.1 4059319 4060710 R cytoplasmic membrane protein that functions as a monomer; catalyzes the active transport of sugar-phosphates such as glucose-6-phosphate with the obligatory exchange of inorganic phosphate or organophosphate; sugar phosphate antiporter complement(4059319..4060710) Escherichia coli S88 7132052 YP_002393661.1 CDS uhpC NC_011742.1 4060848 4062167 R membrane protein regulates uhpT expression; regulatory protein UhpC complement(4060848..4062167) Escherichia coli S88 7130401 YP_002393662.1 CDS uhpB NC_011742.1 4062177 4063679 R Member of the two-component regulatory system UhpB/UhpA involved in the regulation of the uptake of hexose ph; sensory histidine kinase UhpB complement(4062177..4063679) Escherichia coli S88 7130400 YP_002393663.1 CDS uhpA NC_011742.1 4063679 4064269 R response regulator in two-component regulatory system wtih UhpB; phosphorylated UhpA is a positive activator uhpT, a hexose phosphates transporter; DNA-binding transcriptional activator UhpA complement(4063679..4064269) Escherichia coli S88 7130399 YP_002393664.1 CDS ilvN NC_011742.1 4064342 4064632 R with IlvB catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase small subunit; acetolactate synthase 1 regulatory subunit complement(4064342..4064632) Escherichia coli S88 7130398 YP_002393665.1 CDS ilvB NC_011742.1 4064636 4066324 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2989782, 85242083, 92380929, 2989781; Product type e : enzyme; acetolactate synthase catalytic subunit complement(4064636..4066324) Escherichia coli S88 7131629 YP_002393666.1 CDS ivbL NC_011742.1 4066430 4066528 R Evidence 1c : Function experimentally demonstrated in the studied genus; Product type l : leader peptide; ilvB operon leader peptide complement(4066430..4066528) Escherichia coli S88 7131620 YP_002393667.1 CDS emrD NC_011742.1 4066929 4068113 D multidrug efflux protein involved in adaptation to low energy shock; multidrug resistance protein D 4066929..4068113 Escherichia coli S88 7130428 YP_002393668.1 CDS yidF NC_011742.1 4068121 4068618 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(4068121..4068618) Escherichia coli S88 7132393 YP_002393669.1 CDS yidG NC_011742.1 4068615 4068977 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4068615..4068977) Escherichia coli S88 7130835 YP_002393670.1 CDS yidH NC_011742.1 4068967 4069314 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4068967..4069314) Escherichia coli S88 7130836 YP_002393671.1 CDS yidL NC_011742.1 4072702 4073598 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 4072702..4073598 Escherichia coli S88 7130841 YP_002393672.1 CDS yidE NC_011742.1 4073688 4075349 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1356969; Product type pt : putative transporter; hypothetical protein complement(4073688..4075349) Escherichia coli S88 7130842 YP_002393673.1 CDS ECS88_4108 NC_011742.1 4075379 4075549 D Evidence 6 : Doubtful CDS; hypothetical protein 4075379..4075549 Escherichia coli S88 7130834 YP_002393674.1 CDS ibpB NC_011742.1 4075546 4075974 R 16 kDa heat shock protein B; associates with aggregated proteins, together with ibpA, to stabilize and protect them from irreversible denaturation and extensive proteolysis during heat shock and oxidative stress; ATP-independent; heat shock chaperone IbpB complement(4075546..4075974) Escherichia coli S88 7132936 YP_002393675.1 CDS ibpA NC_011742.1 4076086 4076499 R with IbpB associates with aggregated proteins to stabilize and protect them from irreversible denaturation and extensive proteolysis during heat shock and oxidative stress; heat shock protein IbpA complement(4076086..4076499) Escherichia coli S88 7131605 YP_002393676.1 CDS yidQ NC_011742.1 4076805 4077137 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 4076805..4077137 Escherichia coli S88 7131604 YP_002393677.1 CDS yidR NC_011742.1 4077141 4078355 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4077141..4078355) Escherichia coli S88 7130843 YP_002393678.1 CDS cbrA NC_011742.1 4078456 4079556 D FAD/NAD(P)-binding domain; putative oxidoreductase 4078456..4079556 Escherichia coli S88 7130844 YP_002393679.1 CDS dgoT NC_011742.1 4079517 4080809 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 79020349; Product type t : transporter; D-galactonate transporter complement(4079517..4080809) Escherichia coli S88 7129164 YP_002393680.1 CDS dgoD NC_011742.1 4080929 4082077 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 79020349; Product type e : enzyme; galactonate dehydratase complement(4080929..4082077) Escherichia coli S88 7130197 YP_002393681.1 CDS dgoA NC_011742.1 4082074 4082691 R catalyzes the formation of D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-galactonate 6-phosphate; functions in galactonate metabolism; 2-dehydro-3-deoxy-6-phosphogalactonate aldolase complement(4082074..4082691) Escherichia coli S88 7130194 YP_002393682.1 CDS dgoK NC_011742.1 4082675 4083553 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 79020349; Product type e : enzyme; 2-oxo-3-deoxygalactonate kinase complement(4082675..4083553) Escherichia coli S88 7130193 YP_002393683.1 CDS dgoR NC_011742.1 4083550 4084239 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 79020349; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(4083550..4084239) Escherichia coli S88 7130195 YP_002393684.1 CDS yidX NC_011742.1 4084500 4085174 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; hypothetical protein 4084500..4085174 Escherichia coli S88 7130196 YP_002393685.1 CDS yidA NC_011742.1 4085218 4086030 R YidA; catalyzes the dephosphorylation of erythrose 4-phosphate (preferred substrate), mannose 1-phosphate and p-nitrophenyl phosphate; hydrolyzes the alpha-D-glucose-1-phosphate but not the beta form; member of the haloacid dehalogenase-like hydrolases superfamily and Cof family of proteins; sugar phosphatase complement(4085218..4086030) Escherichia coli S88 7130845 YP_002393686.1 CDS yidB NC_011742.1 4086145 4086543 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4086145..4086543) Escherichia coli S88 7130830 YP_002393687.1 CDS gyrB NC_011742.1 4086783 4089197 R negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit B complement(4086783..4089197) Escherichia coli S88 7130831 YP_002393688.1 CDS recF NC_011742.1 4089226 4090299 R Required for DNA replication; binds preferentially to single-stranded, linear DNA; recombination protein F complement(4089226..4090299) Escherichia coli S88 7128884 YP_002393689.1 CDS dnaN NC_011742.1 4090299 4091399 R binds the polymerase to DNA and acts as a sliding clamp; DNA polymerase III subunit beta complement(4090299..4091399) Escherichia coli S88 7131807 YP_002393690.1 CDS dnaA NC_011742.1 4091404 4092807 R binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself.; chromosomal replication initiation protein complement(4091404..4092807) Escherichia coli S88 7130227 YP_002393691.1 CDS rpmH NC_011742.1 4093414 4093554 D in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 4093414..4093554 Escherichia coli S88 7130220 YP_002393692.1 CDS rnpA NC_011742.1 4093571 4093930 D protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus; this enzyme also cleaves other RNA substrates; ribonuclease P 4093571..4093930 Escherichia coli S88 7133772 YP_002393693.1 CDS yidD NC_011742.1 4093894 4094151 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4093894..4094151 Escherichia coli S88 7132751 YP_002393694.1 CDS yidC NC_011742.1 4094154 4095800 D 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; putative inner membrane protein translocase component YidC 4094154..4095800 Escherichia coli S88 7130833 YP_002393695.1 CDS trmE NC_011742.1 4095906 4097270 D 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; tRNA modification GTPase TrmE 4095906..4097270 Escherichia coli S88 7130832 YP_002393696.1 CDS tnaC NC_011742.1 4097512 4097586 D Evidence 1c : Function experimentally demonstrated in the studied genus; Product type l : leader peptide; tryptophanase leader peptide 4097512..4097586 Escherichia coli S88 7130340 YP_002393697.1 CDS tnaA NC_011742.1 4097807 4099222 D tryptophan indole-lyase; catalyzes the formation of indole and pyruvate from tryptophan; tryptophanase 4097807..4099222 Escherichia coli S88 7133483 YP_002393698.1 CDS tnaB NC_011742.1 4099314 4100561 D tryptophan transporter of low affinity; tryptophan permease TnaB 4099314..4100561 Escherichia coli S88 7133481 YP_002393699.1 CDS mdtL NC_011742.1 4100693 4101868 D Confers resistance to chloramphenicol; multidrug efflux system protein MdtL 4100693..4101868 Escherichia coli S88 7133482 YP_002393700.1 CDS yidZ NC_011742.1 4101843 4102802 D Involved in anaerobic NO protection; DNA-binding transcriptional regulator YidZ 4101843..4102802 Escherichia coli S88 7128800 YP_002393701.1 CDS yieE NC_011742.1 4102947 4103708 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphopantetheinyl transferase 4102947..4103708 Escherichia coli S88 7130846 YP_002393702.1 CDS yieF NC_011742.1 4103730 4104296 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14766567; Product type e : enzyme; chromate reductase, Class I, flavoprotein 4103730..4104296 Escherichia coli S88 7130847 YP_002393703.1 CDS yieG NC_011742.1 4104349 4105686 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4104349..4105686) Escherichia coli S88 7130848 YP_002393704.1 CDS yieH NC_011742.1 4105853 4106518 D YieH; catalyzes the dephosphorylation of phosphoenolpyruvate, AMP and p-nitrophenyl phosphate; purine and pyrimidine nucleotides are secondary substrates; member of the haloacid dehalogenase-like hydrolases superfamily; 6-phosphogluconate phosphatase 4105853..4106518 Escherichia coli S88 7130849 YP_002393705.1 CDS yieI NC_011742.1 4106585 4107058 D might be involved in hypersensitivity to nitrofurzone; putative inner membrane protein 4106585..4107058 Escherichia coli S88 7130850 YP_002393706.1 CDS yieK NC_011742.1 4107140 4107862 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative 6-phosphogluconolactonase complement(4107140..4107862) Escherichia coli S88 7130851 YP_002393707.1 CDS yieL NC_011742.1 4107877 4109073 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative xylanase complement(4107877..4109073) Escherichia coli S88 7130852 YP_002393708.1 CDS bglH NC_011742.1 4109073 4110689 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10027967; Product type t : transporter; carbohydrate-specific outer membrane porin, cryptic complement(4109073..4110689) Escherichia coli S88 7130853 YP_002393709.1 CDS bglB NC_011742.1 4110775 4112169 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87222180, 88297127, 92334140, 3034860, 3309161; Product type e : enzyme; cryptic phospho-beta-glucosidase B complement(4110775..4112169) Escherichia coli S88 7129117 YP_002393710.1 CDS bglF NC_011742.1 4112188 4114062 R phosphoenolpyruvate-dependent sugar phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIB is phosphorylated by IIA and then transfers the phosphoryl group to the sugar; IIC forms the translocation channel; PTS system beta-glucoside-specific transporter subunits IIABC complement(4112188..4114062) Escherichia coli S88 7129114 YP_002393711.1 CDS bglG NC_011742.1 4114196 4115032 R positive regulator of the beta-glucoside operon; transcriptional antiterminator; transcriptional antiterminator BglG complement(4114196..4115032) Escherichia coli S88 7129115 YP_002393712.1 CDS phoU NC_011742.1 4115318 4116043 R regulates several genes involved in high affinity phosphate uptake; under conditions of high phosphate concentrations downregulates the PHO regulon; transcriptional regulator PhoU complement(4115318..4116043) Escherichia coli S88 7129116 YP_002393713.1 CDS pstB NC_011742.1 4116058 4116831 R ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation; phosphate transporter ATP-binding protein complement(4116058..4116831) Escherichia coli S88 7133729 YP_002393714.1 CDS pstA NC_011742.1 4116922 4117812 R Part of the ABC transporter complex PstABCS responsible for inorganic phosphate (Pi) uptake under Pi starvation conditions; phosphate transporter permease subunit PtsA complement(4116922..4117812) Escherichia coli S88 7130811 YP_002393715.1 CDS pstC NC_011742.1 4117812 4118771 R part of the ATP-dependent phosphate uptake system PstABCS responsible for inorganic phosphate (Pi) uptake under Pi starvation conditions; phosphate transporter permease subunit PstC complement(4117812..4118771) Escherichia coli S88 7130810 YP_002393716.1 CDS pstS NC_011742.1 4118858 4119898 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90133909, 2215649, 6321434, 6365894, 9228942, 9298646, 9671506; Product type t : transporter; phosphate ABC transporter periplasmic substrate-binding protein PstS complement(4118858..4119898) Escherichia coli S88 7130812 YP_002393717.1 CDS glmS NC_011742.1 4120212 4122041 R Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source; glucosamine--fructose-6-phosphate aminotransferase complement(4120212..4122041) Escherichia coli S88 7130813 YP_002393718.1 CDS glmU NC_011742.1 4122202 4123572 R forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis; bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase complement(4122202..4123572) Escherichia coli S88 7132221 YP_002393719.1 CDS atpC NC_011742.1 4123926 4124345 R part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane; F0F1 ATP synthase subunit epsilon complement(4123926..4124345) Escherichia coli S88 7132222 YP_002393720.1 CDS atpD NC_011742.1 4124366 4125748 R Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit; F0F1 ATP synthase subunit beta complement(4124366..4125748) Escherichia coli S88 7129968 YP_002393721.1 CDS atpG NC_011742.1 4125775 4126638 R Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit; F0F1 ATP synthase subunit gamma complement(4125775..4126638) Escherichia coli S88 7129969 YP_002393722.1 CDS atpA NC_011742.1 4126689 4128230 R produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit; F0F1 ATP synthase subunit alpha complement(4126689..4128230) Escherichia coli S88 7129972 YP_002393723.1 CDS atpH NC_011742.1 4128243 4128776 R Produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex; F0F1 ATP synthase subunit delta complement(4128243..4128776) Escherichia coli S88 7129966 YP_002393724.1 CDS atpF NC_011742.1 4128791 4129261 R Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.; F0F1 ATP synthase subunit B complement(4128791..4129261) Escherichia coli S88 7129973 YP_002393725.1 CDS atpE NC_011742.1 4129323 4129562 R Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0; F0F1 ATP synthase subunit C complement(4129323..4129562) Escherichia coli S88 7129971 YP_002393726.1 CDS atpB NC_011742.1 4129609 4130424 R Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0; F0F1 ATP synthase subunit A complement(4129609..4130424) Escherichia coli S88 7129970 YP_002393727.1 CDS atpI NC_011742.1 4130433 4130813 R Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit I associates with the membrane and may be involved with cation translocation; F0F1 ATP synthase subunit I complement(4130433..4130813) Escherichia coli S88 7129967 YP_002393728.1 CDS gidB NC_011742.1 4131430 4132053 R glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA; 16S rRNA methyltransferase GidB complement(4131430..4132053) Escherichia coli S88 7129974 YP_002393729.1 CDS gidA NC_011742.1 4132117 4134006 R 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; tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA complement(4132117..4134006) Escherichia coli S88 7132205 YP_002393730.1 CDS mioC NC_011742.1 4134385 4134828 R An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group; flavodoxin complement(4134385..4134828) Escherichia coli S88 7132204 YP_002393731.1 CDS asnC NC_011742.1 4134918 4135376 R transcriptional repressor of asnA which codes for aspartate-ammonia ligase; DNA-binding transcriptional regulator AsnC complement(4134918..4135376) Escherichia coli S88 7128839 YP_002393732.1 CDS asnA NC_011742.1 4135528 4136520 D catalyzes the formation of asparagine from aspartate and ammonia; asparagine synthetase AsnA 4135528..4136520 Escherichia coli S88 7129948 YP_002393733.1 CDS yieM NC_011742.1 4136525 4137976 R contains a von Willibrand factor type A domain; stimulates the ATPase activity of RavA; hypothetical protein complement(4136525..4137976) Escherichia coli S88 7129946 YP_002393734.1 CDS ravA NC_011742.1 4137970 4139466 R interacts with LdcI, lysine decarboxylase; may be active in late log/ early stationary phase; regulatory ATPase RavA complement(4137970..4139466) Escherichia coli S88 7130854 YP_002393735.1 CDS trkD NC_011742.1 4139689 4141557 D Responsible for the low-affinity transport of potassium into the cell; involved in potassium ion uptake under hyper-osmotic stress at a low pH; potassium transport protein Kup 4139689..4141557 Escherichia coli S88 7131784 YP_002393736.1 CDS rbsD NC_011742.1 4141724 4142143 D cytoplasmic mutarotase that catalyzes the conversion between beta-pyran and beta-furan forms of D-ribose; RbsD is required for efficient ribose utilization in E. coli; rbsD-mutant E. coli strains are unable to use ribose as a sole carbon source; D-ribose pyranase 4141724..4142143 Escherichia coli S88 7130335 YP_002393737.1 CDS rbsA NC_011742.1 4142151 4143656 D with RbsBCD acts to import ribose into the cell; RbsA contains 2 ATP-binding domain; D-ribose transporter ATP binding protein 4142151..4143656 Escherichia coli S88 7131791 YP_002393738.1 CDS rbsC NC_011742.1 4143661 4144626 D functions to transport ribose at high affinity; forms a complex with RbsA2C2B; ribose ABC transporter permease protein 4143661..4144626 Escherichia coli S88 7131788 YP_002393739.1 CDS rbsB NC_011742.1 4144651 4145541 D periplasmic substrate-binding component of the ATP-dependent ribose transport system; D-ribose transporter subunit RbsB 4144651..4145541 Escherichia coli S88 7131790 YP_002393740.1 CDS rbsK NC_011742.1 4145667 4146596 D catalyzes the formation of D-ribose 5-phosphate from ribose; ribokinase 4145667..4146596 Escherichia coli S88 7131789 YP_002393741.1 CDS rbsR NC_011742.1 4146600 4147592 D DNA-binding transcriptional repressor of ribose metabolism; transcriptional repressor RbsR 4146600..4147592 Escherichia coli S88 7131792 YP_002393742.1 CDS hsrA NC_011742.1 4147558 4148985 R Evidence 2b : Function of strongly homologous gene; PubMedId : 20218988, 12107133; Product type t : transporter; multidrug or homocysteine efflux system complement(4147558..4148985) Escherichia coli S88 7131793 YP_002393743.1 CDS yieP NC_011742.1 4149008 4149700 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator complement(4149008..4149700) Escherichia coli S88 7131398 YP_002393744.1 CDS hdfR NC_011742.1 4155501 4156340 R Negatively regulates the transcription of the flagellar master operon flhDC by binding to the upstream region of the operon; transcriptional regulator HdfR complement(4155501..4156340) Escherichia coli S88 7129898 YP_002393745.1 CDS yifE NC_011742.1 4156459 4156797 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4156459..4156797 Escherichia coli S88 7128893 YP_002393746.1 CDS yifB NC_011742.1 4156822 4158372 R among the AAA+ ATPases, the YifB protease family belongs to the Helix 2 insert clade; unknown function; putative ATP-dependent protease complement(4156822..4158372) Escherichia coli S88 7130857 YP_002393747.1 CDS ilvL NC_011742.1 4158695 4158793 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87174741; Product type l : leader peptide; ilvG operon leader peptide 4158695..4158793 Escherichia coli S88 7130856 YP_002393748.1 CDS ilvG NC_011742.1 4158933 4160579 D catalyzes the formation of 2-acetolactate from pyruvate; also known as acetolactate synthase large subunit; acetolactate synthase 2 catalytic subunit 4158933..4160579 Escherichia coli S88 7131627 YP_002393749.1 CDS ilvM NC_011742.1 4160576 4160839 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92332418, 92380929, 1569580, 3550695, 3897211; Product type e : enzyme; acetolactate synthase 2 regulatory subunit 4160576..4160839 Escherichia coli S88 7131624 YP_002393750.1 CDS ilvE NC_011742.1 4160859 4161788 D catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; branched-chain amino acid aminotransferase 4160859..4161788 Escherichia coli S88 7131628 YP_002393751.1 CDS ilvD NC_011742.1 4161853 4163703 D catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase 4161853..4163703 Escherichia coli S88 7131623 YP_002393752.1 CDS ilvA NC_011742.1 4163706 4165250 D threonine deaminase; threonine dehydratase; in Escherichia coli, IlvA is part of the isoleucine biosynthetic pathway; threonine dehydratase 4163706..4165250 Escherichia coli S88 7131622 YP_002393753.1 CDS ilvY NC_011742.1 4165247 4166137 R participates in controlling several genes involved in isoleucine and valine biosynthesis; activates the transcription of the ilvC gene in the presence of acetolactate or acetohydroxybutyrate; DNA-binding transcriptional regulator IlvY complement(4165247..4166137) Escherichia coli S88 7131619 YP_002393754.1 CDS ilvC NC_011742.1 4166287 4167762 D catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis; ketol-acid reductoisomerase 4166287..4167762 Escherichia coli S88 7131630 YP_002393755.1 CDS ppiC NC_011742.1 4167808 4168089 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94215709, 7878732, 7925971, 8163020; Product type e : enzyme; peptidyl-prolyl cis-trans isomerase C (rotamase C) complement(4167808..4168089) Escherichia coli S88 7131621 YP_002393756.1 CDS rep NC_011742.1 4168176 4170197 D single-stranded DNA-dependent ATPase; initiates unwinding at a nick in the DNA; involved in DNA replication; ATP-dependent DNA helicase Rep 4168176..4170197 Escherichia coli S88 7130762 YP_002393757.1 CDS gpp NC_011742.1 4170244 4171728 R catalyzes the conversion of guanosine 5'-triphosphate,3'-diphosphate (pppGpp) to guanosine 5'-diphosphate,3'-diphosphate (ppGpp); pppGpp and ppGpp control the stringent response during amino acid starvation; guanosine pentaphosphate phosphohydrolase complement(4170244..4171728) Escherichia coli S88 7131817 YP_002393758.1 CDS ECS88_4201 NC_011742.1 4171734 4171913 R Evidence 6 : Doubtful CDS; hypothetical protein complement(4171734..4171913) Escherichia coli S88 7130063 YP_002393759.1 CDS rhlB NC_011742.1 4171864 4173129 R enables ATP-dependent unwinding of double stranded RNA as a component of the RNA degradosome, a multi-enzyme complex important in RNA processing and messenger RNA degradation; ATP-dependent RNA helicase RhlB complement(4171864..4173129) Escherichia coli S88 7132937 YP_002393760.1 CDS trxA NC_011742.1 4173260 4173589 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90202710, 91154193, 92250497, 99175138, 10489448, 1094461, 10947986, 1561103, 2181145, 2193685, 3891733, 4616096, 4883076, 6098320, 6099324, 7812718, 8098620, 8253691; Product type c : carrier; thioredoxin 4173260..4173589 Escherichia coli S88 7132707 YP_002393761.1 CDS rhoL NC_011742.1 4173730 4173831 D Evidence 1c : Function experimentally demonstrated in the studied genus; Product type l : leader peptide; putative rho operon leader peptide 4173730..4173831 Escherichia coli S88 7130355 YP_002393762.1 CDS rho NC_011742.1 4173916 4175175 D An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 4173916..4175175 Escherichia coli S88 7132710 YP_002393763.1 CDS rfe NC_011742.1 4175415 4176518 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92114763, 94245613, 94292435, 10629198, 11024259, 11700352, 11832520, 1722555, 1730666; Product type e : enzyme; UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase 4175415..4176518 Escherichia coli S88 7132709 YP_002393764.1 CDS wzzE NC_011742.1 4176530 4177576 D Enterobacterial Common Antigen (ECA) polysaccharide chain length modulation protein; lipopolysaccharide biosynthesis protein WzzE 4176530..4177576 Escherichia coli S88 7132690 YP_002393765.1 CDS rffE NC_011742.1 4177632 4178762 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90212314, 90337949, 92112804, 94042873, 11106477, 7559340, 8170390, 8226648; Product type e : enzyme; UDP-N-acetyl glucosamine-2-epimerase 4177632..4178762 Escherichia coli S88 7132511 YP_002393766.1 CDS wecC NC_011742.1 4178759 4180021 D catalyzes the oxidation of UDP-N-acetyl-D-mannosamine to UDP-N-acetylmannosaminuronic acid; UDP-N-acetyl-D-mannosamine dehydrogenase 4178759..4180021 Escherichia coli S88 7132695 YP_002393767.1 CDS rffG NC_011742.1 4180021 4181088 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88086930, 90212314, 90337949, 92112804, 92174908, 94018634, 94042873, 7559340; Product type e : enzyme; dTDP-glucose 4,6-dehydratase 4180021..4181088 Escherichia coli S88 7132694 YP_002393768.1 CDS rffH NC_011742.1 4181107 4181988 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94292435, 96032389; Product type e : enzyme; glucose-1-phosphate thymidylyltransferase 4181107..4181988 Escherichia coli S88 7132696 YP_002393769.1 CDS rffC NC_011742.1 4182095 4182640 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90212314, 90337949, 92112804, 8366065; Product type e : enzyme; TDP-fucosamine acetyltransferase 4182095..4182640 Escherichia coli S88 7132697 YP_002393770.1 CDS rffA NC_011742.1 4182645 4183775 D catalyzes the formation of dTDP-D-fucosamine from dTDP-4-oxo-6-deoxy-D-glucose in enterobacterial common antigen biosynthesis; TDP-4-oxo-6-deoxy-D-glucose transaminase 4182645..4183775 Escherichia coli S88 7132693 YP_002393771.1 CDS wzxE NC_011742.1 4183777 4185027 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12621029, 20044778; Product type t : transporter; O-antigen translocase 4183777..4185027 Escherichia coli S88 7132692 YP_002393772.1 CDS rffT NC_011742.1 4185024 4186103 D catalyzes the synthesis of a lipid-linked intermediate involved in ECA synthesis; 4-alpha-L-fucosyltransferase 4185024..4186103 Escherichia coli S88 7132508 YP_002393773.1 CDS wzyE NC_011742.1 4186100 4187452 D enterobacterial common antigen polymerase; putative common antigen polymerase 4186100..4187452 Escherichia coli S88 7132699 YP_002393774.1 CDS rffM NC_011742.1 4187455 4188195 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88086874, 90337949, 92112804; Product type e : enzyme; putative UDP-N-acetyl-D-mannosaminuronic acid transferase 4187455..4188195 Escherichia coli S88 7132510 YP_002393775.1 CDS yifK NC_011742.1 4188386 4189771 D uncharacterized member of the amino acid-polyamine-organocation (APC) superfamily of amino acid transporters; unknown function; putative transport protein YifK 4188386..4189771 Escherichia coli S88 7132698 YP_002393776.1 CDS aslB NC_011742.1 4190457 4191692 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 11222759, 2180918, 12419807, 14749327; Product type pr : putative regulator; regulator of arylsulfatase activity 4190457..4191692 Escherichia coli S88 7129903 YP_002393777.1 CDS aslA NC_011742.1 4191850 4193505 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 16766528, 92358234, 15477040; Product type e : enzyme; arylsulfatase-like enzyme complement(4191850..4193505) Escherichia coli S88 7129944 YP_002393778.1 CDS hemY NC_011742.1 4194184 4195380 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 89041586; Product type pe : putative enzyme; putative protoheme IX biogenesis protein complement(4194184..4195380) Escherichia coli S88 7131350 YP_002393779.1 CDS hemX NC_011742.1 4195383 4196570 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 89098348, 92358234, 3054815, 3062586, 9298646; Product type pe : putative enzyme; putative uroporphyrinogen III C-methyltransferase complement(4195383..4196570) Escherichia coli S88 7128907 YP_002393780.1 CDS hemD NC_011742.1 4196592 4197332 R catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane; functions in tetrapyrrole and heme biosynthesis; uroporphyrinogen-III synthase complement(4196592..4197332) Escherichia coli S88 7128906 YP_002393781.1 CDS hemC NC_011742.1 4197329 4198270 R transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase complement(4197329..4198270) Escherichia coli S88 7128899 YP_002393782.1 CDS cyaA NC_011742.1 4198657 4201203 D catalyzes transfer of adenylyl group of ATP from pyrophosphate to the 3'-hydroxyl group to form cyclic AMP; adenylate cyclase 4198657..4201203 Escherichia coli S88 7128898 YP_002393783.1 CDS cyaY NC_011742.1 4201243 4201563 R defects in the mitochondrial frataxin protein cause Friedreich ataxis which is an autosomal recessive neurodegenerative disease; based on phylogenomic distribution this protein may have a role in iron-sulfur cluster protein assembly; frataxin-like protein complement(4201243..4201563) Escherichia coli S88 7130519 YP_002393784.1 CDS ECS88_4231 NC_011742.1 4201611 4202927 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(4201611..4202927) Escherichia coli S88 7130520 YP_002393785.1 CDS yifL NC_011742.1 4204582 4204785 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; putative lipoprotein 4204582..4204785 Escherichia coli S88 7130986 YP_002393786.1 CDS dapF NC_011742.1 4204822 4205646 D involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate; diaminopimelate epimerase 4204822..4205646 Escherichia coli S88 7130859 YP_002393787.1 CDS yigA NC_011742.1 4205643 4206350 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4205643..4206350 Escherichia coli S88 7130568 YP_002393788.1 CDS xerC NC_011742.1 4206347 4207243 D site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs; site-specific tyrosine recombinase XerC 4206347..4207243 Escherichia coli S88 7130860 YP_002393789.1 CDS yigB NC_011742.1 4207243 4207959 D YigB; member of the haloacid dehalogenase (HAD)-like hydrolases superfamily of protein; unknown function; flavin mononucleotide phosphatase 4207243..4207959 Escherichia coli S88 7132520 YP_002393790.1 CDS uvrD NC_011742.1 4208043 4210205 D unwinds DNA duplexes with 3' to 5' polarity with respect to the bound strand and initiates unwinding most effectively when a single-stranded region is present; involved in the post-incision events of nucleotide excision repair and methyl-directed mismatch repair.; DNA-dependent helicase II 4208043..4210205 Escherichia coli S88 7130861 YP_002393791.1 CDS ECS88_4240 NC_011742.1 4210250 4211152 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(4210250..4211152) Escherichia coli S88 7132461 YP_002393792.1 CDS yigE NC_011742.1 4211235 4211999 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4211235..4211999) Escherichia coli S88 7130987 YP_002393793.1 CDS corA NC_011742.1 4212369 4213319 D responsible for the influx of magnesium ions; magnesium/nickel/cobalt transporter CorA 4212369..4213319 Escherichia coli S88 7130862 YP_002393794.1 CDS ECS88_4243 NC_011742.1 4213355 4213852 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4213355..4213852) Escherichia coli S88 7131949 YP_002393795.1 CDS ECS88_4244 NC_011742.1 4213849 4214697 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4213849..4214697) Escherichia coli S88 7130988 YP_002393796.1 CDS rarD NC_011742.1 4215008 4215898 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative chloramphenicol resistance permease complement(4215008..4215898) Escherichia coli S88 7130989 YP_002393797.1 CDS yigI NC_011742.1 4215950 4216417 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4215950..4216417) Escherichia coli S88 7131783 YP_002393798.1 CDS pldA NC_011742.1 4216582 4217451 D catalyzes the hydrolysis of phosphatidylcholine; phospholipase A 4216582..4217451 Escherichia coli S88 7130863 YP_002393799.1 CDS rhtC NC_011742.1 4219320 4219940 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 99313167, 10386596, 3027506; Product type t : transporter; threonine efflux system 4219320..4219940 Escherichia coli S88 7131813 YP_002393800.1 CDS rhtB NC_011742.1 4220001 4220621 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 99313167, 10386596; Product type t : transporter; homoserine/homoserine lactone efflux protein complement(4220001..4220621) Escherichia coli S88 7132713 YP_002393801.1 CDS pldB NC_011742.1 4220732 4221754 D lecithinase B; catalyzes the conversion of 1-lysophosphatidylcholine to glycerophosphocholine; can also hydrolyze 2-acyl glycerophosphoethanolamine and other substrates; lysophospholipase L2 4220732..4221754 Escherichia coli S88 7132712 YP_002393802.1 CDS yigL NC_011742.1 4221762 4222562 D purine and pyrimidine nucleotides are secondary substrates; yigL expression is regulated by heat shock, osmotic shock and starvation of glucose, phosphate or ammonium; putative sugar phosphatase 4221762..4222562 Escherichia coli S88 7133739 YP_002393803.1 CDS yigM NC_011742.1 4222638 4223537 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 4222638..4223537 Escherichia coli S88 7130864 YP_002393804.1 CDS metR NC_011742.1 4223425 4224378 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90384950, 96303520, 2205852, 2643109; Product type r : regulator; DNA-binding transcriptional activator, homocysteine-binding complement(4223425..4224378) Escherichia coli S88 7130865 YP_002393805.1 CDS metE NC_011742.1 4224496 4226757 D catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine; 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase 4224496..4226757 Escherichia coli S88 7128824 YP_002393806.1 CDS ECS88_4258 NC_011742.1 4226926 4227186 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4226926..4227186) Escherichia coli S88 7128813 YP_002393807.1 CDS ECS88_4259 NC_011742.1 4227246 4227503 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4227246..4227503) Escherichia coli S88 7130990 YP_002393808.1 CDS ECS88_4262 NC_011742.1 4229085 4229675 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4229085..4229675 Escherichia coli S88 7130993 YP_002393809.1 CDS ptsG NC_011742.1 4229717 4231225 D Evidence 2b : Function of strongly homologous gene; PubMedId : 9200688; Product type t : transporter; fused glucose-specific PTS enzymes: IIBcomponent and IIC component 4229717..4231225 Escherichia coli S88 7130994 YP_002393810.1 CDS ECS88_4264 NC_011742.1 4231276 4233273 D 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; transketolase 4231276..4233273 Escherichia coli S88 7131739 YP_002393811.1 CDS ECS88_4265 NC_011742.1 4233303 4234148 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4233303..4234148) Escherichia coli S88 7130995 YP_002393812.1 CDS ECS88_4266 NC_011742.1 4234349 4235254 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcritional regulator complement(4234349..4235254) Escherichia coli S88 7130996 YP_002393813.1 CDS ECS88_4267 NC_011742.1 4235332 4236555 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative permease; putative Purine-cytosine permease and related proteins complement(4235332..4236555) Escherichia coli S88 7130997 YP_002393814.1 CDS ECS88_4268 NC_011742.1 4236581 4236970 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4236581..4236970) Escherichia coli S88 7130998 YP_002393815.1 CDS ECS88_4269 NC_011742.1 4236987 4238030 R catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP; carbamate kinase complement(4236987..4238030) Escherichia coli S88 7130999 YP_002393816.1 CDS ECS88_4270 NC_011742.1 4237936 4239411 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4237936..4239411) Escherichia coli S88 7131000 YP_002393817.1 CDS ECS88_4271 NC_011742.1 4239357 4240916 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; Putative enzyme, Putative Succinyl-CoA synthetase, alpha subunit complement(4239357..4240916) Escherichia coli S88 7131001 YP_002393818.1 CDS ECS88_4272 NC_011742.1 4241011 4241871 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4241011..4241871) Escherichia coli S88 7131002 YP_002393819.1 CDS ECS88_4273 NC_011742.1 4241877 4242545 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative Isochorismate hydrolase complement(4241877..4242545) Escherichia coli S88 7131003 YP_002393820.1 CDS ysgA NC_011742.1 4242802 4243611 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12676709; Product type pe : putative enzyme; putative hydrolase complement(4242802..4243611) Escherichia coli S88 7131004 YP_002393821.1 CDS udp NC_011742.1 4243873 4244637 D catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate; involved in the pyrimidine salvage pathway; uridine phosphorylase 4243873..4244637 Escherichia coli S88 7131864 YP_002393822.1 CDS ECS88_4276 NC_011742.1 4244672 4246162 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4244672..4246162) Escherichia coli S88 7130391 YP_002393823.1 CDS ECS88_4277 NC_011742.1 4246175 4246684 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative permease subunit complement(4246175..4246684) Escherichia coli S88 7131005 YP_002393824.1 CDS ECS88_4278 NC_011742.1 4246698 4247672 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative periplasmic binding protein complement(4246698..4247672) Escherichia coli S88 7131006 YP_002393825.1 CDS ECS88_4279 NC_011742.1 4247697 4248401 R catalyzes the formation of D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-galactonate 6-phosphate; functions in galactonate metabolism; 2-dehydro-3-deoxy-6-phosphogalactonate aldolase complement(4247697..4248401) Escherichia coli S88 7131007 YP_002393826.1 CDS ECS88_4280 NC_011742.1 4248316 4249320 R Evidence 2b : Function of strongly homologous gene; Product type e : enzyme; acidic carbohydrate kinase complement(4248316..4249320) Escherichia coli S88 7131008 YP_002393827.1 CDS ECS88_4281 NC_011742.1 4249344 4250198 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator complement(4249344..4250198) Escherichia coli S88 7131009 YP_002393828.1 CDS rmuC NC_011742.1 4250328 4251755 D YigN; nuclease that may cleave DNA structures arising during the recombination of short-inverted repeats and thereby prevents the inversion of the internal sequence; transcription is induced by DNA-damaging agents such as nalidixic acid or mitomycin C in a LexA-dependent manner; DNA recombination protein RmuC 4250328..4251755 Escherichia coli S88 7131010 YP_002393829.1 CDS ubiE NC_011742.1 4251850 4252605 D Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone; ubiquinone/menaquinone biosynthesis methyltransferase 4251850..4252605 Escherichia coli S88 7132739 YP_002393830.1 CDS yigP NC_011742.1 4252619 4253224 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4252619..4253224 Escherichia coli S88 7130384 YP_002393831.1 CDS ubiB NC_011742.1 4253221 4254861 D an Escherichia coli mutant results in accumulation of octaprenylphenol and no ubiquinone; functions in the formation of 2-octaprenyl-6-hydroxy-phenol from 2-octaprenylphenol in ubiquinone (coenzyme Q) biosynthesis; similar to eukaryotic proteins that exhibit kinase functions; putative ubiquinone biosynthesis protein UbiB 4253221..4254861 Escherichia coli S88 7130866 YP_002393832.1 CDS tatA NC_011742.1 4254940 4255209 D TatA; similar to TatE that is found in some proteobacteria; part of system that translocates proteins with a conserved twin arginine motif across the inner membrane; capable of translocating folded substrates typically those with bound cofactors; similar to a protein import system in thylakoid membranes; twin arginine translocase protein A 4254940..4255209 Escherichia coli S88 7130381 YP_002393833.1 CDS tatB NC_011742.1 4255213 4255728 D mediates the export of protein precursors bearing twin-arginine signal peptides; sec-independent translocase 4255213..4255728 Escherichia coli S88 7131262 YP_002393834.1 CDS tatC NC_011742.1 4255731 4256507 D with TatABE forms the twin-arginine translocation complex which is involved in the transport of proteins across the cytoplasmic membrane; twin-arginine protein translocation system subunit TatC 4255731..4256507 Escherichia coli S88 7131263 YP_002393835.1 CDS tatD NC_011742.1 4256549 4257331 D magnesium dependent; not involved in the Sec-independent protein export system; DNase TatD 4256549..4257331 Escherichia coli S88 7131264 YP_002393836.1 CDS rfaH NC_011742.1 4257328 4257816 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92011415, 92250420, 92261317, 1584020, 12007406; Product type r : regulator; transcriptional activator RfaH complement(4257328..4257816) Escherichia coli S88 7131265 YP_002393837.1 CDS ubiD NC_011742.1 4257983 4259476 D catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol; 3-octaprenyl-4-hydroxybenzoate decarboxylase 4257983..4259476 Escherichia coli S88 7131819 YP_002393838.1 CDS fre NC_011742.1 4259522 4260223 D NAD(P)H-flavin reductase; catalyzes the reversible oxidation/reduction of NAD(P) and flavine mononucleotide; in Salmonella and E. coli this protein also reduces aquacob(III)alamin to cob(II)alamin; FMN reductase 4259522..4260223 Escherichia coli S88 7130383 YP_002393839.1 CDS fadA NC_011742.1 4260506 4261669 R FadA; fatty acid oxidation complex component beta; functions in a heterotetramer with FadB; similar to FadI2J2 complex; functions in beta-oxidation of fatty acids; 3-ketoacyl-CoA thiolase complement(4260506..4261669) Escherichia coli S88 7132828 YP_002393840.1 CDS fadB NC_011742.1 4261679 4263868 R includes enoyl-CoA hydratase, delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase, and 3-hydroxybutyryl-CoA epimerase; catalyzes the formation of an hydroxyacyl-CoA by addition of water on enoyl-CoA; also exhibits 3-hydroxyacyl-CoA epimerase and 3-hydroxyacyl-CoA dehydrogenase activities; forms a heterotetramer with FadA; similar to FadI2J2 complex; functions in beta-oxidation of fatty acids; multifunctional fatty acid oxidation complex subunit alpha complement(4261679..4263868) Escherichia coli S88 7129440 YP_002393841.1 CDS pepQ NC_011742.1 4264058 4265389 D catalyzes the hydrolysis of dipeptides with a proline at the C-terminal; also catalyzes the low efficiency hydrolysis of organophosphate di- and tri-esters; proline dipeptidase 4264058..4265389 Escherichia coli S88 7129441 YP_002393842.1 CDS yigZ NC_011742.1 4265389 4266003 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 15103642; Product type pf : putative factor; hypothetical protein 4265389..4266003 Escherichia coli S88 7133675 YP_002393843.1 CDS trkH NC_011742.1 4266042 4267493 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91100357, 2243799, 7896723; Product type t : transporter; potassium transporter 4266042..4267493 Escherichia coli S88 7130867 YP_002393844.1 CDS hemG NC_011742.1 4267505 4268050 D catalyzes the oxidation of protoporphyrinogen IX to form protoporphyrin IX; protoporphyrinogen oxidase 4267505..4268050 Escherichia coli S88 7130336 YP_002393845.1 CDS mobB NC_011742.1 4273630 4274142 R in Escherichia coli the MobB protein is not essential but has been found to interact with multiple proteins involved in the molybdopterin guanine dinucleotide cofactor biosynthesis pathway; molybdopterin-guanine dinucleotide biosynthesis protein B complement(4273630..4274142) Escherichia coli S88 7129851 YP_002393846.1 CDS mobA NC_011742.1 4274139 4274723 R in Escherichia coli MobA links a guanosine 5'-phosphate to molydopterin to form molybdopterin guanine dinucleotide during molybdenum cofactor biosynthesis; molybdopterin-guanine dinucleotide biosynthesis protein MobA complement(4274139..4274723) Escherichia coli S88 7128854 YP_002393847.1 CDS yihD NC_011742.1 4274793 4275062 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4274793..4275062 Escherichia coli S88 7128853 YP_002393848.1 CDS yihE NC_011742.1 4275139 4276125 D catalyzes the phosphorylation of protein substrates at serine and threonine residues in vitro; specific substrate in vivo has not been identified yet; plays a role in long-term cell survival and expression of surface appendages; serine/threonine protein kinase 4275139..4276125 Escherichia coli S88 7130869 YP_002393849.1 CDS dsbA NC_011742.1 4276142 4276768 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12498799, 93264419, 94016574, 94206930, 99298180, 10210188, 1429594, 1740115, 1934062, 8413591, 8494885, 8521518, 9194175, 9298646, 9300489, 9572841, 9600841, 9655827; Product type e : enzyme; periplasmic protein disulfide isomerase I 4276142..4276768 Escherichia coli S88 7130870 YP_002393850.1 CDS yihF NC_011742.1 4276923 4278353 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4276923..4278353 Escherichia coli S88 7130239 YP_002393851.1 CDS yihG NC_011742.1 4278394 4279326 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative acyltransferase complement(4278394..4279326) Escherichia coli S88 7130871 YP_002393852.1 CDS polA NC_011742.1 4279690 4282476 D has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair; DNA polymerase I 4279690..4282476 Escherichia coli S88 7130872 YP_002393853.1 CDS engB NC_011742.1 4282858 4283454 R binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential; ribosome biogenesis GTP-binding protein YsxC complement(4282858..4283454) Escherichia coli S88 7130631 YP_002393854.1 CDS yihI NC_011742.1 4284072 4284581 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4284072..4284581 Escherichia coli S88 7130504 YP_002393855.1 CDS hemN NC_011742.1 4284770 4286143 D catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 4284770..4286143 Escherichia coli S88 7130873 YP_002393856.1 CDS glnG NC_011742.1 4286503 4287912 R response regulator of a two-component regulatory system involved in the activation of nitrogen assimilation genes; interacts with sigma-54; nitrogen regulation protein NR(I) complement(4286503..4287912) Escherichia coli S88 7128905 YP_002393857.1 CDS glnL NC_011742.1 4287924 4288973 R sensory histidine kinase in two-component regulatory system with GlnG; acts as a signal transducer which responds to the nitrogen level of cell and modulates the activity of ntrC by phosphorylation/dephosphorylation; nitrogen regulation protein NR(II) complement(4287924..4288973) Escherichia coli S88 7130008 YP_002393858.1 CDS glnA NC_011742.1 4289147 4290556 R forms a homododecamer; forms glutamine from ammonia and glutamate with the conversion of ATP to ADP and phosphate; also functions in the assimilation of ammonia; highly regulated protein controlled by the addition/removal of adenylyl groups by adenylyltransferase from specific tyrosine residues; addition of adenylyl groups results in inactivation of the enzyme; glutamine synthetase complement(4289147..4290556) Escherichia coli S88 7130011 YP_002393859.1 CDS bipA NC_011742.1 4290929 4292752 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9642082, 7783627, 9298646, 9622352; Product type f : factor; GTP-binding protein 4290929..4292752 Escherichia coli S88 7130004 YP_002393860.1 CDS ECS88_4322 NC_011742.1 4292859 4293647 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; Putative DEOR-type transcriptional regulator complement(4292859..4293647) Escherichia coli S88 7129126 YP_002393861.1 CDS ECS88_4323 NC_011742.1 4293687 4294634 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative sugar kinase complement(4293687..4294634) Escherichia coli S88 7131011 YP_002393862.1 CDS ECS88_4324 NC_011742.1 4294686 4295633 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase with NAD(P)-binding Rossmann-fold domain, putative 3-hydroxyisobutyrate dehydrogenase 4294686..4295633 Escherichia coli S88 7131012 YP_002393863.1 CDS ECS88_4325 NC_011742.1 4295658 4296545 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative aldolase yihT 4295658..4296545 Escherichia coli S88 7131013 YP_002393864.1 CDS ECS88_4326 NC_011742.1 4296578 4297588 D Evidence 4 : Homologs of previously reported genes of unknown function; Conserved hypothetical protein, putative dehydrogenase, putative GroES-like protein 4296578..4297588 Escherichia coli S88 7131014 YP_002393865.1 CDS ECS88_4327 NC_011742.1 4297658 4299091 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 4297658..4299091 Escherichia coli S88 7131015 YP_002393866.1 CDS ECS88_4328 NC_011742.1 4299190 4300539 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transport protein (shikimate homolog) 4299190..4300539 Escherichia coli S88 7131016 YP_002393867.1 CDS ECS88_4329 NC_011742.1 4300472 4301416 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative Galactose mutarotase and related enzymes 4300472..4301416 Escherichia coli S88 7131017 YP_002393868.1 CDS yihX NC_011742.1 4301557 4302156 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; phosphatase 4301557..4302156 Escherichia coli S88 7131018 YP_002393869.1 CDS rbn NC_011742.1 4302150 4303022 D RNase BN; required for 3' maturation of certain phage T4-encoded tRNAs; forms a dimer; specific for immature tRNA substrates containing incorrect residues within the universal CCA sequence; 3' to 5' exoribonuclease; ribonuclease BN 4302150..4303022 Escherichia coli S88 7130874 YP_002393870.1 CDS dtd NC_011742.1 4303019 4303456 D hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine; D-tyrosyl-tRNA(Tyr) deacylase 4303019..4303456 Escherichia coli S88 7131787 YP_002393871.1 CDS yiiD NC_011742.1 4303453 4304442 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative acetyltransferase 4303453..4304442 Escherichia coli S88 7132365 YP_002393872.1 CDS ECS88_4334 NC_011742.1 4304506 4305489 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative lipase complement(4304506..4305489) Escherichia coli S88 7130875 YP_002393873.1 CDS ECS88_4335 NC_011742.1 4305643 4305954 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4305643..4305954 Escherichia coli S88 7131019 YP_002393874.1 CDS ECS88_4336 NC_011742.1 4305955 4306245 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative transcriptional regulator 4305955..4306245 Escherichia coli S88 7131020 YP_002393875.1 CDS ECS88_4337 NC_011742.1 4306604 4306882 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4306604..4306882 Escherichia coli S88 7131021 YP_002393876.1 CDS yiiE NC_011742.1 4307278 4307496 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator 4307278..4307496 Escherichia coli S88 7131022 YP_002393877.1 CDS fdhE NC_011742.1 4307712 4308641 R required for the formation of active formate dehydrogenase; formate dehydrogenase accessory protein FdhE complement(4307712..4308641) Escherichia coli S88 7130876 YP_002393878.1 CDS fdoI NC_011742.1 4308638 4309273 R cytochrome b556(FDO) component; heme containing; formate dehydrogenase-O subunit gamma complement(4308638..4309273) Escherichia coli S88 7129452 YP_002393879.1 CDS fdoH NC_011742.1 4309270 4310172 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91317715, 8522521, 9852007; Product type c : carrier; formate dehydrogenase-O, Fe-S subunit complement(4309270..4310172) Escherichia coli S88 7129459 YP_002393880.1 CDS fdoG NC_011742.1 4310185 4313235 R Evidence 1c : Function experimentally demonstrated in the studied genus; Product type e : enzyme; formate dehydrogenase-O, large subunit complement(4310185..4313235) Escherichia coli S88 7129458 YP_002393881.1 CDS fdhD NC_011742.1 4313429 4314262 D involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth; formate dehydrogenase accessory protein 4313429..4314262 Escherichia coli S88 7129457 YP_002393882.1 CDS ECS88_4347 NC_011742.1 4315392 4316786 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative glycoporin 4315392..4316786 Escherichia coli S88 7130878 YP_002393883.1 CDS yiiL NC_011742.1 4316827 4317141 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15060078; Product type e : enzyme; L-rhamnose mutarotase complement(4316827..4317141) Escherichia coli S88 7131023 YP_002393884.1 CDS rhaD NC_011742.1 4317151 4317975 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90128204, 93374854, 8396120; Product type e : enzyme; rhamnulose-1-phosphate aldolase complement(4317151..4317975) Escherichia coli S88 7130879 YP_002393885.1 CDS rhaA NC_011742.1 4318252 4319511 R catalyzes the formation of L-rhamnulose from L-rhamnose; L-rhamnose isomerase complement(4318252..4319511) Escherichia coli S88 7132702 YP_002393886.1 CDS rhaB NC_011742.1 4319508 4320977 R catalyzes the ATP-dependent phosphorylation of rhamnulose; rhamnulokinase complement(4319508..4320977) Escherichia coli S88 7132700 YP_002393887.1 CDS rhaS NC_011742.1 4321265 4322101 D activates the expression of the rhaBAD operon and rhaT gene; transcriptional activator RhaS 4321265..4322101 Escherichia coli S88 7132701 YP_002393888.1 CDS rhaT NC_011742.1 4323117 4324151 R transports L-rhamnose and L-lyxose into the cell; rhamnose-proton symporter complement(4323117..4324151) Escherichia coli S88 7132704 YP_002393889.1 CDS sodA NC_011742.1 4324436 4325056 D SodA; manganese binding; only present under aerobic conditions; destroys free radicals; superoxide dismutase 4324436..4325056 Escherichia coli S88 7132706 YP_002393890.1 CDS kdgT NC_011742.1 4325316 4326299 D transports degraded pectin products into the bacterial cell; 2-keto-3-deoxygluconate permease 4325316..4326299 Escherichia coli S88 7130616 YP_002393891.1 CDS yiiM NC_011742.1 4326448 4327122 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4326448..4327122 Escherichia coli S88 7130439 YP_002393892.1 CDS cpxA NC_011742.1 4327228 4328601 R part of two-component CpxA/CpxR system; senses envelope stress; upregulates a number of periplasmic folding and trafficking factors; two-component sensor protein complement(4327228..4328601) Escherichia coli S88 7130880 YP_002393893.1 CDS cpxR NC_011742.1 4328598 4329296 R response regulator in two-component regulatory system with CpxA; part of the envelope stress response system; DNA-binding transcriptional regulator CpxR complement(4328598..4329296) Escherichia coli S88 7131955 YP_002393894.1 CDS cpxP NC_011742.1 4329446 4329946 D repressor of the Cpx envelope stress response pathway which occurs via periplasmic interactions with CpxA; CpxP is degraded by DegP protease especially in the presence of misfolded substrates; periplasmic repressor CpxP 4329446..4329946 Escherichia coli S88 7131957 YP_002393895.1 CDS fieF NC_011742.1 4330095 4330997 D member of cation diffusion facilitator family; CDF; membrane-bound; induced by both zinc and iron, but does not induce resistance to zinc; can transport zinc(II) in a proton-dependent manner; instead this protein induces iron resistance; forms dimers; ferrous iron efflux protein F 4330095..4330997 Escherichia coli S88 7131956 YP_002393896.1 CDS pfkA NC_011742.1 4331178 4332140 D catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis; 6-phosphofructokinase 4331178..4332140 Escherichia coli S88 7129490 YP_002393897.1 CDS sbp NC_011742.1 4332460 4333449 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91161616, 2002055, 3158524, 8774726, 9298646; Product type t : transporter; sulfate transporter subunit 4332460..4333449 Escherichia coli S88 7133678 YP_002393898.1 CDS cdh NC_011742.1 4333556 4334311 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 86008270, 2995360, 3158524; Product type e : enzyme; CDP-diacylglycerol pyrophosphatase 4333556..4334311 Escherichia coli S88 7131369 YP_002393899.1 CDS tpiA NC_011742.1 4334366 4335133 R Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate; triosephosphate isomerase complement(4334366..4335133) Escherichia coli S88 7129177 YP_002393900.1 CDS yiiQ NC_011742.1 4335241 4335840 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4335241..4335840) Escherichia coli S88 7133502 YP_002393901.1 CDS yiiR NC_011742.1 4335941 4336381 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 4335941..4336381 Escherichia coli S88 7130881 YP_002393902.1 CDS yiiS NC_011742.1 4336593 4336892 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4336593..4336892 Escherichia coli S88 7130882 YP_002393903.1 CDS yiiT NC_011742.1 4336919 4337347 D with UspC and Usp E is involved in resistance to UV radiation; universal stress protein UspD 4336919..4337347 Escherichia coli S88 7130883 YP_002393904.1 CDS fpr NC_011742.1 4337352 4338098 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93194782, 94092163, 95050480, 95362685, 1400248, 2834327, 7961651, 8449868, 9149148; Product type e : enzyme; ferredoxin-NADP reductase complement(4337352..4338098) Escherichia coli S88 7130884 YP_002393905.1 CDS glpX NC_011742.1 4338195 4339205 R type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese; fructose 1,6-bisphosphatase II complement(4338195..4339205) Escherichia coli S88 7132822 YP_002393906.1 CDS glpK NC_011742.1 4339376 4340884 R Converts glycerol and ADP to glycerol-3-phosphate and ADP; glycerol kinase complement(4339376..4340884) Escherichia coli S88 7130028 YP_002393907.1 CDS glpF NC_011742.1 4340907 4341752 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12629974, 12948772, 14646142, 15004242, 90094250, 92210584, 11039922, 11101882, 11226336, 11964478, 1372899, 2544860, 6998951; Product type t : transporter; glycerol facilitator complement(4340907..4341752) Escherichia coli S88 7130024 YP_002393908.1 CDS yiiU NC_011742.1 4342177 4342422 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4342177..4342422 Escherichia coli S88 7130022 YP_002393909.1 CDS rraA NC_011742.1 4342507 4342992 R regulator of RNase E; increases half-life and abundance of RNAs; interacts with RNase E possibly inhibiting catalytic activity; ribonuclease activity regulator protein RraA complement(4342507..4342992) Escherichia coli S88 7130885 YP_002393910.1 CDS menA NC_011742.1 4343085 4344011 R catalyzes the formation of dimethylmenaquinone from 1,4-dihydroxy-2-naphthoate and octaprenyl diphosphate; 1,4-dihydroxy-2-naphthoate octaprenyltransferase complement(4343085..4344011) Escherichia coli S88 7133805 YP_002393911.1 CDS hslU NC_011742.1 4344078 4345409 R heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease ATP-binding subunit HslU complement(4344078..4345409) Escherichia coli S88 7128803 YP_002393912.1 CDS hslV NC_011742.1 4345419 4345949 R heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease peptidase subunit complement(4345419..4345949) Escherichia coli S88 7131396 YP_002393913.1 CDS ftsN NC_011742.1 4346042 4347001 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9282742, 93285993, 8509333; Product type cp : cell process; essential cell division protein FtsN complement(4346042..4347001) Escherichia coli S88 7131397 YP_002393914.1 CDS cytR NC_011742.1 4347093 4348118 R negatively controls the transcription initiation of genes such as deoCABD, udp, and cdd encoding catabolizing enzymes and nupC, nupG, and tsx encoding transporting and pore-forming proteins; DNA-binding transcriptional regulator CytR complement(4347093..4348118) Escherichia coli S88 7132853 YP_002393915.1 CDS priA NC_011742.1 4348274 4350472 R binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity; primosome assembly protein PriA complement(4348274..4350472) Escherichia coli S88 7130551 YP_002393916.1 CDS rpmE NC_011742.1 4350675 4350887 D 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; 50S ribosomal protein L31 4350675..4350887 Escherichia coli S88 7130776 YP_002393917.1 CDS yiiX NC_011742.1 4350948 4351556 R member of the NlpC/P60 superfamily of peptidases; putative peptidoglycan peptidase complement(4350948..4351556) Escherichia coli S88 7133769 YP_002393918.1 CDS metJ NC_011742.1 4351616 4352071 R when combined with S-adenosylmethionine represses the expression of the methionine regulon and of proteins involved in S-adenosylmethionine synthesis; transcriptional repressor protein MetJ complement(4351616..4352071) Escherichia coli S88 7130886 YP_002393919.1 CDS metB NC_011742.1 4352210 4353370 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87326410, 90148970, 3307782, 6361020, 9843488; Product type e : enzyme; cystathionine gamma-synthase, PLP-dependent 4352210..4353370 Escherichia coli S88 7128818 YP_002393920.1 CDS metL NC_011742.1 4353373 4355805 D multifunctional homodimeric enzyme that catalyzes the phosphorylation of aspartate to form aspartyl-4-phosphate as well as conversion of aspartate semialdehyde to homoserine; functions in a number of amino acid biosynthetic pathways; bifunctional aspartate kinase II/homoserine dehydrogenase II 4353373..4355805 Escherichia coli S88 7128811 YP_002393921.1 CDS tsx NC_011742.1 4356023 4356883 R Evidence 1b : Function experimentally demonstrated in the studied species; Product type m : membrane component; nucleoside channel phage T6/colicin K receptor complement(4356023..4356883) Escherichia coli S88 7128821 YP_002393922.1 CDS ECS88_4393 NC_011742.1 4356960 4358585 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases complement(4356960..4358585) Escherichia coli S88 7130362 YP_002393923.1 CDS ECS88_4394 NC_011742.1 4358620 4360173 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative 5'-nucleotidase complement(4358620..4360173) Escherichia coli S88 7131024 YP_002393924.1 CDS ECS88_4395 NC_011742.1 4360403 4361527 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4360403..4361527) Escherichia coli S88 7131025 YP_002393925.1 CDS ECS88_4396 NC_011742.1 4361654 4363213 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative phosphoesterase 4361654..4363213 Escherichia coli S88 7131026 YP_002393926.1 CDS metF NC_011742.1 4363595 4364485 D MTHFR; catalyzes NADH-linked reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate using FAD as a cofactor; 5,10-methylenetetrahydrofolate reductase 4363595..4364485 Escherichia coli S88 7131027 YP_002393927.1 CDS katG NC_011742.1 4364814 4366994 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90292022, 94209230, 3045098; Product type e : enzyme; catalase/hydroperoxidase HPI(I) 4364814..4366994 Escherichia coli S88 7128814 YP_002393928.1 CDS yijE NC_011742.1 4367088 4367993 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative permease 4367088..4367993 Escherichia coli S88 7130432 YP_002393929.1 CDS yijF NC_011742.1 4368020 4368637 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4368020..4368637) Escherichia coli S88 7130888 YP_002393930.1 CDS gldA NC_011742.1 4368913 4370016 R forms dimers and octamers; involved in conversion of glycerol to dihydroxy-acetone; glycerol dehydrogenase complement(4368913..4370016) Escherichia coli S88 7130889 YP_002393931.1 CDS fsaB NC_011742.1 4370027 4370689 R similar to transaldolase from Escherichia coli; many organisms have multiple copies; fructose-6-phosphate aldolase complement(4370027..4370689) Escherichia coli S88 7132212 YP_002393932.1 CDS ptsA NC_011742.1 4370701 4373202 R Evidence 2b : Function of strongly homologous gene; PubMedId : 95291446, 7773398; Product type t : transporter; fused putative PTS enzymes: Hpr component ; enzyme I component ; enzyme IIA component complement(4370701..4373202) Escherichia coli S88 7132843 YP_002393933.1 CDS frwC NC_011742.1 4373511 4374590 D FrwC with FrwB, FrwD and PtsA forms a PEP-dependent sugar phosphotransferase system permease which may phosphorylate and transport sugars into the cell; forms translocation channel and contains the specific substrate-binding site; putative fructose-like permease EIIC subunit 2 4373511..4374590 Escherichia coli S88 7130818 YP_002393934.1 CDS frwB NC_011742.1 4374605 4374925 D FrwB with FrwC, FrwD and PtsA forms a PEP-dependent sugar phosphotransferase system (PTS) permease which may phosphorylate and transport sugars into the cell; cytoplasmic protein that interacts with complex EIIA; contains the second phosphorylation site of the PTS; putative PTS system fructose-like transporter subunit EIIB 4374605..4374925 Escherichia coli S88 7132840 YP_002393935.1 CDS pflD NC_011742.1 4374976 4377273 D involved in production of D-lactate from glucose under microaerobic conditions; cytoplasmic protein; putative formate acetyltransferase 2 4374976..4377273 Escherichia coli S88 7132839 YP_002393936.1 CDS pflC NC_011742.1 4377239 4378117 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95291446, 14673546, 7773398; Product type e : enzyme; pyruvate formate lyase II activase 4377239..4378117 Escherichia coli S88 7133683 YP_002393937.1 CDS frwD NC_011742.1 4378119 4378460 D FrwD with FrwB, FrwC and PtsA forms a PEP-dependent sugar phosphotransferase system permease which may phosphorylate and transport sugars into the cell; phosphorylated by EIIA; FrwB homolog; putative fructose-like phosphotransferase EIIB subunit 3 4378119..4378460 Escherichia coli S88 7133682 YP_002393938.1 CDS yijO NC_011742.1 4378447 4379298 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(4378447..4379298) Escherichia coli S88 7132841 YP_002393939.1 CDS yijP NC_011742.1 4379524 4381257 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 10456927; Product type pm : putative membrane component; hypothetical protein complement(4379524..4381257) Escherichia coli S88 7130890 YP_002393940.1 CDS ppc NC_011742.1 4381440 4384091 R catalyzes the formation of oxaloacetate from phosphoenolpyruvate; phosphoenolpyruvate carboxylase complement(4381440..4384091) Escherichia coli S88 7130891 YP_002393941.1 CDS argE NC_011742.1 4384393 4385544 R catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine in arginine biosynthesis; acetylornithine deacetylase complement(4384393..4385544) Escherichia coli S88 7130753 YP_002393942.1 CDS argC NC_011742.1 4385698 4386702 D catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate; N-acetyl-gamma-glutamyl-phosphate reductase 4385698..4386702 Escherichia coli S88 7133095 YP_002393943.1 CDS argB NC_011742.1 4386713 4387486 D catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase 4386713..4387486 Escherichia coli S88 7133093 YP_002393944.1 CDS argH NC_011742.1 4387547 4388920 D catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase 4387547..4388920 Escherichia coli S88 7133092 YP_002393945.1 CDS rspA NC_011742.1 4389418 4390632 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 93341455, 94310441; Product type pe : putative enzyme; putative enolase/dehydratase 4389418..4390632 Escherichia coli S88 7133097 YP_002393946.1 CDS ECS88_4417 NC_011742.1 4390699 4391982 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; Putative transporter 4390699..4391982 Escherichia coli S88 7133817 YP_002393947.1 CDS oxyR NC_011742.1 4392234 4393151 D Activates the expression of a regulon of hydrogen peroxide-inducible genes such as katG, gor, ahpC, ahpF, oxyS, dps, fur and grxA; DNA-binding transcriptional regulator OxyR 4392234..4393151 Escherichia coli S88 7133151 YP_002393948.1 CDS sthA NC_011742.1 4393134 4394534 R catalyzes the conversion of NADPH to NADH; soluble pyridine nucleotide transhydrogenase complement(4393134..4394534) Escherichia coli S88 7133150 YP_002393949.1 CDS ECS88_4420 NC_011742.1 4394864 4396030 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 7730270; Product type e : enzyme; Hippurate hydrolase (Benzoylglycine amidohydrolase) (Hippuricase) 4394864..4396030 Escherichia coli S88 7131231 YP_002393950.1 CDS ECS88_4421 NC_011742.1 4396073 4397389 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative proton/ carboxylic acid permease 4396073..4397389 Escherichia coli S88 7131029 YP_002393951.1 CDS fabR NC_011742.1 4397439 4398143 D negatively controls the expression of fabA and fabB, genes involved in the unsaturated fatty acid biosynthesis; DNA-binding transcriptional repressor FabR 4397439..4398143 Escherichia coli S88 7131030 YP_002393952.1 CDS yijD NC_011742.1 4398143 4398502 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein 4398143..4398502 Escherichia coli S88 7129438 YP_002393953.1 CDS trmA NC_011742.1 4398542 4399642 R catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs; tRNA (uracil-5-)-methyltransferase complement(4398542..4399642) Escherichia coli S88 7130887 YP_002393954.1 CDS btuB NC_011742.1 4400011 4401855 D involved in the active translocation of vitamin B12 (cyanocobalamin) across the outer membrane to the periplasmic space; vitamin B12/cobalamin outer membrane transporter 4400011..4401855 Escherichia coli S88 7129862 YP_002393955.1 CDS murI NC_011742.1 4401800 4402657 D converts L-glutamate to D-glutamate, a component of peptidoglycan; glutamate racemase 4401800..4402657 Escherichia coli S88 7129136 YP_002393956.1 CDS murB NC_011742.1 4408180 4409208 D catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis; UDP-N-acetylenolpyruvoylglucosamine reductase 4408180..4409208 Escherichia coli S88 7129852 YP_002393957.1 CDS birA NC_011742.1 4409205 4410170 D catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon; biotin--protein ligase 4409205..4410170 Escherichia coli S88 7129631 YP_002393958.1 CDS coaA NC_011742.1 4410199 4411149 R catalyzes the formation of (R)-4'-phosphopantothenate in coenzyme A biosynthesis; pantothenate kinase complement(4410199..4411149) Escherichia coli S88 7129127 YP_002393959.1 CDS tufB NC_011742.1 4412067 4413251 D 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; elongation factor Tu 4412067..4413251 Escherichia coli S88 7129911 YP_002393960.1 CDS secE NC_011742.1 4413481 4413864 D forms a complex with SecY and SecG; SecYEG forms a putative protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force; preprotein translocase subunit SecE 4413481..4413864 Escherichia coli S88 7130367 YP_002393961.1 CDS nusG NC_011742.1 4413866 4414411 D Modulates Rho-dependent transcription termination; transcription antitermination protein NusG 4413866..4414411 Escherichia coli S88 7131381 YP_002393962.1 CDS rplK NC_011742.1 4414570 4414998 D binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 4414570..4414998 Escherichia coli S88 7133118 YP_002393963.1 CDS rplA NC_011742.1 4415002 4415706 D in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA; 50S ribosomal protein L1 4415002..4415706 Escherichia coli S88 7132771 YP_002393964.1 CDS rplJ NC_011742.1 4415998 4416495 D binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 4415998..4416495 Escherichia coli S88 7132763 YP_002393965.1 CDS rplL NC_011742.1 4416562 4416927 D 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; 50S ribosomal protein L7/L12 4416562..4416927 Escherichia coli S88 7132770 YP_002393966.1 CDS rpoB NC_011742.1 4417247 4421275 D 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; DNA-directed RNA polymerase subunit beta 4417247..4421275 Escherichia coli S88 7133751 YP_002393967.1 CDS rpoC NC_011742.1 4421352 4425575 D 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; DNA-directed RNA polymerase subunit beta' 4421352..4425575 Escherichia coli S88 7133775 YP_002393968.1 CDS thiH NC_011742.1 4425815 4426948 R in Escherichia coli this enzyme functions in thiamine biosynthesis along with thiFSGI and iscS; with ThiFSG catalyzes the formation of thiazole phosphate from tyrosine, cysteine and 1-deoxy-D-xylulose-5-phosphate; forms a complex with ThiG; contains an iron-sulfur center; thiamine biosynthesis protein ThiH complement(4425815..4426948) Escherichia coli S88 7133776 YP_002393969.1 CDS thiG NC_011742.1 4426945 4427715 R functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate; thiazole synthase complement(4426945..4427715) Escherichia coli S88 7131296 YP_002393970.1 CDS thiS NC_011742.1 4427717 4427917 R with ThiF, ThiG, and ThiO catalyzes the formation of the thiazole moiety of thiamine pyrophosphate; sulfur carrier protein ThiS complement(4427717..4427917) Escherichia coli S88 7131295 YP_002393971.1 CDS thiF NC_011742.1 4427901 4428656 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8432721, 94089392, 98298179, 10082377, 9632726; Product type e : enzyme; thiamin (thiazole moiety) biosynthesis protein complement(4427901..4428656) Escherichia coli S88 7131302 YP_002393972.1 CDS thiE NC_011742.1 4428649 4429284 R catalyzes the formation of thiamine monophosphate from 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate; thiamine-phosphate pyrophosphorylase complement(4428649..4429284) Escherichia coli S88 7131294 YP_002393973.1 CDS thiC NC_011742.1 4429284 4431179 R required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC complement(4429284..4431179) Escherichia coli S88 7131293 YP_002393974.1 CDS rsd NC_011742.1 4431412 4431888 R binds specifically to the major sigma factor sigma 70; active in stationary phase; anti-RNA polymerase sigma 70 factor complement(4431412..4431888) Escherichia coli S88 7129863 YP_002393975.1 CDS nudC NC_011742.1 4431983 4432756 D can catalyze hydrolysis of broad range of dinucleotide pyrophosphates but prefers reduced form of NADH; requires divalent metal ions such as magnesium and manganese and produces two mononucleoside 5'-phosphates; NADH pyrophosphatase 4431983..4432756 Escherichia coli S88 7133808 YP_002393976.1 CDS hemE NC_011742.1 4432796 4433860 D catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase 4432796..4433860 Escherichia coli S88 7129751 YP_002393977.1 CDS nfi NC_011742.1 4433870 4434541 D Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA; cleaves DNA containing urea residues, AP sites, base mismatches, insertion/deletion mismatches, flaps, and pseudo-Y structures; endonuclease V 4433870..4434541 Escherichia coli S88 7128900 YP_002393978.1 CDS yjaG NC_011742.1 4434584 4435174 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4434584..4435174 Escherichia coli S88 7129700 YP_002393979.1 CDS hupA NC_011742.1 4435361 4435633 D histone-like DNA-binding protein; transcriptional regulator HU subunit alpha 4435361..4435633 Escherichia coli S88 7130894 YP_002393980.1 CDS yjaH NC_011742.1 4435646 4436341 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4435646..4436341 Escherichia coli S88 7131404 YP_002393981.1 CDS zraP NC_011742.1 4436343 4436762 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 98362023, 9694902; Product type pf : putative factor; zinc resistance protein complement(4436343..4436762) Escherichia coli S88 7130895 YP_002393982.1 CDS zraS NC_011742.1 4437000 4438376 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21140164, 89327164, 92255260, 11243806, 2666400; Product type r : regulator; sensor protein ZraS 4437000..4438376 Escherichia coli S88 7131891 YP_002393983.1 CDS zraR NC_011742.1 4438373 4439698 D DNA-binding response regulator in two-component regulatory system with ZraS; response regulator/sigma54 interaction protein; transcriptional regulatory protein ZraR 4438373..4439698 Escherichia coli S88 7131893 YP_002393984.1 CDS purD NC_011742.1 4439695 4440984 R catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; phosphoribosylamine--glycine ligase complement(4439695..4440984) Escherichia coli S88 7131892 YP_002393985.1 CDS purH NC_011742.1 4440996 4442585 R involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase complement(4440996..4442585) Escherichia coli S88 7131747 YP_002393986.1 CDS yjaA NC_011742.1 4448289 4448672 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 2412207; hypothetical protein 4448289..4448672 Escherichia coli S88 7129853 YP_002393987.1 CDS yjaB NC_011742.1 4448736 4449179 R Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; hypothetical protein complement(4448736..4449179) Escherichia coli S88 7130892 YP_002393988.1 CDS metA NC_011742.1 4449336 4450265 D catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase 4449336..4450265 Escherichia coli S88 7130893 YP_002393989.1 CDS aceB NC_011742.1 4450534 4452135 D Catalyzes the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle; malate synthase 4450534..4452135 Escherichia coli S88 7128810 YP_002393990.1 CDS aceA NC_011742.1 4452165 4453469 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91295197, 92112731, 92353108, 2836370, 3049537, 3060852, 3276689, 3290857, 3291954, 7826335; Product type e : enzyme; isocitrate lyase 4452165..4453469 Escherichia coli S88 7132031 YP_002393991.1 CDS aceK NC_011742.1 4453518 4455242 D catalyzes the phosphorylation/dephosphorylation of the enzyme isocitrate dehydrogenase on a specific serine which regulates activity; unphosphorylated IDH is fully active when cells are grown on glucose while the enzyme becomes phosphorylated and inactive in the presence of acetate or ethanol; bifunctional isocitrate dehydrogenase kinase/phosphatase protein 4453518..4455242 Escherichia coli S88 7132030 YP_002393992.1 CDS iclR NC_011742.1 4455259 4456083 R regulates the glyoxylate bypass operon (aceBAK), which encodes isocitrate lyase, malate synthase and isocitrate dehydrogenase kinase/phosphorylase; transcriptional repressor IclR complement(4455259..4456083) Escherichia coli S88 7132034 YP_002393993.1 CDS metH NC_011742.1 4456283 4459966 D one of two methionine synthases in Escherichia coli; MetH catalyzes a methyl transfer reaction from methyltetrahydrofolate to homocysteine to create methionine; requires zinc for activity; B12-dependent methionine synthase 4456283..4459966 Escherichia coli S88 7131613 YP_002393994.1 CDS ECS88_4484 NC_011742.1 4460020 4460346 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4460020..4460346 Escherichia coli S88 7128816 YP_002393995.1 CDS ECS88_4485 NC_011742.1 4460389 4460838 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4460389..4460838 Escherichia coli S88 7131031 YP_002393996.1 CDS yjbB NC_011742.1 4461009 4462640 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 4461009..4462640 Escherichia coli S88 7131032 YP_002393997.1 CDS pepE NC_011742.1 4462730 4463419 R alpha-aspartyl dipeptidase; catalyzes the hydrolysis of dipeptides with an N-terminal aspartate residue; belongs to peptidase S51 family; peptidase E complement(4462730..4463419) Escherichia coli S88 7130897 YP_002393998.1 CDS ECS88_4488 NC_011742.1 4463801 4465042 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 7947968, 7652212; Product type e : enzyme; L-sorbose 1-phosphate reductase complement(4463801..4465042) Escherichia coli S88 7133672 YP_002393999.1 CDS ECS88_4489 NC_011742.1 4465082 4465936 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 7947968, 7700234; Product type t : transporter; sorbose permease IID component complement(4465082..4465936) Escherichia coli S88 7131033 YP_002394000.1 CDS ECS88_4490 NC_011742.1 4465917 4466714 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 7947968, 7700234; Product type t : transporter; sorbose permease IIC component (PTS system) complement(4465917..4466714) Escherichia coli S88 7131034 YP_002394001.1 CDS ECS88_4491 NC_011742.1 4466780 4467274 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 7947968, 7700234, 12662934; Product type t : transporter; sorbose-specific phosphotransferase enzyme IIB component (PTS system) complement(4466780..4467274) Escherichia coli S88 7131035 YP_002394002.1 CDS ECS88_4492 NC_011742.1 4467274 4467681 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 7947968; Product type t : transporter; sorbose-specific phosphotransferase enzyme IIA component (PTS system) complement(4467274..4467681) Escherichia coli S88 7131036 YP_002394003.1 CDS ECS88_4493 NC_011742.1 4467691 4468497 R Converts D-sorbitol-dphosphate to D-fructose-6-phosphate; sorbitol-6-phosphate 2-dehydrogenase complement(4467691..4468497) Escherichia coli S88 7131037 YP_002394004.1 CDS ECS88_4494 NC_011742.1 4468567 4469598 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 7947968; Product type r : regulator; sorbitol/sorbose operon activator complement(4468567..4469598) Escherichia coli S88 7131038 YP_002394005.1 CDS yjbC NC_011742.1 4469862 4470734 D catalyzes the synthesis of pseudouridine from U-2604 in the 23S ribosomal RNA; 23S rRNA pseudouridine synthase F 4469862..4470734 Escherichia coli S88 7131039 YP_002394006.1 CDS yjbD NC_011742.1 4470735 4471007 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4470735..4471007) Escherichia coli S88 7130898 YP_002394007.1 CDS lysC NC_011742.1 4471260 4472609 R catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; functions in amino acid biosynthesis; lysine sensitive; aspartate kinase III complement(4471260..4472609) Escherichia coli S88 7130899 YP_002394008.1 CDS pgi NC_011742.1 4473134 4474783 D 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; glucose-6-phosphate isomerase 4473134..4474783 Escherichia coli S88 7129864 YP_002394009.1 CDS ECS88_4499 NC_011742.1 4475262 4475510 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4475262..4475510) Escherichia coli S88 7133690 YP_002394010.1 CDS yjbF NC_011742.1 4475638 4476276 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type lp : lipoprotein; putative lipoprotein 4475638..4476276 Escherichia coli S88 7131040 YP_002394011.1 CDS yjbG NC_011742.1 4476273 4477010 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4476273..4477010 Escherichia coli S88 7130900 YP_002394012.1 CDS yjbH NC_011742.1 4477010 4479106 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative porin 4477010..4479106 Escherichia coli S88 7130901 YP_002394013.1 CDS ECS88_4503 NC_011742.1 4479153 4479431 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(4479153..4479431) Escherichia coli S88 7131581 YP_002394014.1 CDS ECS88_4504 NC_011742.1 4479491 4479649 D Evidence 6 : Doubtful CDS; hypothetical protein 4479491..4479649 Escherichia coli S88 7131041 YP_002394015.1 CDS yjbA NC_011742.1 4479646 4480056 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10986267; Product type pm : putative membrane component; phosphate-starvation-inducible protein PsiE 4479646..4480056 Escherichia coli S88 7131042 YP_002394016.1 CDS malG NC_011742.1 4480150 4481040 R with MalKFE is involved in the transport of maltose into the cell; maltose transporter permease complement(4480150..4481040) Escherichia coli S88 7130896 YP_002394017.1 CDS malF NC_011742.1 4481055 4482599 R with MalKGE is involved in maltose transport into the cell; maltose transporter membrane protein complement(4481055..4482599) Escherichia coli S88 7129408 YP_002394018.1 CDS malE NC_011742.1 4482753 4483943 R functions in the MalKFGE ABC transporter complex to transport maltose into the cell by using ATP hydrolysis; maltose ABC transporter periplasmic protein complement(4482753..4483943) Escherichia coli S88 7129407 YP_002394019.1 CDS malK NC_011742.1 4484308 4485423 D with malEFG is involved in import of maltose/maltodextrin; maltose/maltodextrin transporter ATP-binding protein 4484308..4485423 Escherichia coli S88 7129406 YP_002394020.1 CDS lamB NC_011742.1 4485495 4486835 D porin involved in the transport of maltose and maltodextrins; maltoporin 4485495..4486835 Escherichia coli S88 7129410 YP_002394021.1 CDS malM NC_011742.1 4487158 4488078 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87141162, 2434655, 6086106; Product type pt : putative transporter; maltose regulon periplasmic protein 4487158..4488078 Escherichia coli S88 7130474 YP_002394022.1 CDS ubiC NC_011742.1 4488257 4488754 D catalyzes the formation of 4-hydroxybenzoate from chorismate; chorismate pyruvate lyase 4488257..4488754 Escherichia coli S88 7129411 YP_002394023.1 CDS ubiA NC_011742.1 4488767 4489639 D catalyzes the conversion of 4-Hydroxybenzoate into 3-octaprenyl-4-hydroxybenzoate, as part of the ubiquinone biosynthesis pathway; 4-hydroxybenzoate octaprenyltransferase 4488767..4489639 Escherichia coli S88 7130382 YP_002394024.1 CDS plsB NC_011742.1 4489792 4492215 R PlsB; catalyzes the formation of 1-acyl-sn-glycerol 3-phosphate by transfering the acyl moiety from acyl-CoA; glycerol-3-phosphate acyltransferase complement(4489792..4492215) Escherichia coli S88 7130380 YP_002394025.1 CDS dgkA NC_011742.1 4492386 4492754 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10220339, 6257698, 86278195, 88111690, 2984194, 6309817, 8071224; Product type e : enzyme; diacylglycerol kinase 4492386..4492754 Escherichia coli S88 7133740 YP_002394026.1 CDS lexA NC_011742.1 4492864 4493472 D Represses a number of genes involved in the response to DNA damage; LexA repressor 4492864..4493472 Escherichia coli S88 7130192 YP_002394027.1 CDS dinF NC_011742.1 4493491 4494870 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87165788; Product type cp : cell process; DNA-damage-inducible SOS response protein 4493491..4494870 Escherichia coli S88 7130491 YP_002394028.1 CDS yjbJ NC_011742.1 4494986 4495195 D unknown function; highly abundant protein in vivo; overexpressed under high NaCl concentrations; part of the sigma S regulon; non-essential; putative stress-response protein 4494986..4495195 Escherichia coli S88 7130207 YP_002394029.1 CDS zur NC_011742.1 4495237 4495752 R Acts as a negative controlling element, employing Zn(2+) as a cofactor to bind the operator of the repressed genes znuACB; zinc uptake transcriptional repressor complement(4495237..4495752) Escherichia coli S88 7131663 YP_002394030.1 CDS yjbN NC_011742.1 4495908 4496903 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 22095566; Product type e : enzyme; tRNA-dihydrouridine synthase A 4495908..4496903 Escherichia coli S88 7131895 YP_002394031.1 CDS pspG NC_011742.1 4496827 4497279 D coordinately regulated along with pspA; PspF-dependent induction in response to secretin overexpression in Yersinia; phage shock protein G 4496827..4497279 Escherichia coli S88 7131664 YP_002394032.1 CDS qor NC_011742.1 4497444 4498427 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94089392, 7602590; Product type e : enzyme; quinone oxidoreductase, NADPH-dependent complement(4497444..4498427) Escherichia coli S88 7131665 YP_002394033.1 CDS ECS88_4524 NC_011742.1 4498533 4500698 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase complement(4498533..4500698) Escherichia coli S88 7131772 YP_002394034.1 CDS ECS88_4525 NC_011742.1 4500571 4501971 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transmembrane transport protein complement(4500571..4501971) Escherichia coli S88 7131043 YP_002394035.1 CDS ECS88_4526 NC_011742.1 4502062 4502841 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative Enoyl-CoA hydratase/carnithine racemase complement(4502062..4502841) Escherichia coli S88 7131044 YP_002394036.1 CDS ECS88_4527 NC_011742.1 4502834 4504405 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative Acyl CoA:acetate/3-ketoacid CoA transferase, alpha and beta subunits complement(4502834..4504405) Escherichia coli S88 7131045 YP_002394037.1 CDS ECS88_4528 NC_011742.1 4504634 4505695 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator 4504634..4505695 Escherichia coli S88 7131046 YP_002394038.1 CDS dnaB NC_011742.1 4505768 4507183 D unwinds double stranded DNA; replicative DNA helicase 4505768..4507183 Escherichia coli S88 7131047 YP_002394039.1 CDS alr NC_011742.1 4507236 4508315 D converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer; alanine racemase 4507236..4508315 Escherichia coli S88 7130221 YP_002394040.1 CDS ECS88_4531 NC_011742.1 4508338 4508895 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 4508338..4508895 Escherichia coli S88 7133049 YP_002394041.1 CDS ECS88_4532 NC_011742.1 4508868 4509890 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator 4508868..4509890 Escherichia coli S88 7131048 YP_002394042.1 CDS tyrB NC_011742.1 4509972 4511165 D catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate; aromatic amino acid aminotransferase 4509972..4511165 Escherichia coli S88 7131049 YP_002394043.1 CDS sucA NC_011742.1 4511272 4514091 D SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide; 2-oxoglutarate dehydrogenase E1 component 4511272..4514091 Escherichia coli S88 7130375 YP_002394044.1 CDS sucB NC_011742.1 4514124 4515278 D Evidence 2b : Function of strongly homologous gene; PubMedId : 10739245, 6376124; Product type e : enzyme; dihydrolipoamide succinyltransferase (E2 component) 4514124..4515278 Escherichia coli S88 7131234 YP_002394045.1 CDS ECS88_4536 NC_011742.1 4515290 4516708 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative dihydrolipoyl dehydrogenase, E3 component (lpd-like) 4515290..4516708 Escherichia coli S88 7131236 YP_002394046.1 CDS sucC NC_011742.1 4516730 4517899 D Evidence 1b : Function experimentally demonstrated in the studied species; Product type e : enzyme; Succinyl-CoA synthetase beta chain (SCS-beta) 4516730..4517899 Escherichia coli S88 7131050 YP_002394047.1 CDS sucD NC_011742.1 4517912 4518784 D Evidence 1b : Function experimentally demonstrated in the studied species; Product type e : enzyme; Succinyl-CoA synthetase alpha chain (SCS-alpha) 4517912..4518784 Escherichia coli S88 7131238 YP_002394048.1 CDS ECS88_4539 NC_011742.1 4518990 4520495 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative membrane protein; putative transporter 4518990..4520495 Escherichia coli S88 7131240 YP_002394049.1 CDS ECS88_4540 NC_011742.1 4520369 4521580 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; Putative malate/L-lactate dehydrogenases 4520369..4521580 Escherichia coli S88 7131051 YP_002394050.1 CDS ECS88_4543 NC_011742.1 4522920 4524740 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2134335; Product type prc : putative receptor; putative C4-dicarboxylate transport sensor protein (dctB-like) complement(4522920..4524740) Escherichia coli S88 7130168 YP_002394051.1 CDS aphA NC_011742.1 4525017 4525730 D Class B; non-specific; catalyzes the dephosphorylation of organic phosphomonoesters; also has phosphotransferase activity; acid phosphatase/phosphotransferase 4525017..4525730 Escherichia coli S88 7131053 YP_002394052.1 CDS yjbQ NC_011742.1 4525841 4526257 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 11972052; hypothetical protein 4525841..4526257 Escherichia coli S88 7133074 YP_002394053.1 CDS yjbR NC_011742.1 4526261 4526617 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4526261..4526617 Escherichia coli S88 7131666 YP_002394054.1 CDS uvrA NC_011742.1 4526652 4529474 R 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; excinuclease ABC subunit A complement(4526652..4529474) Escherichia coli S88 7131667 YP_002394055.1 CDS ssb NC_011742.1 4529728 4530264 D binds to single stranded DNA and PriA helcase facilitate replication restart; single-stranded DNA-binding protein 4529728..4530264 Escherichia coli S88 7132458 YP_002394056.1 CDS yjcB NC_011742.1 4530363 4530644 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4530363..4530644) Escherichia coli S88 7130648 YP_002394057.1 CDS yjcC NC_011742.1 4531073 4532659 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative signal transduction protein (EAL domain containing protein) 4531073..4532659 Escherichia coli S88 7131668 YP_002394058.1 CDS soxS NC_011742.1 4532662 4532985 R regulates genes involved in response to oxidative stress; DNA-binding transcriptional regulator SoxS complement(4532662..4532985) Escherichia coli S88 7131669 YP_002394059.1 CDS soxR NC_011742.1 4533071 4533535 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91210176, 91360349, 94139656, 9564045, 10207625, 12670967, 1653416, 1708380, 7673113, 8065907, 8306957, 8631739, 8969171, 9019397, 9092651, 9204707; Product type r : regulator; DNA-binding transcriptional dual regulator, Fe-S center for redox-sensing 4533071..4533535 Escherichia coli S88 7130623 YP_002394060.1 CDS yjcD NC_011742.1 4534082 4535431 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative permease 4534082..4535431 Escherichia coli S88 7131351 YP_002394061.1 CDS yjcE NC_011742.1 4535582 4537231 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 21557160, 11479290; Product type pt : putative transporter; putative cation/proton antiporter 4535582..4537231 Escherichia coli S88 7131670 YP_002394062.1 CDS ECS88_4557 NC_011742.1 4537267 4538151 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator (LysR family) complement(4537267..4538151) Escherichia coli S88 7131671 YP_002394063.1 CDS ECS88_4558 NC_011742.1 4538255 4538665 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4538255..4538665 Escherichia coli S88 7131054 YP_002394064.1 CDS ECS88_4559 NC_011742.1 4538658 4539347 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4538658..4539347 Escherichia coli S88 7131055 YP_002394065.1 CDS actP NC_011742.1 4539386 4541035 R member of the sodium:solute symporter family; cotranscribed with the acs gene which encodes acetyl coenzyme A synthase; mutations affect acetate uptake; acetate permease complement(4539386..4541035) Escherichia coli S88 7131056 YP_002394066.1 CDS yjcH NC_011742.1 4541032 4541346 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 14563880; Product type pm : putative membrane component; hypothetical protein complement(4541032..4541346) Escherichia coli S88 7132049 YP_002394067.1 CDS acs NC_011742.1 4541638 4543596 R Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA; acetyl-CoA synthetase complement(4541638..4543596) Escherichia coli S88 7131672 YP_002394068.1 CDS nrfA NC_011742.1 4543988 4545424 D catalyzes the formate-dependent reduction of nitrite to ammonia; cytochrome C552; cytochrome c552 4543988..4545424 Escherichia coli S88 7132048 YP_002394069.1 CDS nrfB NC_011742.1 4545469 4546035 D part of nitrite reductase complex; NrfB is active at high nitrate conditions; NrfA, B, C, and D are essential for the formate-dependent nitrite reduction to ammonia; cytochrome c nitrite reductase pentaheme subunit 4545469..4546035 Escherichia coli S88 7129741 YP_002394070.1 CDS nrfC NC_011742.1 4546032 4546703 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94335626, 8057835; Product type c : carrier; formate-dependent nitrite reductase, 4Fe4S subunit 4546032..4546703 Escherichia coli S88 7129742 YP_002394071.1 CDS nrfD NC_011742.1 4546700 4547656 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91058381, 94335626, 8057835; Product type e : enzyme; formate-dependent nitrite reductase, membrane subunit 4546700..4547656 Escherichia coli S88 7129743 YP_002394072.1 CDS nrfE NC_011742.1 4547736 4549394 D with NrfF and NrfG catalyzes the insertion of heme into cytochrome c552; heme lyase subunit NrfE 4547736..4549394 Escherichia coli S88 7129744 YP_002394073.1 CDS nrfF NC_011742.1 4549387 4549770 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91058381, 94335626, 9593308, 8057835, 8842153; Product type f : factor; formate-dependent nitrite reductase complex subunit NrfF 4549387..4549770 Escherichia coli S88 7129745 YP_002394074.1 CDS nrfG NC_011742.1 4549767 4550363 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91058381, 94335626, 9593308, 8057835, 8842153; Product type f : factor; formate-dependent nitrite reductase complex subunit NrfG 4549767..4550363 Escherichia coli S88 7129746 YP_002394075.1 CDS gltP NC_011742.1 4550706 4552019 D carrier protein part of the Na(+)-independent, binding-protein-independent glutamate-aspartate transport system; glutamate/aspartate:proton symporter 4550706..4552019 Escherichia coli S88 7129747 YP_002394076.1 CDS yjcO NC_011742.1 4552167 4552856 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4552167..4552856) Escherichia coli S88 7130036 YP_002394077.1 CDS ECS88_4572 NC_011742.1 4552967 4553671 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ABC transporter ATP-binding protein (yddO) complement(4552967..4553671) Escherichia coli S88 7131673 YP_002394078.1 CDS ECS88_4573 NC_011742.1 4553658 4554554 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative dipeptide/oligopeptide/nickel transport system, ATPase component complement(4553658..4554554) Escherichia coli S88 7131057 YP_002394079.1 CDS ECS88_4574 NC_011742.1 4554487 4555320 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative dipeptide/nickel transporter, Inner membrane permease subunit (yddQ) complement(4554487..4555320) Escherichia coli S88 7131058 YP_002394080.1 CDS ECS88_4575 NC_011742.1 4555320 4556462 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative dipeptide/nickel transporter, Inner membrane permease subunit precursor (yddR) complement(4555320..4556462) Escherichia coli S88 7131059 YP_002394081.1 CDS ECS88_4576 NC_011742.1 4556469 4558037 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative ABC-type dipeptide transport system, periplasmic component complement(4556469..4558037) Escherichia coli S88 7131060 YP_002394082.1 CDS fdhF NC_011742.1 4558412 4560559 R Evidence 1c : Function experimentally demonstrated in the studied genus; Product type e : enzyme; formate dehydrogenase-H, selenopolypeptide subunit complement(4558412..4560559) Escherichia coli S88 7131061 YP_002394083.1 CDS yjcP NC_011742.1 4560757 4562223 R part of a multidrug efflux system involved in resistance to acriflavin, puromycin, erytjhromycin and tetraphenylarsonium chloride; member of the outer membrane factor (OMF) family; putative outer membrane efflux protein MdtP complement(4560757..4562223) Escherichia coli S88 7129453 YP_002394084.1 CDS yjcQ NC_011742.1 4562220 4564271 R possibly part of a tripartite efflux system composed of MdtN, MdtO and MdtP which could be involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride; multidrug efflux system protein MdtO complement(4562220..4564271) Escherichia coli S88 7131674 YP_002394085.1 CDS yjcR NC_011742.1 4564271 4565302 R with MdtO and MdtP is involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride; multidrug resistance protein MdtN complement(4564271..4565302) Escherichia coli S88 7131675 YP_002394086.1 CDS ECS88_4582 NC_011742.1 4565321 4565644 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative membrane protein; putative Formate dehydrogenase H complement(4565321..4565644) Escherichia coli S88 7131676 YP_002394087.1 CDS yjcS NC_011742.1 4565804 4567789 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1587481; Product type pe : putative enzyme; putative alkyl sulfatase complement(4565804..4567789) Escherichia coli S88 7131062 YP_002394088.1 CDS alsK NC_011742.1 4568064 4568993 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20026827, 9401019; Product type e : enzyme; D-allose kinase complement(4568064..4568993) Escherichia coli S88 7131677 YP_002394089.1 CDS alsE NC_011742.1 4568977 4569672 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20026827, 9401019; Product type e : enzyme; allulose-6-phosphate 3-epimerase complement(4568977..4569672) Escherichia coli S88 7133055 YP_002394090.1 CDS alsA NC_011742.1 4570642 4572174 R with AlsBC acts to import allose into the cell; AlsA contain 2 ATP-binding domains; D-allose transporter ATP-binding protein complement(4570642..4572174) Escherichia coli S88 7133053 YP_002394091.1 CDS alsB NC_011742.1 4572301 4573236 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20026827, 9401019, 10064713, 8576032; Product type t : transporter; D-allose transporter subunit complement(4572301..4573236) Escherichia coli S88 7133050 YP_002394092.1 CDS rpiR NC_011742.1 4573295 4574185 R involved in rpiB and als operon repression; DNA-binding transcriptional repressor RpiR complement(4573295..4574185) Escherichia coli S88 7133051 YP_002394093.1 CDS rpiB NC_011742.1 4574544 4574993 D catalyzes the interconversion of ribose 5-phosphate to ribulose 5-phosphate; enzyme from E. coli shows allose 6-phosphate isomerase activity; ribose-5-phosphate isomerase B 4574544..4574993 Escherichia coli S88 7132762 YP_002394094.1 CDS yjdP NC_011742.1 4575062 4575391 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4575062..4575391 Escherichia coli S88 7132761 YP_002394095.1 CDS phnP NC_011742.1 4575419 4576177 R required for the use of phosphonates and phosphite as phosphorus sources; carbon-phosphorus lyase complex accessory protein complement(4575419..4576177) Escherichia coli S88 7131686 YP_002394096.1 CDS phnO NC_011742.1 4576179 4576613 R PhnO in Salmonella enterica catalyzes the acetylation of a range of aminoalkylphosphonic acids; part of the biochemical pathway that enables the cell to use phosphonates as a phosphorus source; Escherichia coli uses a different mechanism of phosphonate catabolism where PhnO is not essential and seems to play a regulatory role; aminoalkylphosphonic acid N-acetyltransferase complement(4576179..4576613) Escherichia coli S88 7133721 YP_002394097.1 CDS phnN NC_011742.1 4576600 4577157 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12700258, 91100346, 93273711, 93328121, 9650256, 1840580, 2155230; Product type e : enzyme; ribose 1,5-bisphosphokinase complement(4576600..4577157) Escherichia coli S88 7133720 YP_002394098.1 CDS phnM NC_011742.1 4577157 4578293 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 91100346, 93273711, 93328121, 9650256, 1840580, 2155230; Product type e : enzyme; carbon-phosphorus lyase complex subunit complement(4577157..4578293) Escherichia coli S88 7133719 YP_002394099.1 CDS phnL NC_011742.1 4578290 4578970 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93122525, 93273711, 93328121, 9650256, 1840580, 2155230; Product type e : enzyme; carbon-phosphorus lyase complex subunit complement(4578290..4578970) Escherichia coli S88 7133718 YP_002394100.1 CDS phnK NC_011742.1 4579081 4579839 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93122525, 93273711, 93328121, 9650256, 1840580, 2155230; Product type e : enzyme; phosphonate C-P lyase system protein PhnK complement(4579081..4579839) Escherichia coli S88 7133717 YP_002394101.1 CDS phnJ NC_011742.1 4579836 4580681 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93122525, 93273711, 93328121, 9650256, 1840580, 2155230; Product type e : enzyme; carbon-phosphorus lyase complex subunit complement(4579836..4580681) Escherichia coli S88 7133716 YP_002394102.1 CDS phnI NC_011742.1 4580674 4581738 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93122525, 93273711, 93328121, 9650256, 1840580, 2155230; Product type e : enzyme; carbon-phosphorus lyase complex subunit complement(4580674..4581738) Escherichia coli S88 7133715 YP_002394103.1 CDS phnH NC_011742.1 4581738 4582322 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93122525, 93273711, 93328121, 9650256, 1840580, 2155230; Product type e : enzyme; carbon-phosphorus lyase complex subunit complement(4581738..4582322) Escherichia coli S88 7133714 YP_002394104.1 CDS phnG NC_011742.1 4582319 4582771 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93122525, 93273711, 93328121, 9650256, 1840580, 2155230; Product type e : enzyme; carbon-phosphorus lyase complex subunit complement(4582319..4582771) Escherichia coli S88 7133713 YP_002394105.1 CDS phnF NC_011742.1 4582772 4583497 R may be involved in phosphonate uptake and biodegradation; phosphonate metabolism transcriptional regulator PhnF complement(4582772..4583497) Escherichia coli S88 7133712 YP_002394106.1 CDS phnE NC_011742.1 4583518 4584360 R Evidence 2b : Function of strongly homologous gene; Product type t : transporter; phosphonates transport system, permease protein complement(4583518..4584360) Escherichia coli S88 7133711 YP_002394107.1 CDS phnD NC_011742.1 4584403 4585419 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93122525, 93273711, 93328121, 9650256, 1840580, 2155230; Product type t : transporter; phosphonate/organophosphate ester transporter subunit ; periplasmic binding component of ABC superfamily complement(4584403..4585419) Escherichia coli S88 7133710 YP_002394108.1 CDS phnC NC_011742.1 4585444 4586232 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93122525, 93273711, 93328121, 9650256, 1840580, 2155230; Product type t : transporter; phosphonate/organophosphate ester transporter subunit complement(4585444..4586232) Escherichia coli S88 7133709 YP_002394109.1 CDS phnB NC_011742.1 4586365 4586808 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 93328121, 9650256, 2155230; hypothetical protein complement(4586365..4586808) Escherichia coli S88 7133708 YP_002394110.1 CDS ECS88_4609 NC_011742.1 4586968 4587450 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 9650256, 2155230; Product type pt : putative transporter; putative alkylphosphonate uptake protein in phosphonate metabolism complement(4586968..4587450) Escherichia coli S88 7133707 YP_002394111.1 CDS yjdA NC_011742.1 4587706 4589934 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4587706..4589934 Escherichia coli S88 7131063 YP_002394112.1 CDS yjcZ NC_011742.1 4589931 4590809 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4589931..4590809 Escherichia coli S88 7131679 YP_002394113.1 CDS proP NC_011742.1 4591073 4592575 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10049386, 12525168, 92165733, 93132799, 9871325, 99376621, 8421314; Product type t : transporter; proline/glycine betaine transporter 4591073..4592575 Escherichia coli S88 7131678 YP_002394114.1 CDS basS NC_011742.1 4592752 4593843 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94110256, 8282725; Product type r : regulator; sensor protein BasS/PmrB complement(4592752..4593843) Escherichia coli S88 7130787 YP_002394115.1 CDS basR NC_011742.1 4593853 4594521 R response regulator in two-component regulatory system with BasS; DNA-binding transcriptional regulator BasR complement(4593853..4594521) Escherichia coli S88 7129989 YP_002394116.1 CDS eptA NC_011742.1 4594518 4596161 R with ZipA and an unidentified 24 kDa protein forms a complex involved in cell division; putative cell division protein complement(4594518..4596161) Escherichia coli S88 7129988 YP_002394117.1 CDS adiC NC_011742.1 4596265 4597602 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12867448; Product type t : transporter; arginine:agmatin antiporter complement(4596265..4597602) Escherichia coli S88 7132413 YP_002394118.1 CDS adiY NC_011742.1 4597739 4598500 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : c; Product type r : regulator; DNA-binding transcriptional activator complement(4597739..4598500) Escherichia coli S88 7132056 YP_002394119.1 CDS adiA NC_011742.1 4598836 4601106 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 93186686, 2830169, 4204273, 8383109; Product type e : enzyme; biodegradative arginine decarboxylase complement(4598836..4601106) Escherichia coli S88 7132057 YP_002394120.1 CDS melR NC_011742.1 4601302 4602210 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90060832, 9108148, 1445207, 2684786, 2830169; Product type r : regulator; DNA-binding transcriptional regulator MelR complement(4601302..4602210) Escherichia coli S88 7132055 YP_002394121.1 CDS melA NC_011742.1 4602493 4603848 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 87174747, 88162811, 90248411, 2831880, 3031590, 6329200; Product type e : enzyme; alpha-galactosidase, NAD(P)-binding 4602493..4603848 Escherichia coli S88 7128802 YP_002394122.1 CDS yjdF NC_011742.1 4603845 4604495 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(4603845..4604495) Escherichia coli S88 7128801 YP_002394123.1 CDS fumB NC_011742.1 4604618 4606264 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 86142617, 88193096, 89255123, 2656658; Product type e : enzyme; anaerobic class I fumarate hydratase (fumarase B) complement(4604618..4606264) Escherichia coli S88 7131681 YP_002394124.1 CDS dcuB NC_011742.1 4606342 4607682 R functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to DcuA; DcuA and DcuB function as independent and mutually redundant C4-dicarboxylate (aspartate, malate, fumarate and succinate) transporters; anaerobic C4-dicarboxylate transporter complement(4606342..4607682) Escherichia coli S88 7132154 YP_002394125.1 CDS dcuR NC_011742.1 4608253 4608972 R response regulator in two-component regulatory system with DcuS; phosphorylated DcuR activates transcription of genes involved in anaerobic fumarate respiration; DNA-binding transcriptional activator DcuR complement(4608253..4608972) Escherichia coli S88 7130170 YP_002394126.1 CDS dcuS NC_011742.1 4608969 4610600 R C4-dicarboxylate-sensing histidine kinase; part of two-component regulatory system with DcuR; regulates anaerobic fumarate respiration; sensory histidine kinase DcuS complement(4608969..4610600) Escherichia coli S88 7130172 YP_002394127.1 CDS yjdI NC_011742.1 4610781 4611011 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4610781..4611011 Escherichia coli S88 7130173 YP_002394128.1 CDS yjdJ NC_011742.1 4611023 4611295 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative acyltransferase with acyl-CoA N-acyltransferase domain 4611023..4611295 Escherichia coli S88 7131682 YP_002394129.1 CDS yjdK NC_011742.1 4611523 4611819 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4611523..4611819 Escherichia coli S88 7131683 YP_002394130.1 CDS lysU NC_011742.1 4612139 4613656 R class II; inducible; 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; induced by high temperature, anaerobiosis, and low pH; 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; lysyl-tRNA synthetase complement(4612139..4613656) Escherichia coli S88 7131684 YP_002394131.1 CDS yjdL NC_011742.1 4613893 4615350 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter complement(4613893..4615350) Escherichia coli S88 7129398 YP_002394132.1 CDS cadA NC_011742.1 4615409 4617556 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92105022, 92210511, 1370290, 1556085, 4204273; Product type e : enzyme; lysine decarboxylase 1 complement(4615409..4617556) Escherichia coli S88 7131685 YP_002394133.1 CDS cadB NC_011742.1 4617636 4618970 R antiporter protein responsible for lysine import and cadaverine export; member of the lysine-dependent acid resistance system 4 (AR4); inner membrane protein; lysine/cadaverine antiporter complement(4617636..4618970) Escherichia coli S88 7129148 YP_002394134.1 CDS cadC NC_011742.1 4619336 4620874 R regulates the cadBA operon; DNA-binding transcriptional activator CadC complement(4619336..4620874) Escherichia coli S88 7129149 YP_002394135.1 CDS ECS88_4638 NC_011742.1 4621161 4621379 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 4621161..4621379 Escherichia coli S88 7129150 YP_002394136.1 CDS ECS88_4639 NC_011742.1 4621706 4622269 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4621706..4622269) Escherichia coli S88 7131064 YP_002394137.1 CDS yeeW NC_011742.1 4622354 4622776 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4622354..4622776) Escherichia coli S88 7131146 YP_002394138.1 CDS yeeV NC_011742.1 4622773 4623150 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14594833; Product type h : extrachromosomal origin; toxin of the YeeV-YeeU toxin-antitoxin system; CP4-44 prophage complement(4622773..4623150) Escherichia coli S88 7132973 YP_002394139.1 CDS yeeU NC_011742.1 4623239 4623607 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14594833; Product type h : extrachromosomal origin; antitoxin of the YeeV-YeeU toxin-antitoxin system; CP4-44 prophage complement(4623239..4623607) Escherichia coli S88 7132970 YP_002394140.1 CDS yeeT NC_011742.1 4623687 4623908 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CP4-44 prophage complement(4623687..4623908) Escherichia coli S88 7132966 YP_002394141.1 CDS yeeS NC_011742.1 4623995 4624441 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11053371; Product type pf : putative factor; putative DNA repair protein; CP4-44 prophage complement(4623995..4624441) Escherichia coli S88 7132962 YP_002394142.1 CDS ECS88_4645 NC_011742.1 4624486 4625037 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; Putative antirestriction protein complement(4624486..4625037) Escherichia coli S88 7132958 YP_002394143.1 CDS ECS88_4646 NC_011742.1 4625231 4626049 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4625231..4626049) Escherichia coli S88 7130329 YP_002394144.1 CDS ECS88_4647 NC_011742.1 4626139 4626372 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4626139..4626372) Escherichia coli S88 7132608 YP_002394145.1 CDS ECS88_4648 NC_011742.1 4626378 4627163 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein complement(4626378..4627163) Escherichia coli S88 7132609 YP_002394146.1 CDS ECS88_4649 NC_011742.1 4627206 4627886 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative HTH-type transcriptional regulator yfjR complement(4627206..4627886) Escherichia coli S88 7132610 YP_002394147.1 CDS ECS88_4650 NC_011742.1 4628089 4628973 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putataive GTPase complement(4628089..4628973) Escherichia coli S88 7132611 YP_002394148.1 CDS ECS88_4651 NC_011742.1 4629074 4630297 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4629074..4630297 Escherichia coli S88 7132612 YP_002394149.1 CDS ECS88_4652 NC_011742.1 4631750 4632481 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4631750..4632481 Escherichia coli S88 7132613 YP_002394150.1 CDS ECS88_4653 NC_011742.1 4632639 4633403 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4632639..4633403 Escherichia coli S88 7132614 YP_002394151.1 CDS ECS88_4654 NC_011742.1 4633472 4633705 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4633472..4633705 Escherichia coli S88 7132615 YP_002394152.1 CDS ECS88_4655 NC_011742.1 4633741 4633932 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4633741..4633932) Escherichia coli S88 7132616 YP_002394153.1 CDS ECS88_4657 NC_011742.1 4634454 4635518 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4634454..4635518 Escherichia coli S88 7131643 YP_002394154.1 CDS ECS88_4658 NC_011742.1 4635618 4635989 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4635618..4635989 Escherichia coli S88 7132618 YP_002394155.1 CDS ECS88_4659 NC_011742.1 4636261 4636470 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4636261..4636470 Escherichia coli S88 7132619 YP_002394156.1 CDS ECS88_4661 NC_011742.1 4636963 4637604 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein with microcompartments protein domain complement(4636963..4637604) Escherichia coli S88 7132621 YP_002394157.1 CDS metK NC_011742.1 4637553 4638704 R catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase complement(4637553..4638704) Escherichia coli S88 7132622 YP_002394158.1 CDS ECS88_4664 NC_011742.1 4638833 4639888 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4638833..4639888) Escherichia coli S88 7128820 YP_002394159.1 CDS ECS88_4665 NC_011742.1 4639905 4641167 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein with histidine kinase domain complement(4639905..4641167) Escherichia coli S88 7132623 YP_002394160.1 CDS ECS88_4667 NC_011742.1 4641717 4642238 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative maturase-related protein complement(4641717..4642238) Escherichia coli S88 7129865 YP_002394161.1 CDS ECS88_4669 NC_011742.1 4642266 4642805 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative maturase-related protein complement(4642266..4642805) Escherichia coli S88 7132625 YP_002394162.1 CDS ECS88_4670 NC_011742.1 4643291 4644196 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative membrane protein; putative permease complement(4643291..4644196) Escherichia coli S88 7132626 YP_002394163.1 CDS ECS88_4671 NC_011742.1 4644333 4645250 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 3053170; Product type pe : putative enzyme; putative pyruvate formate-lyase 3-activating enzyme complement(4644333..4645250) Escherichia coli S88 7132627 YP_002394164.1 CDS ECS88_4672 NC_011742.1 4645359 4647911 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative Formate C-acetyltransferase complement(4645359..4647911) Escherichia coli S88 7132628 YP_002394165.1 CDS ECS88_4673 NC_011742.1 4647960 4648670 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 8626329; conserved hypothetical protein with intracelllular protease 1 domain complement(4647960..4648670) Escherichia coli S88 7132629 YP_002394166.1 CDS ECS88_4674 NC_011742.1 4648546 4648845 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4648546..4648845) Escherichia coli S88 7132630 YP_002394167.1 CDS ECS88_4675 NC_011742.1 4648869 4650386 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 7868611, 10464203; Product type pe : putative enzyme; putative acetaldehyde/propionaldehyde dehydrogenase (eutE-like) complement(4648869..4650386) Escherichia coli S88 7132631 YP_002394168.1 CDS ECS88_4676 NC_011742.1 4650447 4651232 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative propanediol utilization protein, polyhedral bodies (pduB-like) complement(4650447..4651232) Escherichia coli S88 7132632 YP_002394169.1 CDS ECS88_4677 NC_011742.1 4651254 4651586 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10498708; Product type ps : putative structure; putative propanediol utilization protein, polyhedral bodies (pduA-like) complement(4651254..4651586) Escherichia coli S88 7132633 YP_002394170.1 CDS ECS88_4678 NC_011742.1 4651820 4653127 R catalyzes the formation of propanoyl phosphate from propanoate and ATP; TdcD also has acetate kinase activities and functions in anaerobic threonine catabolism; propionate/acetate kinase complement(4651820..4653127) Escherichia coli S88 7132634 YP_002394171.1 CDS ECS88_4680 NC_011742.1 4653045 4653542 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4653045..4653542) Escherichia coli S88 7132635 YP_002394172.1 CDS ECS88_4681 NC_011742.1 4653570 4653839 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type ps : putative structure; putative Ethanolamine utilization protein (eutN-like) complement(4653570..4653839) Escherichia coli S88 7132636 YP_002394173.1 CDS ECS88_4682 NC_011742.1 4653851 4654576 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4653851..4654576) Escherichia coli S88 7132637 YP_002394174.1 CDS ECS88_4683 NC_011742.1 4654560 4655318 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative ethanolamine utilization protein (eutJ-like) complement(4654560..4655318) Escherichia coli S88 7132638 YP_002394175.1 CDS ECS88_4684 NC_011742.1 4655373 4656059 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 10498708; hypothetical protein complement(4655373..4656059) Escherichia coli S88 7132639 YP_002394176.1 CDS ECS88_4685 NC_011742.1 4656199 4657317 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative propanol dehydrogenase complement(4656199..4657317) Escherichia coli S88 7132640 YP_002394177.1 CDS ECS88_4686 NC_011742.1 4657766 4658167 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4657766..4658167 Escherichia coli S88 7132641 YP_002394178.1 CDS ECS88_4687 NC_011742.1 4658188 4658496 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4658188..4658496 Escherichia coli S88 7132642 YP_002394179.1 CDS ECS88_4688 NC_011742.1 4658549 4658740 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4658549..4658740) Escherichia coli S88 7132643 YP_002394180.1 CDS ECS88_4689 NC_011742.1 4659188 4659316 D Evidence 6 : Doubtful CDS; hypothetical protein 4659188..4659316 Escherichia coli S88 7132644 YP_002394181.1 CDS ECS88_4690 NC_011742.1 4659333 4659770 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein 4659333..4659770 Escherichia coli S88 7132645 YP_002394182.1 CDS ECS88_4691 NC_011742.1 4659842 4660240 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4659842..4660240 Escherichia coli S88 7132646 YP_002394183.1 CDS ECS88_4692 NC_011742.1 4660254 4660355 D Evidence 6 : Doubtful CDS; hypothetical protein 4660254..4660355 Escherichia coli S88 7132647 YP_002394184.1 CDS ECS88_4693 NC_011742.1 4660479 4662077 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 4660479..4662077 Escherichia coli S88 7132648 YP_002394185.1 CDS ECS88_4694 NC_011742.1 4662209 4663993 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4662209..4663993 Escherichia coli S88 7132649 YP_002394186.1 CDS ECS88_4695 NC_011742.1 4663993 4664745 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4663993..4664745 Escherichia coli S88 7132650 YP_002394187.1 CDS ECS88_4696 NC_011742.1 4664727 4666046 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4664727..4666046 Escherichia coli S88 7132651 YP_002394188.1 CDS ECS88_4697 NC_011742.1 4666043 4666768 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative DNAse 4666043..4666768 Escherichia coli S88 7132652 YP_002394189.1 CDS ECS88_4698 NC_011742.1 4666990 4667187 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 4666990..4667187 Escherichia coli S88 7132653 YP_002394190.1 CDS ECS88_4699 NC_011742.1 4667321 4667896 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4667321..4667896) Escherichia coli S88 7132654 YP_002394191.1 CDS ECS88_4700 NC_011742.1 4667904 4669232 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4667904..4669232) Escherichia coli S88 7132655 YP_002394192.1 CDS ECS88_4702 NC_011742.1 4669573 4670385 R Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; Transposase insF for insertion sequence IS3A/B/C/D/E/fA complement(4669573..4670385) Escherichia coli S88 7132657 YP_002394193.1 CDS ECS88_4703 NC_011742.1 4670442 4670765 R Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase ORF A, IS3 family complement(4670442..4670765) Escherichia coli S88 7132658 YP_002394194.1 CDS ECS88_4704 NC_011742.1 4670799 4671176 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative Zn-dependent alcohol dehydrogenases complement(4670799..4671176) Escherichia coli S88 7132659 YP_002394195.1 CDS ECS88_4705 NC_011742.1 4671539 4671763 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(4671539..4671763) Escherichia coli S88 7132660 YP_002394196.1 CDS ECS88_4706 NC_011742.1 4671799 4672158 R Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase InsB (ORF2) IS1 complement(4671799..4672158) Escherichia coli S88 7132661 YP_002394197.1 CDS ECS88_4707 NC_011742.1 4672185 4672457 R Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase InsA (ORF1) IS1 complement(4672185..4672457) Escherichia coli S88 7132662 YP_002394198.1 CDS ECS88_4708 NC_011742.1 4672710 4674179 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative membrane protein of unknown function 4672710..4674179 Escherichia coli S88 7132663 YP_002394199.1 CDS ECS88_4709 NC_011742.1 4674284 4676653 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative Orn/Lys/Arg decarboxylase 4674284..4676653 Escherichia coli S88 7132664 YP_002394200.1 CDS ECS88_4710 NC_011742.1 4676728 4678227 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative membrane protein; putative Amino acid transporters 4676728..4678227 Escherichia coli S88 7132665 YP_002394201.1 CDS insA NC_011742.1 4678370 4678645 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9689094; Product type h : extrachromosomal origin; IS1 repressor protein InsA 4678370..4678645 Escherichia coli S88 7132666 YP_002394202.1 CDS insB NC_011742.1 4678564 4679067 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9689094; Product type h : extrachromosomal origin; IS1 transposase InsAB' 4678564..4679067 Escherichia coli S88 7131636 YP_002394203.1 CDS ECS88_4713 NC_011742.1 4679534 4680085 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; Putative HTH-type transcriptional regulator complement(4679534..4680085) Escherichia coli S88 7131639 YP_002394204.1 CDS insB NC_011742.1 4681060 4681563 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9689094; Product type h : extrachromosomal origin; IS1 transposase InsAB' complement(4681060..4681563) Escherichia coli S88 7132669 YP_002394205.1 CDS insA NC_011742.1 4681482 4681757 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9689094; Product type h : extrachromosomal origin; IS1 repressor protein InsA complement(4681482..4681757) Escherichia coli S88 7131640 YP_002394206.1 CDS ECS88_4719 NC_011742.1 4682287 4683360 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 10411725; Product type pe : putative enzyme; SHI-2 pathogenicity island protein complement(4682287..4683360) Escherichia coli S88 7131637 YP_002394207.1 CDS ECS88_4720 NC_011742.1 4683586 4684851 R Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; integrase complement(4683586..4684851) Escherichia coli S88 7132670 YP_002394208.1 CDS yjdC NC_011742.1 4685231 4685806 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 1370290; Product type pr : putative regulator; putative transcriptional regulator complement(4685231..4685806) Escherichia coli S88 7129920 YP_002394209.1 CDS dipZ NC_011742.1 4685843 4687540 R two electrons are transferred from cytoplasmic NADPH to thioredoxin and then to the inner membrane protein DsbD which keeps the disulfide isomerase DsbC in a reduced state in the oxidizing periplasm; DsbC in turns rearranges incorrectly made disulfide bonds in the periplasm; thiol:disulfide interchange protein precursor complement(4685843..4687540) Escherichia coli S88 7131680 YP_002394210.1 CDS cutA NC_011742.1 4687516 4687854 R copper binding protein required for copper tolerance; involved in resistance toward heavy metals; divalent-cation tolerance protein CutA complement(4687516..4687854) Escherichia coli S88 7130210 YP_002394211.1 CDS dcuA NC_011742.1 4687970 4689271 R functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to dcuB; anaerobic C4-dicarboxylate transporter complement(4687970..4689271) Escherichia coli S88 7130515 YP_002394212.1 CDS aspA NC_011742.1 4689389 4690825 R catalyzes the formation of fumarate from aspartate; aspartate ammonia-lyase complement(4689389..4690825) Escherichia coli S88 7130169 YP_002394213.1 CDS fxsA NC_011742.1 4691162 4691638 D F exclusion of bacteriophage T7; overproduction of this protein in Escherichia coli inhibits the F plasmid-mediated exclusion of bacteriophage T7; interacts with the F plasmid-encoded PifA protein; inner membrane protein; FxsA 4691162..4691638 Escherichia coli S88 7129950 YP_002394214.1 CDS yjeH NC_011742.1 4691654 4692910 R uncharacterized member of the APC superfamily of amino acid transporters; unknown function; inner membrane protein YjeH complement(4691654..4692910) Escherichia coli S88 7132158 YP_002394215.1 CDS groES NC_011742.1 4693186 4693479 D 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; co-chaperonin GroES 4693186..4693479 Escherichia coli S88 7131689 YP_002394216.1 CDS groEL NC_011742.1 4693523 4695169 D 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; chaperonin GroEL 4693523..4695169 Escherichia coli S88 7130071 YP_002394217.1 CDS yjeI NC_011742.1 4695307 4695660 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4695307..4695660 Escherichia coli S88 7130070 YP_002394218.1 CDS yjeJ NC_011742.1 4695710 4696579 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4695710..4696579) Escherichia coli S88 7131690 YP_002394219.1 CDS yjeK NC_011742.1 4696814 4697842 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2019591, 10629195; Product type pe : putative enzyme; putative lysine aminomutase complement(4696814..4697842) Escherichia coli S88 7131691 YP_002394220.1 CDS efp NC_011742.1 4697884 4698450 D Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 4697884..4698450 Escherichia coli S88 7131692 YP_002394221.1 CDS ecnA NC_011742.1 4698502 4698627 D acts as and antidote to the bacteriolytic entericidin B in the EcnAB toxin-antitoxin complex; entericidin A 4698502..4698627 Escherichia coli S88 7132386 YP_002394222.1 CDS ecnB NC_011742.1 4698738 4698884 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 98344100, 9677290; Product type lp : lipoprotein; entericidin B membrane lipoprotein 4698738..4698884 Escherichia coli S88 7132376 YP_002394223.1 CDS sugE NC_011742.1 4699060 4699377 D member of the SMR family of proton-dependent drug efflux transporters; quaternary ammonium compound efflux pump; confers resistance to cetylpyridinium, cetyldimethylethyl ammonium and cetrimide cations; quaternary ammonium compound-resistance protein SugE 4699060..4699377 Escherichia coli S88 7132377 YP_002394224.1 CDS blc NC_011742.1 4699374 4699907 R lipocalin; globomycin-sensitive outer membrane lipoprotein; outer membrane lipoprotein Blc complement(4699374..4699907) Escherichia coli S88 7131248 YP_002394225.1 CDS ampC NC_011742.1 4699996 4701129 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 92212899, 97464439, 99421326, 10595535, 6795623, 7041115, 9819201; Product type e : enzyme; beta-lactamase complement(4699996..4701129) Escherichia coli S88 7129129 YP_002394226.1 CDS frdD NC_011742.1 4701192 4701551 R in conjunction with FrdC acts to anchor the catalytic components of the fumarate reductase to the cytoplasmic membrane; fumarate reductase subunit D complement(4701192..4701551) Escherichia coli S88 7133061 YP_002394227.1 CDS frdC NC_011742.1 4701562 4701957 R part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; the catalytic subunits are similar to succinate dehydrogenase SdhAB; fumarate reductase subunit C complement(4701562..4701957) Escherichia coli S88 7132827 YP_002394228.1 CDS frdB NC_011742.1 4701968 4702702 R part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; the catalytic subunits are similar to succinate dehydrogenase SdhAB; fumarate reductase iron-sulfur subunit complement(4701968..4702702) Escherichia coli S88 7132826 YP_002394229.1 CDS frdA NC_011742.1 4702695 4704503 R part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; the catalytic subunits are similar to succinate dehydrogenase SdhAB; fumarate reductase flavoprotein subunit complement(4702695..4704503) Escherichia coli S88 7132825 YP_002394230.1 CDS poxA NC_011742.1 4704828 4705805 D lysine--tRNA ligase beta chain; poxA; class II aminoacyl tRNA synthetase; catalyzes a two-step reaction; first charging a lysine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; lysyl-tRNA synthetase 4704828..4705805 Escherichia coli S88 7132824 YP_002394231.1 CDS yjeM NC_011742.1 4706024 4707526 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter 4706024..4707526 Escherichia coli S88 7130750 YP_002394232.1 CDS yjeN NC_011742.1 4707589 4707903 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4707589..4707903 Escherichia coli S88 7131693 YP_002394233.1 CDS yjeO NC_011742.1 4707900 4708214 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 4707900..4708214 Escherichia coli S88 7131694 YP_002394234.1 CDS yjeP NC_011742.1 4708245 4711568 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; hypothetical protein complement(4708245..4711568) Escherichia coli S88 7131695 YP_002394235.1 CDS psd NC_011742.1 4711590 4712558 R catalyzes the decarboxylation of phosphatidyl-L-serine to phosphatidylethanoleamine; phosphatidylserine decarboxylase complement(4711590..4712558) Escherichia coli S88 7131696 YP_002394236.1 CDS rsgA NC_011742.1 4712655 4713707 R EngC; RsgA; CpgA; circularly permuted GTPase; ribosome small subunit-dependent GTPase A; has the pattern G4-G1-G3 as opposed to other GTPases; interacts strongly with 30S ribosome which stimulates GTPase activity; ribosome-associated GTPase complement(4712655..4713707) Escherichia coli S88 7130801 YP_002394237.1 CDS orn NC_011742.1 4713802 4714347 D 3'-5' exoribonuclease specific for small oligoribonuclotides; oligoribonuclease 4713802..4714347 Escherichia coli S88 7133813 YP_002394238.1 CDS yjeS NC_011742.1 4715126 4716265 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pc : putative carrier; putative Fe-S electron transport protein complement(4715126..4716265) Escherichia coli S88 7129915 YP_002394239.1 CDS yjeF NC_011742.1 4716264 4717811 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein 4716264..4717811 Escherichia coli S88 7131697 YP_002394240.1 CDS yjeE NC_011742.1 4717783 4718244 D possibly involved in cell wall synthesis; putative ATPase 4717783..4718244 Escherichia coli S88 7131688 YP_002394241.1 CDS amiB NC_011742.1 4718263 4719600 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21348478, 87242501, 1594459, 7511774; Product type e : enzyme; N-acetylmuramoyl-l-alanine amidase II 4718263..4719600 Escherichia coli S88 7131687 YP_002394242.1 CDS mutL NC_011742.1 4719610 4721457 D This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. Promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex; DNA mismatch repair protein 4719610..4721457 Escherichia coli S88 7133058 YP_002394243.1 CDS miaA NC_011742.1 4721450 4722400 D 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; tRNA delta(2)-isopentenylpyrophosphate transferase 4721450..4722400 Escherichia coli S88 7129640 YP_002394244.1 CDS hfq NC_011742.1 4722486 4722794 D Stimulates the elongation of poly(A) tails; RNA-binding protein Hfq 4722486..4722794 Escherichia coli S88 7128831 YP_002394245.1 CDS hflX NC_011742.1 4722870 4724150 D involved in modulation of proteins HflK and HflC; part of the hflA locus (high frequency of lysogenization) which governs the lysis-lysogeny decision of bacteriophage lambda by controlling stability of the phage cII protein; putative GTPase HflX 4722870..4724150 Escherichia coli S88 7128913 YP_002394246.1 CDS hflK NC_011742.1 4724236 4725495 D with HflC inhibits proteolysis of lambda cII protein by FtsH; FtsH protease regulator HflK 4724236..4725495 Escherichia coli S88 7128912 YP_002394247.1 CDS hflC NC_011742.1 4725498 4726502 D with HflK inhibits proteolysis of lambda cII protein by FtsH; FtsH protease regulator HflC 4725498..4726502 Escherichia coli S88 7128911 YP_002394248.1 CDS yjeT NC_011742.1 4726584 4726781 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 4726584..4726781 Escherichia coli S88 7128909 YP_002394249.1 CDS purA NC_011742.1 4726885 4728183 D catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase 4726885..4728183 Escherichia coli S88 7131698 YP_002394250.1 CDS nsrR NC_011742.1 4728388 4728813 D negatively regulates the transcription of genes upregulated by nitrosative stress; transcriptional repressor NsrR 4728388..4728813 Escherichia coli S88 7131744 YP_002394251.1 CDS rnr NC_011742.1 4728852 4731293 D 3'-5'exoribonuclease that acts nonspecifically on poly(A), poly(U) and ribosomal RNAs; exoribonuclease R 4728852..4731293 Escherichia coli S88 7129748 YP_002394252.1 CDS rlmB NC_011742.1 4731385 4732116 D Specifically methylates the ribose of guanosine 2251 in 23S rRNA; 23S rRNA (guanosine-2'-O-)-methyltransferase 4731385..4732116 Escherichia coli S88 7132753 YP_002394253.1 CDS yjfI NC_011742.1 4732243 4732644 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4732243..4732644 Escherichia coli S88 7132728 YP_002394254.1 CDS yjfJ NC_011742.1 4732663 4733361 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator effector protein 4732663..4733361 Escherichia coli S88 7131701 YP_002394255.1 CDS yjfK NC_011742.1 4733411 4734070 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4733411..4734070 Escherichia coli S88 7131702 YP_002394256.1 CDS yjfL NC_011742.1 4734088 4734486 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 4734088..4734486 Escherichia coli S88 7131703 YP_002394257.1 CDS yjfM NC_011742.1 4734496 4735134 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4734496..4735134 Escherichia coli S88 7131704 YP_002394258.1 CDS yjfC NC_011742.1 4735137 4736300 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative synthetase/amidase 4735137..4736300 Escherichia coli S88 7131705 YP_002394259.1 CDS aidB NC_011742.1 4736384 4738009 D catalyzes the formation of 3-methylcrotonyl-CoA from isovaleryl-CoA; isovaleryl CoA dehydrogenase 4736384..4738009 Escherichia coli S88 7131699 YP_002394260.1 CDS yjfN NC_011742.1 4738126 4738401 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4738126..4738401) Escherichia coli S88 7133037 YP_002394261.1 CDS yjfO NC_011742.1 4738550 4738879 R in Escherichia coli, mutation of this gene affects biofilm maturation, stress response, and motility; putative biofilm stress and motility protein A complement(4738550..4738879) Escherichia coli S88 7131706 YP_002394262.1 CDS yjfP NC_011742.1 4739061 4739810 D YjfP; esterase activity towards palmitoyl-CoA and pNP-butyrate in vitro; unknown function and substrate in vivo; esterase 4739061..4739810 Escherichia coli S88 7131707 YP_002394263.1 CDS ulaR NC_011742.1 4739807 4740562 R negative regulator of ulaG and ulaABCDEF; transcriptional repressor UlaR complement(4739807..4740562) Escherichia coli S88 7131708 YP_002394264.1 CDS ulaG NC_011742.1 4740670 4741734 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12644495, 15808744; Product type pe : putative enzyme; putative L-ascorbate 6-phosphate lactonase complement(4740670..4741734) Escherichia coli S88 7132061 YP_002394265.1 CDS ulaA NC_011742.1 4742089 4743486 D membrane component; functions with enzymes IIB (sgaB; ulaB) and IIA (sgaA; ulaC) enzyme I and HPr for anaerobic utilization and uptake of L-ascorbate; sgaTBA are regulated by yifQ as well as Crp and Fnr; PTS system ascorbate-specific transporter subunit IIC 4742089..4743486 Escherichia coli S88 7130412 YP_002394266.1 CDS ulaB NC_011742.1 4743502 4743807 D involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake; PTS system L-ascorbate-specific transporter subunit IIB 4743502..4743807 Escherichia coli S88 7130406 YP_002394267.1 CDS ulaC NC_011742.1 4743817 4744281 D involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake; PTS system L-ascorbate-specific transporter subunit IIA 4743817..4744281 Escherichia coli S88 7130407 YP_002394268.1 CDS ulaD NC_011742.1 4744295 4744945 D catalyzes the formation of L-xylulose-5-phosphate from 3-keto-L-gulonate-6-phosphate in anaerobic L-ascorbate utilization; 3-keto-L-gulonate-6-phosphate decarboxylase 4744295..4744945 Escherichia coli S88 7130408 YP_002394269.1 CDS ulaE NC_011742.1 4744955 4745809 D UlaE; catalyzes the epimerization of L-ribulose-5-phosphate into L-xylulose-5-phosphate; part of the anaerobic L-ascorbate degradation pathway; L-xylulose 5-phosphate 3-epimerase 4744955..4745809 Escherichia coli S88 7130409 YP_002394270.1 CDS sgaE NC_011742.1 4745809 4746495 D catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate in the anaerobic catabolism of L-ascorbate; links the arabinose metabolic pathway to the pentose phosphate pathway and allows the bacteria to use arabinose as an energy source; L-ribulose-5-phosphate 4-epimerase 4745809..4746495 Escherichia coli S88 7130410 YP_002394271.1 CDS yjfY NC_011742.1 4746624 4746899 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4746624..4746899) Escherichia coli S88 7130411 YP_002394272.1 CDS rpsF NC_011742.1 4747227 4747622 D binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 4747227..4747622 Escherichia coli S88 7131709 YP_002394273.1 CDS priB NC_011742.1 4747629 4747943 D binds single-stranded DNA at the primosome assembly site; primosomal replication protein N 4747629..4747943 Escherichia coli S88 7133789 YP_002394274.1 CDS rpsR NC_011742.1 4747948 4748175 D binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit; 30S ribosomal protein S18 4747948..4748175 Escherichia coli S88 7130777 YP_002394275.1 CDS rplI NC_011742.1 4748217 4748666 D in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 4748217..4748666 Escherichia coli S88 7133801 YP_002394276.1 CDS ECS88_4790 NC_011742.1 4749068 4749559 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4749068..4749559 Escherichia coli S88 7132769 YP_002394277.1 CDS ECS88_4791 NC_011742.1 4749562 4750830 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4749562..4750830 Escherichia coli S88 7132672 YP_002394278.1 CDS ECS88_4792 NC_011742.1 4750973 4752250 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative Hexuronate transporter complement(4750973..4752250) Escherichia coli S88 7132673 YP_002394279.1 CDS ECS88_4795 NC_011742.1 4754412 4755953 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative CoA transferase complement(4754412..4755953) Escherichia coli S88 7132676 YP_002394280.1 CDS ECS88_4796 NC_011742.1 4755963 4756745 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative acyl-CoA hydratase complement(4755963..4756745) Escherichia coli S88 7132677 YP_002394281.1 CDS ECS88_4797 NC_011742.1 4756749 4757591 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative enzyme complement(4756749..4757591) Escherichia coli S88 7132678 YP_002394282.1 CDS ECS88_4798 NC_011742.1 4757601 4758434 R catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-(acyl-carrier-protein) reductase complement(4757601..4758434) Escherichia coli S88 7132679 YP_002394283.1 CDS ytfA NC_011742.1 4758581 4759252 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator 4758581..4759252 Escherichia coli S88 7132680 YP_002394284.1 CDS ytfB NC_011742.1 4759236 4759874 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8559074; Product type ps : putative structure; putative cell envelope opacity-associated protein complement(4759236..4759874) Escherichia coli S88 7131865 YP_002394285.1 CDS fklB NC_011742.1 4760093 4760713 D FKBP-type; rotamase; catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides; peptidyl-prolyl cis-trans isomerase 4760093..4760713 Escherichia coli S88 7131866 YP_002394286.1 CDS cycA NC_011742.1 4761022 4762434 D involved in the transport across the cytoplasmic membrane of D-alanine, D-serine and glycine; D-alanine/D-serine/glycine permease 4761022..4762434 Escherichia coli S88 7129508 YP_002394287.1 CDS ytfE NC_011742.1 4762479 4763141 R Involved in anaerobic NO protection and iron metabolism; iron-sulfur cluster repair di-iron protein complement(4762479..4763141) Escherichia coli S88 7130523 YP_002394288.1 CDS ytfF NC_011742.1 4763249 4764223 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4763249..4764223) Escherichia coli S88 7131867 YP_002394289.1 CDS ytfG NC_011742.1 4764323 4765183 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14747727; Product type e : enzyme; NAD(P)H:quinone oxidoreductase complement(4764323..4765183) Escherichia coli S88 7131868 YP_002394290.1 CDS ytfH NC_011742.1 4765272 4765652 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 20088838; Product type pr : putative regulator; putative transcriptional regulator 4765272..4765652 Escherichia coli S88 7131869 YP_002394291.1 CDS cpdB NC_011742.1 4765775 4767718 R periplasmic enzyme; functions during ribonucleic acid degradation; 2',3'-cyclic nucleotides are first converted to 3'-nucleotide and then cleaved to yield a ribonucleotide and a phosphate; bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein complement(4765775..4767718) Escherichia coli S88 7131870 YP_002394292.1 CDS cysQ NC_011742.1 4767908 4768648 D catalyzes the formation of AMP from adenosine-3',5'-bisphosphate; adenosine-3'(2'),5'-bisphosphate nucleotidase 4767908..4768648 Escherichia coli S88 7131952 YP_002394293.1 CDS ytfJ NC_011742.1 4768638 4769195 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 9298646; Product type pr : putative regulator; putative transcriptional regulator complement(4768638..4769195) Escherichia coli S88 7130546 YP_002394294.1 CDS ytfK NC_011742.1 4769520 4769726 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4769520..4769726 Escherichia coli S88 7131871 YP_002394295.1 CDS ytfL NC_011742.1 4769788 4771131 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4769788..4771131) Escherichia coli S88 7131872 YP_002394296.1 CDS msrA NC_011742.1 4771454 4772092 R this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress; methionine sulfoxide reductase A complement(4771454..4772092) Escherichia coli S88 7131873 YP_002394297.1 CDS ytfM NC_011742.1 4772298 4774031 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative outer membrane protein and surface antigen 4772298..4774031 Escherichia coli S88 7129616 YP_002394298.1 CDS ytfN NC_011742.1 4774028 4777807 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4774028..4777807 Escherichia coli S88 7131874 YP_002394299.1 CDS ytfP NC_011742.1 4777810 4778151 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4777810..4778151 Escherichia coli S88 7131875 YP_002394300.1 CDS ppa NC_011742.1 4778531 4779061 R catalyzes the hydrolysis of pyrophosphate to phosphate; inorganic pyrophosphatase complement(4778531..4779061) Escherichia coli S88 7131876 YP_002394301.1 CDS ytfQ NC_011742.1 4779371 4780327 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 9298646; Product type pt : putative transporter; putative sugar transporter subunit: periplasmic-binding component of ABC superfamily 4779371..4780327 Escherichia coli S88 7130752 YP_002394302.1 CDS ytfR NC_011742.1 4780467 4781969 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sugar transporter subunit: ATP-binding component of ABC superfamily 4780467..4781969 Escherichia coli S88 7131877 YP_002394303.1 CDS ytfT NC_011742.1 4781983 4783005 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative sugar transporter subunit: membrane component of ABC superfamily 4781983..4783005 Escherichia coli S88 7131878 YP_002394304.1 CDS yjfF NC_011742.1 4782992 4783987 D membrane component of a putative sugar ABC transporter system; inner membrane ABC transporter permease protein YjfF 4782992..4783987 Escherichia coli S88 7131879 YP_002394305.1 CDS fbp NC_011742.1 4784020 4785018 R catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate; fructose-1,6-bisphosphatase complement(4784020..4785018) Escherichia coli S88 7131700 YP_002394306.1 CDS mpl NC_011742.1 4785194 4786567 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96404780, 2843822, 7984428, 8808921; Product type e : enzyme; UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase 4785194..4786567 Escherichia coli S88 7129449 YP_002394307.1 CDS yjgA NC_011742.1 4786723 4787274 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4786723..4787274) Escherichia coli S88 7129598 YP_002394308.1 CDS pmbA NC_011742.1 4787368 4788720 D protease involved in proteolytic processing of the antibiotic Microcin B17 and in sensitivity to the DNA gyrase inhibitor LetD; peptidase PmbA 4787368..4788720 Escherichia coli S88 7131710 YP_002394309.1 CDS cybC NC_011742.1 4788903 4789289 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1761034, 8499452, 10393541; Product type c : carrier; soluble cytochrome b562 4788903..4789289 Escherichia coli S88 7133744 YP_002394310.1 CDS nrdG NC_011742.1 4789334 4789798 R activates anaerobic ribonucleoside-triphosphate reductase under anaerobic conditions; anaerobic ribonucleotide reductase-activating protein complement(4789334..4789798) Escherichia coli S88 7130522 YP_002394311.1 CDS nrdD NC_011742.1 4789956 4792094 R Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates; anaerobic ribonucleoside triphosphate reductase complement(4789956..4792094) Escherichia coli S88 7129737 YP_002394312.1 CDS treC NC_011742.1 4792488 4794143 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90264345, 93302496, 8083158, 8421692; Product type e : enzyme; trehalose-6-phosphate hydrolase complement(4792488..4794143) Escherichia coli S88 7129734 YP_002394313.1 CDS treB NC_011742.1 4794193 4795614 R phosphoenolpyruvate-dependent sugar phosphotransferase system; catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane; IIB is phosphorylated by IIA and then transfers the phosphoryl group to the sugar; IIC forms the translocation channel; PTS system trehalose(maltose)-specific transporter subunits IIBC complement(4794193..4795614) Escherichia coli S88 7133508 YP_002394314.1 CDS treR NC_011742.1 4795733 4796680 R regulates genes involved in trehalose metabolism; binds the intermediate trehalose-6-phosphate; binds a dimer; regulates treBC operon; trehalose repressor complement(4795733..4796680) Escherichia coli S88 7133507 YP_002394315.1 CDS mgtA NC_011742.1 4797059 4799755 D P-type ATPase involved in magnesium influx; magnesium-transporting ATPase MgtA 4797059..4799755 Escherichia coli S88 7130332 YP_002394316.1 CDS yjgF NC_011742.1 4799961 4800347 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12515541, 10493123, 10595546, 9298646; Product type pe : putative enzyme; ketoacid-binding protein complement(4799961..4800347) Escherichia coli S88 7128830 YP_002394317.1 CDS pyrI NC_011742.1 4800420 4800881 R involved in the allosteric regulation of aspartate carbamoyltransferase; aspartate carbamoyltransferase regulatory subunit complement(4800420..4800881) Escherichia coli S88 7131713 YP_002394318.1 CDS pyrB NC_011742.1 4800894 4801829 R catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase catalytic subunit complement(4800894..4801829) Escherichia coli S88 7131770 YP_002394319.1 CDS pyrL NC_011742.1 4801833 4801967 R Evidence 1c : Function experimentally demonstrated in the studied genus; Product type l : leader peptide; pyrBI operon leader peptide complement(4801833..4801967) Escherichia coli S88 7131763 YP_002394320.1 CDS yjgH NC_011742.1 4802248 4802643 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative mRNA endoribonuclease complement(4802248..4802643) Escherichia coli S88 7131771 YP_002394321.1 CDS yjgI NC_011742.1 4802774 4803487 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; oxidoreductase complement(4802774..4803487) Escherichia coli S88 7131714 YP_002394322.1 CDS yjgJ NC_011742.1 4803558 4804151 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator 4803558..4804151 Escherichia coli S88 7131715 YP_002394323.1 CDS yjgK NC_011742.1 4804296 4804748 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 11115104; hypothetical protein 4804296..4804748 Escherichia coli S88 7131716 YP_002394324.1 CDS ECS88_4840 NC_011742.1 4804871 4806454 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; length varies in various strains; absent from some 4804871..4806454 Escherichia coli S88 7131717 YP_002394325.1 CDS argI NC_011742.1 4806627 4807631 R catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; E. coli K12 has two genes, argF and argI, capable of producing functional ornithine carbamoyltransferase. When both are active in the same cell, the two gene products form a family of four hybrid trimeric isoenzymes designated, FFF, FFI, FII, and III.; ornithine carbamoyltransferase subunit I complement(4806627..4807631) Escherichia coli S88 7132681 YP_002394326.1 CDS yjgD NC_011742.1 4807793 4808209 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4807793..4808209 Escherichia coli S88 7133098 YP_002394327.1 CDS yjgM NC_011742.1 4808255 4808758 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative acetyltransferase complement(4808255..4808758) Escherichia coli S88 7131712 YP_002394328.1 CDS yjgN NC_011742.1 4808951 4810147 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 4808951..4810147 Escherichia coli S88 7131718 YP_002394329.1 CDS valS NC_011742.1 4810201 4813056 R 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; valyl-tRNA synthetase complement(4810201..4813056) Escherichia coli S88 7131719 YP_002394330.1 CDS holC NC_011742.1 4813056 4813499 R binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB; DNA polymerase III subunit chi complement(4813056..4813499) Escherichia coli S88 7132471 YP_002394331.1 CDS pepA NC_011742.1 4813853 4815364 R catalyzes the removal of N-terminal amino acids preferably leucine from various peptides; leucyl aminopeptidase complement(4813853..4815364) Escherichia coli S88 7128943 YP_002394332.1 CDS yjgP NC_011742.1 4815631 4816731 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 4815631..4816731 Escherichia coli S88 7132938 YP_002394333.1 CDS yjgQ NC_011742.1 4816731 4817813 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein 4816731..4817813 Escherichia coli S88 7131720 YP_002394334.1 CDS yjgR NC_011742.1 4817932 4819434 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative ATPase complement(4817932..4819434) Escherichia coli S88 7131721 YP_002394335.1 CDS yjgB NC_011742.1 4819564 4820583 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 12147722; Product type pe : putative enzyme; putative alcohol dehydrogenase, Zn-dependent and NAD(P)-binding complement(4819564..4820583) Escherichia coli S88 7131722 YP_002394336.1 CDS ECS88_4852 NC_011742.1 4820658 4820864 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4820658..4820864) Escherichia coli S88 7131711 YP_002394337.1 CDS ECS88_4853 NC_011742.1 4821397 4822221 D Evidence 4 : Homologs of previously reported genes of unknown function; Conserved hypothetical protein, putative phage-related protein 4821397..4822221 Escherichia coli S88 7129916 YP_002394338.1 CDS ECS88_4854 NC_011742.1 4822270 4822896 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative lysogenic conversion protein from Bacteriophage P2-EC53 complement(4822270..4822896) Escherichia coli S88 7132683 YP_002394339.1 CDS ECS88_4855 NC_011742.1 4822907 4823293 D Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase ORF A, IS3 family 4822907..4823293 Escherichia coli S88 7132684 YP_002394340.1 CDS insI NC_011742.1 4823213 4824364 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9689094, 6092059; Product type e : enzyme; IS30 transposase; KpLE2 phage-like element complement(4823213..4824364) Escherichia coli S88 7132685 YP_002394341.1 CDS insO NC_011742.1 4824495 4825094 D Evidence 7 : Gene remnant; Product type pe : putative enzyme; transposase ORF B (fragment), IS911 4824495..4825094 Escherichia coli S88 7132741 YP_002394342.1 CDS yjhV NC_011742.1 4825260 4825673 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; KpLE2 phage-like element 4825260..4825673 Escherichia coli S88 7132686 YP_002394343.1 CDS fecE NC_011742.1 4826231 4826998 R Part of the FecBCDE citrate-dependent iron (III) transport system; iron-dicitrate transporter ATP-binding subunit complement(4826231..4826998) Escherichia coli S88 7131734 YP_002394344.1 CDS fecD NC_011742.1 4826999 4828465 R Evidence 2b : Function of strongly homologous gene; PubMedId : 2651410; Product type t : transporter; iron-dicitrate transporter subunit ; membrane component of ABC superfamily complement(4826999..4828465) Escherichia coli S88 7129466 YP_002394345.1 CDS fecC NC_011742.1 4827952 4828950 R part of the FecBCDE citrate-dependent iron (III) transport system; iron-dicitrate transporter permease subunit complement(4827952..4828950) Escherichia coli S88 7129465 YP_002394346.1 CDS fecB NC_011742.1 4828947 4829849 R part of the ABC transporter involved in the uptake of citrate-dependent Fe(3+); iron-dicitrate transporter substrate-binding subunit complement(4828947..4829849) Escherichia coli S88 7129464 YP_002394347.1 CDS fecA NC_011742.1 4829894 4832218 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 90105402, 91072220, 92269759, 2836368; Product type t : transporter; ferric citrate outer membrane transporter; KpLE2 phage-like element complement(4829894..4832218) Escherichia coli S88 7129463 YP_002394348.1 CDS fecR NC_011742.1 4832305 4833258 R with FecA forms the FecAR signal transduction system; ferric citrate binds FecA and transmits a signal across the outer membrane to FecR. FecR transmits a signal across the cytoplasmic membrane and activates the sigma 70 protein FecI that directs the RNA polymerase to express the fecABCDE operon; fec operon regulator FecR complement(4832305..4833258) Escherichia coli S88 7129462 YP_002394349.1 CDS fecI NC_011742.1 4833255 4833776 R Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor regulates the genes for iron dicitrate transport; RNA polymerase sigma factor FecI complement(4833255..4833776) Escherichia coli S88 7129468 YP_002394350.1 CDS insA NC_011742.1 4834068 4834346 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1849492; Product type r : regulator; IS1 repressor protein InsA; KpLE2 phage-like element 4834068..4834346 Escherichia coli S88 7129467 YP_002394351.1 CDS ECS88_4873 NC_011742.1 4836504 4837877 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative exported protein 4836504..4837877 Escherichia coli S88 7132687 YP_002394352.1 CDS ECS88_4877 NC_011742.1 4839561 4839908 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative transposase ORF2, IS66 family complement(4839561..4839908) Escherichia coli S88 7132528 YP_002394353.1 CDS ECS88_4878 NC_011742.1 4839905 4840306 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative transposase, IS3 family complement(4839905..4840306) Escherichia coli S88 7132529 YP_002394354.1 CDS ECS88_4879 NC_011742.1 4840640 4841161 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4840640..4841161) Escherichia coli S88 7132530 YP_002394355.1 CDS ECS88_4880 NC_011742.1 4841062 4841469 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4841062..4841469) Escherichia coli S88 7132531 YP_002394356.1 CDS ECS88_4881 NC_011742.1 4841723 4842328 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4841723..4842328) Escherichia coli S88 7132532 YP_002394357.1 CDS ECS88_4883 NC_011742.1 4842869 4843033 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(4842869..4843033) Escherichia coli S88 7132533 YP_002394358.1 CDS ECS88_4884 NC_011742.1 4843037 4843213 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative transcriptional regulator complement(4843037..4843213) Escherichia coli S88 7132534 YP_002394359.1 CDS ECS88_4885 NC_011742.1 4843514 4843780 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(4843514..4843780) Escherichia coli S88 7132535 YP_002394360.1 CDS ECS88_4886 NC_011742.1 4843726 4844127 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 4843726..4844127 Escherichia coli S88 7132536 YP_002394361.1 CDS ECS88_4887 NC_011742.1 4844207 4844824 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4844207..4844824 Escherichia coli S88 7132537 YP_002394362.1 CDS ECS88_4888 NC_011742.1 4844996 4845193 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 4844996..4845193 Escherichia coli S88 7132538 YP_002394363.1 CDS ECS88_4889 NC_011742.1 4846228 4846941 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4846228..4846941 Escherichia coli S88 7132539 YP_002394364.1 CDS ECS88_4890 NC_011742.1 4846963 4847898 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein with GTPase domain 4846963..4847898 Escherichia coli S88 7132540 YP_002394365.1 CDS ECS88_4891 NC_011742.1 4848195 4851116 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 9103983, 2661530, 10931336, 10094691; Product type m : membrane component; antigen 43 precursor (AG43) (Fluffing protein) 4848195..4851116 Escherichia coli S88 7132541 YP_002394366.1 CDS ECS88_4892 NC_011742.1 4851151 4851345 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4851151..4851345 Escherichia coli S88 7132542 YP_002394367.1 CDS ECS88_4893 NC_011742.1 4851500 4852318 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4851500..4852318 Escherichia coli S88 7132543 YP_002394368.1 CDS ECS88_4894 NC_011742.1 4852279 4853133 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative antirestriction protein 4852279..4853133 Escherichia coli S88 7132544 YP_002394369.1 CDS yeeS NC_011742.1 4853179 4853625 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11053371; Product type pf : putative factor; putative DNA repair protein; CP4-44 prophage 4853179..4853625 Escherichia coli S88 7132545 YP_002394370.1 CDS yeeT NC_011742.1 4853688 4853909 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CP4-44 prophage 4853688..4853909 Escherichia coli S88 7132959 YP_002394371.1 CDS ECS88_4897 NC_011742.1 4853909 4854022 D Evidence 6 : Doubtful CDS; hypothetical protein 4853909..4854022 Escherichia coli S88 7132963 YP_002394372.1 CDS ECS88_4898 NC_011742.1 4854113 4854862 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative transposase ORF2, IS21 family complement(4854113..4854862) Escherichia coli S88 7132546 YP_002394373.1 CDS ECS88_4899 NC_011742.1 4854874 4856415 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative transposase ORF1, IS21 family complement(4854874..4856415) Escherichia coli S88 7132547 YP_002394374.1 CDS yeeU NC_011742.1 4856658 4857026 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 14594833; Product type h : extrachromosomal origin; antitoxin of the YeeV-YeeU toxin-antitoxin system; CP4-44 prophage 4856658..4857026 Escherichia coli S88 7132548 YP_002394375.1 CDS mtnK NC_011742.1 4857954 4859213 D phosphorylates methylthioribose to form methylthioribose-1-phosphate; involved in methionine salvage pathway; methylthioribose kinase 4857954..4859213 Escherichia coli S88 7132967 YP_002394376.1 CDS mtnA NC_011742.1 4859223 4860338 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 15102328; Product type e : enzyme; methyl-thioribose-1-phosphate isomerase 4859223..4860338 Escherichia coli S88 7129625 YP_002394377.1 CDS mtnB NC_011742.1 4860369 4861010 D catalyzes the formation of glycerone phosphate and (S)-lactaldehyde from L-fuculose 1-phosphate; L-fuculose phosphate aldolase 4860369..4861010 Escherichia coli S88 7129623 YP_002394378.1 CDS ECS88_4904 NC_011742.1 4861114 4862118 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative integral membrane protein; putative sugar permease 4861114..4862118 Escherichia coli S88 7129624 YP_002394379.1 CDS yjhU NC_011742.1 4862159 4863145 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator; KpLE2 phage-like element complement(4862159..4863145) Escherichia coli S88 7132549 YP_002394380.1 CDS ECS88_4906 NC_011742.1 4863245 4863436 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(4863245..4863436) Escherichia coli S88 7131733 YP_002394381.1 CDS yjhF NC_011742.1 4863492 4864841 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter; KpLE2 phage-like element complement(4863492..4864841) Escherichia coli S88 7132550 YP_002394382.1 CDS yjhG NC_011742.1 4864948 4866915 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; hypothetical protein complement(4864948..4866915) Escherichia coli S88 7131724 YP_002394383.1 CDS yjhH NC_011742.1 4866926 4867831 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 11425723; Product type pe : putative enzyme; putative lyase/synthase (dapA-like); KpLE2 phage-like element complement(4866926..4867831) Escherichia coli S88 7131725 YP_002394384.1 CDS yjhI NC_011742.1 4867836 4868624 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator; KpLE2 phage-like element complement(4867836..4868624) Escherichia coli S88 7131726 YP_002394385.1 CDS sgcR NC_011742.1 4868927 4869709 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator; KpLE2 phage-like element complement(4868927..4869709) Escherichia coli S88 7131727 YP_002394386.1 CDS sgcE NC_011742.1 4869726 4870358 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; epimerase complement(4869726..4870358) Escherichia coli S88 7130595 YP_002394387.1 CDS sgcA NC_011742.1 4870370 4870801 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative phosphotransferase enzyme IIA component; KpLE2 phage-like element complement(4870370..4870801) Escherichia coli S88 7130593 YP_002394388.1 CDS sgcQ NC_011742.1 4870932 4871738 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative nucleoside triphosphatase; KpLE2 phage-like element complement(4870932..4871738) Escherichia coli S88 7131352 YP_002394389.1 CDS sgcC NC_011742.1 4871751 4873064 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative phosphotransferase enzyme IIC component; KpLE2 phage-like element complement(4871751..4873064) Escherichia coli S88 7130594 YP_002394390.1 CDS sgcB NC_011742.1 4873076 4873354 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative enzyme IIB component of PTS; KpLE2 phage-like element complement(4873076..4873354) Escherichia coli S88 7130592 YP_002394391.1 CDS sgcX NC_011742.1 4873351 4874472 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative endoglucanase with Zn-dependent exopeptidase domain; KpLE2 phage-like element complement(4873351..4874472) Escherichia coli S88 7130591 YP_002394392.1 CDS yjhP NC_011742.1 4875258 4876004 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative methyltransferase; KpLE2 phage-like element complement(4875258..4876004) Escherichia coli S88 7130596 YP_002394393.1 CDS yjhQ NC_011742.1 4876060 4876605 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative acetyltransferase; KpLE2 phage-like element complement(4876060..4876605) Escherichia coli S88 7131728 YP_002394394.1 CDS yjhX NC_011742.1 4876617 4876874 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4876617..4876874) Escherichia coli S88 7131729 YP_002394395.1 CDS ECS88_4923 NC_011742.1 4877365 4877496 R Evidence 6 : Doubtful CDS; hypothetical protein complement(4877365..4877496) Escherichia coli S88 7131735 YP_002394396.1 CDS yjhR NC_011742.1 4877836 4878852 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 96367099; Product type pf : putative factor; putative frameshift suppressor; KpLE2 phage-like element 4877836..4878852 Escherichia coli S88 7132552 YP_002394397.1 CDS yjhS NC_011742.1 4879435 4880415 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4879435..4880415) Escherichia coli S88 7131730 YP_002394398.1 CDS yjhT NC_011742.1 4880480 4881586 R Evidence 4 : Homologs of previously reported genes of unknown function; N-acetylneuraminic acid mutarotase complement(4880480..4881586) Escherichia coli S88 7131731 YP_002394399.1 CDS yjhA NC_011742.1 4881606 4882322 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15743943; Product type t : transporter; N-acetylnuraminic acid outer membrane channel protein complement(4881606..4882322) Escherichia coli S88 7131732 YP_002394400.1 CDS ECS88_4929 NC_011742.1 4883121 4883516 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4883121..4883516) Escherichia coli S88 7131723 YP_002394401.1 CDS fimB NC_011742.1 4883776 4884378 D inversion of on/off regulator of fimA; tyrosine recombinase 4883776..4884378 Escherichia coli S88 7132553 YP_002394402.1 CDS fimE NC_011742.1 4884855 4885451 D inversion of on/off regulator of fimA; tyrosine recombinase 4884855..4885451 Escherichia coli S88 7129494 YP_002394403.1 CDS fimA NC_011742.1 4885932 4886486 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6146599, 6147250, 90220509, 93106965, 2858471, 6123483; Product type s : structure; major type 1 subunit fimbrin (pilin) 4885932..4886486 Escherichia coli S88 7129497 YP_002394404.1 CDS fimI NC_011742.1 4886551 4887090 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12897022, 11673421, 6147250; Product type s : structure; type 1 pilus biosynthesis fimbrial protein 4886551..4887090 Escherichia coli S88 7129493 YP_002394405.1 CDS fimC NC_011742.1 4887127 4887852 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20450729, 90220509, 93155127, 93391362, 1363735, 8104335, 8636962, 9783748; Product type f : factor; chaperone, periplasmic 4887127..4887852 Escherichia coli S88 7129501 YP_002394406.1 CDS fimD NC_011742.1 4887919 4890555 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12842468, 90220509, 1970114; Product type f : factor; outer membrane usher protein, type 1 fimbrial synthesis 4887919..4890555 Escherichia coli S88 7129495 YP_002394407.1 CDS fimF NC_011742.1 4890565 4891095 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89056689, 92394896, 1970114, 2890081; Product type s : structure; minor component of type 1 fimbriae 4890565..4891095 Escherichia coli S88 7129496 YP_002394408.1 CDS fimG NC_011742.1 4891108 4891611 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89056689, 92394896, 2890081; Product type s : structure; minor component of type 1 fimbriae 4891108..4891611 Escherichia coli S88 7129498 YP_002394409.1 CDS fimH NC_011742.1 4891631 4892533 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 89056689, 93155127, 93391362, 1971261, 2890081, 2900235; Product type s : structure; minor component of type 1 fimbriae 4891631..4892533 Escherichia coli S88 7129499 YP_002394410.1 CDS gntP NC_011742.1 4892706 4894049 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 96125229, 15516583, 8550444; Product type t : transporter; fructuronate transporter complement(4892706..4894049) Escherichia coli S88 7129500 YP_002394411.1 CDS uxuA NC_011742.1 4894389 4895573 D catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate; mannonate dehydratase 4894389..4895573 Escherichia coli S88 7130051 YP_002394412.1 CDS uxuB NC_011742.1 4895654 4897114 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 73203083, 77222076, 14401695; Product type e : enzyme; D-mannonate oxidoreductase, NAD-binding 4895654..4897114 Escherichia coli S88 7132466 YP_002394413.1 CDS uxuR NC_011742.1 4897329 4898102 D regulates the expression of uxuBA; DNA-binding transcriptional repressor UxuR 4897329..4898102 Escherichia coli S88 7132467 YP_002394414.1 CDS yjiC NC_011742.1 4898243 4899073 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4898243..4899073) Escherichia coli S88 7132468 YP_002394415.1 CDS ECS88_4944 NC_011742.1 4899636 4899779 D Evidence 6 : Doubtful CDS; hypothetical protein 4899636..4899779 Escherichia coli S88 7131737 YP_002394416.1 CDS iraD NC_011742.1 4899745 4900137 D inhibitor of RssB activity in response to DNA damage; blocks degradation of stationary phase sigma factor RpoS; DNA replication/recombination/repair protein 4899745..4900137 Escherichia coli S88 7132554 YP_002394417.1 CDS yjiE NC_011742.1 4900130 4901041 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(4900130..4901041) Escherichia coli S88 7131738 YP_002394418.1 CDS iadA NC_011742.1 4901106 4902278 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 95181377, 7876157; Product type e : enzyme; isoaspartyl dipeptidase complement(4901106..4902278) Escherichia coli S88 7130902 YP_002394419.1 CDS yjiG NC_011742.1 4902291 4902752 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(4902291..4902752) Escherichia coli S88 7131602 YP_002394420.1 CDS yjiH NC_011742.1 4902749 4903432 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4902749..4903432) Escherichia coli S88 7131065 YP_002394421.1 CDS kptA NC_011742.1 4903682 4904266 D in yeast cells this enzyme removes the 2'-phosphate from RNA via an intermediate in which the phosphate is ADP-ribosylated by NAD followed by a presumed transesterification to release the RNA and generate ADP-ribose 1''-2''-cyclic phosphate; functions in tRNA splicing; the function and substrate of bacterial enzymes in organisms that do not perform splicing is unknown; RNA 2'-phosphotransferase-like protein 4903682..4904266 Escherichia coli S88 7131066 YP_002394422.1 CDS ECS88_4952 NC_011742.1 4904387 4909627 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; putative invasin/intimin protein complement(4904387..4909627) Escherichia coli S88 7130467 YP_002394423.1 CDS yjiJ NC_011742.1 4909838 4911016 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4909838..4911016) Escherichia coli S88 7132555 YP_002394424.1 CDS yjiK NC_011742.1 4911087 4911962 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; hypothetical protein complement(4911087..4911962) Escherichia coli S88 7131067 YP_002394425.1 CDS ECS88_4955 NC_011742.1 4912183 4914276 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4912183..4914276) Escherichia coli S88 7131068 YP_002394426.1 CDS ECS88_4956 NC_011742.1 4914472 4914726 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(4914472..4914726) Escherichia coli S88 7132556 YP_002394427.1 CDS ECS88_4957 NC_011742.1 4914588 4914854 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4914588..4914854) Escherichia coli S88 7132557 YP_002394428.1 CDS hgdC NC_011742.1 4914851 4915618 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 8365476, 7607244, 15654892; Product type e : enzyme; ATPase, activator of (R)-hydroxyglutaryl-CoA dehydratase complement(4914851..4915618) Escherichia coli S88 7132558 YP_002394429.1 CDS yjiM NC_011742.1 4915628 4916779 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 3691501, 11106419; Product type pe : putative enzyme; putative 2-hydroxyglutaryl-CoA dehydratase (hgdB-like) complement(4915628..4916779) Escherichia coli S88 7128914 YP_002394430.1 CDS yjiN NC_011742.1 4916895 4918175 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4916895..4918175) Escherichia coli S88 7131069 YP_002394431.1 CDS yjiO NC_011742.1 4918216 4919448 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 21450803; Product type t : transporter; multidrug efflux system protein complement(4918216..4919448) Escherichia coli S88 7131070 YP_002394432.1 CDS ECS88_4962 NC_011742.1 4919915 4920859 D Evidence 4 : Homologs of previously reported genes of unknown function; Conserved hypothetical protein, putative transposase 4919915..4920859 Escherichia coli S88 7131071 YP_002394433.1 CDS yjiR NC_011742.1 4921102 4922514 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; fused putative DNA-binding transcriptional regulator ; putative aminotransferase complement(4921102..4922514) Escherichia coli S88 7132559 YP_002394434.1 CDS yjiS NC_011742.1 4922691 4922855 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4922691..4922855 Escherichia coli S88 7131072 YP_002394435.1 CDS yjiW NC_011742.1 4922897 4923292 R involved in the degradation of RNA; may be involved in the recycling of RNA during the SOS response; endoribonuclease SymE complement(4922897..4923292) Escherichia coli S88 7131073 YP_002394436.1 CDS ECS88_4966 NC_011742.1 4923450 4926725 R Evidence 2b : Function of strongly homologous gene; PubMedId : 8939428; Product type e : enzyme; type I restriction-modification system (hsdR-like) complement(4923450..4926725) Escherichia coli S88 7131353 YP_002394437.1 CDS ECS88_4967 NC_011742.1 4926808 4928199 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11600708; Product type e : enzyme; type I restriction-modification system (hsdS-like) complement(4926808..4928199) Escherichia coli S88 7132560 YP_002394438.1 CDS ECS88_4968 NC_011742.1 4928189 4929808 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8939428; Product type e : enzyme; putative type I restriction-modification system methyltransferase subunit; (hsdM-like) complement(4928189..4929808) Escherichia coli S88 7132561 YP_002394439.1 CDS ECS88_4970 NC_011742.1 4930418 4931038 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(4930418..4931038) Escherichia coli S88 7132563 YP_002394440.1 CDS ECS88_4971 NC_011742.1 4931208 4931522 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4931208..4931522 Escherichia coli S88 7132564 YP_002394441.1 CDS ECS88_4972 NC_011742.1 4931368 4931811 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4931368..4931811 Escherichia coli S88 7132565 YP_002394442.1 CDS yjiA NC_011742.1 4931852 4932808 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 14696199; Product type pe : putative enzyme; putative GTP-binding protein YjiA complement(4931852..4932808) Escherichia coli S88 7132566 YP_002394443.1 CDS yjiX NC_011742.1 4932819 4933022 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4932819..4933022) Escherichia coli S88 7131736 YP_002394444.1 CDS yjiY NC_011742.1 4933072 4935222 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4933072..4935222) Escherichia coli S88 7131075 YP_002394445.1 CDS tsr NC_011742.1 4935600 4937255 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20015410, 89034150, 91317710, 10466731, 2033064, 6213619, 6402709, 8384293; Product type r : regulator; methyl-accepting chemotaxis protein I, serine sensor receptor 4935600..4937255 Escherichia coli S88 7131076 YP_002394446.1 CDS yjiZ NC_011742.1 4937304 4938665 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative transporter complement(4937304..4938665) Escherichia coli S88 7130360 YP_002394447.1 CDS yjjM NC_011742.1 4938880 4939794 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator complement(4938880..4939794) Escherichia coli S88 7131077 YP_002394448.1 CDS yjjN NC_011742.1 4939933 4940955 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative oxidoreductase, Zn-dependent and NAD(P)-binding 4939933..4940955 Escherichia coli S88 7131083 YP_002394449.1 CDS mdoB NC_011742.1 4941093 4943384 R catalyzes the transfer of phosphoglycerol to the glucan backbone; phosphoglycerol transferase I complement(4941093..4943384) Escherichia coli S88 7131084 YP_002394450.1 CDS yjjA NC_011742.1 4943638 4944132 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4943638..4944132) Escherichia coli S88 7132689 YP_002394451.1 CDS dnaC NC_011742.1 4944181 4944918 R acts to load the DnaB helicase onto the initiation site during DNA replication; DNA replication protein DnaC complement(4944181..4944918) Escherichia coli S88 7131078 YP_002394452.1 CDS dnaT NC_011742.1 4944921 4945460 R This protein is required for primosome-dependent normal DNA replication; it is also involved in inducing stable DNA replication during SOS response. It forms, in concert with dnaB protein and other prepriming proteins dnaC, N, N', N'' a prepriming protein complex on the specific site of the template DNA recognized by protein N'; primosomal protein DnaI complement(4944921..4945460) Escherichia coli S88 7130222 YP_002394453.1 CDS ECS88_4984 NC_011742.1 4945567 4946055 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4945567..4946055) Escherichia coli S88 7130229 YP_002394454.1 CDS yjjP NC_011742.1 4946031 4946801 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type pm : putative membrane component; conserved hypothetical protein; putative inner membrane protein complement(4946031..4946801) Escherichia coli S88 7132567 YP_002394455.1 CDS yjjQ NC_011742.1 4947420 4948145 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; putative DNA-binding transcriptional regulator 4947420..4948145 Escherichia coli S88 7131085 YP_002394456.1 CDS bglJ NC_011742.1 4948157 4948780 D regulator for the transport and utilization of the aromatic beta-glucosides arbutin and silicin; DNA-binding transcriptional activator BglJ 4948157..4948780 Escherichia coli S88 7131086 YP_002394457.1 CDS fhuF NC_011742.1 4948818 4949606 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 11931550, 14756576, 3323834, 9990318; Product type c : carrier; ferric iron reductase involved in ferric hydroximate transport complement(4948818..4949606) Escherichia coli S88 7129118 YP_002394458.1 CDS ECS88_4990 NC_011742.1 4949636 4949983 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4949636..4949983 Escherichia coli S88 7129487 YP_002394459.1 CDS rsmC NC_011742.1 4950612 4951643 R 16S rRNA M2G1207 methyltransferase; one of many enzymes that modify bases of the ribosomal RNA; this enzyme methylates the G at position 1207 of the small ribosomal subunit; 16S ribosomal RNA m2G1207 methyltransferase complement(4950612..4951643) Escherichia coli S88 7129917 YP_002394460.1 CDS holD NC_011742.1 4951746 4952159 D with the chi subunit binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB; DNA polymerase III subunit psi 4951746..4952159 Escherichia coli S88 7133815 YP_002394461.1 CDS rimI NC_011742.1 4952128 4952574 D alanine acetyltransferase that specifically acetylates ribosomal protein S18; ribosomal-protein-alanine N-acetyltransferase 4952128..4952574 Escherichia coli S88 7128944 YP_002394462.1 CDS yjjG NC_011742.1 4952589 4953266 D manganese-dependent 5'-nucleotidase; specific for 5'-UMP, 5'-dUMP, and 5'-dTMP; member of haloacid dehalogenase (HAD)-like hydrolase superfamily; nucleotidase 4952589..4953266 Escherichia coli S88 7132723 YP_002394463.1 CDS ECS88_4996 NC_011742.1 4953652 4954866 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative integrase 4953652..4954866 Escherichia coli S88 7131079 YP_002394464.1 CDS ECS88_4997 NC_011742.1 4955242 4956258 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(4955242..4956258) Escherichia coli S88 7132569 YP_002394465.1 CDS ECS88_4998 NC_011742.1 4956805 4957425 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein from phage origin complement(4956805..4957425) Escherichia coli S88 7132570 YP_002394466.1 CDS yfdS NC_011742.1 4957425 4957787 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage complement(4957425..4957787) Escherichia coli S88 7132571 YP_002394467.1 CDS yfdR NC_011742.1 4957778 4958314 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage complement(4957778..4958314) Escherichia coli S88 7129839 YP_002394468.1 CDS yfdQ NC_011742.1 4958442 4959266 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage complement(4958442..4959266) Escherichia coli S88 7129837 YP_002394469.1 CDS ECS88_5002 NC_011742.1 4959332 4959880 R Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein complement(4959332..4959880) Escherichia coli S88 7129834 YP_002394470.1 CDS ECS88_5003 NC_011742.1 4960417 4961109 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative transcriptional regulator from phage origin complement(4960417..4961109) Escherichia coli S88 7132572 YP_002394471.1 CDS ECS88_5004 NC_011742.1 4961207 4961467 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 4961207..4961467 Escherichia coli S88 7132573 YP_002394472.1 CDS ymfL NC_011742.1 4961460 4962011 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative nucleic acid-binding protein; e14 prophage 4961460..4962011 Escherichia coli S88 7132574 YP_002394473.1 CDS ECS88_5007 NC_011742.1 4962008 4963159 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 4962008..4963159 Escherichia coli S88 7131129 YP_002394474.1 CDS ECS88_5008 NC_011742.1 4963156 4963380 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 4963156..4963380 Escherichia coli S88 7132575 YP_002394475.1 CDS ECS88_5009 NC_011742.1 4963338 4964195 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; replication protein from phage origin 4963338..4964195 Escherichia coli S88 7132576 YP_002394476.1 CDS yfdN NC_011742.1 4964198 4964686 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; CPS-53 (KpLE1) prophage 4964198..4964686 Escherichia coli S88 7132577 YP_002394477.1 CDS ECS88_5011 NC_011742.1 4964653 4965012 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin with LexA DNA binding domain 4964653..4965012 Escherichia coli S88 7129831 YP_002394478.1 CDS ECS88_5012 NC_011742.1 4965009 4965398 D Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 8648624; Product type h : extrachromosomal origin; Crossover junction endodeoxyribonuclease from phage origin 4965009..4965398 Escherichia coli S88 7132578 YP_002394479.1 CDS ECS88_5013 NC_011742.1 4965418 4966215 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from phage origin 4965418..4966215 Escherichia coli S88 7132579 YP_002394480.1 CDS ECS88_5014 NC_011742.1 4966217 4967212 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4966217..4967212 Escherichia coli S88 7132580 YP_002394481.1 CDS ydfT NC_011742.1 4967226 4967978 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative antitermination protein Q; Qin prophage 4967226..4967978 Escherichia coli S88 7132581 YP_002394482.1 CDS cspF NC_011742.1 4968394 4968606 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9484881, 8022261, 9439003; Product type h : extrachromosomal origin; cold shock protein; Qin prophage complement(4968394..4968606) Escherichia coli S88 7129339 YP_002394483.1 CDS cspB NC_011742.1 4968907 4969122 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 94293754, 94293756, 9439003; Product type h : extrachromosomal origin; cold shock protein; Qin prophage 4968907..4969122 Escherichia coli S88 7130498 YP_002394484.1 CDS essQ NC_011742.1 4969875 4970090 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pf : putative factor; putative S lysis protein; Qin prophage 4969875..4970090 Escherichia coli S88 7130494 YP_002394485.1 CDS ECS88_5019 NC_011742.1 4970074 4970646 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 4970074..4970646 Escherichia coli S88 7132420 YP_002394486.1 CDS ydfQ NC_011742.1 4970968 4971501 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative membrane-associated lysozyme; Qin prophage 4970968..4971501 Escherichia coli S88 7132582 YP_002394487.1 CDS ydfP NC_011742.1 4971498 4971995 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein; Qin prophage 4971498..4971995 Escherichia coli S88 7129337 YP_002394488.1 CDS cspI NC_011742.1 4972359 4972571 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9484881; Product type h : extrachromosomal origin; cold shock protein; Qin prophage 4972359..4972571 Escherichia coli S88 7129335 YP_002394489.1 CDS ECS88_5023 NC_011742.1 4972804 4973073 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4972804..4973073 Escherichia coli S88 7130501 YP_002394490.1 CDS ECS88_5024 NC_011742.1 4973153 4973419 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4973153..4973419 Escherichia coli S88 7132583 YP_002394491.1 CDS ECS88_5025 NC_011742.1 4973715 4973921 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; hypothetical protein 4973715..4973921 Escherichia coli S88 7132584 YP_002394492.1 CDS ECS88_5026 NC_011742.1 4974474 4974965 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from putative prophage 4974474..4974965 Escherichia coli S88 7132585 YP_002394493.1 CDS ECS88_5027 NC_011742.1 4974965 4977067 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative DNA packaging protein of putative prophage ( terminase large subunit) 4974965..4977067 Escherichia coli S88 7132586 YP_002394494.1 CDS ECS88_5028 NC_011742.1 4977058 4977276 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from putative prophage 4977058..4977276 Escherichia coli S88 7132587 YP_002394495.1 CDS ECS88_5029 NC_011742.1 4977204 4978784 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative portal protein (head-tail preconnector protein) from putative prophage 4977204..4978784 Escherichia coli S88 7132588 YP_002394496.1 CDS ECS88_5030 NC_011742.1 4978537 4980756 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative ATP-dependent Clp protease proteolytic subunit (Endopeptidase Clp) 4978537..4980756 Escherichia coli S88 7132589 YP_002394497.1 CDS ECS88_5031 NC_011742.1 4980798 4981166 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from putative prophage 4980798..4981166 Escherichia coli S88 7132590 YP_002394498.1 CDS ECS88_5032 NC_011742.1 4981159 4981434 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein from putative prophage 4981159..4981434 Escherichia coli S88 7132591 YP_002394499.1 CDS ECS88_5033 NC_011742.1 4981446 4982024 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein Z (GPZ) of prophage 4981446..4982024 Escherichia coli S88 7132592 YP_002394500.1 CDS ECS88_5034 NC_011742.1 4982009 4982422 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein U 4982009..4982422 Escherichia coli S88 7132593 YP_002394501.1 CDS ECS88_5035 NC_011742.1 4982358 4983176 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Major tail protein V 4982358..4983176 Escherichia coli S88 7132594 YP_002394502.1 CDS ECS88_5036 NC_011742.1 4983195 4983623 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative minor tail component of putative prophage 4983195..4983623 Escherichia coli S88 7132595 YP_002394503.1 CDS ECS88_5037 NC_011742.1 4983632 4983961 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative minor tail protein T of putative prophage 4983632..4983961 Escherichia coli S88 7132596 YP_002394504.1 CDS ECS88_5038 NC_011742.1 4983903 4986998 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative tail length tape measure protein from putative prophage 4983903..4986998 Escherichia coli S88 7132597 YP_002394505.1 CDS ECS88_5039 NC_011742.1 4986998 4987327 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein M 4986998..4987327 Escherichia coli S88 7132598 YP_002394506.1 CDS ECS88_5040 NC_011742.1 4987337 4988035 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Minor tail protein L 4987337..4988035 Escherichia coli S88 7132599 YP_002394507.1 CDS ECS88_5041 NC_011742.1 4987998 4988783 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative tail fiber component K of prophage 4987998..4988783 Escherichia coli S88 7132600 YP_002394508.1 CDS ECS88_5042 NC_011742.1 4988681 4989328 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Tail assembly protein I from putative prophage 4988681..4989328 Escherichia coli S88 7132601 YP_002394509.1 CDS ECS88_5043 NC_011742.1 4989344 4992784 D Evidence 2b : Function of strongly homologous gene; Product type h : extrachromosomal origin; Host specificity protein J 4989344..4992784 Escherichia coli S88 7132602 YP_002394510.1 CDS ECS88_5044 NC_011742.1 4992852 4993451 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 2144037; Product type h : extrachromosomal origin; Putative Lom-like outer membrane protein of phage origin 4992852..4993451 Escherichia coli S88 7132603 YP_002394511.1 CDS ECS88_5045 NC_011742.1 4993510 4995894 D Evidence 4 : Homologs of previously reported genes of unknown function; Product type h : extrachromosomal origin; conserved hypothetical protein, putative side tail fiber protein homolog from prophage 4993510..4995894 Escherichia coli S88 7132604 YP_002394512.1 CDS ECS88_5046 NC_011742.1 4995894 4996175 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4995894..4996175 Escherichia coli S88 7132605 YP_002394513.1 CDS ECS88_5047 NC_011742.1 4996185 4996889 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4996185..4996889 Escherichia coli S88 7132606 YP_002394514.1 CDS ECS88_5048 NC_011742.1 4996900 4997193 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 4996900..4997193 Escherichia coli S88 7132607 YP_002394515.1 CDS pinR NC_011742.1 4997421 4998011 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 14687564; Product type pe : putative enzyme; putative site-specific recombinase; DNA invertase; Rac prophage complement(4997421..4998011) Escherichia coli S88 7131289 YP_002394516.1 CDS ydfK NC_011742.1 4998328 4998594 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative DNA-binding transcriptional regulator; Qin prophage complement(4998328..4998594) Escherichia coli S88 7133734 YP_002394517.1 CDS ECS88_5053 NC_011742.1 4999170 4999418 R Evidence 2b : Function of strongly homologous gene; PubMedId : 11230150; Product type f : factor; DNA damage-inducible protein in prophage (dinI-like) complement(4999170..4999418) Escherichia coli S88 7129334 YP_002394518.1 CDS prfC NC_011742.1 4999611 5001224 D stimulates the release of release factors 1 and 2 from the ribosome after hydrolysis of the ester bond in peptidyl-tRNA has occurred; GDP/GTP-binding protein; peptide chain release factor 3 4999611..5001224 Escherichia coli S88 7129843 YP_002394519.1 CDS osmY NC_011742.1 5001617 5002222 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1317380, 8253679, 9298646, 9600841; Product type cp : cell process; periplasmic protein 5001617..5002222 Escherichia coli S88 7130774 YP_002394520.1 CDS ytjA NC_011742.1 5002331 5002510 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 5002331..5002510 Escherichia coli S88 7133146 YP_002394521.1 CDS yjjU NC_011742.1 5002632 5003705 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative esterase 5002632..5003705 Escherichia coli S88 7131880 YP_002394522.1 CDS yjjV NC_011742.1 5003702 5004481 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative deoxyribonuclease YjjV 5003702..5004481 Escherichia coli S88 7131087 YP_002394523.1 CDS yjjW NC_011742.1 5004901 5005764 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative pyruvate formate lyase activating enzyme complement(5004901..5005764) Escherichia coli S88 7131088 YP_002394524.1 CDS yjjI NC_011742.1 5005736 5007286 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(5005736..5007286) Escherichia coli S88 7131089 YP_002394525.1 CDS deoC NC_011742.1 5007544 5008323 D catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate; deoxyribose-phosphate aldolase 5007544..5008323 Escherichia coli S88 7131080 YP_002394526.1 CDS deoA NC_011742.1 5008450 5009772 D Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate; thymidine phosphorylase 5008450..5009772 Escherichia coli S88 7130186 YP_002394527.1 CDS deoB NC_011742.1 5009824 5011047 D catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose; phosphopentomutase 5009824..5011047 Escherichia coli S88 7130184 YP_002394528.1 CDS deoD NC_011742.1 5011104 5011823 D catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate; purine nucleoside phosphorylase 5011104..5011823 Escherichia coli S88 7130185 YP_002394529.1 CDS yjjJ NC_011742.1 5011990 5013321 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr : putative regulator; hypothetical protein 5011990..5013321 Escherichia coli S88 7130187 YP_002394530.1 CDS lplA NC_011742.1 5013322 5014338 R Catalyzes both the ATP-dependent activation of exogenously supplied lipoate to lipoyl-AMP and the transfer of the activated lipoyl on the lipoate-dependent enzymes. Creates an amide linkage that joins the free carboxyl group of lipoic acid to the epsilon-amino group of a specific lysine residue in lipoyl domain of apoproteins; lipoate-protein ligase A complement(5013322..5014338) Escherichia coli S88 7131081 YP_002394531.1 CDS ytjB NC_011742.1 5014366 5015010 R Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 2684780; hypothetical protein complement(5014366..5015010) Escherichia coli S88 7129376 YP_002394532.1 CDS serB NC_011742.1 5015116 5016084 D catalyzes the formation of serine from O-phosphoserine; phosphoserine phosphatase 5015116..5016084 Escherichia coli S88 7131881 YP_002394533.1 CDS radA NC_011742.1 5016133 5017515 D Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents; DNA repair protein RadA 5016133..5017515 Escherichia coli S88 7130580 YP_002394534.1 CDS nadR NC_011742.1 5017536 5018768 D catalyzes the formation of NAD(+) from nicotinamide ribonucleotide; nicotinamide-nucleotide adenylyltransferase 5017536..5018768 Escherichia coli S88 7131782 YP_002394535.1 CDS ECS88_5072 NC_011742.1 5018782 5019192 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 5018782..5019192 Escherichia coli S88 7129655 YP_002394536.1 CDS ECS88_5073 NC_011742.1 5019194 5019478 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 5019194..5019478 Escherichia coli S88 7129844 YP_002394537.1 CDS yjjK NC_011742.1 5019534 5021201 R ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence; putative ABC transporter ATP-binding protein complement(5019534..5021201) Escherichia coli S88 7129845 YP_002394538.1 CDS slt NC_011742.1 5021408 5023345 D catalyzes the cleavage of the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine residues in peptidoglycan; lytic murein transglycosylase 5021408..5023345 Escherichia coli S88 7131082 YP_002394539.1 CDS trpR NC_011742.1 5023435 5023761 D When complexed with L-tryptophan it binds the operator region of the trp operon and prevents the initiation of transcription; Trp operon repressor 5023435..5023761 Escherichia coli S88 7130606 YP_002394540.1 CDS yjjX NC_011742.1 5023834 5024361 R pyrophosphatase; has activity against dUTP and dITP; the crystal structure of the Vibrio protein showed similarity to Methanococcus janaschii Mj0226; in Vibrio cholerae this gene is part of the Mba operon that is involved in regulation and maintenance of biofilms; in Escherichia coli overexpression of this gene leads to resistance to an HMP analog; NTPase complement(5023834..5024361) Escherichia coli S88 7130349 YP_002394541.1 CDS ytjC NC_011742.1 5024413 5025060 D catalyzes reactions involving the transfer of phospho groups between the three carbon atoms of phosphoglycerate; phosphoglycerate mutase 5024413..5025060 Escherichia coli S88 7131090 YP_002394542.1 CDS rob NC_011742.1 5025057 5025926 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 20264525, 20309711, 93194823, 96405618, 8449900; Product type r : regulator; DNA-binding transcriptional activator complement(5025057..5025926) Escherichia coli S88 7131882 YP_002394543.1 CDS creA NC_011742.1 5026137 5026610 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 3531171, 8449900; hypothetical protein 5026137..5026610 Escherichia coli S88 7132755 YP_002394544.1 CDS creB NC_011742.1 5026623 5027312 D response regulator in two-component regulatory system with CreC; CreB protein is phosphorylated by sensor protein phospho-CreC; involved in catabolic regulation; DNA-binding response regulator CreB 5026623..5027312 Escherichia coli S88 7131960 YP_002394545.1 CDS creC NC_011742.1 5027312 5028736 D part of a two-component regulatory system with CreB or PhoB; involved in catabolic regulation; sensory histidine kinase CreC 5027312..5028736 Escherichia coli S88 7131961 YP_002394546.1 CDS creD NC_011742.1 5028794 5030146 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 88216172, 2835585, 2984198, 3531171; Product type m : membrane component; hypothetical protein 5028794..5030146 Escherichia coli S88 7131962 YP_002394547.1 CDS arcA NC_011742.1 5030206 5030922 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15028693, 21167794, 21317451, 91008980, 91358353, 92380937, 9514749, 9632255, 2984198, 7565118, 9298646; Product type r : regulator; two-component response regulator complement(5030206..5030922) Escherichia coli S88 7131963 YP_002394548.1 CDS yjtD NC_011742.1 5031558 5032244 D member of the SPOUT superfamily of methyltransferases; putative RNA methyltransferase 5031558..5032244 Escherichia coli S88 7133089 YP_002401008.1 CDS int NC_011747.1 132 872 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative site-specific recombinase 132..872 Escherichia coli S88 7119360 YP_002401009.1 CDS repA NC_011747.1 1157 2134 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8356112, 2651415, 8320218; Product type e : enzyme; RepFIB replication protein RepA complement(1157..2134) Escherichia coli S88 7119428 YP_002401010.1 CDS pECS88_0003 NC_011747.1 2543 2839 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2543..2839) Escherichia coli S88 7119362 YP_002401011.1 CDS pECS88_0004 NC_011747.1 2808 3029 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(2808..3029) Escherichia coli S88 7119361 YP_002401013.1 CDS pECS88_0006 NC_011747.1 3494 3883 D Evidence 7 : Gene remnant; conserved hypothetical protein, putative fragment of ImpB UV protection protein 3494..3883 Escherichia coli S88 7119363 YP_002401014.1 CDS pECS88_0007 NC_011747.1 4063 4566 R Evidence 2b : Function of strongly homologous gene; PubMedId : 375010, 1849492; Product type pe : putative enzyme; transposase InsB (ORF2) IS1 complement(4063..4566) Escherichia coli S88 7119364 YP_002401015.1 CDS pECS88_0008 NC_011747.1 4485 4709 R Evidence 2b : Function of strongly homologous gene; PubMedId : 375010, 1849492; Product type pe : putative enzyme; transposase InsA (ORF1) IS1 complement(4485..4709) Escherichia coli S88 7119365 YP_002401016.1 CDS iutA NC_011747.1 5285 7486 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 4313071, 6456229, 7044820, 7042696, 6749806; Product type rc : receptor; Ferric aerobactin receptor precusor IutA complement(5285..7486) Escherichia coli S88 7119366 YP_002401017.1 CDS iucD NC_011747.1 7568 8845 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3275632, 10064136; Product type e : enzyme; L-lysine 6-monooxigenase IucD complement(7568..8845) Escherichia coli S88 7119439 YP_002401018.1 CDS iucC NC_011747.1 8842 10584 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3087960; Product type e : enzyme; Aerobactin siderophore biosynthesis protein IucC complement(8842..10584) Escherichia coli S88 7119438 YP_002401019.1 CDS iucB NC_011747.1 10584 11531 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3087960; Product type e : enzyme; N(6)-hydroxylysine acetylase IucB complement(10584..11531) Escherichia coli S88 7119437 YP_002401020.1 CDS iucA NC_011747.1 11532 13319 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3087960; Product type e : enzyme; Aerobactin siderophore biosynthesis protein IucA complement(11532..13319) Escherichia coli S88 7119436 YP_002401021.1 CDS shiF NC_011747.1 13392 14585 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative membrane transport protein ShiF 13392..14585 Escherichia coli S88 7119435 YP_002401022.1 CDS pECS88_0015 NC_011747.1 14965 15345 R may be involved in chromosome condensation; overexpression in Escherichia coli protects against decondensation by camphor; overexpressing the protein results in an increase in supercoiling; camphor resistance protein CrcB complement(14965..15345) Escherichia coli S88 7119445 YP_002401023.1 CDS pECS88_0016 NC_011747.1 15417 15689 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(15417..15689) Escherichia coli S88 7119367 YP_002401024.1 CDS pECS88_0017 NC_011747.1 15686 16120 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative enolase complement(15686..16120) Escherichia coli S88 7119368 YP_002401025.1 CDS sitD NC_011747.1 16588 17445 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6514154; Product type m : membrane component; SitD protein, Iron transport protein, inner membrane component complement(16588..17445) Escherichia coli S88 7119369 YP_002401026.1 CDS sitC NC_011747.1 17442 18299 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6514154; Product type m : membrane component; SitC protein, iron transport protein, inner membrane component complement(17442..18299) Escherichia coli S88 7119449 YP_002401027.1 CDS sitB NC_011747.1 18296 19123 R Evidence 2b : Function of strongly homologous gene; PubMedId : 16514154; Product type t : transporter; SitB protein, iron transport protein, ATP-binding component complement(18296..19123) Escherichia coli S88 7119448 YP_002401028.1 CDS sitA NC_011747.1 19123 20037 R Evidence 2b : Function of strongly homologous gene; PubMedId : 16514154; Product type t : transporter; SitA protein, iron transport protein, periplasmic-binding protein complement(19123..20037) Escherichia coli S88 7119447 YP_002401029.1 CDS pECS88_0023 NC_011747.1 20160 20351 R Evidence 6 : Doubtful CDS; hypothetical protein complement(20160..20351) Escherichia coli S88 7119446 YP_002401030.1 CDS insA NC_011747.1 20393 20668 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9689094; Product type h : extrachromosomal origin; IS1 repressor protein InsA 20393..20668 Escherichia coli S88 7119370 YP_002401031.1 CDS pECS88_0026 NC_011747.1 21101 21775 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(21101..21775) Escherichia coli S88 7119426 YP_002401032.1 CDS pECS88_0027 NC_011747.1 21933 22127 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein; putative exported protein 21933..22127 Escherichia coli S88 7119371 YP_002401033.1 CDS pECS88_0028 NC_011747.1 22203 22682 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(22203..22682) Escherichia coli S88 7119372 YP_002401034.1 CDS pECS88_0029 NC_011747.1 22800 23249 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 22800..23249 Escherichia coli S88 7119373 YP_002401035.1 CDS pECS88_0030 NC_011747.1 23866 25368 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 23866..25368 Escherichia coli S88 7119374 YP_002401036.1 CDS pECS88_0031 NC_011747.1 25594 25785 D Evidence 6 : Doubtful CDS; hypothetical protein 25594..25785 Escherichia coli S88 7119375 YP_002401037.1 CDS pECS88_0035 NC_011747.1 27444 27668 D Evidence 2b : Function of strongly homologous gene; PubMedId : 375010, 1849492; Product type pe : putative enzyme; transposase InsA (ORF1) IS1 27444..27668 Escherichia coli S88 7119376 YP_002401038.1 CDS insB NC_011747.1 27587 28090 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9689094; Product type h : extrachromosomal origin; transposase 27587..28090 Escherichia coli S88 7119377 YP_002401039.1 CDS sopA NC_011747.1 28381 29556 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3029390, 2670941, 10564491; Product type h : extrachromosomal origin; plasmid-partitioning protein SopA 28381..29556 Escherichia coli S88 7119427 YP_002401040.1 CDS sopB NC_011747.1 29556 30527 D SopB; plasmid-partitioning protein 29556..30527 Escherichia coli S88 7119450 YP_002401041.1 CDS pECS88_0039 NC_011747.1 31055 31216 R Evidence 6 : Doubtful CDS; hypothetical protein complement(31055..31216) Escherichia coli S88 7119451 YP_002401042.1 CDS pECS88_0040 NC_011747.1 31244 31591 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 31244..31591 Escherichia coli S88 7119378 YP_002401043.1 CDS pECS88_0041 NC_011747.1 31654 32235 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 31654..32235 Escherichia coli S88 7119379 YP_002401044.1 CDS pECS88_0042 NC_011747.1 32721 33692 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, putative transposase IS110 family complement(32721..33692) Escherichia coli S88 7119380 YP_002401045.1 CDS pECS88_0043 NC_011747.1 33844 34014 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(33844..34014) Escherichia coli S88 7119381 YP_002401046.1 CDS yubI NC_011747.1 34073 34519 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative antirestriction protein 34073..34519 Escherichia coli S88 7119382 YP_002401047.1 CDS pECS88_0045 NC_011747.1 34609 34980 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 34609..34980 Escherichia coli S88 7119500 YP_002401048.1 CDS pECS88_0046 NC_011747.1 34980 35162 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 34980..35162 Escherichia coli S88 7119383 YP_002401049.1 CDS ydbA NC_011747.1 36438 37799 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 36438..37799 Escherichia coli S88 7119384 YP_002401050.1 CDS ydcA NC_011747.1 37847 38410 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative adenine-specific DNA methylase 37847..38410 Escherichia coli S88 7119492 YP_002401051.1 CDS ssb NC_011747.1 39216 39848 D Evidence 2b : Function of strongly homologous gene; Product type cp : cell process; single-stranded DNA-binding protein 39216..39848 Escherichia coli S88 7119493 YP_002401052.1 CDS yubL NC_011747.1 39784 40044 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 39784..40044 Escherichia coli S88 7119452 YP_002401053.1 CDS pECS88_0052 NC_011747.1 40381 41922 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative transposase ORF1, IS21 family 40381..41922 Escherichia coli S88 7119501 YP_002401054.1 CDS pECS88_0053 NC_011747.1 41934 42683 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; Putative transposase ORF2, IS21 family 41934..42683 Escherichia coli S88 7119385 YP_002401055.1 CDS ycjA NC_011747.1 42799 44652 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type h : extrachromosomal origin; putative DNA-binding protein involved in plasmid partitioning (ParB-like partition protein) 42799..44652 Escherichia coli S88 7119386 YP_002401056.1 CDS psiB NC_011747.1 44704 45141 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 9987116, 10537187; Product type h : extrachromosomal origin; plasmid SOS inhibition protein B 44704..45141 Escherichia coli S88 7119491 YP_002401057.1 CDS psiA NC_011747.1 45138 45857 D PsiA; plasmid SOS inhibition protein A 45138..45857 Escherichia coli S88 7119442 YP_002401058.1 CDS flmC NC_011747.1 45991 46290 D Mok; similar to F leading maintenance protein C; modulator of post-segregation killing protein 45991..46290 Escherichia coli S88 7119421 YP_002401059.1 CDS yubN NC_011747.1 46532 46849 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein YubN complement(46532..46849) Escherichia coli S88 7119422 YP_002401060.1 CDS yubO NC_011747.1 47193 47480 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 47193..47480 Escherichia coli S88 7119502 YP_002401061.1 CDS yubP NC_011747.1 47518 48420 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 47518..48420 Escherichia coli S88 7119503 YP_002401062.1 CDS yubQ NC_011747.1 48716 49225 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; lytic transglycosylase complement(48716..49225) Escherichia coli S88 7119504 YP_002401063.1 CDS traM NC_011747.1 49640 50023 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15995191; Product type f : factor; conjugal transfer protein TraM 49640..50023 Escherichia coli S88 7119505 YP_002401064.1 CDS traJ NC_011747.1 50129 50899 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15388431; Product type r : regulator; conjugal transfer transcriptional regulator TraJ 50129..50899 Escherichia coli S88 7119465 YP_002401065.1 CDS traY NC_011747.1 50992 51393 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 7915817, 6368316, 8807284; Product type e : enzyme; conjugal transfer protein TraY 50992..51393 Escherichia coli S88 7119420 YP_002401066.1 CDS traA NC_011747.1 51426 51791 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6090426, 7915817, 2999074; Product type s : structure; conjugal transfer pilin subunit TraA 51426..51791 Escherichia coli S88 7119476 YP_002401067.1 CDS traL NC_011747.1 51806 52117 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6090426, 7915817, 2564189, 8655498; Product type m : membrane component; conjugal transfer pilus assembly protein TraL 51806..52117 Escherichia coli S88 7119453 YP_002401068.1 CDS traE NC_011747.1 52139 52705 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6090426, 7915817; Product type m : membrane component; conjugal transfer pilus assembly protein TraE 52139..52705 Escherichia coli S88 7119464 YP_002401069.1 CDS traK NC_011747.1 52692 53420 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8655498; Product type s : structure; conjugal transfer protein TraK 52692..53420 Escherichia coli S88 7119457 YP_002401070.1 CDS traB NC_011747.1 53420 54847 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 7915817, 8655498; Product type s : structure; conjugal transfer pilus assembly protein TraB 53420..54847 Escherichia coli S88 7119463 YP_002401071.1 CDS traP NC_011747.1 54837 55427 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component; conjugal transfer protein TraP 54837..55427 Escherichia coli S88 7119454 YP_002401072.1 CDS trbD NC_011747.1 55381 55611 D Evidence 4 : Homologs of previously reported genes of unknown function; conjugal transfer protein TrbD 55381..55611 Escherichia coli S88 7119467 YP_002401073.1 CDS trbG NC_011747.1 55623 55874 D Evidence 4 : Homologs of previously reported genes of unknown function; conjugal transfer protein TrbG 55623..55874 Escherichia coli S88 7119479 YP_002401074.1 CDS traV NC_011747.1 55871 56386 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8021201, 7915817; Product type lp : lipoprotein; conjugal transfer protein TraV 55871..56386 Escherichia coli S88 7119481 YP_002401075.1 CDS traR NC_011747.1 56521 56742 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 8021201; Product type pf : putative factor; conjugal transfer protein TraR 56521..56742 Escherichia coli S88 7119473 YP_002401076.1 CDS traC NC_011747.1 56902 59529 D similar to VirB4; conjugal transfer ATP-binding protein TraC 56902..59529 Escherichia coli S88 7119469 YP_002401077.1 CDS trbI NC_011747.1 59526 59912 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15292150; Product type m : membrane component; conjugal transfer protein TrbI 59526..59912 Escherichia coli S88 7119455 YP_002401078.1 CDS traW NC_011747.1 59909 60541 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15292150, 1355084, 7915817, 2198250; Product type s : structure; conjugal transfer pilus assembly protein TraW 59909..60541 Escherichia coli S88 7119482 YP_002401079.1 CDS traU NC_011747.1 60538 61530 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2198250, 7915817, 2050638, 1355084; Product type s : structure; conjugal transfer pilus assembly protein TraU 60538..61530 Escherichia coli S88 7119474 YP_002401080.1 CDS trbC NC_011747.1 61536 62177 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2050638, 7915817, 2198250, 1593622; Product type s : structure; conjugal transfer pilus assembly protein TrbC 61536..62177 Escherichia coli S88 7119472 YP_002401081.1 CDS traN NC_011747.1 62174 63982 D TraN; TrhN; involved in stabilizing mating pairs during plasmid conjugation; F plasmid TraN appears to recognize OmpA in the recipient cell; conjugal transfer mating pair stabilization protein TraN 62174..63982 Escherichia coli S88 7119478 YP_002401082.1 CDS trbE NC_011747.1 64006 64266 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 12533481, 1593622, 7915817; Product type m : membrane component; conjugal transfer protein TrbE 64006..64266 Escherichia coli S88 7119466 YP_002401083.1 CDS traF NC_011747.1 64229 65002 D type IV secretion system pilus assembly protein; similar to F plasmid TraF; conjugal pilus assembly protein TraF 64229..65002 Escherichia coli S88 7119480 YP_002401084.1 CDS traQ NC_011747.1 65484 65768 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2536655, 7915817; Product type m : membrane component; conjugal transfer pilin chaperone TraQ 65484..65768 Escherichia coli S88 7119458 YP_002401085.1 CDS trbB NC_011747.1 65755 66300 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; PubMedId : 16321931, 2536655, 7915817; Product type pe : putative enzyme; conjugal transfer protein TrbB 65755..66300 Escherichia coli S88 7119468 YP_002401086.1 CDS trbJ NC_011747.1 66230 66592 D Evidence 2b : Function of strongly homologous gene; PubMedId : 8444814, 7899511, 10438776; Product type m : membrane component; conjugal transfer protein TrbJ 66230..66592 Escherichia coli S88 7119477 YP_002401087.1 CDS traH NC_011747.1 66589 67965 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1348105, 7915817, 2656408; Product type s : structure; conjugal transfer pilus assembly protein TraH 66589..67965 Escherichia coli S88 7119483 YP_002401088.1 CDS traG NC_011747.1 67962 70472 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1348105, 7915817; Product type m : membrane component; conjugal transfer mating pair stabilization protein TraG 67962..70472 Escherichia coli S88 7119460 YP_002401089.1 CDS traS NC_011747.1 70791 71306 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3323526; Product type m : membrane component; surface exclusion inner membrane protein TraS 70791..71306 Escherichia coli S88 7119459 YP_002401090.1 CDS traT NC_011747.1 71239 72069 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 1359384, 3323526, 7915817, 2087219, 6995306, 9696748, 1730875, 6238226; Product type m : membrane component; conjugal transfer surface exclusion protein TraT 71239..72069 Escherichia coli S88 7119470 YP_002401091.1 CDS traD NC_011747.1 72321 74474 D type IV secretion system coupling protein; similar to F plasmid TraD; conjugal transfer protein TraD 72321..74474 Escherichia coli S88 7119471 YP_002401092.1 CDS traI NC_011747.1 74474 79744 D cleaves origin of transfer and unwinds; oriT relaxase; conjugal transfer nickase/helicase TraI 74474..79744 Escherichia coli S88 7119456 YP_002401093.1 CDS traX NC_011747.1 79764 80510 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 8444800, 7768788, 1916281, 7915817, 2164585; Product type e : enzyme; conjugal transfer pilus acetylation protein TraX 79764..80510 Escherichia coli S88 7119461 YP_002401094.1 CDS finO NC_011747.1 80514 81125 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2164585, 1916281, 7915817, 8807284, 1374147, 10876242, 3027040, 2951652; Product type r : regulator; conjugal transfer fertility inhibition protein FinO 80514..81125 Escherichia coli S88 7119475 YP_002401095.1 CDS yigA NC_011747.1 81263 81475 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 81263..81475 Escherichia coli S88 7119419 YP_002401096.1 CDS yigB NC_011747.1 81658 82119 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative nuclease YigB 81658..82119 Escherichia coli S88 7119496 YP_002401097.1 CDS repA2 NC_011747.1 82164 82424 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 6261081, 7003300, 3019092, 7029525, 2445727, 2580099, 1865183; Product type r : regulator; replication protein 82164..82424 Escherichia coli S88 7119497 YP_002401098.1 CDS repA1 NC_011747.1 82705 83574 D RepA; replication protein 82705..83574 Escherichia coli S88 7119411 YP_002401099.1 CDS yacA NC_011747.1 84490 84759 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein YacA, possible repressor 84490..84759 Escherichia coli S88 7119443 YP_002401100.1 CDS yacB NC_011747.1 84756 85037 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative plasmid stabilisation system protein YacB 84756..85037 Escherichia coli S88 7119484 YP_002401101.1 CDS yacC NC_011747.1 85083 85931 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; putative exoribonuclease YacC 85083..85931 Escherichia coli S88 7119486 YP_002401102.1 CDS cia NC_011747.1 86117 87997 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 7972047, 9009197; Product type m : membrane component; Colicin-Ia 86117..87997 Escherichia coli S88 7119488 YP_002401103.1 CDS imm NC_011747.1 88019 88354 R Evidence 2b : Function of strongly homologous gene; PubMedId : 3531169, 7972047; Product type m : membrane component; Colicin-Ia immunity protein complement(88019..88354) Escherichia coli S88 7119410 YP_002401104.1 CDS ybaA NC_011747.1 88483 88740 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein YbaA 88483..88740 Escherichia coli S88 7119424 YP_002401105.1 CDS ydeA NC_011747.1 88760 89350 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein YdeA complement(88760..89350) Escherichia coli S88 7119489 YP_002401106.1 CDS ydfA NC_011747.1 89347 89607 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein YdfA complement(89347..89607) Escherichia coli S88 7119494 YP_002401107.1 CDS pECS88_0110 NC_011747.1 89900 90352 D Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pe : putative enzyme; Putative acetyltransferase 89900..90352 Escherichia coli S88 7119495 YP_002401108.1 CDS pECS88_0111 NC_011747.1 90408 90674 R Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein, predicted dehydrogenase complement(90408..90674) Escherichia coli S88 7119387 YP_002401109.1 CDS pECS88_0112 NC_011747.1 90942 91346 R Evidence 4 : Homologs of previously reported genes of unknown function; putative dehydrogenase complement(90942..91346) Escherichia coli S88 7119388 YP_002401110.1 CDS pECS88_0113 NC_011747.1 91318 91761 R Evidence 4 : Homologs of previously reported genes of unknown function; putative dehydrogenase complement(91318..91761) Escherichia coli S88 7119389 YP_002401111.1 CDS cvi NC_011747.1 91880 92116 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 3034857; Product type m : membrane component; colicin V immunity protein 91880..92116 Escherichia coli S88 7119390 YP_002401112.1 CDS cvaC NC_011747.1 92094 92405 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2249654, 9743528, 7952189, 8204625; Product type f : factor; Colicin V precursor (Microcin V bacteriocin) 92094..92405 Escherichia coli S88 7119415 YP_002401113.1 CDS cvaB NC_011747.1 92575 94671 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 2249654, 9743528; Product type t : transporter; Colicin V secretion/processing ATP-binding protein CvaB complement(92575..94671) Escherichia coli S88 7119414 YP_002401114.1 CDS cvaA NC_011747.1 94664 95938 R Evidence 2b : Function of strongly homologous gene; PubMedId : 2249654, 7592380; Product type t : transporter; Colicin V secretion protein CvaA complement(94664..95938) Escherichia coli S88 7119413 YP_002401115.1 CDS pECS88_0118 NC_011747.1 96346 96555 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(96346..96555) Escherichia coli S88 7119412 YP_002401116.1 CDS yacA NC_011747.1 96549 96818 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein YacA, possible repressor 96549..96818 Escherichia coli S88 7119391 YP_002401117.1 CDS pECS88_0123 NC_011747.1 97964 98998 D catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive; phospho-2-dehydro-3-deoxyheptonate aldolase 97964..98998 Escherichia coli S88 7119490 YP_002401118.1 CDS iroN NC_011747.1 99851 102013 D Fep; Cbt; Cbr; FeuB; FepA; PfeA; IroN; BfeA; outer membrane receptor of ferric enterobactin and colicins B and D; interacts with the TonB-ExbBD complex which catalyzes the translocation of the siderophore to the periplasmic space; outer membrane receptor FepA 99851..102013 Escherichia coli S88 7119392 YP_002401119.1 CDS iroE NC_011747.1 102058 103014 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12655053, 12761110; Product type e : enzyme; IroE, putative hydrolase complement(102058..103014) Escherichia coli S88 7119433 YP_002401120.1 CDS iroD NC_011747.1 103099 104328 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12655053, 12761110; Product type e : enzyme; IroD, putative ferric enterochelin esterase complement(103099..104328) Escherichia coli S88 7119432 YP_002401121.1 CDS iroC NC_011747.1 104432 108091 R Evidence 2b : Function of strongly homologous gene; PubMedId : 12655053, 12761110; Product type t : transporter; IroC, ATP binding cassette (ABC) transporter homolog complement(104432..108091) Escherichia coli S88 7119431 YP_002401122.1 CDS iroB NC_011747.1 108231 109346 R Evidence 2a : Function of homologous gene experimentally demonstrated in an other organism; PubMedId : 12655053, 12761110; Product type e : enzyme; IroB, putative glucosyltransferase complement(108231..109346) Escherichia coli S88 7119430 YP_002401123.1 CDS pECS88_0130 NC_011747.1 110582 111217 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(110582..111217) Escherichia coli S88 7119429 YP_002401124.1 CDS pECS88_0131 NC_011747.1 111327 111632 R Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein complement(111327..111632) Escherichia coli S88 7119393 YP_002401125.1 CDS pECS88_0132 NC_011747.1 112196 112378 D Evidence 5 : No homology to any previously reported sequences; hypothetical protein 112196..112378 Escherichia coli S88 7119394 YP_002401126.1 CDS iss NC_011747.1 112492 112785 R Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 10737659, 2144037, 7868598; Product type lp : lipoprotein; Iss (Increased serum survival) complement(112492..112785) Escherichia coli S88 7119395 YP_002401127.1 CDS yqiG NC_011747.1 113412 113777 D IS2 OrfA; forms an overlapping reading frame with orfB; may form a fusion protein OrfAB due to ribosomal frameshifting; both OrfA and OrfAB bind terminal inverted repeats; insertion sequence 2 OrfA protein 113412..113777 Escherichia coli S88 7119434 YP_002401128.1 CDS yqiG NC_011747.1 113735 114640 D Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase ORF 2, IS2 113735..114640 Escherichia coli S88 7119498 YP_002401129.1 CDS pECS88_0136 NC_011747.1 115306 115449 D Evidence 6 : Doubtful CDS; hypothetical protein 115306..115449 Escherichia coli S88 7119499 YP_002401130.1 CDS pECS88_0137 NC_011747.1 115864 117057 D Evidence 4 : Homologs of previously reported genes of unknown function; conserved hypothetical protein; putative GTPase 115864..117057 Escherichia coli S88 7119396 YP_002401131.1 CDS pECS88_0138 NC_011747.1 117190 117507 D Evidence 7 : Gene remnant; Product type pe : putative enzyme; putative transposase ORF B (fragment), IS2 117190..117507 Escherichia coli S88 7119397 YP_002401132.1 CDS pECS88_0139 NC_011747.1 117694 118560 D Evidence 7 : Gene remnant; Product type pe : putative enzyme; putative transposase (fragment) 117694..118560 Escherichia coli S88 7119398 YP_002401133.1 CDS pECS88_0142 NC_011747.1 119120 119308 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 119120..119308 Escherichia coli S88 7119401 YP_002401134.1 CDS pECS88_0143 NC_011747.1 119318 120259 D Evidence 4 : Homologs of previously reported genes of unknown function; hypothetical protein 119318..120259 Escherichia coli S88 7119402 YP_002401135.1 CDS etsC NC_011747.1 121056 122426 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative type I secretion outer membrane protein EtsC complement(121056..122426) Escherichia coli S88 7119403 YP_002401136.1 CDS etsB NC_011747.1 122430 124370 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; putative type I secretion ATP binding protein EtsB complement(122430..124370) Escherichia coli S88 7119418 YP_002401137.1 CDS etsA NC_011747.1 124367 125575 R Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt : putative transporter; Putative type I secretion membrane-fusion protein EtsA complement(124367..125575) Escherichia coli S88 7119417 YP_002401138.1 CDS pECS88_0151 NC_011747.1 127008 127898 R Evidence 2b : Function of strongly homologous gene; PubMedId : 2832386; Product type pe : putative enzyme; transposase ORF B, IS3 family, IS51 group complement(127008..127898) Escherichia coli S88 7119405 YP_002401139.1 CDS pECS88_0152 NC_011747.1 127895 128221 R Evidence 2b : Function of strongly homologous gene; Product type pe : putative enzyme; transposase ORF A, IS3 family, IS51 group complement(127895..128221) Escherichia coli S88 7119406 YP_002401140.1 CDS pECS88_0154 NC_011747.1 129343 129732 R Evidence 5 : No homology to any previously reported sequences; hypothetical protein complement(129343..129732) Escherichia coli S88 7119408 YP_002401141.1 CDS ompT NC_011747.1 129836 130789 D outer membrane protease; involved in virulence in many organisms; OmpT; IcsP; SopA; Pla; PgtE; omptin; in Escherichia coli OmpT can degrade antimicrobial peptides; in Yersinia Pla activates plasminogen during infection; in Shigella flexneria SopA cleaves the autotransporter IcsA; outer membrane protease 129836..130789 Escherichia coli S88 7119409 YP_002401142.1 CDS hlyF NC_011747.1 131222 132331 D Evidence 1b : Function experimentally demonstrated in the studied species; PubMedId : 15992275; Product type e : enzyme; hemolysin HlyF 131222..132331 Escherichia coli S88 7119440 YP_002401143.1 CDS pECS88_0157 NC_011747.1 132394 133302 D Evidence 4 : Homologs of previously reported genes of unknown function; PubMedId : 15992275; conserved hypothetical protein; putative Mig-14 protein 132394..133302 Escherichia coli S88 7119423 ECS88_tRNA1 tRNA ECS88_tRNA1 NC_011742.1 230133 230209 D tRNA-Ile 230133..230209 Escherichia coli S88 7129270 ECS88_tRNA2 tRNA ECS88_tRNA2 NC_011742.1 230252 230327 D tRNA-Ala 230252..230327 Escherichia coli S88 7129866 ECS88_tRNA3 tRNA ECS88_tRNA3 NC_011742.1 233675 233751 D tRNA-Asp 233675..233751 Escherichia coli S88 7129849 ECS88_tRNA4 tRNA ECS88_tRNA4 NC_011742.1 241898 241974 D tRNA-Asp 241898..241974 Escherichia coli S88 7130228 ECS88_tRNA5 tRNA ECS88_tRNA5 NC_011742.1 295064 295139 D tRNA-Thr 295064..295139 Escherichia coli S88 7130784 ECS88_tRNA6 tRNA ECS88_tRNA6 NC_011742.1 364658 364738 D tRNA-OTHER 364658..364738 Escherichia coli S88 7130309 ECS88_tRNA7 tRNA ECS88_tRNA7 NC_011742.1 558414 558490 D tRNA-Arg 558414..558490 Escherichia coli S88 7129102 ECS88_tRNA8 tRNA ECS88_tRNA8 NC_011742.1 574100 574175 D tRNA-Met 574100..574175 Escherichia coli S88 7130670 ECS88_tRNA9 tRNA ECS88_tRNA9 NC_011742.1 574183 574259 D tRNA-Arg 574183..574259 Escherichia coli S88 7132000 ECS88_tRNA10 tRNA ECS88_tRNA10 NC_011742.1 574273 574349 D tRNA-Arg 574273..574349 Escherichia coli S88 7132011 ECS88_tRNA91 tRNA ECS88_tRNA91 NC_011742.1 711248 711322 R tRNA-Gln complement(711248..711322) Escherichia coli S88 7130385 ECS88_tRNA90 tRNA ECS88_tRNA90 NC_011742.1 711360 711434 R tRNA-Gln complement(711360..711434) Escherichia coli S88 7132013 ECS88_tRNA89 tRNA ECS88_tRNA89 NC_011742.1 711483 711559 R tRNA-Met complement(711483..711559) Escherichia coli S88 7132012 ECS88_tRNA88 tRNA ECS88_tRNA88 NC_011742.1 711575 711649 R tRNA-Gln complement(711575..711649) Escherichia coli S88 7132010 ECS88_tRNA87 tRNA ECS88_tRNA87 NC_011742.1 711684 711758 R tRNA-Gln complement(711684..711758) Escherichia coli S88 7132009 ECS88_tRNA86 tRNA ECS88_tRNA86 NC_011742.1 711782 711866 R tRNA-Leu complement(711782..711866) Escherichia coli S88 7130710 ECS88_tRNA85 tRNA ECS88_tRNA85 NC_011742.1 711877 711953 R tRNA-Met complement(711877..711953) Escherichia coli S88 7132007 ECS88_tRNA11 tRNA ECS88_tRNA11 NC_011742.1 784314 784389 D tRNA-Lys 784314..784389 Escherichia coli S88 7131221 ECS88_tRNA12 tRNA ECS88_tRNA12 NC_011742.1 784425 784500 D tRNA-Val 784425..784500 Escherichia coli S88 7129868 ECS88_tRNA13 tRNA ECS88_tRNA13 NC_011742.1 784503 784578 D tRNA-Lys 784503..784578 Escherichia coli S88 7129869 ECS88_tRNA14 tRNA ECS88_tRNA14 NC_011742.1 784630 784705 D tRNA-Val 784630..784705 Escherichia coli S88 7129870 ECS88_tRNA15 tRNA ECS88_tRNA15 NC_011742.1 784709 784784 D tRNA-Lys 784709..784784 Escherichia coli S88 7129871 ECS88_tRNA16 tRNA ECS88_tRNA16 NC_011742.1 784833 784908 D tRNA-Lys 784833..784908 Escherichia coli S88 7129872 ECS88_tRNA17 tRNA ECS88_tRNA17 NC_011742.1 784942 785017 D tRNA-Lys 784942..785017 Escherichia coli S88 7129873 ECS88_tRNA84 tRNA ECS88_tRNA84 NC_011742.1 935526 935613 R tRNA-Ser complement(935526..935613) Escherichia coli S88 7130729 ECS88_tRNA83 tRNA ECS88_tRNA83 NC_011742.1 1031502 1031589 R tRNA-Ser complement(1031502..1031589) Escherichia coli S88 7130163 ECS88_tRNA82 tRNA ECS88_tRNA82 NC_011742.1 1083508 1083595 R tRNA-Ser complement(1083508..1083595) Escherichia coli S88 7131424 ECS88_tRNA81 tRNA ECS88_tRNA81 NC_011742.1 1304354 1304438 R tRNA-Tyr complement(1304354..1304438) Escherichia coli S88 7131309 ECS88_tRNA80 tRNA ECS88_tRNA80 NC_011742.1 1304472 1304556 R tRNA-Tyr complement(1304472..1304556) Escherichia coli S88 7132002 ECS88_tRNA18 tRNA ECS88_tRNA18 NC_011742.1 1346648 1346723 D tRNA-Met 1346648..1346723 Escherichia coli S88 7129194 ECS88_tRNA19 tRNA ECS88_tRNA19 NC_011742.1 1346821 1346897 D tRNA-Arg 1346821..1346897 Escherichia coli S88 7129875 ECS88_tRNA20 tRNA ECS88_tRNA20 NC_011742.1 1710627 1710703 D tRNA-Val 1710627..1710703 Escherichia coli S88 7133205 ECS88_tRNA21 tRNA ECS88_tRNA21 NC_011742.1 1710708 1710784 D tRNA-Val 1710708..1710784 Escherichia coli S88 7129878 ECS88_tRNA79 tRNA ECS88_tRNA79 NC_011742.1 1943996 1944082 R tRNA-Leu complement(1943996..1944082) Escherichia coli S88 7131835 ECS88_tRNA78 tRNA ECS88_tRNA78 NC_011742.1 1944095 1944168 R tRNA-Cys complement(1944095..1944168) Escherichia coli S88 7131999 ECS88_tRNA77 tRNA ECS88_tRNA77 NC_011742.1 1944223 1944298 R tRNA-Gly complement(1944223..1944298) Escherichia coli S88 7131998 ECS88_tRNA76 tRNA ECS88_tRNA76 NC_011742.1 1997147 1997236 R tRNA-Ser complement(1997147..1997236) Escherichia coli S88 7133641 ECS88_tRNA22 tRNA ECS88_tRNA22 NC_011742.1 1998228 1998303 D tRNA-Asn 1998228..1998303 Escherichia coli S88 7132950 ECS88_tRNA75 tRNA ECS88_tRNA75 NC_011742.1 2038121 2038196 R tRNA-Asn complement(2038121..2038196) Escherichia coli S88 7132954 ECS88_tRNA23 tRNA ECS88_tRNA23 NC_011742.1 2039945 2040020 D tRNA-Asn 2039945..2040020 Escherichia coli S88 7132955 ECS88_tRNA24 tRNA ECS88_tRNA24 NC_011742.1 2042353 2042428 D tRNA-Asn 2042353..2042428 Escherichia coli S88 7129649 ECS88_tRNA25 tRNA ECS88_tRNA25 NC_011742.1 2322084 2322160 D tRNA-Pro 2322084..2322160 Escherichia coli S88 7129775 ECS88_tRNA26 tRNA ECS88_tRNA26 NC_011742.1 2493119 2493193 D tRNA-Arg 2493119..2493193 Escherichia coli S88 7129827 ECS88_tRNA74 tRNA ECS88_tRNA74 NC_011742.1 2573594 2573669 R tRNA-Ala complement(2573594..2573669) Escherichia coli S88 7133510 ECS88_tRNA73 tRNA ECS88_tRNA73 NC_011742.1 2573709 2573784 R tRNA-Ala complement(2573709..2573784) Escherichia coli S88 7131994 ECS88_tRNA27 tRNA ECS88_tRNA27 NC_011742.1 2576483 2576558 D tRNA-Val 2576483..2576558 Escherichia coli S88 7130038 ECS88_tRNA28 tRNA ECS88_tRNA28 NC_011742.1 2576603 2576678 D tRNA-Val 2576603..2576678 Escherichia coli S88 7129885 ECS88_tRNA29 tRNA ECS88_tRNA29 NC_011742.1 2576725 2576800 D tRNA-Val 2576725..2576800 Escherichia coli S88 7129886 ECS88_tRNA30 tRNA ECS88_tRNA30 NC_011742.1 2576805 2576880 D tRNA-Lys 2576805..2576880 Escherichia coli S88 7129887 ECS88_tRNA72 tRNA ECS88_tRNA72 NC_011742.1 2771898 2771973 R tRNA-Glu complement(2771898..2771973) Escherichia coli S88 7133418 ECS88_tRNA71 tRNA ECS88_tRNA71 NC_011742.1 2908922 2908998 R tRNA-Arg complement(2908922..2908998) Escherichia coli S88 7132077 ECS88_tRNA70 tRNA ECS88_tRNA70 NC_011742.1 2909062 2909138 R tRNA-Arg complement(2909062..2909138) Escherichia coli S88 7131991 ECS88_tRNA69 tRNA ECS88_tRNA69 NC_011742.1 2909202 2909278 R tRNA-Arg complement(2909202..2909278) Escherichia coli S88 7131990 ECS88_tRNA68 tRNA ECS88_tRNA68 NC_011742.1 2909343 2909419 R tRNA-Arg complement(2909343..2909419) Escherichia coli S88 7131988 ECS88_tRNA67 tRNA ECS88_tRNA67 NC_011742.1 2909423 2909515 R tRNA-Ser complement(2909423..2909515) Escherichia coli S88 7131987 ECS88_tRNA31 tRNA ECS88_tRNA31 NC_011742.1 3033607 3033683 D tRNA-Met 3033607..3033683 Escherichia coli S88 7128842 ECS88_tRNA32 tRNA ECS88_tRNA32 NC_011742.1 3033717 3033793 D tRNA-Met 3033717..3033793 Escherichia coli S88 7129890 ECS88_tRNA33 tRNA ECS88_tRNA33 NC_011742.1 3033827 3033903 D tRNA-Met 3033827..3033903 Escherichia coli S88 7129891 ECS88_tRNA66 tRNA ECS88_tRNA66 NC_011742.1 3109710 3109783 R tRNA-Gly complement(3109710..3109783) Escherichia coli S88 7132086 ECS88_tRNA34 tRNA ECS88_tRNA34 NC_011742.1 3219801 3219876 D tRNA-Phe 3219801..3219876 Escherichia coli S88 7132090 ECS88_tRNA35 tRNA ECS88_tRNA35 NC_011742.1 3431106 3431181 D tRNA-Met 3431106..3431181 Escherichia coli S88 7132230 ECS88_tRNA65 tRNA ECS88_tRNA65 NC_011742.1 3525740 3525816 R tRNA-Met complement(3525740..3525816) Escherichia coli S88 7132247 ECS88_tRNA64 tRNA ECS88_tRNA64 NC_011742.1 3529594 3529680 R tRNA-Leu complement(3529594..3529680) Escherichia coli S88 7132259 ECS88_tRNA63 tRNA ECS88_tRNA63 NC_011742.1 3629076 3629151 R tRNA-Thr complement(3629076..3629151) Escherichia coli S88 7129847 ECS88_tRNA62 tRNA ECS88_tRNA62 NC_011742.1 3632465 3632540 R tRNA-Ala complement(3632465..3632540) Escherichia coli S88 7133417 ECS88_tRNA61 tRNA ECS88_tRNA61 NC_011742.1 3632583 3632659 R tRNA-Ile complement(3632583..3632659) Escherichia coli S88 7131981 ECS88_tRNA60 tRNA ECS88_tRNA60 NC_011742.1 3923409 3923485 R tRNA-Pro complement(3923409..3923485) Escherichia coli S88 7130232 ECS88_tRNA36 tRNA ECS88_tRNA36 NC_011742.1 4049371 4049461 D tRNA-Sec 4049371..4049461 Escherichia coli S88 7130823 ECS88_tRNA37 tRNA ECS88_tRNA37 NC_011742.1 4151808 4151883 D tRNA-Glu 4151808..4151883 Escherichia coli S88 7129271 ECS88_tRNA38 tRNA ECS88_tRNA38 NC_011742.1 4155245 4155321 D tRNA-Asp 4155245..4155321 Escherichia coli S88 7129850 ECS88_tRNA39 tRNA ECS88_tRNA39 NC_011742.1 4155330 4155405 D tRNA-Trp 4155330..4155405 Escherichia coli S88 7129897 ECS88_tRNA40 tRNA ECS88_tRNA40 NC_011742.1 4189874 4189950 D tRNA-Arg 4189874..4189950 Escherichia coli S88 7130858 ECS88_tRNA41 tRNA ECS88_tRNA41 NC_011742.1 4190009 4190084 D tRNA-His 4190009..4190084 Escherichia coli S88 7129900 ECS88_tRNA42 tRNA ECS88_tRNA42 NC_011742.1 4190105 4190191 D tRNA-Leu 4190105..4190191 Escherichia coli S88 7129901 ECS88_tRNA43 tRNA ECS88_tRNA43 NC_011742.1 4190234 4190310 D tRNA-Pro 4190234..4190310 Escherichia coli S88 7129902 ECS88_tRNA44 tRNA ECS88_tRNA44 NC_011742.1 4270035 4270111 D tRNA-Ile 4270035..4270111 Escherichia coli S88 7129434 ECS88_tRNA45 tRNA ECS88_tRNA45 NC_011742.1 4270154 4270229 D tRNA-Ala 4270154..4270229 Escherichia coli S88 7129904 ECS88_tRNA46 tRNA ECS88_tRNA46 NC_011742.1 4404659 4404734 D tRNA-Glu 4404659..4404734 Escherichia coli S88 7128947 ECS88_tRNA47 tRNA ECS88_tRNA47 NC_011742.1 4411511 4411586 D tRNA-Thr 4411511..4411586 Escherichia coli S88 7131938 ECS88_tRNA48 tRNA ECS88_tRNA48 NC_011742.1 4411595 4411679 D tRNA-Tyr 4411595..4411679 Escherichia coli S88 7129907 ECS88_tRNA49 tRNA ECS88_tRNA49 NC_011742.1 4411796 4411870 D tRNA-Gly 4411796..4411870 Escherichia coli S88 7129908 ECS88_tRNA50 tRNA ECS88_tRNA50 NC_011742.1 4411877 4411952 D tRNA-Thr 4411877..4411952 Escherichia coli S88 7129909 ECS88_tRNA51 tRNA ECS88_tRNA51 NC_011742.1 4444829 4444904 D tRNA-Glu 4444829..4444904 Escherichia coli S88 7128948 ECS88_tRNA59 tRNA ECS88_tRNA59 NC_011742.1 4685049 4685124 R tRNA-Phe complement(4685049..4685124) Escherichia coli S88 7132671 ECS88_tRNA52 tRNA ECS88_tRNA52 NC_011742.1 4714558 4714633 D tRNA-Gly 4714558..4714633 Escherichia coli S88 7133142 ECS88_tRNA53 tRNA ECS88_tRNA53 NC_011742.1 4714670 4714745 D tRNA-Gly 4714670..4714745 Escherichia coli S88 7129913 ECS88_tRNA54 tRNA ECS88_tRNA54 NC_011742.1 4714781 4714856 D tRNA-Gly 4714781..4714856 Escherichia coli S88 7129914 ECS88_tRNA55 tRNA ECS88_tRNA55 NC_011742.1 4820779 4820863 D tRNA-Leu 4820779..4820863 Escherichia coli S88 7132682 ECS88_tRNA58 tRNA ECS88_tRNA58 NC_011742.1 4950022 4950108 R tRNA-Leu complement(4950022..4950108) Escherichia coli S88 7132568 ECS88_tRNA57 tRNA ECS88_tRNA57 NC_011742.1 4950143 4950229 R tRNA-Leu complement(4950143..4950229) Escherichia coli S88 7129919 ECS88_tRNA56 tRNA ECS88_tRNA56 NC_011742.1 4950258 4950344 R tRNA-Leu complement(4950258..4950344) Escherichia coli S88 7129918 ECS88_16S_3 rRNA ECS88_16S_3 NC_011742.1 228523 230064 D ribosomal RNA 16S 228523..230064 Escherichia coli S88 7130045 ECS88_23S_3 rRNA ECS88_23S_3 NC_011742.1 230502 233405 D ribosomal RNA 23S 230502..233405 Escherichia coli S88 7129877 ECS88_5S_4 rRNA ECS88_5S_4 NC_011742.1 233504 233623 D ribosomal RNA 5S 233504..233623 Escherichia coli S88 7133419 ECS88_5S_3 rRNA ECS88_5S_3 NC_011742.1 2768587 2768706 R ribosomal RNA 5S complement(2768587..2768706) Escherichia coli S88 7130923 ECS88_23S_2 rRNA ECS88_23S_2 NC_011742.1 2768801 2771704 R ribosomal RNA 23S complement(2768801..2771704) Escherichia coli S88 7129848 ECS88_16S_2 rRNA ECS88_16S_2 NC_011742.1 2772059 2773600 R ribosomal RNA 16S complement(2772059..2773600) Escherichia coli S88 7131992 ECS88_5S_2 rRNA ECS88_5S_2 NC_011742.1 3628923 3629035 R ribosomal RNA 5S complement(3628923..3629035) Escherichia coli S88 7132020 ECS88_5S_1 rRNA ECS88_5S_1 NC_011742.1 3629164 3629283 R ribosomal RNA 5S complement(3629164..3629283) Escherichia coli S88 7131982 ECS88_23S_1 rRNA ECS88_23S_1 NC_011742.1 3629378 3632281 R ribosomal RNA 23S complement(3629378..3632281) Escherichia coli S88 7129846 ECS88_16S_1 rRNA ECS88_16S_1 NC_011742.1 3632728 3634269 R ribosomal RNA 16S complement(3632728..3634269) Escherichia coli S88 7131862 ECS88_16S_4 rRNA ECS88_16S_4 NC_011742.1 4150181 4151722 D ribosomal RNA 16S 4150181..4151722 Escherichia coli S88 7130855 ECS88_23S_4 rRNA ECS88_23S_4 NC_011742.1 4152077 4154980 D ribosomal RNA 23S 4152077..4154980 Escherichia coli S88 7129896 ECS88_5S_5 rRNA ECS88_5S_5 NC_011742.1 4155074 4155193 D ribosomal RNA 5S 4155074..4155193 Escherichia coli S88 7133420 ECS88_16S_5 rRNA ECS88_16S_5 NC_011742.1 4268425 4269966 D ribosomal RNA 16S 4268425..4269966 Escherichia coli S88 7128902 ECS88_23S_5 rRNA ECS88_23S_5 NC_011742.1 4270413 4273316 D ribosomal RNA 23S 4270413..4273316 Escherichia coli S88 7129905 ECS88_5S_6 rRNA ECS88_5S_6 NC_011742.1 4273410 4273529 D ribosomal RNA 5S 4273410..4273529 Escherichia coli S88 7133421 ECS88_16S_6 rRNA ECS88_16S_6 NC_011742.1 4403031 4404573 D ribosomal RNA 16S 4403031..4404573 Escherichia coli S88 7129637 ECS88_23S_6 rRNA ECS88_23S_6 NC_011742.1 4404928 4407831 D ribosomal RNA 23S 4404928..4407831 Escherichia coli S88 7129906 ECS88_5S_7 rRNA ECS88_5S_7 NC_011742.1 4407926 4408045 D ribosomal RNA 5S 4407926..4408045 Escherichia coli S88 7133422 ECS88_16S_7 rRNA ECS88_16S_7 NC_011742.1 4443202 4444743 D ribosomal RNA 16S 4443202..4444743 Escherichia coli S88 7131750 ECS88_23S_7 rRNA ECS88_23S_7 NC_011742.1 4445098 4448001 D ribosomal RNA 23S 4445098..4448001 Escherichia coli S88 7129912 ECS88_5S_8 rRNA ECS88_5S_8 NC_011742.1 4448095 4448214 D ribosomal RNA 5S 4448095..4448214 Escherichia coli S88 7133423