1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Feature Locustag K-12 Gene name K-12 Locus name K-12 Synonyms of locus names K-12 Locustag MG1655 Left nucleotide MG1655 Right nucleotide MG1655 Direction of Transcription MG1655 Comment on gene boundary MG1655 Locustag W3110 Left nucleotide W3110 Right nucleotide W3110 Direction of Transcription W3110 Comment on gene boundary W3110 Type of gene product Gene product description Comment gene product description Evidence Literature Cell location Context (genetic element) Enzyme Nomenclature (EC number) Cofactor Protein complex Transporter Classification Transcription regulator family Proteases Signal peptide predictions Signal Peptide Cleavage Sites Transmembrane segments 1 Transmembrane segments 2 TM protein C-term location Transcriptional unit(s) regulated Operons with attenuation regulation Modularized function Structure (PDB) id COG assignment SCOP assignment PFAM assignment TIGRFAM assignment GO cellular component GO cellular process GO molecular function CDS ECK0001 thrL thrL b0001 190 255 + (no change) JW4367 4646522 4646587 + l thr operon leader peptide E 6277952 -!- 6818426 Cytoplasmic TIGR02077;thr_lead_pep: thr operon leader peptide;2.2e-05;codon 1-21 GO:0009088 threonine biosynthesis CDS ECK0002 thrA thrA Hs -!- thrA1 -!- thrA2 -!- thrD b0002 337 2799 + (no change) JW0001 337 2799 + e fused aspartokinase I -!- homoserine dehydrogenase I threonine sensitive E 1598232 -!- 353521 -!- 78130080 -!- 85080024 -!- 89274327 -!- 387092 -!- 390305 -!- 6298218 -!- 7003595 Cytoplasmic 2.7.2.4 -!- 1.1.1.3 monomeric multimer; aspartate kinase I / homoserine dehydrogenase I (b0002) fused: aspartokinase I (aa1-461) -!- homoserine dehydrogenase (aa 464-820) COG0527;Aspartokinases -!- COG0460;Homoserine dehydrogenase "53633; Carbamate kinase-like -!- 51735; NAD(P)-binding Rossmann-fold domains -!- 55347; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain" "PF00696;AA kinase family;2.3e-65;codon 1-284 -!- PF01842;ACT;8.4e-08;codon 316-384 -!- PF01842;ACT;1.2e-09;codon 397-468 -!- PF03447;Homoserine dehydrogenase, NAD binding;2.3e-65;codon 479-612 -!- PF00742;Homoserine dehydrogenase;1.8e-107;codon 614-811" TIGR00657;asp_kinases: aspartate kinase;2.4e-244;codon 1-461 GO:0005737 cytoplasm GO:0009088 threonine biosynthesis -!- GO:0009086 methionine biosynthesis -!- GO:0009090 homoserine biosynthesis CDS ECK0003 thrB thrB b0003 2801 3733 + (no change) JW0002 2801 3733 + e homoserine kinase E 76165260 -!- 81150470 Cytoplasmic 2.7.1.39 Mg2+ monomeric multimer; homoserine kinase (b0003) COG0083;Homoserine kinase 54211; Ribosomal protein S5 domain 2-like -!- 55060; GHMP Kinase PF00288;GHMP kinases putative ATP-binding protei;2e-40;codon 81-274 TIGR00191;thrB: homoserine kinase;3.6e-193;codon 2-310 GO:0005737 cytoplasm GO:0009088 threonine biosynthesis CDS ECK0004 thrC thrC b0004 3734 5020 + (no change) JW0003 3734 5020 + e threonine synthase E 6316258 -!- 94058249 -!- 9298646 -!- 9600841 -!- 1598232 -!- 6150934 Cytoplasmic 4.2.3.1 COG0498;Threonine synthase 53686; Tryptophan synthase beta subunit-like PLP-dependent enzymes PF00291;Pyridoxal-phosphate dependent enzyme;1.3e-31;codon 77-378 TIGR00260;thrC: threonine synthase;2.3e-186;codon 52-398 GO:0005737 cytoplasm GO:0009088 threonine biosynthesis CDS ECK0005 yaaX yaaX b0005 5234 5530 + (no change) JW0004 5234 5530 + o predicted protein C 1-23 regulated by attenuation (yaaX) CDS ECK0006 yaaA yaaA b0006 5683 6459 - (no change) JW0005 5683 6459 - o conserved protein C Cytoplasmic COG3022;Uncharacterized protein conserved in bacteria PF03883;Protein of unknown function (DUF328);2.4e-188;codon 1-256 CDS ECK0007 yaaJ yaaJ b0007 6529 7959 - (no change) JW0006 6529 7959 - pt predicted transporter C Integral Membrane Protein 11 9 COG1115;Na+/alanine symporter PF01235;Sodium:alanine symporter family;3e-295;codon 40-458 TIGR00835;agcS: amino acid carrier protein;7.9e-276;codon 13-441 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0008 talB talB yaaK b0008 8238 9191 + (no change) JW0007 8238 9191 + e transaldolase B E 8332529 -!- 92334977 -!- 11298760 -!- 7592346 -!- 8805555 -!- 9007983 -!- 9298646 Cytoplasmic 2.2.1.2 monomeric multimer; transaldolase B (b0008) 1ONR COG0176;Transaldolase 51569; Aldolase PF00923;Transaldolase;2.6e-183;codon 13-313 TIGR00874;talAB: transaldolase;4e-249;codon 3-317 GO:0005737 cytoplasm "GO:0009052 pentose-phosphate shunt, non-oxidative branch" CDS ECK0009 mog mog bisD -!- chlG -!- mogA -!- yaaG b0009 9306 9893 + (no change) JW0008 9306 9893 + pf predicted molybdochelatase C 10636880 -!- 90148107 -!- 93133126 -!- 93368423 -!- 96312378 -!- 8088525 -!- 8400364 Cytoplasmic 1DI7 COG0521;Molybdopterin biosynthesis enzymes 53218; Molybdenum cofactor biosynthesis proteins PF00994;Probable molybdopterin binding domain;3e-41;codon 4-146 TIGR00177;molyb_syn: molybdenum cofactor synthesis do;2.7e-43;codon 3-148 GO:0005737 cytoplasm GO:0006777 Mo-molybdopterin cofactor biosynthesis CDS ECK0010 yaaH yaaH b0010 9928 10494 - (no change) JW0009 9928 10494 - pm conserved inner membrane protein associated with acetate transport C Integral Membrane Protein 9.B.33; The YaaH (YaaH) Family 6 6 in COG1584;Predicted membrane protein PF01184;GPR1/FUN34/yaaH family;7.8e-130;codon 1-188 CDS ECK0011 yaaW yaaW htgA -!- htpY b0011 10643 11356 - (no change) JW0010 10643 11356 - o conserved protein C Cytoplasmic COG4735;Uncharacterized protein conserved in bacteria PF03667;Uncharacterised protein family (UPF0174);5.5e-147;codon 39-235 CDS ECK0012 htgA htgA htpY -!- groPAB -!- groPC -!- groPF b0012 10830 11315 + start codon change JW5001 10830 11315 + o predicted protein C 92013929 -!- 93239687 -!- 94003405 -!- 8478327 GO:0006457 protein folding -!- GO:0006350 transcription -!- GO:0009266 response to temperature GO:0016563 transcriptional activator activity CDS ECK0013 yaaI yaaI b0013 11382 11786 - (no change) JW0012 11382 11786 - o predicted protein C Periplasmic 1-22 CDS ECK0014 dnaK dnaK grpF -!- seg -!- lop -!- groPAB -!- groPC -!- groPF -!- grpC b0014 12163 14079 + (no change) JW0013 12163 14079 + f "chaperone Hsp70, co-chaperone with DnaJ" E ############################################################################################################################################################################################################################################################### Cytoplasmic heteromultimer; DnaJ/DnaK/GrpE (b0014-b0015-b2614) 1.A.33; The Cation Channel-forming Heat Shock Protein-70 (Hsp70) Family COG0443;Molecular chaperone 53067; Actin-like ATPase domain PF00012;Hsp70 protein;0;codon 4-604 GO:0005737 cytoplasm GO:0006457 protein folding -!- GO:0006970 response to osmotic stress CDS ECK0015 dnaJ dnaJ groP -!- grpC b0015 14168 15298 + (no change) JW0014 14168 15298 + f "chaperone Hsp40, co-chaperone with DnaK" E 92236754 -!- 92274451 -!- 94038895 -!- 9822822 -!- 10210198 -!- 10891270 -!- 1826368 -!- 3003084 -!- 3003085 -!- 8764403 Cytoplasmic heteromultimer; DnaJ/DnaK/GrpE (b0014-b0015-b2614) COG0484;DnaJ-class molecular chaperone with C-terminal Zn finger domain PF00226;DnaJ domain;1.4e-40;codon 5-70 -!- PF00684;DnaJ central domain (4 repeats);1.1e-49;codon 131-211 -!- PF01556;DnaJ C terminal region;3.6e-76;codon 224-345 GO:0005737 cytoplasm GO:0006457 protein folding CDS ECK0016 insL insL-3 yi81-3 b2394 2512353 2513465 + start codon change JW5390 2519777 2520889 + IS ph predicted transposase IS186 C IS186 COG3385;FOG: Transposase and inactivated derivatives PF01609;Transposase DDE domain;5e-45;codon 113-350 CDS ECK0016 insL insL-2 yi81-2 b0582 607288 608400 + (no change) JW0572 607288 608400 + h IS186/IS421 transposase E 9689094 IS186 COG3385;FOG: Transposase and inactivated derivatives PF01609;Transposase DDE domain;5e-45;codon 111-348 CDS ECK0016 insL insL-1 yi81-1 b0016 15445 16557 + (no change) JW0015 15445 16557 + h IS186/IS421 transposase E 9689094 IS186 COG3385;FOG: Transposase and inactivated derivatives PF01609;Transposase DDE domain;5e-45;codon 111-348 CDS ECK0017 hokC hokC gef b4412 16751 16903 - (no change) JW5002 16751 16903 - m "toxic membrane protein, small" CDS overlaps with mokC E 12824883 -!- 92048480 -!- 92048481 -!- 99291074 -!- 10361310 -!- 1943700 -!- 2693900 monomeric multimer; Gef dimer (b4412) 9.B.6; The Toxic Hok/Gef Protein (Hok/Gef) Family PF01848;Hok/gef family;2.6e-26;codon 2-50 CDS ECK0018 mokC mokC gefL -!- gef b0018 16751 16960 - (no change) JW5879 16751 16960 - "shorter is hokC, longer is mokC" r "regulatory protein for HokC, overlaps CDS of hokC" E 90136075 -!- 92048480 -!- 92048481 -!- 99291074 PF01848;Hok/gef family;2.6e-26;codon 21-69 misc_RNA ECK0019 sokC sokC sof b4413 16952 17006 + (no change) JWR0224 16952 17006 + n "regulatory, antisense RNA" blocks mokC and hokC translation E 99291074 CDS ECK0020 nhaA nhaA ant -!- antA -!- hyc b0019 17489 18655 + (no change) JW0018 17489 18655 + t sodium-proton antiporter E 91250446 -!- 92283803 -!- 93131914 Integral Membrane Protein 2.A.33; The NhaA Na+:H+ Antiporter (NhaA) Family 10 11 in COG3004;Na+/H+ antiporter PF06965;Na+/H+ antiporter;1.6e-260;codon 4-380 TIGR00773;NhaA: Na+/H+ antiporter NhaA;1e-287;codon 7-380 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009268 response to pH CDS ECK0021 nhaR nhaR yaaB -!- antO b0020 18715 19620 + (no change) JW0019 18715 19620 + r DNA-binding transcriptional activator E 92268083 -!- 94193576 -!- 2429258 -!- 3413113 -!- 8168494 Cytoplasmic LysR nhaA -!- osmC COG0583;Transcriptional regulator PF00126;Bacterial regulatory helix-turn-helix protei;1e-17;codon 8-67 GO:0005737 cytoplasm GO:0006350 transcription -!- GO:0009268 response to pH GO:0016563 transcriptional activator activity CDS ECK0022 insB insB unique to W3110 0 0 JW2285 2411473 2411976 - IS1 -!- W3110 specific region h IS1 element protein E IS1 ECK0022 insB insB-7 b4576 4516744 4517247 + pseudogene; interrupted by frameshift JW4255+JW4256 4523401 4523904 + ancestral gene su IS1 transposase InsAB' (pseudogene) IS1 CDS ECK0022 insB insB-7_2 b4564 4517038 4517247 + pseudogene fragment -!- new JW4256 4523695 4523904 + pseudogene h "IS1 transposase InsAB', C-ter fragment (pseudogene)" E IS1 PF03400;Transposase_27: IS1 transposase;6.8e-26;codon 1-69 CDS ECK0022 insB insB-7_1 b4563 4516744 4517037 + pseudogene fragment -!- new JW4255 4523401 4523694 + pseudogene h "IS1 transposase InsAB', N-ter fragment (pseudogene)" E IS1 PF03400;Transposase_27: IS1 transposase;1.3e-11;codon 37-97 CDS ECK0022 insB insB-6 b3445 3581700 3582203 + (no change) JW3409 4056235 4056738 - h IS1 transposase InsAB' E 9689094 IS1 PF03400;IS1 transposase;2.9e-112;codon 37-167 CDS ECK0022 insB insB-5 b1893 1976542 1977045 - (no change) unique to MG1655 336 336 - "IS1 is inserted in strain MG, but IS5 is inserted at this region in strain W" h IS1 transposase InsAB' E 9689094 IS1 "COG1662;Transposase and inactivated derivatives, IS1 family" PF03400;IS1 transposase;2.9e-112;codon 37-167 CDS ECK0022 insB insB-4 b0988 1049250 1049753 + (no change) JW0972 1050449 1050952 + h IS1 transposase InsAB' E 9689094 IS1 "COG1662;Transposase and inactivated derivatives, IS1 family" PF03400;IS1 transposase;1.2e-111;codon 37-167 CDS ECK0022 insB insB-3 b0274 289873 290376 - (no change) JW0268 289873 290376 - h CP4-6 prophage; IS1 transposase InsAB' E 9689094 cryptic prophage CP4-6 -!- IS1 "COG1662;Transposase and inactivated derivatives, IS1 family" PF03400;IS1 transposase;1.3e-111;codon 37-167 CDS ECK0022 insB insB-2 b0264 278402 278905 - (no change) JW0256 278402 278905 - h CP4-6 prophage; IS1 transposase InsAB' E 9689094 cryptic prophage CP4-6 -!- IS1 "COG1662;Transposase and inactivated derivatives, IS1 family" PF03400;IS1 transposase;1.3e-111;codon 37-167 CDS ECK0022 insB insB-1 b0021 19811 20314 - (no change) JW0020 19811 20314 - h IS1 transposase InsAB' E 9689094 IS1 "COG1662;Transposase and inactivated derivatives, IS1 family" PF03400;IS1 transposase;2.9e-112;codon 37-167 CDS ECK0023 insA insA unique to W3110 0 0 JW2286 2411895 2412170 - IS1 -!- W3110 specific region h IS1 element protein E IS1 CDS ECK0023 insA insA-4 b4516 1049056 1049331 + new JW0971 1050255 1050530 + IS h IS1 repressor protein InsA E 46689; Homeodomain-like CDS ECK0023 insA insA-7 b4294 4516550 4516825 + (no change) JW4254 4523207 4523482 + h KpLE2 phage-like element; IS1 repressor protein InsA E 1849492 KpLE2 phage-like element -!- IS1 46689; Homeodomain-like PF03811;Insertion element protein;3.6e-63;codon 1-88 CDS ECK0023 insA insA-6 b3444 3581506 3581781 + (no change) JW3408 4056657 4056932 - h IS1 repressor protein InsA E 9689094 IS1 COG3677;Transposase and inactivated derivatives 46689; Homeodomain-like PF03811;Insertion element protein;7.1e-68;codon 1-88 CDS ECK0023 insA insA-5 b1894 1976964 1977239 - (no change) unique to MG1655 336 336 - "IS1 is inserted in strain MG, but IS5 is inserted at this region in strain W" h IS1 repressor protein InsA E 9689094 IS1 COG3677;Transposase and inactivated derivatives 46689; Homeodomain-like PF03811;Insertion element protein;7.1e-68;codon 1-88 CDS ECK0023 insA insA-3 b0275 290295 290570 - (no change) JW0269 290295 290570 - h CP4-6 prophage; IS1 repressor protein InsA E 9689094 cryptic prophage CP4-6 -!- IS1 COG3677;Transposase and inactivated derivatives 46689; Homeodomain-like PF03811;Insertion element protein;4.3e-67;codon 1-88 CDS ECK0023 insA insA-2 b0265 278824 279099 - (no change) JW0257 278824 279099 - h CP4-6 prophage; IS1 repressor protein InsA E 9689094 cryptic prophage CP4-6 -!- IS1 COG3677;Transposase and inactivated derivatives 46689; Homeodomain-like PF03811;Insertion element protein;4.3e-67;codon 1-88 CDS ECK0023 insA insA-1 b0022 20233 20508 - (no change) JW0021 20233 20508 - h IS1 repressor protein InsA E 9689094 IS1 COG3677;Transposase and inactivated derivatives 46689; Homeodomain-like PF03811;Insertion element protein;7.1e-68;codon 1-88 CDS ECK0024 rpsT rpsT sup(s20) -!- supS20 b0023 20815 21078 - (no change) JW0022 20815 21078 - s 30S ribosomal subunit protein S20 E 92011603 -!- 93138304 -!- 93247500 -!- 10094780 -!- 12244297 -!- 12809609 -!- 2429258 -!- 2985604 -!- 6267039 -!- 786731 Cytoplasmic regulated by attenuation (rpsT) 1P87 COG0268;Ribosomal protein S20 46992; Ribosomal protein S20 PF01649;Ribosomal protein S20;6.1e-46;codon 2-85 TIGR00029;S20: ribosomal protein S20;2.4e-47;codon 1-87 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006412 protein biosynthesis GO:0003735 structural constituent of ribosome CDS ECK0025 yaaY yaaY b0024 21181 21399 + (no change) JW5003 21181 21399 + o predicted protein C Membrane Anchored regulated by attenuation (yaaY-ribF) CDS ECK0026 ribF ribF yaaC b0025 21407 22348 + (no change) JW0023 21407 22348 + e bifunctional riboflavin kinase and FAD synthetase E 2985604 -!- 9743119 Cytoplasmic 2.7.1.26 -!- 2.7.7.2 COG0196;FAD synthase 52374; Nucleotidylyl transferase PF06574;Riboflavin kinase (Flavokinase);5.5e-86;codon 16-168 -!- PF01687;Riboflavin kinase / FAD synthetase;4.1e-69;codon 184-308 TIGR00083;ribF: riboflavin biosynthesis protein RibF;1.9e-187;codon 19-308 GO:0005737 cytoplasm CDS ECK0027 ileS ileS ilvS b0026 22391 25207 + (no change) JW0024 22391 25207 + e isoleucyl-tRNA synthetase E 91222233 -!- 93065273 -!- 2985604 -!- 6374664 -!- 6378662 -!- 6390679 -!- 7929087 -!- 9554847 -!- 2011499 Cytoplasmic 6.1.1.5 Zn2+ COG0060;Isoleucyl-tRNA synthetase 47323; Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases -!- 50677; ValRS/IleRS editing domain -!- 52374; Nucleotidylyl transferase "PF00133;tRNA synthetases class I (I, L, M and V);0;codon 27-641 -!- PF06827;Zinc finger found in FPG and IleRS;5.3e-14;codon 898-927" TIGR00392;ileS: isoleucyl-tRNA synthetase;0;codon 22-780 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK0028 lspA lspA dapB -!- ileS b0027 25207 25701 + (no change) JW0025 25207 25701 + e prolipoprotein signal peptidase (signal peptidase II) E 91373397 -!- 6378662 Integral Membrane Protein 3.4.23.36 A8 family; signal peptidase II 4 4 in COG0597;Lipoprotein signal peptidase PF01252;Signal peptidase (SPase) II;9.2e-91;codon 10-164 TIGR00077;lspA: lipoprotein signal peptidase;3.6e-94;codon 1-164 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0029 fkpB fkpB slpA -!- yaaD b0028 25826 26275 + (no change) JW0026 25826 26275 + e FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase) E 97332650 -!- 2011499 Cytoplasmic 5.2.1.8 COG1047;FKBP-type peptidyl-prolyl cis-trans isomerases 2 54534; FKBP-like PF00254;FKBP-type peptidyl-prolyl cis-trans isomeras;2.7e-10;codon 1-141 GO:0005737 cytoplasm GO:0006457 protein folding CDS ECK0030 ispH ispH lytB -!- yaaE b0029 26277 27227 + (no change) JW0027 26277 27227 + c "1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase, 4Fe-4S protein" E 12198182 -!- 12706830 -!- 21311595 -!- 21574179 -!- 21819424 -!- 93163053 -!- 98196746 Cytoplasmic 1.17.1.2 Co2+ -!- FAD -!- NADH COG0761;Penicillin tolerance protein PF02401;LytB protein;1e-192;codon 3-285 TIGR00216;ispH_lytB: 4-hydroxy-3-methylbut-2-enyl dip;9.4e-131;codon 2-285 GO:0005737 cytoplasm GO:0042493 response to drug CDS ECK0031 rihC rihC yaaF b0030 27293 28207 + (no change) JW0028 27293 28207 + e ribonucleoside hydrolase 3 E 21125610 Cytoplasmic 3.2.2.- COG1957;Inosine-uridine nucleoside N-ribohydrolase 53590; Nucleoside hydrolase PF01156;Inosine-uridine preferring nucleoside hy;1.3e-179;codon 2-304 GO:0009226 nucleotide-sugar biosynthesis CDS ECK0032 dapB dapB b0031 28374 29195 + (no change) JW0029 28374 29195 + e dihydrodipicolinate reductase E 74169519 -!- 85054974 -!- 6377309 -!- 7893645 -!- 9398235 Cytoplasmic 1.3.1.26 monomeric multimer; dihydrodipicolinate reductase (b0031) COG0289;Dihydrodipicolinate reductase "51735; NAD(P)-binding Rossmann-fold domains -!- 55347; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain" "PF01113;Dihydrodipicolinate reductase, N-terminus;1.7e-60;codon 6-129 -!- PF05173;Dihydrodipicolinate reductase, C-terminus;2.2e-82;codon 132-269" TIGR00036;dapB: dihydrodipicolinate reductase;3.8e-176;codon 5-271 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009089 lysine biosynthesis via diaminopimelate CDS ECK0033 carA carA arg+ura -!- cap -!- pyrA -!- arg b0032 29651 30799 + (no change) JW0030 29651 30799 + e "carbamoyl phosphate synthetase small subunit, glutamine amidotransferase" E 91113685 -!- 91217057 -!- 92172854 -!- 10029528 -!- 10089390 -!- 10428826 -!- 10587438 -!- 1334233 -!- 6308632 -!- 6330744 -!- 6377309 -!- 9174345 -!- 9298646 -!- 9636022 Cytoplasmic 6.3.5.5 Mg2+ heteromultimer; carbamoyl phosphate synthetase (b0033-b0032) C26 family; non-peptidase homologues 1CE8 COG0505;Carbamoylphosphate synthase small subunit "52021; Carbamoyl phosphate synthetase, small subunit N-terminal domain -!- 52317; Class I glutamine amidotransferase-like" PF00988;Carbamoyl-phosphate synthase small ch;2.3e-93;codon 4-151 -!- PF00117;Glutamine amidotransferase class-I;1e-75;codon 195-373 TIGR01368;CPSaseIIsmall: carbamoyl-phosphate synt;9.1e-249;codon 5-376 GO:0006526 arginine biosynthesis -!- GO:0006221 pyrimidine nucleotide biosynthesis CDS ECK0034 carB carB arg+ura -!- cap -!- pyrA b0033 30817 34038 + (no change) JW0031 30817 34038 + e carbamoyl-phosphate synthase large subunit E 91110549 -!- 91113685 -!- 91159438 -!- 91217057 -!- 91332909 -!- 92172854 -!- 99357782 -!- 10029528 -!- 10089390 -!- 10587438 -!- 6308632 -!- 6330744 -!- 6377309 -!- 9174345 -!- 9636022 Periplasmic 6.3.5.5 Mg2+ heteromultimer; carbamoyl phosphate synthetase (b0033-b0032) 1KEE COG0458;Carbamoylphosphate synthase large subunit (split gene in MJ) "48108; Carbamoyl phosphate synthetase, large subunit connection domain -!- 52335; Methylglyoxal synthase-like -!- 52440; Biotin carboxylase N-terminal domain-like -!- 56059; Glutathione synthetase ATP-binding domain-like" PF00289;Carbamoyl-phosphate synthase L chain;6.2e-64;aa 6-126 -!- PF02786;Carbamoyl-phosphate synthase L chain;3.3e-136;aa 128-364 -!- PF02787;Carbamoyl-phosphate synthetase large chain;2.3e-68;aa 424-547 -!- PF00289;Carbamoyl-phosphate synthase L chain;3.8e-26;aa 558-672 -!- PF02786;Carbamoyl-phosphate synthase L chain;3e-26;aa 674-895 -!- PF02142;MGS-like domain;6.3e-32;aa 956-1042 TIGR01369;CPSaseII_lrg: carbamoyl-phosphate syntha;0;codon 2-1054 GO:0006526 arginine biosynthesis -!- GO:0006221 pyrimidine nucleotide biosynthesis CDS ECK0035 caiF caiF b0034 34300 34695 + start codon change JW0033 34300 34695 + r DNA-binding transcriptional activator E 96200092 Cytoplasmic caiTABCDE -!- fixABCX GO:0005737 cytoplasm GO:0009310 amine catabolism -!- GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0036 caiE caiE b0035 34781 35371 - start codon change JW5004 34781 35371 - pe predicted acyl transferase stimulates activity of carnitine racemase and carnitine dehydrogenase C 95115548 "COG0663;Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily" 51161; Trimeric LpxA-like enzymes PF00132;Bacterial transferase hexapeptide (three rep;1.1;codon 35-52 -!- PF00132;Bacterial transferase hexapeptide (three rep;13;codon 78-95 -!- PF00132;Bacterial transferase hexapeptide (three rep;0.014;codon 101-118 GO:0009310 amine catabolism -!- GO:0042413 carnitine catabolism CDS ECK0037 caiD caiD yaaL b0036 35377 36270 - (no change) JW0035 35377 36270 - e crotonobetainyl CoA hydratase E 21435666 -!- 97189569 -!- 7815937 Cytoplasmic 4.2.1.- COG1024;Enoyl-CoA hydratase/carnithine racemase 52096; ClpP/crotonase PF00378;Enoyl-CoA hydratase/isomerase family;1.4e-87;codon 50-217 GO:0009310 amine catabolism -!- GO:0042413 carnitine catabolism CDS ECK0038 caiC caiC yaaM b0037 36271 37839 - (no change) JW0036 36271 37839 - pe predicted crotonobetaine CoA ligase:carnitine CoA ligase C 97189569 -!- 7815937 Cytoplasmic 6.3.2.- 9.B.17; The Putative Fatty Acid Transporter (FAT) Family 56801; Firefly luciferase-like PF00501;AMP-binding enzyme;2.2e-124;codon 44-456 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009310 amine catabolism CDS ECK0039 caiB caiB yaaN b0038 37898 39115 - (no change) JW0037 37898 39115 - e crotonobetainyl CoA:carnitine CoA transferase E 21435666 -!- 94245624 -!- 95115548 -!- 99227081 -!- 15518548 -!- 10339822 Cytoplasmic 2.8.3.- monomeric multimer; gamma-butyrobetainyl-CoA:carnitine CoA transferase (b0038) COG1804;Predicted acyl-CoA transferases/carnitine dehydratase PF02515;CoA-transferase family III;9e-98;codon 69-260 GO:0005737 cytoplasm GO:0042413 carnitine catabolism -!- GO:0009310 amine catabolism CDS ECK0040 caiA caiA yaaO b0039 39244 40386 - (no change) JW0038 39244 40386 - e "crotonobetaine reductase subunit II, FAD-binding" E 97189569 -!- 99227081 -!- 7815937 Cytoplasmic 1.3.99.- FAD COG1960;Acyl-CoA dehydrogenases "47203; Acyl-CoA dehydrogenase (flavoprotein), C-terminal domain -!- 56645; Acyl-CoA dehydrogenase (flavoprotein), N-terminal and middle domains" "PF02771;Acyl-CoA dehydrogenase, N-terminal doma;3.5e-53;codon 6-119 -!- PF02770;Acyl-CoA dehydrogenase, middle domain;3.9e-58;codon 123-223 -!- PF00441;Acyl-CoA dehydrogenase, C-terminal doma;9.9e-60;codon 227-376" GO:0005737 cytoplasm GO:0006097 glyoxylate cycle -!- GO:0009310 amine catabolism -!- GO:0042413 carnitine catabolism GO:0009054 electron acceptor activity CDS ECK0041 caiT caiT yaaT -!- yaaP b0040 40417 41931 - (no change) JW0039 40417 41931 - pt predicted transporter C 12163501 -!- 9573142 -!- 9871325 -!- 7815937 Integral Membrane Protein 2.A.15; The Betaine/Carnitine/Choline Transporter (BCCT) Family 12 12 COG1292;Choline-glycine betaine transporter PF02028;BCCT family transporter;0;codon 14-501 TIGR00842;bcct: choline/carnitine/betaine transport;4.3e-266;codon 52-501 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK0042 fixA fixA yaaQ b0041 42403 43173 + start codon change JW0040 42403 43173 + pe "predicted electron transfer flavoprotein subunit, ETFP adenine nucleotide-binding domain" role in anaerobic carnitine metabolism C 9573142 -!- 96066354 -!- 12081978 Cytoplasmic "COG2086;Electron transfer flavoprotein, beta subunit" 52431; ETFP adenine nucleotide-binding domain-like PF01012;Electron transfer flavoprotein beta subunit;2.6e-113;codon 13-268 GO:0016052 carbohydrate catabolism CDS ECK0043 fixB fixB yaaR b0042 43188 44129 + (no change) JW0041 43188 44129 + pc "predicted electron transfer flavoprotein, NAD/FAD-binding domain and ETFP adenine nucleotide-binding domain-like" role in anaerobic carnitine metabolism C 9573142 -!- 96066354 -!- 12081978 Cytoplasmic "COG2025;Electron transfer flavoprotein, alpha subunit" 52431; ETFP adenine nucleotide-binding domain-like -!- 52467; DHS-like NAD/FAD-binding domain PF00766;Electron transfer flavoprotein alpha subuni;1.6e-126;codon 6-275 GO:0016052 carbohydrate catabolism CDS ECK0044 fixC fixC yaaS b0043 44180 45466 + (no change) JW0042 44180 45466 + pc predicted oxidoreductase with FAD/NAD(P)-binding domain potential role in carnitine metabolism C 96066354 Cytoplasmic COG0644;Dehydrogenases (flavoproteins) 51905; FAD/NAD(P)-binding domain PF01266;FAD dependent oxidoreductase;2.4e-14;codon 7-330 GO:0042413 carnitine catabolism CDS ECK0045 fixX fixX yaaT b0044 45463 45750 + (no change) JW0043 45463 45750 + pc predicted 4Fe-4S ferredoxin-type protein potential role in anaerobic carnitine metabolism C 96066354 Cytoplasmic COG2440;Ferredoxin-like protein 54862; 4Fe-4S ferredoxins GO:0042413 carnitine catabolism CDS ECK0046 yaaU yaaU yabE b0045 45807 47138 + (no change) JW0044 45807 47138 + pt predicted transporter C Integral Membrane Protein 12 12 in COG0477;Permeases of the major facilitator superfamily PF00083;Sugar (and other) transporter;4.9e-43;codon 19-436 -!- PF07690;Major Facilitator Superfamily;2.2e-32;codon 23-395 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0047 kefF kefF yabF b0046 47246 47776 + (no change) JW0045 47246 47776 + pc flavoprotein subunit for the KefC potassium efflux system C 20507830 Cytoplasmic 2.A.37; The Monovalent Cation:Proton Antiporter-2 (CPA2) Family COG2249;Putative NADPH-quinone reductase (modulator of drug activity B) 52218; Flavoproteins PF02525;Flavodoxin-like fold;2.2e-67;codon 1-172 CDS ECK0048 kefC kefC trkC b0047 47769 49631 + (no change) JW0046 47769 49631 + t potassium:proton antiporter glutathione-regulated E 10092637 -!- 90286917 -!- 91260444 -!- 1325937 -!- 6159575 Integral Membrane Protein 2.A.37; The Monovalent Cation:Proton Antiporter-2 (CPA2) Family 12 13 in "COG0475;Kef-type K+ transport systems, membrane components -!- COG1226;Kef-type K+ transport systems, predicted NAD-binding component" 51735; NAD(P)-binding Rossmann-fold domains PF02254;TrkA-N domain;3.1e-20;codon 401-514 TIGR00932;2a37: potassium efflux system protein;4.6e-144;codon 13-285 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0015386 potassium:hydrogen antiporter activity CDS ECK0049 folA folA tmrA -!- tmr b0048 49823 50302 + (no change) JW0047 49823 50302 + e dihydrofolate reductase E 15139807 -!- 90280385 -!- 91152032 -!- 92008630 -!- 1998681 -!- 2185835 -!- 320005 -!- 350268 -!- 3549289 -!- 6159575 -!- 6815179 -!- 7007370 Cytoplasmic 1.5.1.3 1DDS COG0262;Dihydrofolate reductase 53597; Dihydrofolate reductases PF00186;Dihydrofolate reductase;3.2e-59;codon 1-158 GO:0046656 folic acid biosynthesis -!- GO:0009257 10-formyltetrahydrofolate biosynthesis CDS ECK0050 apaH apaH cfcB b0049 50380 51222 - (no change) JW0048 50380 51222 - e diadenosine tetraphosphatase E 89296933 -!- 89359108 -!- 92037553 -!- 3031429 -!- 6317672 Cytoplasmic 3.6.1.41 COG0639;Diadenosine tetraphosphatase and related serine/threonine protein phosphatases 56300; Metallo-dependent phosphatases PF00149;Calcineurin-like phosphoesterase;2.5e-18;codon 1-150 TIGR00668;apaH: bis(5'-nucleosyl)-tetraphosphatase (sy;2.7e-239;codon 1-279 GO:0005737 cytoplasm "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0051 apaG apaG temP b0050 51229 51606 - (no change) JW0049 51229 51606 - pt protein associated with Co2+ and Mg2+ efflux C 92334977 Cytoplasmic COG2967;Uncharacterized protein affecting Mg2+/Co2+ transport PF04379;Protein of unknown function (DUF525);2.7e-78;codon 1-121 CDS ECK0052 ksgA ksgA rsmA b0051 51609 52430 - (no change) JW0050 51609 52430 - e "S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase" E 12876362 -!- 15136037 -!- 89291753 -!- 9748462 -!- 2670894 -!- 3031429 -!- 3122846 -!- 3905517 Cytoplasmic 2.1.1.- 1QYR COG0030;Dimethyladenosine transferase (rRNA methylation) 53335; S-adenosyl-L-methionine-dependent methyltransferases PF00398;Ribosomal RNA adenine dimethylase;1.4e-110;codon 8-266 TIGR00755;ksgA: dimethyladenosine transferase;1.9e-140;codon 9-264 GO:0005737 cytoplasm GO:0009451 RNA modification -!- GO:0042493 response to drug CDS ECK0053 pdxA pdxA b0052 52427 53416 - (no change) JW0051 52427 53416 - e "4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent" E ############################################################################################################################################################################################################################################################### Cytoplasmic 1.1.1.262 Zn2+ 1PS6 COG1995;Pyridoxal phosphate biosynthesis protein PF04166;Pyridoxal phosphate biosynthetic protein Pdx;2e-191;codon 25-322 TIGR00557;pdxA: 4-hydroxythreonine-4-phosphate dehydro;8e-242;codon 4-325 GO:0005737 cytoplasm GO:0008615 pyridoxine biosynthesis CDS ECK0054 surA surA b0053 53416 54702 - (no change) JW0052 53416 54702 - e peptidyl-prolyl cis-trans isomerase (PPIase) E 21145448 -!- 21588133 -!- 97032152 -!- 2165476 -!- 2670894 -!- 8626309 -!- 9298646 -!- 9600841 Periplasmic 5.2.1.8 428 1M5Y COG0760;Parvulin-like peptidyl-prolyl isomerase 54534; FKBP-like PF00639;PPIC-type PPIASE domain;2.6e-45;codon 178-272 -!- PF00639;PPIC-type PPIASE domain;3.5e-51;codon 289-382 GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0006457 protein folding CDS ECK0055 imp imp ostA -!- yabG b0054 54755 57109 - (no change) JW0053 54755 57109 - f exported protein required for envelope biosynthesis and integrity E 12207697 -!- 95110156 -!- 2547691 -!- 9298646 Periplasmic 1-24 784 COG1452;Organic solvent tolerance protein OstA PF04453;Organic solvent tolerance protein;8e-179;codon 295-697 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0056 djlA djlA yabH b0055 57364 58179 + (no change) JW0054 57364 58179 + f "DnaJ-like protein, membrane anchored" co-chaperone with DnaK E 21269341 -!- 9364917 -!- 9364918 -!- 12664169 -!- 8809778 -!- 11106641 Membrane Anchored COG1076;DnaJ-domain-containing proteins 1 46565; Chaperone J-domain PF00226;DnaJ domain;1.9e-14;codon 205-269 GO:0006457 protein folding CDS ECK0057 yabP yabP b0056 58474 59124 + (no change) JW0055 58474 59124 + o predicted protein C Cytoplasmic CDS ECK0058 yabQ yabQ b0057 59121 59279 + (no change) JW0056 59121 59279 + o predicted protein C Cytoplasmic CDS ECK0059 rluA rluA yabO b0058 59687 60346 - (no change) JW0057 59687 60346 - e pseudouridine synthase for 23S rRNA (position 746) and tRNAphe(position 32) E 99315821 -!- 10529181 -!- 10924141 -!- 7493321 -!- 7958944 Cytoplasmic 4.2.1.70 "COG0564;Pseudouridylate synthases, 23S RNA-specific" PF00849;RNA pseudouridylate synthase;1.7e-62;codon 22-170 GO:0009451 RNA modification CDS ECK0060 hepA hepA rapA -!- yabA b0059 60358 63264 - (no change) JW0058 60358 63264 - f RNA polymerase-associated helicase protein (ATPase and RNA polymerase recycling factor) putative helicase protein A E 11751638 -!- 20357329 -!- 92250435 -!- 92334977 -!- 11772406 -!- 11567013 -!- 2034216 -!- 8382805 -!- 9507009 -!- 9614128 Cytoplasmic 3.6.1.- "COG0553;Superfamily II DNA/RNA helicases, SNF2 family" 52540; P-loop containing nucleotide triphosphate hydrolases "PF04851;Type III restriction enzyme, res subunit;5.8e-06;codon 152-318 -!- PF00176;SNF2 family N-terminal domain;2e-91;codon 157-454 -!- PF00271;Helicase conserved C-terminal domain;2.5e-20;codon 523-601" GO:0009451 RNA modification CDS ECK0061 polB polB dinA b0060 63429 65780 - (no change) JW0059 63429 65780 - e DNA polymerase II E 10217781 -!- 91083835 -!- 91154268 -!- 99362739 -!- 2034216 -!- 2217198 -!- 9079692 Cytoplasmic 2.7.7.7 1Q8I COG0417;DNA polymerase elongation subunit (family B) 53098; Ribonuclease H-like -!- 56672; DNA/RNA polymerases "PF03104;DNA polymerase family B, exonuclease do;1.2e-61;codon 25-296 -!- PF00136;DNA polymerase family B;3.7e-96;codon 368-783" GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication -!- GO:0006281 DNA repair -!- GO:0009314 response to radiation -!- GO:0009432 SOS response CDS ECK0062 araD araD b0061 65855 66550 - (no change) JW0060 65855 66550 - e L-ribulose-5-phosphate 4-epimerase E 87163495 -!- 2034216 -!- 2217198 -!- 2251150 -!- 2261080 Cytoplasmic 5.1.3.4 monomeric multimer; L-ribulose-phosphate 4-epimerase (b0061) regulated by attenuation (araD) 1JDI COG0235;Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases 53639; Class II aldolase PF00596;Class II Aldolase and Adducin N-terminal;2e-106;codon 7-218 TIGR00760;araD: L-ribulose-5-phosphate 4-epimerase;6.2e-167;codon 1-231 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK0063 araA araA b0062 66835 68337 - (no change) JW0061 66835 68337 - e L-arabinose isomerase E 87163495 -!- 91162650 Cytoplasmic 5.3.1.4 monomeric multimer; L-arabinose isomerase (b0062) COG2160;L-arabinose isomerase PF02610;L-arabinose isomerase;0;codon 1-500 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK0064 araB araB b0063 68348 70048 - (no change) JW0062 68348 70048 - e L-ribulokinase E 87163495 -!- 91162650 -!- 189315 -!- 357433 Cytoplasmic 2.7.1.16 monomeric multimer; L-ribulokinase (b0063) COG1069;Ribulose kinase 53067; Actin-like ATPase domain "PF00370;FGGY family of carbohydrate kinases, N-termi;1.5e-06;codon 3-281" TIGR01234;L-ribulokinase: L-ribulokinase;0;codon 2-553 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK0065 araC araC b0064 70387 71265 + (no change) JW0063 70387 71265 + r DNA-binding transcriptional dual regulator E 88097378 -!- 90251626 -!- 91162650 -!- 6160371 -!- 6283093 -!- 7008027 -!- 7019009 -!- 9103202 -!- 9367758 Cytoplasmic monomeric multimer; AraC transcriptional dual regulator (b0064) AraC/XylS araBAD -!- araC -!- araE -!- araFG-araH_1H_2 -!- araJ COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like -!- 51215; Regulatory protein AraC PF02311;AraC-like ligand binding domain;1.5e-29;codon 20-162 -!- PF00165;Bacterial regulatory helix-turn-helix pr;1.1e-11;codon 181-228 -!- PF00165;Bacterial regulatory helix-turn-helix pr;2.2e-13;codon 234-278 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0066 yabI yabI b0065 71351 72115 + (no change) JW5005 71351 72115 + pm conserved inner membrane protein C Integral Membrane Protein 5 5 out COG0586;Uncharacterized membrane-associated protein PF00597;DedA family;1.1e-64;codon 18-178 GO:0009274 cell wall (sensu Bacteria) CDS ECK0067 thiQ thiQ sfuC -!- yabJ b0066 72229 72927 - (no change) JW0065 72229 72927 - t thiamin transporter subunit -!- ATP-binding component of ABC superfamily E 99311269 Cytoplasmic heteromultimer; thiamin ABC transporter (b0066-b0067-b0068) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG3840;ABC-type thiamine transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;6.8e-73;codon 25-206 "TIGR01277;thiQ: ABC transporter, ATP-binding protein,;1.5e-179;codon 2-214" GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009228 thiamin biosynthesis CDS ECK0068 thiP thiP sfuB -!- yabK b0067 72911 74521 - (no change) JW0066 72911 74521 - t fused thiamin transporter subunits of ABC superfamily: membrane components E 99311269 Integral Membrane Protein heteromultimer; thiamin ABC transporter (b0066-b0067-b0068) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 12 12 "fused thiamin transport protein, ABC superfamily: membrane component (aa1-174) -!- membrane component (aa285-536)" "COG1178;ABC-type Fe3+ transport system, permease component" PF00528;Binding-protein-dependent transport syst;1e-06;codon 52-274 -!- PF00528;Binding-protein-dependent transport syst;0.00049;codon 331-535 TIGR01253;thiP: thiamine/thiamine pyrophosphate ABC tr;0;codon 8-525 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009228 thiamin biosynthesis CDS ECK0069 tbpA tbpA sfuA -!- thiB -!- yabI -!- yabL b0068 74497 75480 - (no change) JW0067 74497 75480 - t thiamin transporter subunit -!- periplasmic-binding component of ABC superfamily E 12182833 -!- 4869219 -!- 8432721 -!- 99311269 -!- 9535878 Periplasmic heteromultimer; thiamin ABC transporter (b0066-b0067-b0068) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 327 "COG4143;ABC-type thiamine transport system, periplasmic component" 53850; Periplasmic binding protein-like II TIGR01276;thiB: thiamin/thiamin pyrophosphate ABC tran;2.6e-286;codon 6-327 -!- TIGR01254;sfuA: ABC transporter periplasmic binding pr;8e-227;codon 18-321 GO:0042597 periplasmic space GO:0009228 thiamin biosynthesis CDS ECK0070 sgrR sgrR yabN b0069 75644 77299 - (no change) JW0068 75644 77299 - r DNA-binding transcriptional regulator E 15522088 Cytoplasmic "COG4533;ABC-type uncharacterized transport system, periplasmic component" 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00496;Bacterial extracellular solute-binding prot;2.6e-62;codon 163-492 GO:0042597 periplasmic space misc_RNA ECK0071 sgrS sgrS ryaA b4577 77367 77593 + new JWR0259 77367 77593 + n small antisense RNA degrades ptsG mRNA E 15522088 -!- 15650111 CDS ECK0072 setA setA yabM b0070 77621 78799 + (no change) JW0069 77621 78799 + t broad specificity sugar efflux system E 10438463 -!- 10209755 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in regulated by attenuation (setA) PF07690;Major Facilitator Superfamily;3.1e-23;codon 18-364 TIGR00899;2A0120: sugar efflux transporter;4.8e-259;codon 17-391 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism GO:0015543 lactose/glucose efflux transporter activity CDS ECK0073 leuD leuD b0071 78848 79453 - (no change) JW0070 78848 79453 - e 3-isopropylmalate isomerase subunit E 374346 -!- 9600841 -!- 2993799 Cytoplasmic 4.2.1.33 heteromultimer; isopropylmalate isomerase (b0072-b0071) COG0066;3-isopropylmalate dehydratase small subunit "52016; Aconitase, C-terminal domain" PF00694;Aconitase C-terminal domain;1.5e-67;codon 2-127 "TIGR00171;leuD: 3-isopropylmalate dehydratase, small s;2.5e-115;codon 1-189" GO:0005737 cytoplasm GO:0009098 leucine biosynthesis CDS ECK0074 leuC leuC b0072 79464 80864 - (no change) JW0071 79464 80864 - e "3-isopropylmalate isomerase subunit, dehydratase component" E 374346 -!- 2124684 -!- 2993799 -!- 8119295 -!- 9298646 -!- 9600841 -!- 9740056 Cytoplasmic 4.2.1.33 heteromultimer; isopropylmalate isomerase (b0072-b0071) COG0065;3-isopropylmalate dehydratase large subunit "53732; Aconitase, first 3 domains" PF00330;Aconitase family (aconitate hydratase);9.7e-292;codon 4-457 "TIGR00170;leuC: 3-isopropylmalate dehydratase, large s;0;codon 1-465" GO:0005737 cytoplasm GO:0009098 leucine biosynthesis CDS ECK0075 leuB leuB b0073 80867 81958 - start codon change JW5807 80867 81958 - e 3-isopropylmalate dehydrogenase E 204639 -!- 8119295 -!- 8875643 -!- 9086278 -!- 9298646 Cytoplasmic 1.1.1.85 monomeric multimer; 3-isopropylmalate dehydrogenase (b0073) 53659; Isocitrate & isopropylmalate dehydrogenases PF00180;Isocitrate/isopropylmalate dehydrogenase;9.2e-225;codon 7-356 TIGR00169;leuB: 3-isopropylmalate dehydrogenase;1.7e-275;codon 7-356 GO:0005737 cytoplasm GO:0009098 leucine biosynthesis CDS ECK0076 leuA leuA b0074 81958 83529 - (no change) JW0073 81958 83529 - e 2-isopropylmalate synthase E 4570778 -!- 6195343 -!- 6171647 -!- 9298646 Cytoplasmic 4.1.3.12 K+ monomeric multimer; 2-isopropylmalate synthase (b0074) regulated by attenuation (leuA-leuB-leuC-leuD) COG0119;Isopropylmalate/homocitrate/citramalate synthases 51366; Ribulose-phoshate binding barrel PF00682;HMGL-like;3.2e-153;codon 13-279 TIGR00973;leuA_bact: 2-isopropylmalate synthase;0;codon 4-497 GO:0005737 cytoplasm GO:0009098 leucine biosynthesis CDS ECK0077 leuL leuL leuLP b0075 83622 83708 - (no change) JW0074 83622 83708 - l leu operon leader peptide E 392514 -!- 91154117 Cytoplasmic GO:0005737 cytoplasm GO:0009098 leucine biosynthesis CDS ECK0078 leuO leuO b0076 84368 85312 + start codon change JW0075 84368 85312 + r DNA-binding transcriptional activator part of stringent response E 21270209 -!- 88320486 -!- 3519576 Cytoplasmic LysR leuLABCD 46785; Winged helix -!- 53850; Periplasmic binding protein-like II "PF00126;HTH_1: transcriptional regulator, LysR famil;3e-23;codon 24-83 -!- PF01046;NodD_C_term: NodD transcription activator ca;1.6e-57;codon 168-314 -!- PF03466;LysR_substrate: LysR substrate binding domai;3.5e-07;codon 107-313" GO:0005737 cytoplasm GO:0009098 leucine biosynthesis -!- GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0079 ilvI ilvI b0077 85630 87354 + start codon change JW0076 85630 87354 + e "acetolactate synthase III, large subunit" thiamin-dependent E 89155476 -!- 92380929 -!- 3891724 -!- 6308579 -!- 9298646 Cytoplasmic 2.2.1.6 FAD -!- Mg2+ heteromultimer; acetolactate synthase III / acetohydroxybutanoate synthase III (b0077-b0078) regulated by attenuation (ilvI-ilvH-fruL) 52467; DHS-like NAD/FAD-binding domain -!- 52518; Thiamin diphosphate-binding fold (THDP-binding) "PF02776;Thiamine pyrophosphate enzyme, N-termina;3e-104;codon 34-204 -!- PF00205;Thiamine pyrophosphate enzyme, central d;1.6e-82;codon 225-384" "TIGR00118;acolac_lg: acetolactate synthase, large sub;0;codon 34-600" CDS ECK0080 ilvH ilvH brnP b0078 87357 87848 + (no change) JW0077 87357 87848 + e "acetolactate synthase III, thiamin-dependent, small subunit" E 89033904 -!- 89155476 -!- 92380929 -!- 1851954 -!- 2198273 -!- 6308579 Cytoplasmic 2.2.1.6 FAD -!- Mg2+ heteromultimer; acetolactate synthase III / acetohydroxybutanoate synthase III (b0077-b0078) "COG0440;Acetolactate synthase, small (regulatory) subunit" 55021; Regulatory domain in the aminoacid metabolism PF01842;ACT domain;1.5e-16;codon 3-76 "TIGR00119;acolac_sm: acetolactate synthase, small sub;2.6e-75;codon 1-159" CDS ECK0081 fruR fruR cra -!- fruC -!- shl b0080 88028 89032 + (no change) JW0078 88028 89032 + r DNA-binding transcriptional dual regulator of fru operon and of carbon and energy metabolism E 89384462 -!- 94018607 -!- 94047069 -!- 96421533 -!- 1851954 -!- 2198273 -!- 8655535 -!- 9237914 Cytoplasmic monomeric multimer; FruR transcriptional dual regulator (b0080) GalR/LacI aceBAK -!- adhE -!- edd-eda -!- epd-pgk -!- fruBKA -!- icdA -!- mtlADR -!- nirBDC-cysG -!- pckA -!- pfkA -!- ppsA -!- ptsHI-crr -!- pykF regulated by attenuation (fruR) COG1609;Transcriptional regulators 47413; lambda repressor-like DNA-binding domains -!- 53822; Periplasmic binding protein-like I "PF00356;Bacterial regulatory proteins, lacI fami;5.8e-09;codon 1-26 -!- PF00532;Periplasmic binding proteins and sugar b;3.3e-05;codon 61-329" GO:0005737 cytoplasm GO:0006096 glycolysis -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0082 mraZ mraZ yabB b0081 89634 90092 + (no change) JW0079 89634 90092 + o conserved protein C 20042184 -!- 2187182 Cytoplasmic COG2001;Uncharacterized protein conserved in bacteria PF02381;Domain of unknown function UPF0040 family;8.1e-31;codon 1-76 -!- PF02381;Domain of unknown function UPF0040 family;2.7e-24;codon 77-145 TIGR00242;TIGR00242: mraZ protein;4.7e-77;codon 1-152 CDS ECK0083 mraW mraW yabC b0082 90094 91035 + (no change) JW0080 90094 91035 + e S-adenosyl-dependent methyltransferase activity on membrane-located substrates E 20042184 -!- 10493123 -!- 2187182 -!- 6350821 Cytoplasmic 2.1.1.- COG0275;Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis 53335; S-adenosyl-L-methionine-dependent methyltransferases PF01795;MraW methylase family;1.5e-196;codon 4-311 TIGR00006;TIGR00006: S-adenosyl-methyltransferase Mra;1.8e-218;codon 1-311 GO:0042158 lipoprotein biosynthesis CDS ECK0084 ftsL ftsL yabD -!- mraR b0083 91032 91397 + (no change) JW0081 91032 91397 + cp membrane bound cell division protein at septum containing leucine zipper motif E 10027987 -!- 93077455 -!- 94079315 -!- 1447153 -!- 2187182 -!- 6350821 Membrane Anchored COG3116;Cell division protein PF04999;Cell division protein FtsL;1.1e-65;codon 24-120 TIGR02209;ftsL_broad: cell division protein FtsL;1.3e-37;codon 35-119 CDS ECK0085 ftsI ftsI pbpB -!- sep b0084 91413 93179 + (no change) JW0082 91413 93179 + e transpeptidase involved in septal peptidoglycan synthesis (penicillin-binding protein 3) E 91072213 -!- 92202178 -!- 94095121 -!- 9603865 -!- 9614966 -!- 1332942 -!- 1447153 -!- 2198024 -!- 2677607 -!- 2681146 -!- 3049550 -!- 3911028 -!- 6350821 Membrane Anchored COG0768;Cell division protein FtsI/penicillin-binding protein 2 "56519; Penicillin-binding protein 2x (pbp-2x), N-terminal domain -!- 56601; beta-Lactamase/D-ala carboxypeptidase" PF03717;Penicillin-binding Protein dimerisatio;7.9e-69;codon 66-222 -!- PF00905;Penicillin binding protein transpeptid;1.4e-120;codon 260-555 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009252 peptidoglycan biosynthesis -!- GO:0042493 response to drug CDS ECK0086 murE murE b0085 93166 94653 + (no change) JW0083 93166 94653 + e UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-diaminopimelate ligase E 88273095 -!- 90036700 -!- 91310568 -!- 2198024 -!- 2269304 -!- 2692800 -!- 9166795 6.3.2.13 COG0769;UDP-N-acetylmuramyl tripeptide synthase "53244; MurD-like peptide ligases, peptide-binding domain -!- 53623; MurD-like peptide ligases, catalytic domain -!- 63418; MurE/MurF N-terminal domain" "PF01225;Mur ligase family, catalytic domain;2.2e-87;codon 42-330 -!- PF02875;Mur ligase family, glutamate ligase doma;1.5e-39;codon 339-427" TIGR01085;murE: UDP-N-acetylmuramyl-tripeptide synthet;3.8e-217;codon 19-492 GO:0009274 cell wall (sensu Bacteria) GO:0009252 peptidoglycan biosynthesis CDS ECK0087 murF murF mra b0086 94650 96008 + (no change) JW0084 94650 96008 + e UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase E 88273095 -!- 90248455 -!- 91310568 -!- 97128642 -!- 11090285 -!- 2668880 -!- 9166795 Cytoplasmic 6.3.2.10 COG0770;UDP-N-acetylmuramyl pentapeptide synthase "53244; MurD-like peptide ligases, peptide-binding domain -!- 53623; MurD-like peptide ligases, catalytic domain -!- 63418; MurE/MurF N-terminal domain" "PF01225;Mur ligase family, catalytic domain;7.1e-84;codon 36-304 -!- PF02875;Mur ligase family, glutamate ligase doma;1.3e-20;codon 313-399" TIGR01143;murF: UDP-N-acetylmuramoyl-tripeptide--D-ala;9.2e-197;codon 29-446 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009252 peptidoglycan biosynthesis -!- GO:0000270 peptidoglycan metabolism CDS ECK0088 mraY mraY murX b0087 96002 97084 + (no change) JW0085 96002 97084 + e phospho-N-acetylmuramoyl-pentapeptide transferase E 91123172 -!- 10564498 -!- 215212 -!- 2179861 Integral Membrane Protein 2.7.8.13 10 10 out COG0472;UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N-acetylglucosamine-1-phosphate transferase PF00953;Glycosyl transferase;1.6e-88;codon 98-290 TIGR00445;mraY: phospho-N-acetylmuramoyl-pentapeptide-;7.2e-252;codon 37-360 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009252 peptidoglycan biosynthesis CDS ECK0089 murD murD b0088 97087 98403 + (no change) JW0086 97087 98403 + e UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase E 88273095 -!- 90036700 -!- 91310568 -!- 99330160 -!- 10966819 -!- 1765076 -!- 2129548 -!- 2179861 -!- 2509435 -!- 9218784 Membrane Anchored 6.3.2.9 Mg2+ -!- potassium phosphate COG0771;UDP-N-acetylmuramoylalanine-D-glutamate ligase "51984; UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD, N-terminal domain -!- 53244; MurD-like peptide ligases, peptide-binding domain -!- 53623; MurD-like peptide ligases, catalytic domain" "PF01225;Mur ligase family, catalytic domain;2e-66;codon 42-291 -!- PF02875;Mur ligase family, glutamate ligase doma;1e-17;codon 300-379" TIGR01087;murD: UDP-N-acetylmuramoylalanine--D-glutama;4.3e-173;codon 8-436 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009252 peptidoglycan biosynthesis CDS ECK0090 ftsW ftsW rodA b0089 98403 99647 + (no change) JW0087 98403 99647 + cp integral membrane protein involved in stabilizing FstZ ring during cell division E 90036736 -!- 9603865 -!- 2197603 -!- 7961485 -!- 9006034 -!- 9218774 Integral Membrane Protein 9.B.3; The Putative Bacterial Murein Precursor Exporter (MPE) Family 10 10 in COG0772;Bacterial cell division membrane protein PF01098;Cell cycle protein;3.7e-195;codon 46-403 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0091 murG murG b0090 99644 100711 + (no change) JW0088 99644 100711 + e N-acetylglucosaminyl transferase E 12538870 -!- 88273095 -!- 91310568 -!- 99268472 -!- 10892798 -!- 2187180 -!- 2197603 -!- 8449890 2.4.1.227 1NLM COG0707;UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase 53756; UDP-Glycosyltransferase/glycogen phosphorylase PF03033;Glycosyltransferase family;9.4e-54;codon 8-146 -!- PF04101;Glycosyltransferase family;2.7e-59;codon 184-345 TIGR01133;murG: undecaprenyldiphospho-muramoylpentapep;1.3e-152;codon 1-349 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009252 peptidoglycan biosynthesis CDS ECK0092 murC murC b0091 100765 102240 + (no change) JW0089 100765 102240 + e UDP-N-acetylmuramate:L-alanine ligase E 12876369 -!- 88273095 -!- 91310568 -!- 99330160 -!- 2197603 -!- 7601127 -!- 9166795 Cytoplasmic 6.3.2.8 Mg2+ COG0773;UDP-N-acetylmuramate-alanine ligase "51984; UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD, N-terminal domain -!- 53244; MurD-like peptide ligases, peptide-binding domain -!- 53623; MurD-like peptide ligases, catalytic domain" "PF01225;Mur ligase family, catalytic domain;1.7e-68;codon 55-315 -!- PF02875;Mur ligase family, glutamate ligase doma;1.3e-22;codon 324-422" TIGR01082;murC: UDP-N-acetylmuramate--alanine ligase;1.5e-285;codon 21-476 GO:0009274 cell wall (sensu Bacteria) GO:0009252 peptidoglycan biosynthesis CDS ECK0093 ddlB ddlB ddl b0092 102233 103153 + (no change) JW0090 102233 103153 + e D-alanine:D-alanine ligase E 91129242 -!- 95200896 -!- 1554356 -!- 2197603 -!- 3528126 -!- 7939684 -!- 9054558 Cytoplasmic 6.3.2.4 monomeric multimer; D-alanine-D-alanine ligase B (b0092) 1IOV COG1181;D-alanine-D-alanine ligase and related ATP-grasp enzymes 52440; Biotin carboxylase N-terminal domain-like -!- 56059; Glutathione synthetase ATP-binding domain-like PF01820;D-ala D-ala ligase N-terminus;1.3e-47;codon 3-95 -!- PF07478;D-ala D-ala ligase C-terminus;2.8e-119;codon 96-303 TIGR01205;D_ala_D_alaTIGR: D-alanine--D-alanine;1.5e-179;codon 4-306 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009252 peptidoglycan biosynthesis CDS ECK0094 ftsQ ftsQ b0093 103155 103985 + (no change) JW0091 103155 103985 + cp membrane anchored protein involved in growth of wall at septum E 92021787 -!- 93015653 -!- 9882666 -!- 2995680 -!- 3528126 -!- 6094474 Membrane Anchored COG1589;Cell division septal protein PF03799;Cell division protein FtsQ;3.9e-79;codon 28-247 GO:0019866 inner membrane CDS ECK0095 ftsA ftsA divA b0094 103982 105244 + (no change) JW0092 103982 105244 + cp ATP-binding cell division protein involved in recruitment of FtsK to Z ring E 11847116 -!- 20507805 -!- 93015653 -!- 94079315 -!- 2846985 -!- 2995680 -!- 3000876 -!- 6094474 Cytoplasmic COG0849;Actin-like ATPase involved in cell division 53067; Actin-like ATPase domain PF02491;Cell division protein FtsA;1.8e-74;codon 10-197 -!- PF02491;Cell division protein FtsA;3e-70;codon 199-383 TIGR01174;ftsA: cell division protein FtsA;5.8e-179;codon 9-385 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0096 ftsZ ftsZ sfiB -!- sulB b0095 105305 106456 + (no change) JW0093 105305 106456 + cp GTP-binding tubulin-like cell division protein forms ring at septum E 94018635 -!- 94193533 -!- 94222860 -!- 99248407 -!- 1528267 -!- 1528268 -!- 1944597 -!- 2824434 -!- 2995680 -!- 3000876 -!- 6094474 -!- 8016071 -!- 8083192 -!- 9298646 Cytoplasmic COG0206;Cell division GTPase "52490; Tubulin, GTPase domain -!- 55307; Tubulin, C-terminal domain" "PF00091;Tubulin/FtsZ family, GTPase domain;1.1e-89;codon 11-204 -!- PF03953;Tubulin/FtsZ family, C-terminal domain;1.1e-45;codon 206-332" TIGR00065;ftsZ: cell division protein FtsZ;3.6e-218;codon 1-348 GO:0005737 cytoplasm CDS ECK0097 lpxC lpxC asmB -!- envA b0096 106557 107474 + (no change) JW0094 106557 107474 + e UDP-3-O-acyl N-acetylglucosamine deacetylase E "92021797 -!- 94079315 -!- 99152380 -!- 2824434 -!- 3000876 -!- 8752330 -!- Young K, Silver L, Bramhill D, et al;FASEB Journal;1993;7:1252" Cytoplasmic 3.5.1.- Zn2+ COG0774;UDP-3-O-acyl-N-acetylglucosamine deacetylase PF03331;UDP-3-O-acyl N-acetylglycosamine deacetylase;2.4e-194;codon 2-280 TIGR00325;lpxC: UDP-3-0-acyl N-acetylglucosamine deace;2.9e-172;codon 1-305 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009245 lipid A biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0098 secM secM srrA -!- yacA -!- yccA b0097 107705 108217 + start codon change JW5007 107705 108217 + r regulator of secA translation E 20444210 -!- 21111078 1-57 PF06558;Secretion monitor precursor protein (SecM);9.6e-114;codon 49-195 CDS ECK0099 secA secA azi -!- pea -!- prlD b0098 108279 110984 + (no change) JW0096 108279 110984 + t "preprotein translocase subunit, ATPase" "member of DEAD box family, targets protein precursors to the SecYE core translocon" E 12403785 -!- 91170263 -!- 92135194 -!- 94292446 -!- 9644254 -!- 9705302 -!- 9829959 -!- 2542029 -!- 2824434 -!- 2841285 Cytoplasmic heteromultimer; Sec Protein Secretion Complex (b0098-b0407-b0408-b0409-b3175-b3300-b3609-b3705-b 3981) 3.A.5; The General Secretory Pathway (Sec) Family "COG0653;Preprotein translocase subunit SecA (ATPase, RNA helicase)" 52540; P-loop containing nucleotide triphosphate hydrolases PF07517;SecA DEAD-like domain;7.4e-160;codon 6-402 -!- PF01043;SecA preprotein cross-linking domain;1.1e-85;codon 228-358 -!- PF07516;SecA Wing and Scaffold domain;3e-125;codon 617-831 -!- PF02810;SEC-C motif;6.2e-11;codon 881-901 "TIGR00963;secA: preprotein translocase, SecA subunit;0;codon 28-818" GO:0005737 cytoplasm CDS ECK0100 mutT mutT nudA b0099 111044 111433 + (no change) JW0097 111044 111433 + e "nucleoside triphosphate pyrophosphohydrolase, marked preference for dGTP" E 10218109 -!- 89264540 -!- 90136514 -!- 91225007 -!- 97444511 -!- 1309939 -!- 2841285 -!- 3033442 -!- 3288626 -!- 7578113 -!- 9063868 Cytoplasmic 3.6.1.- Mg2+ -!- Mn2+ 1PUS COG0494;NTP pyrophosphohydrolases including oxidative damage repair enzymes 55811; Nudix PF00293;NUDIX domain;1e-28;codon 4-129 TIGR00586;mutt: mutator mutT protein;2.5e-94;codon 1-128 GO:0005737 cytoplasm GO:0009265 2'-deoxyribonucleotide biosynthesis CDS ECK0101 yacG yacG b0101 111649 111846 - (no change) JW5008 111649 111846 - o conserved protein predicted zinc finger protein C 12211008 -!- 3033442 Cytoplasmic 1LV3 COG3024;Uncharacterized protein conserved in bacteria PF03884;Domain of unknown function (DUF329);5.7e-41;codon 5-64 CDS ECK0102 yacF yacF b0102 111856 112599 - (no change) JW0099 111856 112599 - o conserved protein C Cytoplasmic COG4582;Uncharacterized protein conserved in bacteria PF07072;Protein of unknown function (DUF1342);2e-172;codon 3-247 CDS ECK0103 coaE coaE yacE b0103 112599 113219 - (no change) JW0100 112599 113219 - e dephospho-CoA kinase E 21189301 -!- 10493123 Periplasmic 2.7.1.24 COG0237;Dephospho-CoA kinase 52540; P-loop containing nucleotide triphosphate hydrolases PF01121;Dephospho-CoA kinase;1e-118;codon 3-180 TIGR00152;TIGR00152: dephospho-CoA kinase;2.5e-73;codon 4-191 CDS ECK0104 guaC guaC b0104 113444 114487 + (no change) JW0101 113444 114487 + e GMP reductase E "89061679 -!- Mager J, Magasanik B;J Biol Chem;1960;235(5):1474-1478" Cytoplasmic 1.7.1.7 monomeric multimer; GMP reductase (b0104) COG0516;IMP dehydrogenase/GMP reductase 51412; Inosine monophosphate dehydrogenase (IMPDH) PF00478;IMP dehydrogenase / GMP reductase domain;7.9e-159;codon 8-347 TIGR01305;GMP_reduct_1: guanosine monophosphate re;1.2e-268;codon 2-344 GO:0005737 cytoplasm "GO:0009152 purine ribonucleotide biosynthesis -!- GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0105 hofC hofC hopC -!- yacD b0106 114522 115724 - (no change) JW0102 114522 115724 - s "assembly protein in type IV pilin biogenesis, transmembrane protein" component of type IV pilin biogenesis pathway E 96099298 -!- 2904262 -!- 7959070 Integral Membrane Protein 4 3 out "COG1459;Type II secretory pathway, component PulF" PF00482;Bacterial type II secretion system protein F;1.1e-21;codon 63-186 -!- PF00482;Bacterial type II secretion system protein F;7.7e-17;codon 266-388 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0106 hofB hofB hopB b0107 115714 117099 - (no change) JW0103 115714 117099 - d conserved protein with nucleoside triphosphate hydrolase domain component of type IV pilin biogenesis pathway C 96099298 -!- 7959070 Cytoplasmic "COG2804;Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB" 52540; P-loop containing nucleotide triphosphate hydrolases PF00437;Type II/IV secretion system protein;8e-145;codon 76-354 GO:0009289 fimbria CDS ECK0107 ppdD ppdD b0108 117109 117549 - (no change) JW0104 117109 117549 - ps predicted major pilin subunit component of type IV pilin biogenesis pathway C 20100782 -!- 20271862 -!- 96099298 -!- 7959070 Membrane Anchored "COG4969;Tfp pilus assembly protein, major pilin PilA" 54523; Pilin PF07963;Prokaryotic N-terminal methylation motif;1.8e-08;codon 5-28 GO:0009289 fimbria CDS ECK0108 nadC nadC b0109 117752 118645 - (no change) JW0105 117752 118645 - e quinolinate phosphoribosyltransferase E 4319723 Cytoplasmic 2.4.2.19 Mg2+ monomeric multimer; quinolinate phosphoribosyltransferase (decarboxylating) (b0109) COG0157;Nicotinate-nucleotide pyrophosphorylase "51690; Quinolinic acid phosphoribosyltransferase, C-terminal domain -!- 54675; Quinolinic acid phosphoribosyltransferase, N-terminal domain" "PF02749;Quinolinate phosphoribosyl transferase, N-t;1e-43;codon 40-129 -!- PF01729;Quinolinate phosphoribosyl transferase, C-t;1.3e-102;codon 131-295" TIGR00078;nadC: nicotinate-nucleotide pyrophosphorylas;5.1e-163;codon 26-296 GO:0009435 nicotinamide adenine dinucleotide biosynthesis CDS ECK0109 ampD ampD b0110 118733 119284 + (no change) JW0106 118733 119284 + e N-acetyl-anhydromuranmyl-L-alanine amidase E 90113890 -!- 95047240 -!- 2607970 -!- 7959070 Cytoplasmic 3.5.1.28 COG3023;Negative regulator of beta-lactamase expression PF01510;N-acetylmuramoyl-L-alanine amidase;2.9e-64;codon 17-177 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0000270 peptidoglycan metabolism CDS ECK0110 ampE ampE b0111 119281 120135 + (no change) JW0107 119281 120135 + pm predicted inner membrane protein C 90113890 -!- 2607970 Integral Membrane Protein 5 4 out COG3725;Membrane protein required for beta-lactamase induction GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0111 aroP aroP aroR -!- aroT b0112 120178 121551 - (no change) JW0108 120178 121551 - t aromatic amino acid transporter E 1104763 -!- 90174991 -!- 9150230 Integral Membrane Protein 2.A.3; The Amino Acid-Polyamine-Organocation (APC) Family 12 12 in COG1113;Gamma-aminobutyrate permease and related permeases PF00324;Amino acid permease;3.1e-184;codon 19-457 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009094 L-phenylalanine biosynthesis -!- GO:0006571 tyrosine biosynthesis CDS ECK0112 pdhR pdhR yacB -!- dcuA -!- aceC -!- genA b0113 122092 122856 + (no change) JW0109 122092 122856 + r DNA-binding transcriptional dual regulator E 94085588 -!- 94178454 -!- 94335636 -!- 6343085 Cytoplasmic GntR lldPRD -!- pdhR-aceEF-lpdA -!- yfiD COG2186;Transcriptional regulators 46785; Winged helix "PF00392;Bacterial regulatory proteins, gntR family;3.2e-32;codon 11-74 -!- PF07729;FCD domain;5.9e-31;codon 99-227" GO:0005737 cytoplasm GO:0006096 glycolysis -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK0113 aceE aceE b0114 123017 125680 + (no change) JW0110 123017 125680 + e "pyruvate dehydrogenase, decarboxylase component E1, thiamin-binding" E 89076356 -!- 89247334 -!- 90242938 -!- 11955070 -!- 6343085 -!- 8262214 -!- 9298646 Cytoplasmic 1.2.4.1 Mg2+ heteromultimer; pyruvate dehydrogenase multienzyme complex (b0114-b0115-b0116) -!- monomeric multimer; pyruvate dehydrogenase (b0114) 1RP7 "COG2609;Pyruvate dehydrogenase complex, dehydrogenase (E1) component" 52518; Thiamin diphosphate-binding fold (THDP-binding) -!- 52922; Transketolase C-terminal domain-like "TIGR00759;aceE: 2-oxo-acid dehydrogenase E1 component,;0;codon 4-887" GO:0016052 carbohydrate catabolism -!- GO:0006086 acetyl-CoA biosynthesis from pyruvate -!- GO:0006096 glycolysis -!- GO:0009436 glyoxylate catabolism -!- GO:0009061 anaerobic respiration CDS ECK0114 aceF aceF b0115 125695 127587 + (no change) JW0111 125695 127587 + e "pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2" E 80009188 -!- 92037610 -!- 92207996 -!- 2121129 -!- 2201286 -!- 6345153 -!- 6821375 -!- 9298646 2.3.1.12 Mg2+ heteromultimer; pyruvate dehydrogenase multienzyme complex (b0114-b0115-b0116) "COG0508;Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes" 47005; Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex -!- 51230; Single hybrid motif -!- 52777; CoA-dependent acyltransferases 3 of PF00364;Biotin-requiring enzyme: 1.1e-27;aa 3-74 -!- 1.4e-30;aa 106-177 -!- 4.6e-29;aa 207-278 -!- PF02817;e3 binding domain;1.7e-18;aa 329-365 -!- PF00198;2-oxoacid dehydrogenases acyltransferase (catalytic domain);1.2e-110;aa 397-630 TIGR01348;PDHac_trf_long: pyruvate dehydrogenase;0;codon 3-630 GO:0016052 carbohydrate catabolism -!- GO:0006086 acetyl-CoA biosynthesis from pyruvate -!- GO:0006096 glycolysis -!- GO:0009436 glyoxylate catabolism -!- GO:0009061 anaerobic respiration CDS ECK0115 lpd lpd dhl -!- lpdA b0116 127912 129336 + (no change) JW0112 127912 129336 + e "lipoamide dehydrogenase, E3 component is part of three enzyme complexes" part of pyruvate and 2-oxoglutarate dehydrogenase complexes and glycine cleavage system L protein; binds Zn(II) -!- NADH-dependent E 89134177 -!- 91008999 -!- 6352260 -!- 9298646 -!- Reed LJ;Accounts of Chemical Research;1974;7:40-46 Cytoplasmic 1.8.1.4 Mg2+ heteromultimer; 2-oxoglutarate dehydrogenase complex (b0726-b0727-b0116) -!- heteromultimer; gcv system (b0116-b2903-b2904-b2905) -!- heteromultimer; pyruvate dehydrogenase multienzyme complex (b0114-b0115-b0116) -!- monomeric multimer; dihydrolipoate dehydrogenase / dihydrolipoamide dehydrogenase (b0116) "COG1249;Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes" "51905; FAD/NAD(P)-binding domain -!- 55424; FAD/NAD-linked reductases, dimerisation (C-terminal) domain" PF00070;Pyridine nucleotide-disulphide oxidored;2.9e-96;codon 8-319 -!- PF02852;Pyridine nucleotide-disulphide oxidored;3.2e-52;codon 347-456 TIGR01350;lipoamide_DH: dihydrolipoamide dehydroge;6.5e-176;codon 6-466 GO:0005737 cytoplasm GO:0016052 carb catab -!- GO:0009063 aa catab -!- GO:0006096 glycolysis -!- GO:0006086 acetyl-CoA biosyn -!- GO:0006099 TCA -!- GO:0009060 aerobic resp -!- GO:0009061 anaerobic resp -!- GO:0009257 10-formylTHF biosyn -!- GO:0009436 glyoxylate catab CDS ECK0116 yacH yacH orf(ace) b0117 129407 131260 - (no change) JW0113 129407 131260 - o predicted protein C Periplasmic 1-21 GO:0009274 cell wall (sensu Bacteria) CDS ECK0117 acnB acnB yacI -!- yacJ b0118 131615 134212 + (no change) JW0114 131615 134212 + e bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase E 12473114 -!- 20053887 -!- 9421904 -!- 95093601 -!- 11992126 -!- 8932712 -!- 9298646 Cytoplasmic 4.2.1.3 -!- 4.2.1.99 regulated by attenuation (acnB) COG1049;Aconitase B "52016; Aconitase, C-terminal domain -!- 53732; Aconitase, first 3 domains" PF06434;Aconitate hydratase;8.9e-295;codon 2-382 -!- PF00330;Aconitase family (aconitate hydratase);9e-09;codon 383-818 TIGR00117;acnB: aconitate hydratase;0;codon 1-854 GO:0006099 tricarboxylic acid cycle -!- GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration CDS ECK0118 yacL yacL b0119 134388 134750 + start codon change JW0115 134388 134750 + o conserved protein C 2666401 -!- 7567469 Cytoplasmic regulated by attenuation (yacL) COG3112;Uncharacterized protein conserved in bacteria PF06062;Uncharacterised protein family (UPF0231);5e-78;codon 17-134 CDS ECK0119 speD speD b0120 134788 135582 - (no change) JW0116 134788 135582 - e S-adenosylmethionine decarboxylase E 88058963 -!- 89327165 -!- 2181453 -!- 3546296 Cytoplasmic 4.1.1.50 Mg2+ "adenosylmethionine decarboxylase (b0120-b0120) -!- monomeric multimer; adenosylmethionine decarboxylase, alpha complex (b0120) -!- monomeric multimer; adenosylmethionine decarboxylase, beta complex (b0120)" COG1586;S-adenosylmethionine decarboxylase PF02675;S-adenosylmethionine decarboxylase;6.7e-77;codon 38-169 GO:0006596 polyamine biosynthesis CDS ECK0120 speE speE b0121 135598 136464 - (no change) JW0117 135598 136464 - e spermidine synthase (putrescine aminopropyltransferase) E 88058963 -!- 89327165 -!- 3526348 Cytoplasmic 2.5.1.16 monomeric multimer; spermidine synthase (b0121) COG0421;Spermidine synthase 53335; S-adenosyl-L-methionine-dependent methyltransferases PF01564;Spermine/spermidine synthase;3.1e-135;codon 6-244 TIGR00417;speE: spermidine synthase;4.6e-203;codon 7-278 GO:0006596 polyamine biosynthesis CDS ECK0121 yacC yacC b0122 136570 136917 - start codon change JW0118 136570 136917 - o predicted protein C Periplasmic 1-58 CDS ECK0122 cueO cueO yacK b0123 137083 138633 + (no change) JW0119 137083 138633 + e multicopper oxidase (laccase) E 11867755 -!- 21125583 -!- 21359329 -!- 10493123 -!- 10915804 -!- 11399769 -!- 11527384 -!- 9298646 Periplasmic 1-28 516 COG2132;Putative multicopper oxidases 49503; Cupredoxins PF07732;Multicopper oxidase;4.3e-47;codon 51-167 -!- PF07731;Multicopper oxidase;1.3e-18;codon 378-516 TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.018;codon 1-28 CDS ECK0123 gcd gcd b0124 138835 141225 - (no change) JW0120 138835 141225 - e glucose dehydrogenase E 10359647 -!- 11604400 -!- 14612441 -!- 91035240 -!- 93123180 -!- 93286127 Integral Membrane Protein 1.1.5.2 Mg2+ 5 5 out COG4993;Glucose dehydrogenase 50998; Quinoprotein alcohol dehydrogenase PF01011;PQQ enzyme repeat;3.2e-09;codon 225-262 -!- PF01011;PQQ enzyme repeat;4.2e-06;codon 660-698 -!- PF01011;PQQ enzyme repeat;1e-07;codon 721-759 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006006 glucose metabolism -!- GO:0016052 carbohydrate catabolism GO:0009053 electron donor activity CDS ECK0124 hpt hpt b0125 141431 141967 + start codon change JW5009 141431 141967 + e hypoxanthine phosphoribosyltransferase E 13808016 -!- 339828 -!- 6787390 -!- 6801015 -!- 12070315 Cytoplasmic 2.4.2.8 Mg2+ 1GRV 53271; PRTase-like PF00156;Phosphoribosyl transferase domain;3.7e-38;codon 7-153 TIGR01203;HGPRTase: hypoxanthine phosphoribosyltransfe;4.4e-115;codon 11-178 GO:0005737 cytoplasm "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0125 can can yadF b0126 142008 142670 - (no change) JW0122 142008 142670 - e carbonic anhydrase E 12784642 Cytoplasmic 4.2.1.1 COG0288;Carbonic anhydrase "53056; beta-carbonic anhydrase, cab" PF00484;Carbonic anhydrase;7.8e-59;codon 30-192 CDS ECK0126 yadG yadG b0127 142779 143705 + (no change) JW0123 142779 143705 + pt predicted transporter subunit: ATP-binding component of ABC superfamily C Cytoplasmic heteromultimer; YadG/YadH ABC transporter (b0127-b0128) "COG1131;ABC-type multidrug transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.5e-53;codon 31-212 GO:0005737 cytoplasm CDS ECK0127 yadH yadH b0128 143702 144472 + (no change) JW0124 143702 144472 + pt predicted transporter subunit: membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YadG/YadH ABC transporter (b0127-b0128) 6 6 in "COG0842;ABC-type multidrug transport system, permease component" PF01061;ABC-2 type transporter;4.4e-48;codon 7-219 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0128 yadI yadI agaX b0129 144577 145017 + (no change) JW0125 144577 145017 + pt predicted PTS Enzyme IIA C Cytoplasmic heteromultimer; EIIAga (b0129-b3140-b2416-b2415-b3138-b3139) "COG2893;Phosphotransferase system, mannose/fructose-specific component IIA" "53062; IIA domain of mannose transporter, IIA-Man" PF03610;PTS system fructose IIA component;4.7e-38;codon 2-117 GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system CDS ECK0129 yadE yadE b0130 145081 146310 + (no change) JW0126 145081 146310 + pe predicted polysaccharide deacetylase lipoprotein C 1-19 regulated by attenuation (yadE) COG0726;Predicted xylanase/chitin deacetylase PF01522;Polysaccharide deacetylase;4.7e-29;codon 227-368 CDS ECK0130 panD panD b0131 146314 146694 - (no change) JW0127 146314 146694 - e aspartate 1-decarboxylase E 7037743 -!- 9169598 -!- 9546220 4.1.1.11 monomeric multimer; aspartate 1-decarboxylase (b0131) 1PQE COG0853;Aspartate 1-decarboxylase 50692; ADC-like PF02261;Aspartate decarboxylase;9e-86;codon 1-116 TIGR00223;panD: aspartate 1-decarboxylase;4.8e-103;codon 1-126 GO:0005737 cytoplasm GO:0015937 coenzyme A biosynthesis CDS ECK0131 yadD yadD b0132 146968 147870 + (no change) JW5010 146968 147870 + ph predicted transposase C Cytoplasmic "PF04754;Putative transposase, YhgA-like;6.6e-205;codon 1-276" TIGR01784;T_den_put_tspse: conserved hypothetic;6.4e-123;codon 8-296 CDS ECK0132 panC panC b0133 147944 148795 - (no change) JW0129 147944 148795 - e pantothenate synthetase E 7037743 -!- 12999714 Cytoplasmic 6.3.2.1 K+ -!- Mg2+ monomeric multimer; pantoate-beta-alanine ligase (b0133) COG0414;Panthothenate synthetase 52374; Nucleotidylyl transferase PF02569;Pantoate-beta-alanine ligase;2.3e-198;codon 2-280 TIGR00018;panC: pantoate--beta-alanine ligase;1.1e-206;codon 1-281 -!- TIGR00125;cyt_tran_rel: cytidyltransferase-related;6.9e-06;codon 23-91 GO:0005737 cytoplasm GO:0015937 coenzyme A biosynthesis CDS ECK0133 panB panB ts-9 b0134 148807 149601 - (no change) JW0130 148807 149601 - e 3-methyl-2-oxobutanoate hydroxymethyltransferase E 12837791 -!- 7037743 -!- 93209959 -!- 9298646 Cytoplasmic 2.1.2.11 Mg2+ monomeric multimer; 3-methyl-2-oxobutanoate hydroxymethyltransferase (b0134) COG0413;Ketopantoate hydroxymethyltransferase PF02548;Ketopantoate hydroxymethyltransferase;3.8e-183;codon 2-260 TIGR00222;panB: 3-methyl-2-oxobutanoate hydroxymethylt;6.7e-208;codon 1-264 GO:0005737 cytoplasm GO:0015937 coenzyme A biosynthesis CDS ECK0134 yadC yadC b0135 149715 150953 - (no change) JW0131 149715 150953 - ps predicted fimbrial-like adhesin protein C "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;9e-06;codon 247-412 GO:0009289 fimbria CDS ECK0135 yadK yadK b0136 151003 151599 - (no change) JW0132 151003 151599 - ps predicted fimbrial-like adhesin protein C 49401; Bacterial adhesins CDS ECK0136 yadL yadL b0137 151626 152231 - (no change) JW0133 151626 152231 - ps predicted fimbrial-like adhesin protein C 1-18 49401; Bacterial adhesins PF00419;Fimbrial protein;0.0023;codon 46-201 CDS ECK0137 yadM yadM b0138 152243 152812 - start codon change JW0134 152243 152812 - ps predicted fimbrial-like adhesin protein C Periplasmic 1-37 49401; Bacterial adhesins GO:0009289 fimbria CDS ECK0138 htrE htrE b0139 152829 155426 - (no change) JW0135 152829 155426 - pf predicted outer membrane usher protein C 93352405 Periplasmic 865 "COG3188;P pilus assembly protein, porin PapC" PF00577;Fimbrial Usher protein;0;codon 33-845 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0139 ecpD ecpD b0140 155461 156201 - (no change) JW0136 155461 156201 - pf predicted periplasmic pilin chaperone C 93352405 Periplasmic "COG3121;P pilus assembly protein, chaperone PapD" 49354; PapD-like -!- 49584; Periplasmic chaperone C-domain PF00345;Gram-negative pili assembly chaperone;5.5e-73;codon 26-152 -!- PF02753;Gram-negative pili assembly chaperone;2.3e-29;codon 156-244 GO:0019866 inner membrane GO:0006457 protein folding CDS ECK0140 yadN yadN b0141 156299 156883 - (no change) JW0137 156299 156883 - ps predicted fimbrial-like adhesin protein C Periplasmic 1-23 "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;1.9e-05;codon 28-194 GO:0009289 fimbria CDS ECK0141 folK folK b0142 157253 157732 - (no change) JW0138 157253 157732 - e 2-amino-4-hydroxy-6-hydroxymethyldihyropteridine pyrophosphokinase E 92041593 -!- 92394901 -!- 10378268 -!- 10452528 -!- 2537812 Cytoplasmic 2.7.6.3 Mg2+ 1Q0N "COG0801;7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase" "55083; 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK" "PF01288;7,8-dihydro-6-hydroxymethylpteri n-pyrophosph;2.4e-77;codon 5-133" TIGR01498;folK: 2-amino-4-hydroxy-6-hydroxymethyldihyd;1.8e-75;codon 4-134 GO:0046656 folic acid biosynthesis CDS ECK0142 pcnB pcnB b0143 157729 159126 - start codon change -!- AUU start JW5808 157729 159126 - e poly(A) polymerase I E 10594833 -!- 20300915 -!- 20504447 -!- 21316493 -!- 22195892 -!- 7533264 -!- 93066242 -!- 93342068 -!- 94128084 -!- 95020645 -!- 98445341 -!- 99291044 -!- 1691435 -!- 2537812 Cytoplasmic 2.7.7.19 COG0617;tRNA nucleotidyltransferase/poly(A) polymerase PF01743;Poly A polymerase family;6.9e-85;codon 109-274 TIGR01942;pcnB: poly(A) polymerase;2.1e-197;codon 20-454 GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK0143 yadB yadB b0144 159186 160112 - (no change) JW5892 159186 160112 - e glutamyl-Q tRNA(Asp) synthetase E 15003446 -!- 15150343 -!- 2180916 Cytoplasmic 6.1.1.- 1NZJ COG0008;Glutamyl- and glutaminyl-tRNA synthetases 52374; Nucleotidylyl transferase "PF00749;tRNA synthetases class I (E and Q), cata;3.9e-33;codon 19-301" GO:0006418 amino acid activation CDS ECK0144 dksA dksA msmA b0145 160149 160604 - (no change) JW0141 160149 160604 - r "DNA-binding transcriptional regulator of rRNA transcription, DnaK suppressor protein" E 15294157 -!- 90202727 -!- 2013578 -!- 9298646 -!- 9600841 Cytoplasmic COG1734;DnaK suppressor protein PF01258;Prokaryotic dksA/traR C4-type zinc finge;3.2e-36;codon 76-146 GO:0005737 cytoplasm GO:0006457 protein folding CDS ECK0145 sfsA sfsA sfs1 -!- sfs b0146 160782 161486 - (no change) JW0142 160782 161486 - pr predicted DNA-binding transcriptional regulator of maltose metabolism C 91193225 -!- 2180916 Cytoplasmic "COG1489;DNA-binding protein, stimulates sugar fermentation" PF03749;Sugar fermentation stimulation protein;1.1e-109;codon 13-231 TIGR00230;sfsA: sugar fermentation stimulation protein;9.8e-109;codon 1-234 GO:0016052 carbohydrate catabolism CDS ECK0146 ligT ligT yadP b0147 161501 162031 - start codon change JW5011 161501 162031 - e 2'-5' RNA ligase E 97094878 Cytoplasmic 6.5.1.- "PF02834;2',5' RNA ligase family;5.2e-18;codon 14-92 -!- PF02834;2',5' RNA ligase family;6.5e-09;codon 93-169" TIGR02258;2_5_ligase: 2'-5' RNA ligase;2.9e-69;codon 8-177 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK0147 hrpB hrpB yadO b0148 162105 164534 + start codon change JW0144 162105 164534 + pe predicted ATP-dependent helicase member of DEAD box family C 95206938 Cytoplasmic COG1643;HrpA-like helicases 52540; P-loop containing nucleotide triphosphate hydrolases PF00270;DEAD/DEAH box helicase;2.1e-11;codon 29-182 -!- PF00271;Helicase conserved C-terminal domain;4.2e-09;codon 249-343 -!- PF04408;Helicase associated domain (HA2);2.4e-06;codon 403-490 TIGR01970;DEAH_box_HrpB: ATP-dependent helicase H;0;codon 19-824 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK0148 mrcB mrcB pbpF -!- ponB b0149 164730 167264 + (no change) JW0145 164730 167264 + e fused glycosyl transferase -!- transpeptidase penicillin-binding protein 1b E 20032350 -!- 3882429 -!- 3906031 -!- 99406903 Membrane Anchored 2.4.1.129 -!- 3.4.-.- fused penicillin-binding protein 1b: membrane protein (aa1-200) -!- glycosyl transferase (aa204-382) -!- transpeptidase (aa444-844) COG0744;Membrane carboxypeptidase (penicillin-binding protein) 56601; beta-Lactamase/D-ala carboxypeptidase -!- 56601; beta-Lactamase/D-ala carboxypeptidase -!- 56601; beta-Lactamase/D-ala carboxypeptidase PF00912;Transglycosylase;1.1e-83;codon 195-366 -!- PF00905;Penicillin binding protein transpeptid;6.2e-18;codon 472-748 TIGR02071;PBP_1b: penicillin-binding protein 1B;0;codon 67-795 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0046349 amino sugar biosynthesis -!- GO:0009252 peptidoglycan biosynthesis -!- GO:0042493 response to drug CDS ECK0149 fhuA fhuA T1 -!- T5rec -!- tonA b0150 167484 169727 + (no change) JW0146 167484 169727 + t ferrichrome outer membrane transporter "receptor for colicin M and phages T1, T5 and phi80" E 12383253 -!- 12896986 -!- 12944258 -!- 92276324 -!- 93139053 -!- 93345445 -!- 9613584 -!- 99406910 -!- 10850805 -!- 2823072 -!- 3079747 -!- 7515827 -!- 8617231 -!- 9856937 -!- 9865695 Outer Membrane B-barrel protein heteromultimer; Outer Membrane Ferrichrome Transport System (b0150-b1252-b3005-b3006) -!- heteromultimer; ferrichrome uptake system (b0150-b0151-b0152-b0153-b1252-b3005-b3006) 1.B.14; The Outer Membrane Receptor (OMR) Family 1-33 747 "COG1629;Outer membrane receptor proteins, mostly Fe transport" 56935; Porins PF07715;TonB-dependent Receptor Plug Domain;3.3e-21;codon 75-181 -!- PF00593;TonB dependent receptor;1.6e-26;codon 510-747 TIGR01783;TonB-siderophor: TonB-dependent sider;3.3e-266;codon 78-747 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0150 fhuC fhuC b0151 169778 170575 + (no change) JW0147 169778 170575 + t iron-hydroxamate transporter subunit -!- ATP-binding component of ABC superfamily E 89364703 -!- 91307893 -!- 92202160 -!- 9613584 -!- 2823072 -!- 3301821 Cytoplasmic heteromultimer; ferrichrome uptake system (b0150-b0151-b0152-b0153-b1252-b3005-b3006) -!- heteromultimer; iron (III) hydroxamate ABC transporter (b0151-b0153-b0152) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG1120;ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;3.4e-61;codon 37-224 GO:0005737 cytoplasm CDS ECK0151 fhuD fhuD b0152 170575 171465 + (no change) JW0148 170575 171465 + t iron-hydroxamate transporter subunit -!- periplasmic-binding component of ABC superfamily E 89364703 -!- 91072323 -!- 91307893 -!- 9613584 -!- 10742172 -!- 2823072 -!- 3301821 Periplasmic heteromultimer; ferrichrome uptake system (b0150-b0151-b0152-b0153-b1252-b3005-b3006) -!- heteromultimer; iron (III) hydroxamate ABC transporter (b0151-b0153-b0152) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-30 "COG0614;ABC-type Fe3+-hydroxamate transport system, periplasmic component" 53807; Helical backbone PF01497;Periplasmic binding protein;7.7e-08;codon 35-272 GO:0042597 periplasmic space GO:0006826 iron ion transport CDS ECK0152 fhuB fhuB b0153 171462 173444 + (no change) JW0149 171462 173444 + t fused iron-hydroxamate transporter subunits of ABC superfamily: membrane components E 89364703 -!- 91307893 -!- 92202160 -!- 9613584 -!- 2823072 -!- 3020380 Integral Membrane Protein heteromultimer; ferrichrome uptake system (b0150-b0151-b0152-b0153-b1252-b3005-b3006) -!- heteromultimer; iron (III) hydroxamate ABC transporter (b0151-b0153-b0152) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 20 17 in "fused hydroxamate-dependent iron transport protein, ABC superfamily: membrane component (aa1-330) -!- membrane component (aa331-660)" "COG0609;ABC-type Fe3+-siderophore transport system, permease component" PF01032;FecCD transport family;6.6e-35;codon 29-325 -!- PF01032;FecCD transport family;1.2e-60;codon 355-657 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0153 hemL hemL gsa -!- popC b0154 173602 174882 - (no change) JW0150 173602 174882 - e glutamate-1-semialdehyde aminotransferase (aminomutase) E 91155920 -!- 91258321 -!- 92353044 Cytoplasmic 5.4.3.8 monomeric multimer; glutamate-1-semialdehyde aminotransferase (b0154) COG0001;Glutamate-1-semialdehyde aminotransferase 53383; PLP-dependent transferases PF00202;Aminotransferase class-III;1.7e-120;codon 23-426 "TIGR00713;hemL: glutamate-1-semialdehyde-2,1-aminomuta;0;codon 3-426" CDS ECK0154 clcA clcA eriC -!- yadQ b0155 175107 176528 + (no change) JW5012 175107 176528 + t "chloride channel, voltage-gated" E 10539975 -!- 10648805 -!- 11196649 -!- 11796999 -!- 12384697 Integral Membrane Protein 1.A.11; The Chloride Channel (ClC) Family 11 11 in regulated by attenuation (yadQ) COG0038;Chloride channel protein EriC 56869; Membrane all-alpha PF00654;Voltage gated chloride channel;5.1e-138;codon 85-440 CDS ECK0155 yadR yadR b0156 176610 176954 + (no change) JW0152 176610 176954 + o conserved protein C Cytoplasmic COG0316;Uncharacterized conserved protein PF01521;HesB-like domain;1.6e-58;codon 8-113 TIGR00049;TIGR00049: Iron-sulfur cluster assembly acc;2.6e-61;codon 9-114 CDS ECK0156 yadS yadS b0157 177001 177624 - (no change) JW0153 177001 177624 - pm conserved inner membrane protein C Integral Membrane Protein 7 7 in COG2860;Predicted membrane protein PF03458;UPF0126 domain;3.5e-39;codon 3-88 -!- PF03458;UPF0126 domain;2e-35;codon 90-180 CDS ECK0157 btuF btuF yadT b0158 177662 178462 - (no change) JW0154 177662 178462 - t vitamin B12 transporter subunit: periplasmic-binding component of ABC superfamily E 11790740 Periplasmic heteromultimer; vitamin B12 ABC transporter (b1710-b1709-b1711-b0158) -!- heteromultimer; vitamin B12 transport system (b0158-b1252-b1709-b1710-b1711-b3005-b3006-b3966) 266 1N2Z "COG0614;ABC-type Fe3+-hydroxamate transport system, periplasmic component" 53807; Helical backbone PF01497;Periplasmic binding protein;3.5e-59;codon 24-243 GO:0042597 periplasmic space CDS ECK0158 pfs pfs pfs -!- yadA b0159 178455 179153 - (no change) JW0155 178455 179153 - e 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase E 9524204 -!- 98417441 -!- 2157212 Cytoplasmic 3.2.2.9 -!- 3.2.2.16 monomeric multimer; 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (b0159) COG0775;Nucleoside phosphorylase 53167; Purine and uridine phosphorylases PF01048;Phosphorylase family;4.6e-113;codon 2-226 TIGR01704;MTA/SAH-Nsdase: MTA/SAH nucleosidase;1.7e-200;codon 2-229 "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0159 dgt dgt optA b0160 179237 180754 + (no change) JW0156 179237 180754 + e deoxyguanosine triphosphate triphosphohydrolase E 90136066 -!- 90207273 -!- 90323597 -!- 13563461 -!- 2826481 Cytoplasmic 3.1.5.1 Mg2+ monomeric multimer; deoxyguanosinetriphosphate triphosphohydrolase (b0160) COG0232;dGTP triphosphohydrolase PF01966;HD domain;1.3e-11;codon 66-184 TIGR01353;dGTP_triPase: deoxyguanosinetriphosphate;9.4e-193;codon 28-502 GO:0005737 cytoplasm "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0160 degP degP htrA -!- ptd b0161 180884 182308 + (no change) JW0157 180884 182308 + e "serine endoprotease (protease Do), membrane-associated" E 12057188 -!- 20069954 -!- 90202693 -!- 91222240 -!- 99444919 -!- 12878036 -!- 2157212 -!- 2165018 -!- 3057437 -!- 9600841 -!- 2180903 Periplasmic 3.4.21.- monomeric multimer; serine protease Do (b0161) S1C family; peptidase Do 474 "COG0265;Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain" 50156; PDZ domain-like -!- 50494; Trypsin-like serine proteases PF00089;Trypsin;4.9e-27;codon 95-277 -!- PF00595;PDZ domain (Also known as DHR or GLGF);1.2e-20;codon 279-368 -!- PF00595;PDZ domain (Also known as DHR or GLGF);1.6e-16;codon 385-463 TIGR02037;degP_htrA_DO: protease DO;8.5e-262;codon 39-473 GO:0042597 periplasmic space GO:0009266 response to temperature CDS ECK0161 cdaR cdaR yaeG -!- sdaR b0162 182463 183620 + start codon change JW5013 182463 183620 + r DNA-binding transcriptional activator E 20225875 -!- 10762278 Cytoplasmic cdaR -!- garD -!- gudP -!- yhaUFED-rnpB PF05651;Putative sugar diacid recognition;4.5e-175;codon 12-316 CDS ECK0162 yaeH yaeH b0163 183709 184095 - (no change) JW0159 183709 184095 - o conserved protein C Cytoplasmic CDS ECK0163 yaeI yaeI b0164 184257 185069 - start codon change JW5014 184257 185069 - pe predicted phosphatase C COG1408;Predicted phosphohydrolases 56300; Metallo-dependent phosphatases PF00149;Calcineurin-like phosphoesterase;9.4e-15;codon 26-190 CDS ECK0164 dapD dapD ssa b0166 185123 185947 - (no change) JW0161 185123 185947 - e "2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase" E 71136282 -!- 85054973 -!- 8412694 -!- 9298646 Cytoplasmic 2.3.1.117 monomeric multimer; tetrahydrodipicolinate succinylase (b0166) COG2171;Tetrahydrodipicolinate N-succinyltransferase 51161; Trimeric LpxA-like enzymes 4 of PF00132; Bacterial transferase hexapeptide (three repeats): 28;codon 131-148 -!- 0.77;codon 149-166 -!- 8.1;codon 175-192 -!- 0.34;codon 193-210 "TIGR00965;dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarbo;3.7e-236;codon 3-273" GO:0005737 cytoplasm GO:0009089 lysine biosynthesis via diaminopimelate CDS ECK0165 glnD glnD glnD5 b0167 185978 188650 - (no change) JW0162 185978 188650 - e uridylyltransferase E 92325045 -!- 9737855 -!- 8412694 Cytoplasmic 2.7.7.59 Mg2+ -!- Mn2+ regulated by attenuation (glnD-dapD-b0165-yaeI) COG2844;UTP:GlnB (protein PII) uridylyltransferase 55021; Regulatory domain in the aminoacid metabolism -!- 56699; Nucleotidyltransferases PF01909;Nucleotidyltransferase domain;5.8e-13;codon 70-169 -!- PF01966;HD domain;3.3e-19;codon 468-602 -!- PF01842;ACT domain;1.9e-07;codon 708-783 -!- PF01842;ACT domain;1.4e-07;codon 815-880 TIGR01693;UTase_glnD: protein-P-II uridylyltransfera;0;codon 44-885 GO:0005737 cytoplasm GO:0006807 nitrogen metabolism -!- GO:0006542 glutamine biosynthesis -!- GO:0006464 protein modification CDS ECK0166 map map b0168 188712 189506 - (no change) JW0163 188712 189506 - e methionine aminopeptidase E 87109068 -!- 10387007 -!- 10555963 -!- 8471602 Cytoplasmic 3.4.11.18 Co2+ -!- Fe2+ M24A family; methionyl aminopeptidase 1 regulated by attenuation (map) 1MAT COG0024;Methionine aminopeptidase 55920; Creatinase/aminopeptidase PF00557;metallopeptidase family M24;9e-114;codon 12-250 "TIGR00500;met_pdase_I: methionine aminopeptidase, t;3.3e-179;codon 3-251" GO:0006457 protein folding misc_RNA ECK0167 tff t44 b4414 189712 189847 + (no change) JWR0225 189712 189847 + n small RNA E 21437416 CDS ECK0168 rpsB rpsB b0169 189874 190599 + (no change) JW0164 189874 190599 + s 30S ribosomal subunit protein S2 E 6272196 -!- 10094780 -!- 12244297 -!- 12809609 -!- 1575737 -!- 7023985 -!- 7556101 -!- 9298646 -!- 9716382 Cytoplasmic 1P87 COG0052;Ribosomal protein S2 52313; Ribosomal protein S2 PF00318;Ribosomal protein S2;4.5e-131;codon 9-225 TIGR01011;rpsB_bact: ribosomal protein S2;1.3e-171;codon 3-227 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006412 protein biosynthesis GO:0003735 structural constituent of ribosome CDS ECK0169 tsf tsf b0170 190857 191708 + (no change) JW0165 190857 191708 + f protein chain elongation factor EF-Ts E 6272196 -!- 93054499 -!- 1447125 -!- 8596629 -!- 9298646 -!- 9468511 -!- 9600841 Cytoplasmic regulated by attenuation (tsf) COG0264;Translation elongation factor Ts "46934; UBA-like -!- 54713; Elongation factor Ts (EF-Ts), dimerisation domain" PF00627;UBA/TS-N domain;1.3e-11;codon 4-44 -!- PF00889;Elongation factor TS;4.9e-112;codon 57-263 TIGR00116;tsf: translation elongation factor Ts;3e-185;codon 1-282 GO:0005737 cytoplasm GO:0006412 protein biosynthesis CDS ECK0170 pyrH pyrH smbA -!- umk b0171 191855 192580 + (no change) JW0166 191855 192580 + e uridylate kinase E 169229 -!- 89125613 -!- 94247361 -!- 9677289 -!- 1447125 -!- 7711027 -!- 9457846 Cytoplasmic 2.7.4.- monomeric multimer; uridylate kinase (b0171) regulated by attenuation (pyrH) COG0528;Uridylate kinase 53633; Carbamate kinase-like PF00696;Amino acid kinase family;2.1e-63;codon 10-219 TIGR02075;pyrH_bact: uridylate kinase;1.2e-163;codon 9-240 GO:0005737 cytoplasm "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0171 frr frr rrf b0172 192872 193429 + (no change) JW0167 192872 193429 + f ribosome recycling factor E 90062117 -!- 91317739 -!- 1447125 -!- 8183897 -!- 9298646 Cytoplasmic COG0233;Ribosome recycling factor "55194; Ribosome recycling factor, RRF" PF01765;Ribosome recycling factor;6.9e-101;codon 19-183 TIGR00496;frr: ribosome recycling factor;1.6e-124;codon 10-185 GO:0005737 cytoplasm GO:0006412 protein biosynthesis -!- GO:0009386 translational attenuation CDS ECK0172 dxr dxr ispC -!- yaeM b0173 193521 194717 + (no change) JW0168 193521 194717 + e 1-deoxy-D-xylulose 5-phosphate reductoisomerase E 98374274 -!- 99290045 -!- 10631325 -!- 10787409 -!- 1447125 -!- 7567469 Cytoplasmic 1.1.1.267 Mn2+ monomeric multimer; DXP reductoisomerase (b0173) 1ONP COG0743;1-deoxy-D-xylulose 5-phosphate reductoisomerase "51735; NAD(P)-binding Rossmann-fold domains -!- 55347; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain -!- 69055; 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain" PF02670;1-deoxy-D-xylulose 5-phosphate reduct;1.1e-270;codon 4-389 TIGR00243;Dxr: 1-deoxy-D-xylulose 5-phosphate reductoi;1.2e-304;codon 1-398 CDS ECK0173 ispU ispU uppS -!- rth -!- yaeS b0174 194903 195664 + (no change) JW0169 194903 195664 + e undecaprenyl pyrophosphate synthase E 10217761 -!- 12756244 -!- 9882662 Cytoplasmic 2.5.1.31 Mg2+ "monomeric multimer; undecaprenyl diphosphate synthase / di-trans,poly-cis-decaprenylcistransferase (b0174)" 1V7U COG0020;Undecaprenyl pyrophosphate synthase 64005; Undecaprenyl diphosphate synthase PF01255;Putative undecaprenyl diphosphate syntha;2e-156;codon 24-245 TIGR00055;uppS: undecaprenyl diphosphate synthase;3e-168;codon 19-244 GO:0005737 cytoplasm "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0174 cdsA cdsA cds b0175 195677 196534 + start codon change JW5810 195677 196534 + e CDP-diglyceride synthase E 86008268 -!- 2995359 Integral Membrane Protein 2.7.7.41 K+ -!- Mg2+ 9 8 out COG0575;CDP-diglyceride synthetase PF01148;Cytidylyltransferase family;1.4e-67;codon 17-245 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0008654 phospholipid biosynthesis CDS ECK0175 yaeL yaeL ecf -!- ecfE b0176 196546 197898 + (no change) JW0171 196546 197898 + e zinc metallopeptidase zinc metalloprotease regulates sigma E (RpoE) regulon for extracytoplasmic stress response by degrading R -!- multicopy rpoE suppresses yaeL mutation E 11750129 -!- 14633997 -!- 15066031 -!- 21547928 -!- 15496982 -!- 11274153 -!- 2995358 -!- 7984428 Integral Membrane Protein 3.4.24.- M50B family; RseP peptidase (Escherichia coli) (YAEL protein) 5 4 COG0750;Predicted membrane-associated Zn-dependent proteases 1 50156; PDZ domain-like PF02163;Peptidase family M50;1.3e-76;codon 10-446 -!- PF00595;PDZ domain (Also known as DHR or GLGF);1.9e-15;codon 203-277 TIGR00054: membrane-associated zinc metallo;3.9e-302;codon 2-450 CDS ECK0176 yaeT yaeT up05 -!- ecfK -!- yzzN -!- yzzY b0177 197928 200360 + (no change) JW0172 197928 200360 + d conserved protein predicted outer membrane protein assembly factor C 11274153 -!- 9298646 Periplasmic 1-20 810 COG4775;Outer membrane protein/protective antigen OMA87 5 of PF07244;Surface antigen variable number repeat: 1e-08;codon 48-94 -!- 4.6e-07;codon 119-177 -!- 1.8e-07;codon 208-268 -!- 3e-08;codon 290-347 -!- 2.8e-07;codon 371-426 -!- PF01103;Surface antigen;6.1e-83;codon 438-810 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0177 hlpA hlpA firA -!- ompH -!- skp b0178 200482 200967 + (no change) JW0173 200482 200967 + f periplasmic chaperone for outer membrane proteins E 15101556 -!- 90201355 -!- 97032152 -!- 99386928 -!- 1987124 -!- 2843433 -!- 9298646 -!- 2167239 Periplasmic 1-21 161 1U2M COG2825;Outer membrane protein PF03938;Outer membrane protein (OmpH-like);4.8e-57;codon 2-161 GO:0009274 cell wall (sensu Bacteria) -!- GO:0042597 periplasmic space GO:0006457 protein folding CDS ECK0178 lpxD lpxD fir -!- firA -!- hlpA -!- skp -!- ssc -!- omsA b0179 200971 201996 + (no change) JW0174 200971 201996 + e UDP-3-O-(3-hydroxymyristoyl)-glucosamine N-acyltransferase E 93185653 -!- 93374989 -!- 94179097 -!- 1429432 -!- 1602961 -!- 1987124 Cytoplasmic 2.3.1.- COG1044;UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase 51161; Trimeric LpxA-like enzymes PF04613;UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase;5.6e-52;codon 4-102 -!- 8 of PF00132;Bacterial transferase hexapeptide (three repeats);0.042;codon 109-126 -!- 0.007;codon 127-144 -!- 0.032;codon 145-162 -!- 1.2;codon 163-180 -!- 0.28;codon 200-217 -!- 0.019;codon 222-239 -!- 0.98;codon 240-257 -!- 14;codon 258-275 TIGR01853;lipid_A_lpxD: UDP-3-O-[3-hydroxymyristoy;6.6e-204;codon 8-330 GO:0009245 lipid A biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0179 fabZ fabZ sefA -!- yaeA -!- sabA -!- sfhC b0180 202101 202556 + (no change) JW0175 202101 202556 + e (3R)-hydroxymyristol acyl carrier protein dehydratase E 789345 -!- 8910376 Cytoplasmic 4.2.1.- monomeric multimer; beta-hydroxyacyl-ACP dehydratase (b0180) COG0764;3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases 54637; Thioesterase/thiol ester dehydrase-isomerase PF03061;Thioesterase superfamily;4.4e-22;codon 52-140 TIGR01750;fabZ: beta-hydroxyacyl-(acyl-carrier-protein;5.6e-89;codon 8-147 GO:0005737 cytoplasm CDS ECK0180 lpxA lpxA b0181 202560 203348 + (no change) JW0176 202560 203348 + e UDP-N-acetylglucosamine acetyltransferase E 88058790 -!- 89008361 -!- 90202920 -!- 3277952 -!- 7481807 Cytoplasmic 2.3.1.129 monomeric multimer; UDP-N-acetylglucosamine acyltransferase (b0181) 1LXA COG1043;Acyl-[acyl carrier protein]--UDP-N-acetylglucosamine O-acyltransferase 51161; Trimeric LpxA-like enzymes 7 of PF00132;Bacterial transferase hexapeptide (three repeats): 0.0036;codon 17-34 -!- 0.43;codon 35-52 -!- 0.78;codon 53-70 -!- 7.1;codon 83-100 -!- 7.5;codon 120-137 -!- 7.9;codon 138-155 -!- 9.7;codon 162-179 TIGR01852;lipid_A_lpxA: acyl-[acyl-carrier-protein;2.6e-176;codon 8-261 GO:0005737 cytoplasm GO:0009245 lipid A biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0181 lpxB lpxB pgsB b0182 203348 204496 + (no change) JW0177 203348 204496 + e tetraacyldisaccharide-1-P synthase E 88058790 -!- 89008361 -!- 3277952 Cytoplasmic 2.4.1.182 COG0763;Lipid A disaccharide synthetase 53756; UDP-Glycosyltransferase/glycogen phosphorylase PF02684;Lipid-A-disaccharide synthetase;2.5e-225;codon 9-377 TIGR00215;lpxB: lipid-A-disaccharide synthase;1.2e-190;codon 1-380 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009245 lipid A biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0182 rnhB rnhB b0183 204493 205089 + (no change) JW0178 204493 205089 + e "ribonuclease HII, degrades RNA of DNA-RNA hybrids" E 20250850 -!- 91046040 -!- 3316192 -!- 9888800 Cytoplasmic 3.1.26.4 COG0164;Ribonuclease HII 53098; Ribonuclease H-like PF01351;Ribonuclease HII;6.7e-98;codon 13-190 GO:0005737 cytoplasm GO:0006401 RNA catabolism -!- GO:0006401 RNA catabolism CDS ECK0183 dnaE dnaE polC -!- sdgC b0184 205126 208608 + (no change) JW0179 205126 208608 + e DNA polymerase III alpha subunit E 91250451 -!- 92147649 -!- 92156151 -!- 1575709 -!- 3316192 -!- 7678242 -!- 8375647 Cytoplasmic 2.7.7.7 "heteromultimer; DNA polymerase III, core enzyme (b0184-b0215-b1842)" "COG0587;DNA polymerase III, alpha subunit" 50249; Nucleic acid-binding proteins PF02231;PHP domain N-terminal region;5.3e-29;aa 7-72 -!- PF02811;PHP domain C-terminal region;2.1e-36;aa 80-211 -!- PF07733;Bacterial DNA polymerase III alpha subunit;0;aa 238-735 -!- PF01336;OB-fold nucleic acid binding domain;8.7e-13;aa 999-1073 "TIGR00594;polc: DNA polymerase III, alpha subunit;0;codon 6-1031" GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK0184 accA accA b0185 208621 209580 + (no change) JW0180 208621 209580 + e "acetyl-CoA carboxylase, carboxytransferase, alpha subunit" E 11157970 -!- 92380982 -!- 93123150 -!- 9668099 -!- 9226257 -!- 9298646 6.4.1.2 heteromultimer; acetyl CoA carboxylase (b2316-b0185-b3256-b3255) -!- heteromultimer; acetyl-CoA carboxyltransferase (b0185-b2316) -!- monomeric multimer; carboxyl transferase subunit alpha (b0185) COG0825;Acetyl-CoA carboxylase alpha subunit 52096; ClpP/crotonase PF03255;Acetyl co-enzyme A carboxylase carboxyltrans;2.1e-102;codon 4-151 "TIGR00513;accA: acetyl-CoA carboxylase, carboxyl trans;1.8e-258;codon 1-319" GO:0005737 cytoplasm CDS ECK0185 ldcC ldcC ldc -!- ldcH b0186 209679 211820 + (no change) JW0181 209679 211820 + e "lysine decarboxylase 2, constitutive" E 97480927 -!- 98195734 -!- 98357244 -!- 9226257 -!- 9723924 Cytoplasmic 4.1.1.18 monomeric multimer; lysine decarboxylase 2 (b0186) regulated by attenuation (ldcC-yaeR) COG1982;Arginine/lysine/ornithine decarboxylases 53383; PLP-dependent transferases -!- 55904; Ornithine decarboxylase C-terminal domain "PF03709;Orn/Lys/Arg decarboxylase, N-terminal doma;3.8e-60;codon 1-124 -!- PF01276;Orn/Lys/Arg decarboxylase, major domain;6.4e-283;codon 130-562 -!- PF03711;Orn/Lys/Arg decarboxylase, C-terminal doma;5.1e-89;codon 570-704" GO:0006096 glycolysis -!- GO:0016052 carbohydrate catabolism CDS ECK0186 yaeR yaeR b0187 211877 212266 + start codon change JW0182 211877 212266 + pe predicted lyase C Cytoplasmic 54593; Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase PF00903;Glyoxalase/Bleomycin resistance protein/Di;1.3e-33;codon 15-135 CDS ECK0187 tilS tilS mesJ -!- yaeN b0188 212331 213629 + (no change) JW0183 212331 213629 + e tRNA(Ile)-lysidine synthetase E 14527414 Cytoplasmic 6.1.1.5 COG0037;Predicted ATPase of the PP-loop superfamily implicated in cell cycle control 52402; Adenine nucleotide alpha hydrolases PF01171;PP-loop family;1.6e-107;codon 14-215 CDS ECK0188 rof rof yaeO -!- mesJ b0189 213678 213932 - start codon change JW0184 213678 213932 - f modulator of Rho-dependent transcription termination E 9723924 Cytoplasmic COG4568;Transcriptional antiterminator PF07073;Modulator of Rho-dependent transcription ter;2e-45;codon 9-83 GO:0005737 cytoplasm GO:0006350 transcription CDS ECK0189 yaeP yaeP b4406 213925 214125 - (no change) JW0185 213925 214125 - o conserved protein C Cytoplasmic PF06786;Uncharacterised protein family (UPF0253);1.1e-40;codon 1-66 CDS ECK0190 yaeQ yaeQ b0190 214291 214836 + (no change) JW0186 214291 214836 + o conserved protein C Cytoplasmic COG4681;Uncharacterized protein conserved in bacteria PF07152;YaeQ protein;2e-122;codon 1-181 CDS ECK0191 yaeJ yaeJ b0191 214833 215255 + (no change) JW0187 214833 215255 + d conserved protein C Cytoplasmic COG1186;Protein chain release factor B PF00472;Peptidyl-tRNA hydrolase domain;9.7e-42;codon 3-132 CDS ECK0192 nlpE nlpE cutF b0192 215269 215979 + (no change) JW0188 215269 215979 + lp lipoprotein involved with copper homeostasis and adhesion E 11830644 -!- 95362641 -!- 95362642 Outer membrane Lipoprotein COG3015;Uncharacterized lipoprotein NlpE involved in copper resistance PF04170;Uncharacterized lipoprotein NlpE involved in;7.2e-165;codon 2-222 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0006805 xenobiotic metabolism CDS ECK0193 yaeF yaeF yaeK b0193 216179 217003 - start codon change JW5016 216179 217003 - lp predicted lipoprotein C Outer membrane Lipoprotein CDS ECK0194 proS proS drp -!- drpA b0194 217057 218775 - (no change) JW0190 217057 218775 - e prolyl-tRNA synthetase E 91305088 -!- 1688424 -!- 2203971 -!- 9298646 Cytoplasmic 6.1.1.15 monomeric multimer; prolyl-tRNA synthetase (b0194) COG0442;Prolyl-tRNA synthetase 52954; Anticodon-binding domain of Class II aaRS -!- 55681; Class II aaRS and biotin synthetases -!- 55826; Hypothetical protein HI1434 (YbaK homologue) PF00587;tRNA synthetase class II core domain (;1.2e-60;codon 38-192 -!- PF04073;YbaK / prolyl-tRNA synthetases associa;3.2e-08;codon 249-387 -!- PF03129;Anticodon binding domain;7.9e-28;codon 475-569 TIGR00409;proS_fam_II: prolyl-tRNA synthetase;0;codon 1-569 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK0195 yaeB yaeB b0195 218887 219594 - (no change) JW0191 218887 219594 - o conserved protein C Cytoplasmic COG1720;Uncharacterized conserved protein PF01980;Uncharacterised protein family UPF0066;1.6e-55;codon 18-144 TIGR00104;TIGR00104: conserved hypothetical protein T;1.2e-111;codon 1-150 CDS ECK0196 rcsF rcsF b0196 219591 219995 - (no change) JW0192 219591 219995 - pr "predicted outer membrane protein, signal" signaling system associated with colanic acid synthesis C 93094132 Outer membrane Lipoprotein regulated by attenuation (rcsF-yaeB) GO:0030113 capsule (sensu Bacteria) GO:0009242 colanic acid biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0197 metQ metQ yaeC -!- metD b0197 220113 220928 - (no change) JW0193 220113 220928 - t DL-methionine transporter subunit -!- periplasmic-binding component of ABC superfamily E 12169620 -!- 12218041 -!- 12819857 -!- 1459951 Membrane Lipoprotein heteromultimer; L- and D-methionine uptake ABC permease (b0197-b0198-b0199) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG1464;ABC-type metal ion transport system, periplasmic component/surface antigen" 53850; Periplasmic binding protein-like II PF03180;NLPA lipoprotein;5.2e-149;codon 33-271 "TIGR00363;TIGR00363: lipoprotein, YaeC family;3.8e-184;codon 14-271" GO:0009274 cell wall (sensu Bacteria) -!- GO:0042597 periplasmic space CDS ECK0198 metI metI yaeE -!- metD b0198 220968 221621 - (no change) JW0194 220968 221621 - t DL-methionine transporter subunit -!- membrane component protein of ABC superfamily E 12169620 -!- 12218041 -!- 12819857 Integral Membrane Protein heteromultimer; L- and D-methionine uptake ABC permease (b0197-b0198-b0199) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 5 5 in "COG2011;ABC-type metal ion transport system, permease component" PF00528;Binding-protein-dependent transport syst;1.6e-21;codon 13-216 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0199 metN metN abc -!- metD b0199 221614 222645 - (no change) JW0195 221614 222645 - t DL-methionine transporter subunit -!- ATP-binding component of ABC superfamily E 12169620 -!- 12218041 -!- 94124004 Cytoplasmic heteromultimer; L- and D-methionine uptake ABC permease (b0197-b0198-b0199) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG1135;ABC-type metal ion transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;4.8e-76;codon 31-217 GO:0005737 cytoplasm CDS ECK0200 gmhB gmhB yaeD -!- gmbC -!- gmbX -!- wcbN b0200 222833 223408 + (no change) JW0196 222833 223408 + e "D,D-heptose 1,7-bisphosphate phosphatase" E 11751812 Cytoplasmic COG0241;Histidinol phosphatase and related phosphatases 56784; HAD-like "TIGR00213;GmhB_yaeD: D,D-heptose 1,7-bisphospha;2e-145;codon 5-181 -!- TIGR01656;Histidinol-ppas: histidinol-phosphate;7.1e-39;codon 6-158 -!- TIGR01662;HAD-SF-IIIA: hydrolase, HAD-superfami;7.5e-53;codon 6-158" rRNA ECK0201 rrsH rrsH b0201 223771 225312 + (no change) JWR0001 223771 225312 + n 16S rRNA (rrsH) E 92378996 -!- 93090734 -!- 93277831 tRNA ECK0202 ileV ileV b0202 225381 225457 + (no change) JWR0002 225381 225457 + n tRNA-Ile(GAU) (Isoleucine tRNA1) triplicate E 90230300 tRNA ECK0203 alaV alaV b0203 225500 225575 + (no change) JWR0003 225500 225575 + n tRNA-Ala(UGC) (Alanine tRNA 1B) E 89274211 -!- 92189789 -!- 92279029 rRNA ECK0204 rrlH rrlH b0204 225759 228662 + (no change) JWR0004 225759 228662 + n 23S rRNA (rrlH) E 90356363 -!- 93385117 -!- 94211787 rRNA ECK0205 rrfH rrfH b0205 228756 228875 + (no change) JWR0005 228756 228875 + n 5S rRNA (rrfH) E 89293830 -!- 90356363 -!- 91088242 tRNA ECK0206 aspU aspU b0206 228928 229004 + (no change) JWR0006 228928 229004 + n tRNA-Asp(GUC) (Aspartate tRNA1) triplicate with asp E 90230300 CDS ECK0207 dkgB dkgB yafB b0207 229167 229970 + (no change) JW0197 229167 229970 + e "2,5-diketo-D-gluconate reductase B" E 99357626 -!- 6255418 Cytoplasmic 1.1.1.274 regulated by attenuation (dkgB) "COG0656;Aldo/keto reductases, related to diketogulonate reductase" 51430; NAD(P)-linked oxidoreductase PF00248;Aldo/keto reductase family;1.4e-88;codon 1-252 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK0208 yafC yafC b0208 229967 230881 - (no change) JW0198 229967 230881 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;1.7e-19;codon 5-64 -!- PF03466;LysR substrate binding domain;5.5e-51;codon 88-294 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0209 yafD yafD b0209 231122 231922 + (no change) JW5017 231122 231922 + d conserved protein C 1663890 Cytoplasmic COG3021;Uncharacterized protein conserved in bacteria 56219; DNase I-like PF03372;Endonuclease/Exonuclease/phospha tase fa;1.4e-20;codon 44-259 CDS ECK0210 yafE yafE b0210 231926 232549 + (no change) JW0200 231926 232549 + pe predicted S-adenosyl-L-methionine-dependent methyltransferase C Cytoplasmic COG0500;SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases GO:0009102 biotin biosynthesis CDS ECK0211 mltD mltD dniR -!- yafG b0211 232597 233955 - (no change) JW5018 232597 233955 - pe predicted membrane-bound lytic murein transglycosylase D C 20304905 -!- 92137666 -!- 8203016 Outer membrane Lipoprotein 3.2.1.- 1-37 COG0741;Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) 53955; Lysozyme-like -!- 54106; LysM domain PF06474;MLTD_N;5.2e-40;codon 1-92 -!- PF01464;Transglycosylase SLT domain;3.7e-39;codon 102-218 -!- PF01476;LysM domain;4.6e-18;codon 343-385 -!- PF01476;LysM domain;7.4e-14;codon 402-443 GO:0005737 cytoplasm GO:0009061 anaerobic respiration -!- GO:0017004 cytochrome biogenesis -!- GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0212 gloB gloB yafR b0212 234027 234782 - (no change) JW0202 234027 234782 - pe predicted hydroxyacylglutathione hydrolase C Cytoplasmic "COG0491;Zn-dependent hydrolases, including glyoxylases" 56281; Metallo-hydrolase/oxidoreductase PF00753;Metallo-beta-lactamase superfamily;6.8e-38;codon 11-165 GO:0009438 methylglyoxal metabolism CDS ECK0213 yafS yafS b0213 234816 235538 + start codon change JW0203 234816 235538 + pe predicted S-adenosyl-L-methionine-dependent methyltransferase C Cytoplasmic COG0500;SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases CDS ECK0214 rnhA rnhA cer -!- dasF -!- herA -!- rnh -!- sdrA -!- sin b0214 235535 236002 - (no change) JW0204 235535 236002 - e "ribonuclease HI, degrades RNA of DNA-RNA hybrids" E 91120714 -!- 91326034 -!- 94051590 -!- 1311386 -!- 1646006 -!- 1698262 -!- 2169648 -!- 2171503 -!- 3023634 -!- 6296074 -!- 6316347 -!- 8381958 -!- 8408067 -!- 8527428 -!- 8931125 Cytoplasmic 3.1.26.4 1RCH COG0328;Ribonuclease HI 53098; Ribonuclease H-like PF00075;RNase H;8.5e-72;codon 2-142 GO:0005737 cytoplasm GO:0006401 RNA catabolism -!- GO:0006261 DNA dependent DNA replication -!- GO:0006508 proteolysis and peptidolysis CDS ECK0215 dnaQ dnaQ mutD b0215 236067 236798 + (no change) JW0205 236067 236798 + e DNA polymerase III epsilon subunit E 11772007 -!- 91250451 -!- 92011792 -!- 92156151 -!- 1575709 -!- 3023634 -!- 3540531 -!- 6316347 Cytoplasmic 2.7.7.7 "heteromultimer; DNA polymerase III, core enzyme (b0184-b0215-b1842)" "COG0847;DNA polymerase III, epsilon subunit and related 3'-5' exonucleases" 53098; Ribonuclease H-like PF00929;Exonuclease;1.3e-53;codon 8-175 "TIGR00573;dnaq: exonuclease, DNA polymerase III, ep;2.6e-136;codon 6-225 -!- TIGR01406;dnaQ_proteo: DNA polymerase III, epsilon;1.6e-140;codon 7-243" GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication -!- GO:0006457 protein folding tRNA ECK0216 aspV aspV b0216 236931 237007 + (no change) JWR0007 236931 237007 + n tRNA-Asp(GUC) (Aspartate tRNA1) triplicate with asp E 90230300 CDS ECK0217 yafT yafT b0217 237335 238120 + (no change) JW0206 237335 238120 + pe predicted aminopeptidase C Outer membrane Lipoprotein CDS ECK0218 yafU yafU b0218 238746 239084 - (no change) JW0207 238746 239084 - pm predicted inner membrane protein C Integral Membrane Protein 2 2 in CDS ECK0219 yafF yafF b4503 239190 239378 + new JW0208 239190 239378 + o conserved protein C Cytoplasmic GO:0005737 cytoplasm CDS ECK0220 yafV yafV b0219 239419 240189 - (no change) JW5019 239419 240189 - pe "predicted C-N hydrolase family amidase, NAD(P)-binding" C Cytoplasmic COG0388;Predicted amidohydrolase 56317; Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase PF00795;Carbon-nitrogen hydrolase;4.5e-10;codon 5-166 CDS ECK0221 ivy ivy ykfE -!- up18 b0220 240343 240816 + (no change) JW0210 240343 240816 + pr inhibitor of vertebrate C-lysozyme E 21264642 -!- 11278658 -!- 9868784 -!- 8740179 Periplasmic monomeric multimer; inhibitor of vertebrate C-type lysozyme (b0220) 1-28 157 1GPQ CDS ECK0222 fadE fadE yafH -!- fadF b0221 240859 243303 - start codon change JW5020 240859 243303 - e acyl coenzyme A dehydrogenase E 12057976 -!- 99140134 Integral Membrane Protein 1.3.99.3 1-56 4 2 COG1960;Acyl-CoA dehydrogenases "47203; Acyl-CoA dehydrogenase (flavoprotein), C-terminal domain -!- 56645; Acyl-CoA dehydrogenase (flavoprotein), N-terminal and middle domains" "PF02771;Acyl-CoA dehydrogenase, N-terminal doma;4.3e-05;codon 133-247 -!- PF00441;Acyl-CoA dehydrogenase, C-terminal doma;5.1e-23;codon 372-519" GO:0019395 fatty acid oxidation CDS ECK0223 lpcA lpcA gmhA -!- yafI -!- tfrA b0222 243543 244121 + (no change) JW0212 243543 244121 + e D-sedoheptulose 7-phosphate isomerase E 11751812 -!- 4926688 -!- 785207 Cytoplasmic 5.-.-.- COG0279;Phosphoheptose isomerase 53697; SIS domain PF01380;SIS domain;5.8e-28;codon 38-192 TIGR00441;gmhA: phosphoheptose isomerase;2.6e-140;codon 6-187 GO:0005737 cytoplasm GO:0009244 lipopolysaccharide core region biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0224 yafJ yafJ b0223 244327 245094 + (no change) JW0213 244327 245094 + pe predicted amidotransfease C Cytoplasmic C44 family; non-peptidase homologues COG0121;Predicted glutamine amidotransferase 56235; N-terminal nucleophile aminohydrolases (Ntn hydrolases) PF00310;Glutamine amidotransferases class-II;1.1e-34;codon 2-217 CDS ECK0225 yafK yafK b0224 245065 245805 - (no change) JW0214 245065 245805 - o conserved protein C COG3034;Uncharacterized protein conserved in bacteria PF06104;Bacterial protein of unknown function (DUF94;6.7e-159;codon 30-229 CDS ECK0226 yafQ yafQ b0225 245961 246239 - (no change) JW0215 245961 246239 - pf predicted toxin of the YafQ-DinJ toxin-antitoxin system C 15009896 Cytoplasmic COG3041;Uncharacterized protein conserved in bacteria TIGR00053;TIGR00053: conserved hypothetical protein T;2.2e-55;codon 3-92 CDS ECK0227 dinJ dinJ yebG b0226 246242 246502 - (no change) JW0216 246242 246502 - pf predicted antitoxin of YafQ-DinJ toxin-antitoxin system DNA damage inducible protein C 99451883 Cytoplasmic COG3077;DNA-damage-inducible protein J PF04221;RelB antitoxin;1.8e-42;codon 4-84 GO:0006281 DNA repair CDS ECK0228 yafL yafL b0227 246712 247461 + (no change) JW0217 246712 247461 + lp predicted lipoprotein and C40 family peptidase C C40 family; unassigned peptidases (YafL protein) 1-28 COG0791;Cell wall-associated hydrolases (invasion-associated proteins) PF00877;NlpC/P60 family;5.3e-55;codon 131-241 GO:0009274 cell wall (sensu Bacteria) CDS ECK0229 yafM yafM b0228 247637 248134 + (no change) JW0218 247637 248134 + o conserved protein C Cytoplasmic COG1943;Transposase and inactivated derivatives PF07605;Protein of unknown function (DUF1568);0.00033;codon 52-98 CDS ECK0230 fhiA fhiA b0229 248358 250070 - pseudogene fragment -!- start codon change JW5811 248358 250070 - pseudogene su "flagellar system protein, promoterless fragment (pseudogene)" truncated remnant of second flagellar system Flag-2 C Integral Membrane Protein 3 3 "COG1298;Flagellar biosynthesis pathway, component FlhA" PF00771;FHIPEP family;2e-158;codon 2-572 GO:0019861 flagellum -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0231 mbhA mbhA b0230 250072 250827 + pseudogene fragment -!- start codon change JW5812 250072 250827 + "pseudogene, no initiation codon" su "flagellar system protein, promoterless fragment (pseudogene)" C 15687208 Cytoplasmic COG1360;Flagellar motor protein PF00691;OmpA family;1.7e-19;codon 120-216 GO:0042330 taxis CDS ECK0232 dinB dinB dinB -!- dinP b0231 250898 251953 + (no change) JW0221 250898 251953 + e DNA polymerase IV E 9391106 -!- 99417968 -!- 99429869 -!- 11080171 -!- 11463382 -!- 11587937 -!- 11595180 -!- 11751576 -!- 12045089 -!- 12060704 -!- 6771759 -!- 7596361 Cytoplasmic 2.7.7.7 COG0389;Nucleotidyltransferase/DNA polymerase involved in DNA repair 56672; DNA/RNA polymerases PF00817;impB/mucB/samB family;4.6e-146;codon 7-341 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication -!- GO:0009432 SOS response CDS ECK0233 yafN yafN b0232 252005 252298 + (no change) JW0222 252005 252298 + pf predicted antitoxin of the YafO-YafN toxin-antitoxin system C 12813093 -!- 14594833 Cytoplasmic COG2161;Antitoxin of toxin-antitoxin stability system PF02604;Phd_YefM;5.6e-12;codon 7-76 TIGR01552;phd_fam: prevent-host-death family protein;0.0037;codon 9-57 CDS ECK0234 yafO yafO b0233 252301 252699 + (no change) JW0223 252301 252699 + pf predicted toxin of the YafO-YafN toxin-antitoxin system C 12813093 -!- 14594833 Cytoplasmic CDS ECK0235 yafP yafP b0234 252709 253161 + (no change) JW0224 252709 253161 + pe predicted acyltransferase with acyl-CoA N-acyltransferase domain C 12813093 Cytoplasmic COG0454;Histone acetyltransferase HPA2 and related acetyltransferases 55729; Acyl-CoA N-acyltransferases (Nat) PF00583;Acetyltransferase (GNAT) family;3.1e-10;codon 59-125 CDS ECK0236 ykfJ ykfJ b0235 253467 253733 + (no change) JW0225 253467 253733 + o conserved protein C Cytoplasmic COG1690;Uncharacterized conserved protein CDS ECK0237 prfH prfH b0236 253702 254202 + (no change) JW0226 253702 254202 + pf predicted peptide chain release factor C 93027135 Cytoplasmic COG1186;Protein chain release factor B PF00472;Peptidyl-tRNA hydrolase domain;3.4e-42;codon 59-164 GO:0005737 cytoplasm GO:0006412 protein biosynthesis CDS ECK0238 pepD pepD pepH b0237 254259 255716 - (no change) JW0227 254259 255716 - e aminoacyl-histidine dipeptidase (peptidase D) E 1695895 -!- 21101837 -!- 88121730 -!- 92204123 -!- 2651887 Cytoplasmic 3.4.13.3 monomeric multimer; peptidase D (b0237) M20C family; Xaa-His dipeptidase COG2195;Di- and tripeptidases 53187; Zn-dependent exopeptidases PF07687;Peptidase dimerisation domain;6.1e-16;codon 206-295 TIGR01893;aa-his-dipept: aminoacyl-histidine dipe;2.1e-243;codon 7-483 GO:0005737 cytoplasm CDS ECK0239 gpt gpt glyD -!- gpp -!- gxu b0238 255977 256435 + (no change) JW0228 255977 256435 + e guanine-hypoxanthine phosphoribosyltransferase E 339828 -!- 6787390 -!- 6801015 -!- 3540961 -!- 6100966 -!- 6324102 -!- 6324103 -!- 6396164 -!- 6397401 -!- 9100006 -!- 9743633 Cytoplasmic 2.4.2.22 monomeric multimer; xanthine phosphoribosyltransferase / guanine phosphoribosyltransferase / hypoxanthine phosphoribosyltransferase (b0238) 1A96 COG0503;Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins 53271; PRTase-like PF00156;Phosphoribosyl transferase domain;7.7e-19;codon 1-127 GO:0005737 cytoplasm "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0240 frsA frsA yafA b0239 256527 257771 + (no change) JW0229 256527 257771 + r "hydrolase, binds to enzyme IIA(Glc)" fermentation/respiration switch protein E 15169777 -!- 6397401 Cytoplasmic regulated by attenuation (yafA-crl) COG1073;Hydrolases of the alpha/beta superfamily 53474; alpha/beta-Hydrolases PF06500;Protein of unknown function (DUF1100);0;codon 1-414 CDS ECK0241 crl crl b0240 257829 258230 + (no change) JW0230 257829 258230 + r DNA-binding transcriptional regulator for cryptic genes for curli formation and fibronectin binding E 14978043 -!- 89201357 -!- 93023873 -!- 6341601 Cytoplasmic PF07417;Transcriptional regulator Crl;8e-99;codon 2-133 GO:0009289 fimbria -!- GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0242 phoE phoE ompE b0241 258269 259324 - (no change) JW0231 258269 259324 - t outer membrane phosphoporin protein E E 89178658 -!- 89380253 -!- 92219258 -!- 98090453 -!- 1380671 -!- 1848301 -!- 1848682 -!- 6089111 -!- 6341601 -!- 7679770 Outer Membrane B-barrel protein 1.B.1; The General Bacterial Porin (GBP) Family 1-21 1PHO COG3203;Outer membrane protein (porin) 56935; Porins PF00267;Gram-negative porin;1.1e-201;codon 27-351 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0243 proB proB pro2 -!- pro(2) b0242 259612 260715 + (no change) JW0232 259612 260715 + e gamma-glutamate kinase E 6255065 -!- 89291886 -!- 6089111 -!- 6341601 Cytoplasmic 2.7.2.11 Mg2+ heteromultimer; gamma-glutamyl kinase-GP-reductase multienzyme complex (b0242-b0243) -!- monomeric multimer; gamma-glutamyl kinase (b0242) COG0263;Glutamate 5-kinase 53633; Carbamate kinase-like PF00696;Amino acid kinase family;8.3e-59;codon 5-235 -!- PF01472;PUA domain;3.9e-30;codon 276-350 TIGR01027;proB: glutamate 5-kinase;5.2e-243;codon 5-366 GO:0005737 cytoplasm GO:0006561 proline biosynthesis CDS ECK0244 proA proA proL -!- pro1 -!- pro(1) b0243 260727 261980 + (no change) JW0233 260727 261980 + e gamma-glutamylphosphate reductase E 6255065 -!- 89291886 -!- 1282191 -!- 6089111 -!- 6337636 Cytoplasmic 1.2.1.41 heteromultimer; gamma-glutamyl kinase-GP-reductase multienzyme complex (b0242-b0243) -!- monomeric multimer; glutamate-5-semialdehyde dehydrogenase (b0243) COG0014;Gamma-glutamyl phosphate reductase 53720; ALDH-like TIGR00407;proA: gamma-glutamyl phosphate reductase;1.9e-301;codon 9-406 GO:0005737 cytoplasm GO:0006561 proline biosynthesis tRNA ECK0245 thrW thrW b0244 262095 262170 + (no change) JWR0008 262095 262170 + n tRNA-Thr(CGU) (Threonine tRNA2) E 88312630 -!- 92231971 -!- 93021106 CDS ECK0246 ykfI ykfI b0245 262552 262893 - (no change) JW0234 262552 262893 - h CP4-6 prophage; toxin of the YkfI-YafW toxin-antitoxin system E 14594833 Cytoplasmic cryptic prophage CP4-6 PF06755;Protein of unknown function (DUF1219);3e-44;codon 1-113 CDS ECK0247 yafW yafW b0246 262914 263231 - (no change) JW0235 262914 263231 - h CP4-6 prophage; antitoxin of the YkfI-YafW toxin-antitoxin system E 14594833 Cytoplasmic cryptic prophage CP4-6 PF06154;YagB/YeeU/YfjZ family;1.2e-78;codon 1-105 CDS ECK0248 ykfH ykfH b4504 263250 263471 - new JW5956 263250 263471 - o predicted protein C Cytoplasmic GO:0005737 cytoplasm CDS ECK0249 ykfG ykfG b0247 263480 263956 - (no change) JW0236 263480 263956 - h CP4-6 prophage; predicted DNA repair protein C Cytoplasmic cryptic prophage CP4-6 COG2003;DNA repair proteins "PF04002;RadC, DNA repair protein;2.3e-82;codon 34-158" TIGR00608;radc: DNA repair protein RadC;2.7e-30;codon 2-158 CDS ECK0250 yafX yafX b0248 263972 264430 - (no change) JW5022 263972 264430 - h CP4-6 prophage; predicted protein C Cytoplasmic cryptic prophage CP4-6 PF03230;Antirestriction protein;3e-65;codon 57-152 CDS ECK0251 ykfF ykfF b0249 264528 264767 - (no change) JW5023 264528 264767 - h CP4-6 prophage; predicted protein C Periplasmic cryptic prophage CP4-6 regulated by attenuation (ykfF) PF06006;Bacterial protein of unknown function (DUF90;4.5e-50;codon 2-74 CDS ECK0252 ykfB ykfB b0250 264844 265311 - (no change) JW0239 264844 265311 - h CP4-6 prophage; predicted protein C Periplasmic cryptic prophage CP4-6 CDS ECK0253 yafY yafY b0251 265334 266191 - (no change) JW0240 265334 266191 - h CP4-6 prophage; predicted DNA-binding transcriptional regulator C Inner membrane Lipoprotein cryptic prophage CP4-6 regulated by attenuation (yafY-ykfB) 46785; Winged helix CDS ECK0254 yafZ yafZ b0252 266408 267229 - start codon change JW0242 266408 267229 - h CP4-6 prophage; conserved protein C Cytoplasmic cryptic prophage CP4-6 regulated by attenuation (yafZ) PF06067;Domain of unknown function (DUF932);1.2e-225;codon 6-278 CDS ECK0255 ykfA ykfA b0253 267321 268184 - start codon change JW0243 267321 268184 - h CP4-6 prophage; predicted GTP-binding protein C Cytoplasmic cryptic prophage CP4-6 regulated by attenuation (ykfA) 52540; P-loop containing nucleotide triphosphate hydrolases PF01926;GTPase of unknown function;2.5e-22;codon 38-157 CDS ECK0256 perR perR katC b0254 268513 269406 - (no change) JW0244 268513 269406 - h CP4-6 prophage; predicted DNA-binding transcriptional regulator repressor affecting peroxide resistance C 12878731 -!- 13129938 -!- 9689094 -!- 1200544 Cytoplasmic cryptic prophage CP4-6 COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;9.6e-18;codon 9-68 -!- PF03466;LysR substrate binding domain;1.6e-31;codon 89-292 CDS ECK0257 insN insN-1 yi91a b0255 269466 269870 + (no change) JW5024 269466 269870 + h CP4-6 prophage; partial regulator of insertion element IS911A interrupted by insertion of IS30 element E cryptic prophage CP4-6 -!- IS911A (partial) COG2963;Transposase and inactivated derivatives 46689; Homeodomain-like PF01527;Transposase;2e-15;codon 15-96 CDS ECK0257 insN insN-2 yi91 -!- yi91b b4283 4505220 4505486 + start codon change JW5771 4511877 4512143 + IS h KpLE2 phage-like element; partial regulator of insertion element IS911B. Interrupted by insertion of IS30 element. E KpLE2 phage-like element 46689; Homeodomain-like PF01527;Transposase;7.1e-16;codon 15-96 "TIGR01199;HTH_fis: Helix-turn-helix domain, fis-type;0.016;codon 19-60" CDS ECK0258 insI insI-3 tra8-3 b4284 4505489 4506640 - (no change) JW4244 4512146 4513297 - h KpLE2 phage-like element; IS30 transposase E 9689094 KpLE2 phage-like element -!- IS30 "COG2826;Transposase and inactivated derivatives, IS30 family" 46689; Homeodomain-like -!- 53098; Ribonuclease H-like PF00665;Integrase core domain;2.8e-33;codon 226-376 CDS ECK0258 insI insI-2 tra8-2 b1404 1467382 1468533 + (no change) JW1401 1471072 1472223 + h IS30 transposase E 9689094 IS30 "COG2826;Transposase and inactivated derivatives, IS30 family" 46689; Homeodomain-like -!- 53098; Ribonuclease H-like PF00665;Integrase core domain;2.8e-33;codon 226-376 CDS ECK0258 insI insI-1 tra8-1 b0256 269827 270978 + (no change) JW0246 269827 270978 + h CP4-6 prophage; IS30 transposase E 9689094 cryptic prophage CP4-6 -!- IS30 "COG2826;Transposase and inactivated derivatives, IS30 family" 46689; Homeodomain-like -!- 53098; Ribonuclease H-like PF00665;Integrase core domain;9.4e-34;codon 226-376 CDS ECK0259 insO insO-1 b0257 271054 271479 + (no change) JW0247 271054 271479 + h "CP4-6 prophage; partial transposase of insertion element IS911A, interrupted by insertion of IS30 element." partial transposase of insertion element IS911A. Interrupted by insertion of IS30 element -!- pseudogene E cryptic prophage CP4-6 -!- IS911A (partial) COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like CDS ECK0260 ykfC ykfC b0258 272071 273216 + start codon change JW5813 272071 273216 + h CP4-6 prophage; conserved protein C Cytoplasmic cryptic prophage CP4-6 COG3344;Retron-type reverse transcriptase 56672; DNA/RNA polymerases PF00078;Reverse transcriptase (RNA-dependent DNA pol;3.9e-68;codon 77-332 CDS ECK0261 insH insH unique to W3110 0 0 JW5951 4310431 4311411 + IS5 -!- W3110 specific region h IS5 element protein E IS5 CDS ECK0261 insH insH unique to W3110 0 0 JW5936 3750659 3751639 + IS5 -!- W3110 specific region h IS5 element protein E IS5 CDS ECK0261 insH insH unique to W3110 0 0 JW5935 3746979 3747959 + IS5 -!- W3110 specific region h IS5 element protein E IS5 CDS ECK0261 insH insH unique to W3110 0 0 JW5928 3261202 3262182 + IS5 -!- W3110 specific region h IS5 element protein E IS5 CDS ECK0261 insH insH unique to W3110 0 0 JW5914 2177051 2178031 + IS5 -!- W3110 specific region h IS5 element protein E IS5 CDS ECK0261 insH insH unique to W3110 0 0 JW5895 654281 655261 + IS5 -!- W3110 specific region h IS5 element protein E IS5 CDS ECK0261 insH insH unique to W3110 0 0 JW1882 1980355 1981371 - "IS1 is inserted in strain MG, but IS5 is inserted at this region in strain W -!- W3110 specific region" h IS5 element protein E IS5 CDS ECK0261 insH insH-11 trs5-11 -!- yi52_ b3505 3650205 3651221 - (no change) JW3472 3987217 3988233 + h IS5 transposase and trans-activator E 15766797 -!- 6281654 IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;4.6e-45;codon 151-326 CDS ECK0261 insH insH-10 trs5-10 -!- yi52_ b3218 3363724 3364740 - (no change) JW3185 3365557 3366573 - h IS5 transposase and trans-activator E 15766797 -!- 6281654 IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;4.6e-45;codon 151-326 CDS ECK0261 insH insH-9 yi52_9 -!- trs5-9 b2982 3128200 3129216 + (no change) JW2949 3128834 3129850 + h IS5 transposase and trans-activator E 15766797 -!- 6281654 IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;4.6e-45;codon 151-326 CDS ECK0261 insH insH-8 yi52_8 -!- trs5-8 b2192 2287087 2288103 - (no change) JW2179 2292399 2293415 - h IS5 transposase and trans-activator E 15766797 -!- 6281654 IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;4.6e-45;codon 151-326 CDS ECK0261 insH insH-7 yi52_7 -!- trs5-7 b2030 2099919 2100935 - (no change) JW2014 2104032 2105048 - h IS5 transposase and trans-activator E 15766797 -!- 6281654 IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;4.6e-45;codon 151-326 CDS ECK0261 insH insH-6 yi52_6 -!- trs5-6 b1994 2064329 2065345 - (no change) JW1972 2068442 2069458 - h CP4-44 prophage; IS5 transposase and trans-activator E 15766797 -!- 6281654 cryptic prophage CP4-44 -!- IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;2.2e-44;codon 151-326 CDS ECK0261 insH insH-5 yi52_5 -!- trs5-5 b1370 1425770 1426750 - (no change) JW1363 1429460 1430440 - h Rac prophage; IS5 transposase and trans-activator E 15766797 -!- 6281654 cryptic prophage Rac -!- IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;1.2e-43;codon 139-314 CDS ECK0261 insH insH-4 yi52_4 -!- trs5-4 b1331 1394100 1395116 + (no change) JW1324 1397790 1398806 + h IS5 transposase and trans-activator E 15766797 -!- 6281654 IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;4.6e-45;codon 151-326 CDS ECK0261 insH insH-3 yi52_3 -!- trs5-3 b0656 687220 688236 - (no change) JW0652 688419 689435 - h IS5 transposase and trans-activator E 15766797 -!- 6281654 IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;4.6e-45;codon 151-326 CDS ECK0261 insH insH-2 yi52_2 -!- trs5-2 b0552 573960 574976 - (no change) JW0540 573960 574976 - h DLP12 prophage; IS5 transposase and trans-activator E 15766797 -!- 6281654 cryptic prophage DLP12 -!- IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;4.6e-45;codon 151-326 CDS ECK0261 insH insH-1 trs5 -!- yi52_1 -!- trs5-1 b0259 273325 274341 - (no change) JW0250 273325 274341 - h CP4-6 prophage; IS5 transposase and trans-activator E 15766797 -!- 6281654 cryptic prophage CP4-6 -!- IS5 "COG3039;Transposase and inactivated derivatives, IS5 family" PF01609;Transposase DDE domain;4.6e-45;codon 151-326 CDS ECK0262 mmuP mmuP ykfD b0260 274549 275952 + start codon change JW5027 274549 275952 + h CP4-6 prophage; predicted S-methylmethionine transporter C 9882684 Integral Membrane Protein cryptic prophage CP4-6 2.A.3; The Amino Acid-Polyamine-Organocation (APC) Family 12 12 in regulated by attenuation (mmuP-mmuM) PF00324;Amino acid permease;1.2e-142;codon 26-471 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009086 methionine biosynthesis CDS ECK0263 mmuM mmuM yagD b0261 275939 276871 + (no change) JW0253 275939 276871 + h CP4-6 prophage; S-methylmethionine:homocysteine methyltransferase E 9882684 -!- 10026151 Cytoplasmic cryptic prophage CP4-6 2.1.1.10 -!- 2.1.1. COG2040;Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) PF02574;Homocysteine S-methyltransferase;7.4e-143;codon 16-310 GO:0006071 glycerol metabolism -!- GO:0009086 methionine biosynthesis CDS ECK0264 afuC afuC yagC b0262 276980 278026 - start codon change JW0254 276980 278026 - h CP4-6 prophage; predicted ferric transporter subunit -!- ATP-binding component of ABC superfamily C 8113168 Cytoplasmic cryptic prophage CP4-6 monomeric multimer; abc-38-cplx (b0262) "COG3842;ABC-type spermidine/putrescine transport systems, ATPase components" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.6e-69;codon 36-217 CDS ECK0265 afuB afuB b0263 278038 278400 - (no change) JW0255 278038 278400 - h CP4-6 prophage; predicted ferric trasnporter subunit -!- membrane component of ABC superfamily C Integral Membrane Protein cryptic prophage CP4-6 2 2 in "COG1178;ABC-type Fe3+ transport system, permease component" CDS ECK0266 ykgN ykgN b4505 279248 279586 - new JW0258 279248 279586 - ph predicted IS protein transposase C 46689; Homeodomain-like PF01527;Transposase_8: Transposase;3.5e-33;codon 4-88 "TIGR01199;HTH_fis: Helix-turn-helix domain, fis-type;7e-05;codon 7-48" CDS ECK0267 yagB yagB b0266 279609 279959 - start codon change JW0259 279609 279959 - h CP4-6 prophage; conserved protein C Cytoplasmic cryptic prophage CP4-6 PF06154;YagB/YeeU/YfjZ family;1.1e-89;codon 13-117 CDS ECK0268 yagA yagA b0267 280053 281207 - (no change) JW0260 280053 281207 - h CP4-6 prophage; predicted DNA-binding transcriptional regulator C Cytoplasmic cryptic prophage CP4-6 COG2801;Transposase and inactivated derivatives 46689; Homeodomain-like -!- 53098; Ribonuclease H-like PF00665;Integrase core domain;1.4e-40;codon 137-300 CDS ECK0269 yagE yagE b0268 281481 282410 + (no change) JW0261 281481 282410 + h CP4-6 prophage; predicted lyase/synthase C Cytoplasmic cryptic prophage CP4-6 COG0329;Dihydrodipicolinate synthase/N-acetylneuraminate lyase 51569; Aldolase PF00701;Dihydrodipicolinate synthetase family;2.1e-106;codon 13-307 CDS ECK0270 yagF yagF b0269 282425 284392 + (no change) JW0262 282425 284392 + h CP4-6 prophage; predicted dehydratase C Cytoplasmic cryptic prophage CP4-6 COG0129;Dihydroxyacid dehydratase/phosphogluconate dehydratase 52218; Flavoproteins PF00920;Dehydratase family;1.8e-227;codon 62-638 CDS ECK0271 yagG yagG b0270 284619 286001 + (no change) JW0263 284619 286001 + h CP4-6 prophage; predicted sugar transporter C Integral Membrane Protein cryptic prophage CP4-6 11 12 in regulated by attenuation (yagG-yagH) COG2211;Na+/melibiose symporter and related transporters PF07690;Major Facilitator Superfamily;3e-09;codon 12-385 TIGR00792;gph: sugar (Glycoside-Pentoside-Hexuronide);1.7e-227;codon 9-444 CDS ECK0272 yagH yagH b0271 286013 287623 + (no change) JW0264 286013 287623 + h CP4-6 prophage; predicted xylosidase/arabinosidase C Cytoplasmic cryptic prophage CP4-6 COG3507;Beta-xylosidase PF04616;Glycosyl hydrolases family;4e-167;codon 3-303 CDS ECK0273 yagI yagI b0272 287628 288386 - (no change) JW0265 287628 288386 - h CP4-6 prophage; predicted DNA-binding transcriptional regulator C Cytoplasmic cryptic prophage CP4-6 COG1414;Transcriptional regulator 46785; Winged helix PF01614;Bacterial transcriptional regulator;3.8e-91;codon 62-247 GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK0274 argF argF Arg5 -!- argD b0273 288525 289529 - (no change) JW0266 288525 289529 - h "CP4-6 prophage; ornithine carbamoyltransferase 2, chain F" E 340922 -!- 77028751 -!- 89143794 -!- 3968036 -!- 6382166 -!- 6577418 Cytoplasmic cryptic prophage CP4-6 2.1.3.3 monomeric multimer; ornithine carbamoyltransferase (b0273) regulated by attenuation (argF) COG0078;Ornithine carbamoyltransferase 53671; Aspartate/ornithine carbamoyltransferase "PF02729;Aspartate/ornithine carbamoyltransferase, ca;3.7e-83;codon 7-149 -!- PF00185;Aspartate/ornithine carbamoyltransferase, As;2e-95;codon 154-332" TIGR00658;orni_carb_tr: ornithine carbamoyltransfe;4.8e-222;codon 7-333 GO:0005737 cytoplasm GO:0006526 arginine biosynthesis CDS ECK0275 yagJ yagJ b0276 290724 291455 + (no change) JW0270 290724 291455 + h CP4-6 prophage; predicted protein C Cytoplasmic cryptic prophage CP4-6 CDS ECK0276 yagK yagK b0277 291546 292172 - (no change) JW0271 291546 292172 - h CP4-6 prophage; conserved protein C Cytoplasmic cryptic prophage CP4-6 CDS ECK0277 yagL yagL b0278 292444 293142 - (no change) JW0272 292444 293142 - h CP4-6 prophage; DNA-binding protein E 13129938 -!- 9689094 Cytoplasmic cryptic prophage CP4-6 "COG1961;Site-specific recombinases, DNA invertase Pin homologs" 46689; Homeodomain-like -!- 53041; Resolvase-like CDS ECK0278 yagM yagM b0279 293169 294023 - (no change) JW0273 293169 294023 - h CP4-6 prophage; predicted protein C Cytoplasmic cryptic prophage CP4-6 regulated by attenuation (yagM-yagL) CDS ECK0279 yagN yagN b0280 294363 294803 - (no change) JW0274 294363 294803 - h CP4-6 prophage; predicted protein C Cytoplasmic cryptic prophage CP4-6 CDS ECK0280 intF intF yagO b0281 294920 296320 - (no change) JW0275 294920 296320 - h CP4-6 prophage; predicted phage integrase C Cytoplasmic cryptic prophage CP4-6 COG0582;Integrase 56349; DNA breaking-rejoining enzymes PF00589;Phage integrase family;9.3e-16;codon 273-442 CDS ECK0281 yagP yagP b0282 296605 297015 - (no change) JW0276 296605 297015 - pr predicted transcriptional regulator C Cytoplasmic COG0583;Transcriptional regulator 53850; Periplasmic binding protein-like II "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK0282 yagQ yagQ b0283 296994 297950 - (no change) JW0277 296994 297950 - o conserved protein C Cytoplasmic "COG1975;Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family" PF02625;XdhC and CoxI family;7.3e-30;codon 32-103 CDS ECK0283 yagR yagR b0284 297960 300158 - (no change) JW0278 297960 300158 - pe predicted oxidoreductase with molybdenum-binding domain C Cytoplasmic "COG1529;Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs" 54665; CO dehydrogenase molybdoprotein N-domain-like -!- 56003; Molybdemum cofactor-binding domain PF01315;Aldehyde oxidase and xanthine dehydroge;2.4e-36;codon 34-138 -!- PF02738;Aldehyde oxidase and xanthine dehydroge;1.9e-203;codon 144-668 CDS ECK0284 yagS yagS b0285 300155 301111 - (no change) JW0279 300155 301111 - pe predicted oxidoreductase with FAD-binding domain C Cytoplasmic "COG1319;Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs" 55447; CO dehydrogenase flavoprotein C-terminal domain-like -!- 56176; FAD-binding domain PF00941;FAD binding domain in molybdopterin deh;3.5e-05;codon 2-221 CDS ECK0285 yagT yagT b0286 301108 301797 - (no change) JW0280 301108 301797 - pe "predicted xanthine dehydrogenase, 2Fe-2S subunit" C Cytoplasmic 1-53 "COG2080;Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs" 54292; 2Fe-2S ferredoxin-like PF00111;2Fe-2S iron-sulfur cluster binding domain;4.2e-13;codon 65-125 -!- PF01799;[2Fe-2S] binding domain;2.6e-46;codon 133-222 TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.005;codon 23-50 CDS ECK0286 yagU yagU b0287 302215 302829 + (no change) JW0281 302215 302829 + pm conserved inner membrane protein C Integral Membrane Protein 3 3 in COG3477;Predicted periplasmic/secreted protein PF07274;Protein of unknown function (DUF1440);1.1e-114;codon 21-182 CDS ECK0287 ykgJ ykgJ b0288 303077 303406 - (no change) JW0282 303077 303406 - pc predicted ferredoxin C Periplasmic COG0727;Predicted Fe-S-cluster oxidoreductase PF03692;Uncharacterised protein family (UPF0153);4.5e-30;codon 5-102 GO:0009055 electron carrier activity CDS ECK0288 yagV yagV b0289 303719 304429 - start codon change JW5030 303719 304429 - d conserved protein C 1-36 49354; PapD-like CDS ECK0289 yagW yagW b0290 304398 306041 - (no change) JW0284 304398 306041 - pr predicted receptor C Periplasmic CDS ECK0290 yagX yagX b0291 306031 308556 - (no change) JW0285 306031 308556 - pe predicted aromatic compound dioxygenase C Periplasmic 1-29 49482; Aromatic compound dioxygenase CDS ECK0291 yagY yagY b0292 308582 309250 - (no change) JW0286 308582 309250 - o predicted protein C Periplasmic CDS ECK0292 yagZ yagZ b0293 309308 309895 - (no change) JW0287 309308 309895 - o conserved protein C Periplasmic 1-22 CDS ECK0293 ykgK ykgK b0294 309970 310560 - (no change) JW5031 309970 310560 - pr predicted regulator C Cytoplasmic COG2771;DNA-binding HTH domain-containing proteins "46894; C-terminal, effector domain of the bipartite response regulators" "PF00196;Bacterial regulatory proteins, luxR family;8.6e-07;codon 142-195" CDS ECK0294 ykgL ykgL b0295 311336 311563 + (no change) JW5033 311336 311563 + o predicted protein C Cytoplasmic CDS ECK0295 ykgM ykgM b4506 311598 311738 - new JW5034 311598 311738 - ps predicted ribosomal protein C 57840; Ribosomal protein L36 PF00444;Ribosomal_L36: ribosomal protein L36;0.00013;codon 1-41 TIGR01022;rpmJ_bact: ribosomal protein L36;0.00017; codon 1-41 CDS ECK0296 ykgM ykgM b0296 311738 312001 - (no change) JW5035 311738 312001 - ps predicted ribosomal protein C Cytoplasmic COG0254;Ribosomal protein L31 PF01197;Ribosomal protein L31;1.8e-14;codon 1-80 TIGR00105;L31: ribosomal protein L31;8.3e-15;codon 1-84 GO:0009281 cytosolic ribosome (sensu Bacteria) CDS ECK0297 eaeH eaeH b0297 313581 314468 + (no change) JW0291 313581 314468 + f "attaching and effacing protein, pathogenesis factor" E 12234664 -!- 13129938 -!- 9689094 regulated by attenuation (eaeH-b0298-tra5_5) GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0298 insE insE-5 insE5 b2088 2168251 2168559 + (no change) JW5341 2172364 2172672 + h IS3 element protein InsE E IS3 COG2963;Transposase and inactivated derivatives PF01527;Transposase;4e-06;codon 15-90 CDS ECK0298 insE insE-4 insE4 b1027 1094361 1094669 - (no change) JW5144 1095560 1095868 - h IS3 element protein E IS3 COG2963;Transposase and inactivated derivatives PF01527;Transposase;4e-06;codon 15-90 CDS ECK0298 insE insE-3 insE3 b0540 566056 566364 + (no change) JW5074 566056 566364 + h DLP12 prophage; IS3 element protein InsE E cryptic prophage DLP12 -!- IS3 COG2963;Transposase and inactivated derivatives PF01527;Transposase;4e-06;codon 15-90 CDS ECK0298 insE insE-2 insE2 b0373 391826 392134 - (no change) JW5050 391826 392134 - h IS3 element protein E IS3 COG2963;Transposase and inactivated derivatives PF01527;Transposase;4e-06;codon 15-90 CDS ECK0298 insE insE-1 insE1 b0298 314506 314814 + (no change) JW5036 314506 314814 + h IS3 element protein E IS3 COG2963;Transposase and inactivated derivatives PF01527;Transposase;4e-06;codon 15-90 CDS ECK0299 insF insF-5 insF5 -!- tra5-4 b2089 2168556 2169422 + (no change) JW2073 2172669 2173535 + h IS3 element protein InsF E IS3 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;2.8e-49;codon 124-284 CDS ECK0299 insF insF-4 insF4 -!- tra5-3 b1026 1093498 1094364 - (no change) JW1012 1094697 1095563 - h IS3 element protein InsF E 9689094 IS3 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;2.8e-49;codon 124-284 CDS ECK0299 insF insF-3 insF3 -!- tra5-2 b0541 566361 567227 + (no change) JW0529 566361 567227 + h DLP12 prophage; IS3 element protein InsF E cryptic prophage DLP12 -!- IS3 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;2.8e-49;codon 124-284 CDS ECK0299 insF insF-2 insF2 -!- tra5-1 b0372 390963 391829 - (no change) JW0363 390963 391829 - h IS3 element protein InsF E 9689094 IS3 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;2.8e-49;codon 124-284 CDS ECK0299 insF insF-1 insF1 -!- tra5-5 b0299 314811 315677 + (no change) JW0293 314811 315677 + h IS3 element protein InsF E IS3 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;2.8e-49;codon 124-284 CDS ECK0300 ykgA ykgA b0300 315674 316360 - start codon change JW5037 315674 316360 - pr predicted DNA-binding transcriptional regulator C 20341101 Cytoplasmic AraC/XylS COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like -!- 55136; Probable bacterial effector-binding domain PF00165;Bacterial regulatory helix-turn-helix protei;2.6e-06;codon 20-66 -!- PF00165;Bacterial regulatory helix-turn-helix protei;1.2e-11;codon 72-116 GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK0301 ykgB ykgB b0301 316950 317543 - start codon change JW5038 316950 317543 - pm conserved inner membrane protein C Integral Membrane Protein 4 3 in COG3059;Predicted membrane protein "PF04224;Protein of unknown function, DUF417;3.3e-123;codon 5-185" CDS ECK0302 ykgI ykgI b0303 317555 317791 - start codon change JW5039 317555 317791 - o predicted protein C Periplasmic 1-24 PF07338;Protein of unknown function (DUF1471);9.5e-05;codon 6-83 CDS ECK0303 ykgC ykgC b0304 317900 319225 - start codon change JW5040 317900 319225 - pe predicted oxidoreductase with FAD/NAD(P)-binding domain and dimerization domain C Cytoplasmic regulated by attenuation (ykgC) "COG1249;Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes" "51905; FAD/NAD(P)-binding domain -!- 55424; FAD/NAD-linked reductases, dimerisation (C-terminal) domain" PF00070;Pyridine nucleotide-disulphide oxidored;3.3e-78;codon 14-307 -!- PF02852;Pyridine nucleotide-disulphide oxidored;8.2e-39;codon 337-446 CDS ECK0304 ykgD ykgD b0305 319451 320305 + (no change) JW0298 319451 320305 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic AraC/XylS COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like -!- 51182; RmlC-like PF00165;Bacterial regulatory helix-turn-helix protei;0.00011;codon 181-227 -!- PF00165;Bacterial regulatory helix-turn-helix protei;2.9e-07;codon 233-277 GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0305 ykgE ykgE b0306 320832 321551 + (no change) JW5041 320832 321551 + pe predicted oxidoreductase C Cytoplasmic COG0247;Fe-S oxidoreductase PF02754;Cysteine-rich domain;1.3e-14;codon 26-85 -!- PF02754;Cysteine-rich domain;9.1e-18;codon 155-217 CDS ECK0306 ykgF ykgF b0307 321562 322989 + (no change) JW0300 321562 322989 + pe predicted amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain C Cytoplasmic COG1139;Uncharacterized conserved protein containing a ferredoxin-like domain "46548; alpha-helical ferredoxin -!- 53223; Aminoacid dehydrogenase-like, N-terminal domain" PF00037;4Fe-4S binding domain;0.012;codon 305-326 -!- PF00037;4Fe-4S binding domain;0.015;codon 355-378 TIGR00273;TIGR00273: iron-sulfur cluster binding prot;0;codon 18-453 CDS ECK0307 ykgG ykgG b0308 322982 323677 + start codon change JW5042 322982 323677 + pt predicted transporter C Cytoplasmic "PF02589;Uncharacterized ACR, YkgG family COG1556;3.1e-90;codon 144-279" CDS ECK0308 ykgH ykgH b0310 323920 324588 - (no change) JW0302 323920 324588 - pm predicted inner membrane protein C Integral Membrane Protein 2 2 CDS ECK0309 betA betA b0311 324801 326471 - (no change) JW0303 324801 326471 - e "choline dehydrogenase, a flavoprotein" E 20390040 -!- 89124888 -!- 92065800 -!- 1879697 Cytoplasmic 1.1.99.1 COG2303;Choline dehydrogenase and related flavoproteins "51905; FAD/NAD(P)-binding domain -!- 54373; FAD-linked reductases, C-terminal domain" PF00732;GMC oxidoreductase;9.3e-184;codon 3-293 -!- PF05199;GMC oxidoreductase;3.6e-114;codon 331-527 TIGR01810;betA: choline dehydrogenase;0;codon 4-537 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006578 betaine biosynthesis -!- GO:0006970 response to osmotic stress CDS ECK0310 betB betB b0312 326485 327957 - (no change) JW0304 326485 327957 - e "betaine aldehyde dehydrogenase, NAD-dependent" E 89124888 -!- 90304165 -!- 92065800 -!- 1879697 Cytoplasmic 1.2.1.8 monomeric multimer; betaine aldehyde dehydrogenase (b0312) COG1012;NAD-dependent aldehyde dehydrogenases 53720; ALDH-like PF00171;Aldehyde dehydrogenase family;2e-274;codon 15-483 TIGR01804;BADH: betaine aldehyde dehydrogenase;0;codon 10-477 GO:0006578 betaine biosynthesis -!- GO:0006970 response to osmotic stress CDS ECK0311 betI betI b0313 327971 328558 - (no change) JW0305 327971 328558 - r DNA-binding transcriptional repressor E 89124888 -!- 92065800 Cytoplasmic TetR/AcrR betIBA -!- betT 46689; Homeodomain-like "PF00440;Bacterial regulatory proteins, tetR family;1.7e-15;codon 14-60" GO:0006350 transcription -!- GO:0006970 response to osmotic stress GO:0016564 transcriptional repressor activity CDS ECK0312 betT betT b0314 328687 330720 + (no change) JW0306 328687 330720 + t choline transporter of high affinity E 89124888 -!- 92065800 Integral Membrane Protein 2.A.15; The Betaine/Carnitine/Choline Transporter (BCCT) Family 12 12 COG1292;Choline-glycine betaine transporter PF02028;BCCT family transporter;0;codon 17-503 TIGR00842;bcct: choline/carnitine/betaine transport;1.1e-280;codon 55-503 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006578 betaine biosynthesis CDS ECK0313 yahA yahA b0315 331595 332683 + (no change) JW0307 331595 332683 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic LuxR/UhpA COG2771;DNA-binding HTH domain-containing proteins -!- COG2200;FOG: EAL domain "46894; C-terminal, effector domain of the bipartite response regulators" "PF00196;Bacterial regulatory proteins, luxR family;6.9e-06;codon 22-79 -!- PF00563;EAL domain;1.9e-108;codon 105-346" "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK0314 yahB yahB b0316 332725 333657 - (no change) JW0308 332725 333657 - pr predicted DNA-bindng transcriptional regulator C Periplasmic LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;2.7e-16;codon 7-66 -!- PF03466;LysR substrate binding domain;1.2e-18;codon 90-293 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0315 yahC yahC b0317 333749 334246 - (no change) JW0309 333749 334246 - pm predicted inner membrane protein C Integral Membrane Protein 5 4 in PF06496;Protein of unknown function (DUF1097);2.4e-92;codon 1-162 CDS ECK0316 yahD yahD b0318 334504 335109 + (no change) JW0310 334504 335109 + pr predicted transcriptional regulator with ankyrin domain C Cytoplasmic COG0666;FOG: Ankyrin repeat 48403; Ankyrin repeat PF00023;Ankyrin repeat;1.4e-06;codon 38-70 -!- PF00023;Ankyrin repeat;1.5;codon 107-137 -!- PF00023;Ankyrin repeat;2.7e-05;codon 138-175 CDS ECK0317 yahE yahE b0319 335149 336012 + (no change) JW0311 335149 336012 + o predicted protein C Cytoplasmic CDS ECK0318 yahF yahF b0320 336002 337549 + (no change) JW0312 336002 337549 + pe predicted acyl-CoA synthetase with NAD(P)-binding domain and succinyl-CoA synthetase domain C Cytoplasmic "COG0074;Succinyl-CoA synthetase, alpha subunit" 51735; NAD(P)-binding Rossmann-fold domains -!- 52210; Succinyl-CoA synthetase domains PF06263;Bacterial FdrA protein;2.9e-67;codon 2-515 CDS ECK0319 yahG yahG b0321 337549 338967 + (no change) JW0313 337549 338967 + o conserved protein C PF06545;Protein of unknown function (DUF1116);0;codon 62-472 CDS ECK0320 yahH yahH b0322 339017 339313 + (no change) JW5893 339017 339313 + o predicted protein C CDS ECK0321 yahI yahI b0323 339389 340339 + (no change) JW0315 339389 340339 + pe predicted carbamate kinase-like protein C Cytoplasmic COG0549;Carbamate kinase 53633; Carbamate kinase-like PF00696;Amino acid kinase family;2.6e-91;codon 3-297 GO:0006526 arginine biosynthesis -!- GO:0006221 pyrimidine nucleotide biosynthesis CDS ECK0322 yahJ yahJ b0324 340349 341731 + (no change) JW0316 340349 341731 + pe predicted deaminase with metallo-dependent hydrolase domain C Periplasmic M38 family; unassigned peptidases (YahJ protein) 1-33 COG0402;Cytosine deaminase and related metal-dependent hydrolases 51338; Composite domain of metallo-dependent hydrolases TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.0083;codon 5-36 GO:0009310 amine catabolism CDS ECK0323 yahK yahK b0325 342108 343157 + (no change) JW0317 342108 343157 + pe "predicted oxidoreductase, Zn-dependent and NAD(P)-binding" C Cytoplasmic COG1064;Zn-dependent alcohol dehydrogenases 50129; GroES-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF00107;Zinc-binding dehydrogenase;2e-112;codon 10-343 CDS ECK0324 yahL yahL b0326 343400 344215 + (no change) JW0318 343400 344215 + o predicted protein C Cytoplasmic CDS ECK0325 yahM yahM b0327 344628 344873 + start codon change JW5044 344628 344873 + o predicted protein C Cytoplasmic CDS ECK0326 yahN yahN b0328 344890 345561 - (no change) JW0320 344890 345561 - t neutral amino-acid efflux system E 12879215 Integral Membrane Protein 2.A.76; The Resistance to Homoserine/Threonine (RhtB) Family 6 6 in COG1280;Putative threonine efflux protein PF01810;LysE type translocator;1e-72;codon 28-219 TIGR00949;2A76: Homoserine/Threonine efflux protein;9e-102;codon 33-215 CDS ECK0327 yahO yahO b0329 345708 345983 + (no change) JW0321 345708 345983 + o predicted protein C Periplasmic 1-21 PF07338;Protein of unknown function (DUF1471);7.4e-14;codon 1-89 CDS ECK0328 prpR prpR yahP b0330 346081 347667 - (no change) JW0322 346081 347667 - r DNA-binding transcriptional activator E 9325432 -!- 15805526 Cytoplasmic EBP prpBCDE COG1221;Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain 48283; FIS-like -!- 52540; P-loop containing nucleotide triphosphate hydrolases "PF06506;Propionate catabolism activator;1.5e-93;codon 28-202 -!- PF00158;Sigma-54 interaction domain;6.6e-131;codon 218-452 -!- PF02954;Bacterial regulatory protein, Fis fam;1.6e-05;codon 496-527" "TIGR01199;HTH_fis: Helix-turn-helix domain, fis-type;0.0031;codon 495-527" GO:0005737 cytoplasm GO:0019395 fatty acid oxidation -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK0329 prpB prpB yahQ b0331 347906 348796 + (no change) JW0323 347906 348796 + e 2-methylisocitrate lyase E 11422389 -!- 12473114 -!- 9325432 Cytoplasmic 4.1.3.30 Mg2+ monomeric multimer; 2-methylisocitrate lyase (b0331) COG2513;PEP phosphonomutase and related enzymes 51621; Phosphoenolpyruvate/pyruvate domain GO:0005737 cytoplasm GO:0019395 fatty acid oxidation CDS ECK0330 prpC prpC yahS -!- yzzD b0333 349236 350405 + (no change) JW0324 349236 350405 + e 2-methylcitrate synthase E 12473114 -!- 9579066 -!- 8508809 -!- 9325432 2.3.3.1 monomeric multimer; methylcitrate synthase (b0333) COG0372;Citrate synthase 48256; Citrate synthase PF00285;Citrate synthase;3.9e-102;codon 22-370 TIGR01800;cit_synth_II: 2-methylcitrate synthase/c;3.1e-261;codon 20-388 GO:0005737 cytoplasm GO:0019395 fatty acid oxidation CDS ECK0331 prpD prpD acnC -!- yahT b0334 350439 351890 + (no change) JW0325 350439 351890 + e 2-methylcitrate dehydratase E 12473114 -!- 21642584 Cytoplasmic 4.2.1.79 1SZQ COG2079;Uncharacterized protein involved in propionate catabolism PF03972;MmgE/PrpD family;1.4e-249;codon 13-475 GO:0016052 carbohydrate catabolism CDS ECK0332 prpE prpE yahU b0335 351930 353816 + (no change) JW0326 351930 353816 + pe predicted propionyl-CoA synthetase with ATPase domain C 10411265 COG0365;Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases 56801; Firefly luciferase-like PF00501;AMP-binding enzyme;5.5e-110;codon 85-525 GO:0005737 cytoplasm GO:0019395 fatty acid oxidation CDS ECK0333 codB codB b0336 354146 355405 + (no change) JW0327 354146 355405 + t cytosine transporter E 92349961 Integral Membrane Protein 2.A.39; The Nucleobase:Cation Symporter-1 (NCS1) Family 12 12 in COG1457;Purine-cytosine permease and related proteins "PF02133;Permease for cytosine/purines, uracil,;1.6e-121;codon 11-398" TIGR00800;ncs1: NCS1 nucleoside transporter family;5.4e-130;codon 6-391 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0334 codA codA b0337 355395 356678 + (no change) JW0328 355395 356678 + e cytosine deaminase E 92349961 -!- 8450832 Cytoplasmic 3.5.4.1 Fe2+ -!- Zn2+ M38 family; non-peptidase homologues (cytosine deaminase) 1K70 COG0402;Cytosine deaminase and related metal-dependent hydrolases 51338; Composite domain of metallo-dependent hydrolases -!- 51556; Metallo-dependent hydrolases PF01979;Amidohydrolase family;0.091;codon 53-381 GO:0005737 cytoplasm "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0335 cynR cynR b0338 357015 357914 - (no change) JW5894 357015 357914 - r DNA-binding transcriptional dual regulator E 91242169 -!- 92276346 -!- 94075239 Cytoplasmic LysR cynR -!- cynTSX COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;1.7e-25;codon 3-62 -!- PF03466;LysR substrate binding domain;1.8e-57;codon 86-291 GO:0005737 cytoplasm GO:0006350 transcription -!- GO:0006805 xenobiotic metabolism GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0336 cynT cynT b0339 358023 358682 + (no change) JW0330 358023 358682 + e carbonic anhydrase E 91242169 -!- 92156106 -!- 94075239 -!- 3049588 Cytoplasmic 4.2.1.1 monomeric multimer; carbonate dehydratase (b0339) COG0288;Carbonic anhydrase "53056; beta-carbonic anhydrase, cab" PF00484;Carbonic anhydrase;2.1e-95;codon 27-193 GO:0005737 cytoplasm GO:0009440 cyanate catabolism -!- GO:0006805 xenobiotic metabolism CDS ECK0337 cynS cynS cnt -!- cyaN b0340 358713 359183 + (no change) JW0331 358713 359183 + e cyanate aminohydrolase E 87280031 -!- 91242169 -!- 92156106 -!- 10801492 -!- 2822670 -!- 3049588 -!- 6336748 Cytoplasmic 4.2.1.104 HCO3- monomeric multimer; cyanase (b0340) 1DW9 COG1513;Cyanate lyase 47413; lambda repressor-like DNA-binding domains -!- 55234; Cyanase C-terminal domain PF02560;Cyanate lyase C-terminal domain;2e-57;codon 83-156 TIGR00673;cynS: cyanate hydratase;4.3e-118;codon 1-156 GO:0009440 cyanate catabolism -!- GO:0006807 nitrogen metabolism -!- GO:0006805 xenobiotic metabolism CDS ECK0338 cynX cynX b0341 359216 360370 + (no change) JW0332 359216 360370 + pt predicted cyanate transporter C 91242169 -!- 3049588 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 11 12 COG2807;Cyanate permease PF07690;Major Facilitator Superfamily;4.4e-27;codon 1-345 TIGR00896;CynX: cyanate transporter;4.2e-218;codon 1-353 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009440 cyanate catabolism -!- GO:0006805 xenobiotic metabolism CDS ECK0339 lacA lacA b0342 360473 361084 - (no change) JW0333 360473 361084 - e thiogalactoside acetyltransferase E 789355 -!- 3901000 -!- 3922433 -!- 6444453 -!- 14085376 Cytoplasmic 2.3.1.18 monomeric multimer; galactoside O-acetyltransferase (b0342) 1KRV COG0110;Acetyltransferase (isoleucine patch superfamily) 51161; Trimeric LpxA-like enzymes PF00132;Bacterial transferase hexapeptide (three rep;0.14;codon 95-112 -!- PF00132;Bacterial transferase hexapeptide (three rep;0.18;codon 131-148 -!- PF00132;Bacterial transferase hexapeptide (three rep;0.056;codon 149-166 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK0340 lacY lacY b0343 361150 362403 - (no change) JW0334 361150 362403 - t lactose/galactose transporter E 12893935 -!- 14630326 -!- 90272706 -!- 90366577 -!- 91154204 -!- 10485888 -!- 1644770 -!- 1848449 -!- 2164211 -!- 6444453 -!- 7578103 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 11 in COG0477;Permeases of the major facilitator superfamily PF01306;LacY proton/sugar symporter;0;codon 1-413 -!- PF07690;Major Facilitator Superfamily;1.4e-12;codon 12-374 TIGR00882;2A0105: oligosaccharide:H+ symporter;0;codon 6-401 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK0341 lacZ lacZ b0344 362455 365529 - (no change) JW0335 362455 365529 - e beta-D-galactosidase E "92283812 -!- 11732897 -!- 6246435 -!- 6313347 -!- 6411710 -!- 6420154 -!- 6444453 -!- 8008071 -!- 97298 -!- Wallenfels K, Weil R;Academic Press, NY;1972;617-663" Cytoplasmic 3.2.1.23 monomeric multimer; beta-galactosidase (b0344) 1JZ2 COG3250;Beta-galactosidase/beta-glucuronidase 49303; beta-Galactosidase/glucuronidase domain -!- 49785; Galactose-binding domain-like -!- 51445; (Trans)glycosidases "PF02837;Glycosyl hydrolases family 2, sugar binding;3.4e-94;codon 49-219 -!- PF00703;Glycosyl hydrolases family 2, immunoglobulin-like beta-sandwich;3e-57;codon 221-334 -!- PF02836;Glycosyl hydrolases family 2, TIM barrel;2.3e-196;codon 336-630 -!- PF02929;Beta galactosidase small chain, N term;1.9e-91;codon 736-920 -!- PF02930;Beta galactosidase small chain, C term;4.4e-49;codon 930-1021" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK0342 lacI lacI b0345 365652 366734 - (no change) JW0336 365652 366734 - r DNA-binding transcriptional repressor E 91278090 -!- 93027237 -!- 93066276 -!- 10647179 -!- 1107032 -!- 2040302 -!- 2178920 -!- 2742823 -!- 3064080 -!- 3286877 -!- 355891 -!- 4571224 -!- 4594037 -!- 8046748 -!- 8638105 -!- 8683581 Cytoplasmic GalR/LacI lacZYA 1LBI 47413; lambda repressor-like DNA-binding domains -!- 53822; Periplasmic binding protein-like I "PF00356;Bacterial regulatory proteins, lacI fami;2.5e-11;codon 4-29 -!- PF00532;Periplasmic binding proteins and sugar b;4.6e-10;codon 68-327" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK0343 mhpR mhpR b0346 366811 367758 - (no change) JW0337 366811 367758 - r "DNA-binding transcriptional activator, 3HPP-binding" E 97252486 Cytoplasmic IclR mhpABCDFE regulated by attenuation (mhpR) COG1414;Transcriptional regulator 46785; Winged helix PF01614;Bacterial transcriptional regulator;2.1e-07;codon 108-297 GO:0005737 cytoplasm GO:0019395 fatty acid oxidation -!- GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0344 mhpA mhpA b0347 367835 369499 + (no change) JW0338 367835 369499 + e 3-(3-hydroxyphenyl)propionate hydroxylase E 87008429 -!- 94002258 Cytoplasmic 1.14.13.- COG0654;2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases 51735; NAD(P)-binding Rossmann-fold domains -!- 51905; FAD/NAD(P)-binding domain PF01494;FAD binding domain;5.3e-18;codon 18-155 -!- PF01360;Monooxygenase;1.9e-55;codon 166-354 GO:0019395 fatty acid oxidation CDS ECK0345 mhpB mhpB b0348 369501 370445 + (no change) JW0339 369501 370445 + e "2,3-dihydroxyphenylpropionate 1,2-dioxygenase" E 87008429 -!- 94002258 -!- 8752345 1.13.11.- Fe2+ "monomeric multimer; 3-(2,3-dihydroxyphenyl)propionate dioxygenase (b0348)" 53213; LigB subunit of an aromatic-ring-opening dioxygenase LigAB PF02900;Catalytic LigB subunit of aromatic ring-open;3.5e-132;codon 4-306 GO:0019395 fatty acid oxidation CDS ECK0346 mhpC mhpC b0349 370448 371329 + start codon change JW0340 370448 371329 + e "2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase" E 87008429 -!- 94002258 -!- 15663942 Cytoplasmic 3.7.1.- "S33 family; non-peptidase homologues (2-Hydroxy-6-ketonona-2,4-dienedioic acid hydrolase)" 53474; alpha/beta-Hydrolases PF00561;alpha/beta hydrolase fold;3.3e-33;codon 87-304 GO:0019395 fatty acid oxidation CDS ECK0347 mhpD mhpD mhpS b0350 371339 372148 + start codon change JW0341 371339 372148 + e 2-keto-4-pentenoate hydratase E 87008429 -!- 94002258 -!- 9492273 Cytoplasmic 4.2.1.80 1SV6 COG3971;2-keto-4-pentenoate hydratase 56529; FAH PF01689;Hydratase/decarboxylase;2.3e-147 ;codon 5-223 GO:0019395 fatty acid oxidation CDS ECK0348 mhpF mhpF b0351 372145 373095 + (no change) JW0342 372145 373095 + e "acetaldehyde-CoA dehydrogenase II, NAD-binding" E 87008429 -!- 94002258 1.2.1.10 COG0119;Isopropylmalate/homocitrate/citramalate synthases 51735; NAD(P)-binding Rossmann-fold domains PF02396;Acetaldehyde dehydrogenase;2.5e-249;codon 1-311 GO:0005737 cytoplasm GO:0019395 fatty acid oxidation CDS ECK0349 mhpE mhpE b0352 373092 374105 + (no change) JW0343 373092 374105 + e "4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase, class I" E 87008429 -!- 94002258 -!- 98432850 Cytoplasmic 4.1.3.- COG4569;Acetaldehyde dehydrogenase (acetylating) 51366; Ribulose-phoshate binding barrel PF00682;HMGL-like;1.7e-113;codon 14-270 -!- PF07836;DmpG-like communication domain;1.9e-42;codon 272-335 GO:0019395 fatty acid oxidation CDS ECK0350 mhpT mhpT yaiK b0353 374683 375894 + start codon change JW5046 374683 375894 + pt predicted 3-hydroxyphenylpropionic transporter C Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG0477;Permeases of the major facilitator superfamily PF00083;Sugar (and other) transporter;8.5e-07;codon 17-410 -!- PF07690;Major Facilitator Superfamily;9.6e-50;codon 35-379 TIGR00895;2A0115: benzoate transport;1.7e-180;codon 14-378 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0019395 fatty acid oxidation CDS ECK0351 yaiL yaiL b0354 375996 376535 + start codon change JW0345 375996 376535 + e nucleoprotein/polynucleotide-associated enzyme E 15115803 -!- 12878731 -!- 13129938 Cytoplasmic GO:0005737 cytoplasm CDS ECK0352 frmB frmB yaiM b0355 376759 377592 - (no change) JW0346 376759 377592 - pe predicted esterase C 15466022 Cytoplasmic COG0627;Predicted esterase 53474; alpha/beta-Hydrolases PF00756;Putative esterase;5.5e-120;codon 13-269 CDS ECK0353 frmA frmA adhC b0356 377686 378795 - (no change) JW0347 377686 378795 - e alcohol dehydrogenase class III/glutathione-dependent formaldehyde dehydrogenase E 15466022 -!- 87172301 -!- 1731906 Cytoplasmic 1.1.1.1 -!- 1.2.1.1 Zn2+ "monomeric multimer; formaldehyde dehydrogenase, glutathione-dependent (b0356)" "COG1062;Zn-dependent alcohol dehydrogenases, class III" 50129; GroES-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF00107;Zinc-binding dehydrogenase;1.7e-144;codon 10-369 GO:0005737 cytoplasm GO:0006113 fermentation CDS ECK0354 frmR frmR yaiN b0357 378830 379105 - start codon change JW0348 378830 379105 - r regulator protein that represses frmRAB operon E 15466022 Cytoplasmic COG1937;Uncharacterized protein conserved in bacteria "PF02583;Uncharacterised BCR, COG1937;4.7e-30;codon 35-97" CDS ECK0355 yaiO yaiO b0358 379293 380066 - (no change) JW0349 379293 380066 - o predicted protein C 1-16 CDS ECK0356 yaiX yaiX b0359 380068 380283 - pseudogene -!- start codon change JW0350 380068 380283 - "pseudogene, interrupted by IS" su predicted acyl transferase (pseudogene) predicted glucose-1-phosphate thymidylyltransferase -!- interrupted by IS2A C Cytoplasmic COG0110;Acetyltransferase (isoleucine patch superfamily) 51161; Trimeric LpxA-like enzymes 4 of PF00132;Bacterial transferase hexapeptide (three repeats): 3.6;codon 12-29 -!- 0.086;codon 35-52 -!- 23;codon 94-111 -!- 21;codon 112-129 CDS ECK0357 insC insC unique to W3110 0 0 JW5934 3743807 3744172 - IS2 -!- W3110 specific region h IS2 element protein E IS2 CDS ECK0357 insC insC unique to W3110 0 0 JW5919 2321668 2322033 - IS2 -!- W3110 specific region h IS2 element protein E IS2 CDS ECK0357 insC insC unique to W3110 0 0 JW5902 1301130 1301495 + IS2 -!- W3110 specific region h IS2 element protein E IS2 CDS ECK0357 insC insC unique to W3110 0 0 JW5900 1106496 1106861 - IS2 -!- W3110 specific region h IS2 element protein E IS2 CDS ECK0357 insC insC-6 yi21-6 b4272 4496250 4496660 + (no change) JW4229 4502907 4503317 + h KpLE2 phage-like element; IS2 insertion element repressor InsA E 9689094 KpLE2 phage-like element -!- IS2 COG2963;Transposase and inactivated derivatives 46689; Homeodomain-like PF01527;Transposase;2.6e-34;codon 25-112 CDS ECK0357 insC insC-5 yi21-5 b3044 3184164 3184574 + start codon change JW3012 3184798 3185208 + IS h IS2 insertion element repressor InsA E 9689094 IS2 COG2963;Transposase and inactivated derivatives 46689; Homeodomain-like PF01527;Transposase;2.6e-34;codon 10-97 CDS ECK0357 insC insC-4 yi21-4 b2861 2995257 2995667 - start codon change JW2829 2995891 2996301 - IS h IS2 insertion element repressor InsA E 9689094 IS2 COG2963;Transposase and inactivated derivatives 46689; Homeodomain-like PF01527;Transposase;2.6e-34;codon 10-97 CDS ECK0357 insC insC-3 yi21-3 b1997 2067839 2068249 - (no change) JW1978 2071952 2072362 - h CP4-44 prophage; IS2 insertion element repressor InsA E 9689094 cryptic prophage CP4-44 -!- IS2 46689; Homeodomain-like PF01527;Transposase;2.6e-34;codon 25-112 CDS ECK0357 insC insC -2 yi21-2 b1403 1466808 1467218 - (no change) JW1400 1470498 1470908 - h IS2 insertion element repressor InsA E 9689094 IS2 COG2963;Transposase and inactivated derivatives 46689; Homeodomain-like PF01527;Transposase;2.6e-34;codon 25-112 CDS ECK0357 insC insC -1 yi21-1 b0360 380530 380940 + (no change) JW0351 380530 380940 + h IS2 insertion element repressor InsA E 9689094 IS2 COG2963;Transposase and inactivated derivatives 46689; Homeodomain-like PF01527;Transposase;2.6e-34;codon 25-112 CDS ECK0358 insD insD-3 yi22-3 b1996 2066976 2067881 - (no change) JW1975 2071089 2071994 - h CP4-44 prophage; IS2 insertion element transposase InsAB' location needs redefining- protein encoded by orfA and orfB (ribosomal slippage) E 9689094 cryptic prophage CP4-44 -!- IS2 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;5.5e-34;codon 121-286 CDS ECK0358 insD insD unique to W3110 0 0 JW5933 3742944 3743867 - IS2 -!- W3110 specific region h IS2 element protein E IS2 CDS ECK0358 insD insD unique to W3110 0 0 JW5918 2320805 2321728 - IS2 -!- W3110 specific region h IS2 element protein E IS2 CDS ECK0358 insD insD unique to W3110 0 0 JW5903 1301435 1302358 + IS2 -!- W3110 specific region h IS2 element protein E IS2 CDS ECK0358 insD insD unique to W3110 0 0 JW5899 1105633 1106556 - IS2 -!- W3110 specific region h IS2 element protein E IS2 CDS ECK0358 insD insD-6 yi22-6 b4273 4496618 4497523 + (no change) JW4230 4503275 4504180 + h KpLE2 phage-like element; IS2 insertion element transposase InsAB' E 2830172 KpLE2 phage-like element -!- IS2 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;5.5e-34;codon 121-286 CDS ECK0358 insD insD-5 yi22-5 b3045 3184532 3185437 + (no change) JW3013 3185166 3186071 + h IS2 insertion element transposase InsAB' E 9689094 IS2 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;5.5e-34;codon 121-286 CDS ECK0358 insD insD-4 yi22-4 b2860 2994394 2995299 - (no change) JW2826 2995028 2995933 - h IS2 insertion element transposase InsAB' E 9689094 IS2 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;5.5e-34;codon 121-286 CDS ECK0358 insD insD-2 yi22-2 b1402 1465945 1466850 - (no change) JW1397 1469635 1470540 - h IS2 insertion element transposase InsAB' E 9689094 IS2 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;5.5e-34;codon 121-286 CDS ECK0358 insD insD-1 yi22-1 b0361 380898 381803 + (no change) JW0352 380898 381803 + h IS2 insertion element transposase InsAB' E 9689094 IS2 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;5.5e-34;codon 121-286 CDS ECK0359 yaiF yaiF b0362 381728 382114 - (no change) JW5814 381728 382114 - d predicted protein C 51161; Trimeric LpxA-like enzymes CDS ECK0360 yaiP yaiP b0363 381963 383159 - (no change) JW0355 381963 383159 - pe predicted glucosyltransferase C Integral Membrane Protein 3 4 "COG1215;Glycosyltransferases, probably involved in cell wall biogenesis" 53448; Nucleotide-diphospho-sugar transferases PF00535;Glycosyl transferase;1e-24;codon 33-202 GO:0000271 polysaccharide biosynthesis CDS ECK0361 yaiS yaiS b0364 383283 383840 - start codon change JW0356 383283 383840 - "pseudogene, interrupted by IS" o conserved protein C Cytoplasmic CDS ECK0362 tauA tauA ssiA -!- yaiR b0365 384456 385418 + start codon change JW0357 384456 385418 + t taurine transporter subunit -!- periplasmic-binding component of ABC superfamily E 9401024 -!- 96404792 -!- 8774726 Periplasmic heteromultimer; TauA/TauB/TauC ABC transporter (b0365-b0367-b0366) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-41 320 "COG4521;ABC-type taurine transport system, periplasmic component" 53850; Periplasmic binding protein-like II PF04069;Substrate binding domain of ABC-type glycine;4.2e-44;codon 43-273 TIGR01729;taurine_ABC_bnd: taurine ABC transpor;3.1e-240;codon 44-339 GO:0042597 periplasmic space GO:0006790 sulfur metabolism -!- GO:0009310 amine catabolism CDS ECK0363 tauB tauB ssiB -!- yaiQ b0366 385431 386198 + (no change) JW0358 385431 386198 + t taurine transporter subunit -!- ATP-binding component of ABC superfamily E 9401024 -!- 96404792 Cytoplasmic heteromultimer; TauA/TauB/TauC ABC transporter (b0365-b0367-b0366) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG4525;ABC-type taurine transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.1e-56;codon 27-205 GO:0005737 cytoplasm GO:0006790 sulfur metabolism -!- GO:0009310 amine catabolism CDS ECK0364 tauC tauC ssiC -!- yaiJ b0367 386195 387022 + (no change) JW0359 386195 387022 + t taurine transporter subunit -!- membrane component of ABC superfamily E 9401024 -!- 96404792 Integral Membrane Protein heteromultimer; TauA/TauB/TauC ABC transporter (b0365-b0367-b0366) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 6 6 in "COG0600;ABC-type nitrate/sulfonate/bicarbonate transport system, permease component" PF00528;Binding-protein-dependent transport syst;1.9e-23;codon 80-269 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006790 sulfur metabolism -!- GO:0009310 amine catabolism CDS ECK0365 tauD tauD ssiD -!- yaiG b0368 387019 387870 + (no change) JW0360 387019 387870 + e "taurine dioxygenase, 2-oxoglutarate-dependent" E 9401024 -!- 96404792 -!- 11955067 -!- 2656410 -!- 7984428 -!- 8774726 -!- 9287300 Cytoplasmic 1.14.11.17 Fe2+ monomeric multimer; taurine dioxygenase (b0368) COG2175;Probable taurine catabolism dioxygenase 51197; Clavaminate synthase-like "PF02668;Taurine catabolism dioxygenase TauD, TfdA fa;2.2e-197;codon 5-283" GO:0009310 amine catabolism -!- GO:0006790 sulfur metabolism CDS ECK0366 hemB hemB ncf b0369 387977 388951 - start codon change JW0361 387977 388951 - e porphobilinogen synthase E 91100324 -!- 93143310 -!- 93176130 -!- 10194344 -!- 11444968 -!- 11909869 -!- 2464127 -!- 2656410 Cytoplasmic 4.2.1.24 Zn2+ monomeric multimer; porphobilinogen synthase (b0369) 51569; Aldolase PF00490;Delta-aminolevulinic acid dehydratase;2.1e-236;codon 14-332 CDS ECK0367 ykiB ykiB b0370 389121 389339 - start codon change JW5049 389121 389339 - o predicted protein C CDS ECK0368 yaiT yaiT yaiU b0371 389475 390935 + (no change) JW0362 389475 390935 + o predicted protein C Periplasmic 1-27 CDS ECK0369 yaiU yaiU yaiT b0374 392239 393642 + (no change) JW5051 392239 393642 + o predicted protein C "COG3468;Type V secretory pathway, adhesin AidA" 56935; Porins PF03212;Pertactin;0.003;codon 66-164 -!- PF03797;Autotransporter beta-domain;1.3e-35;codon 203-448 TIGR01414;autotrans_barl: outer membrane autotra;9.7e-87;codon 61-467 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK0370 yaiV yaiV b0375 393685 394353 + (no change) JW0366 393685 394353 + pr predicted DNA-binding transcriptional regulator cAMP-binding C Cytoplasmic 51206; cAMP-binding domain-like GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0371 ampH ampH yaiH b0376 394354 395511 - (no change) JW5052 394354 395511 - e beta-lactamase/D-alanine carboxypeptidase penicillin-binding protein (PBP) E 97464439 -!- 7567469 Periplasmic 3.5.2.6 -!- 3.4.17.8 S12 family; unassigned peptidases (YaiH protein) 1-21 COG1680;Beta-lactamase class C and other penicillin binding proteins 56601; beta-Lactamase/D-ala carboxypeptidase PF00144;Beta-lactamase;4.8e-73;codon 35-372 GO:0042493 response to drug CDS ECK0372 sbmA sbmA b0377 395863 397083 + (no change) JW0368 395863 397083 + pt predicted transporter required for microcin B17 uptake C 87111440 -!- 94143997 Integral Membrane Protein 9.A.18; The Putative Peptide Uptake or Activated Fatty Acid Export Permease (PUP) Family 8 8 in "COG1133;ABC-type long-chain fatty acid transport system, fused permease and ATPase components" PF05992;SbmA/BacA-like family;1.8e-103;codon 34-169 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0373 yaiW yaiW b0378 397096 398190 + (no change) JW0369 397096 398190 + pr predicted DNA-binding transcriptional regulator C Outer membrane Lipoprotein Unclass 1-19 PF07759;Protein of unknown function (DUF1615);7.7e-247;codon 48-364 CDS ECK0374 yaiY yaiY b0379 398249 398557 - (no change) JW0370 398249 398557 - pm predicted inner membrane protein C Integral Membrane Protein 2 2 in CDS ECK0375 yaiZ yaiZ b0380 398817 399029 + start codon change JW5053 398817 399029 + pm predicted inner membrane protein C Integral Membrane Protein 2 2 CDS ECK0376 ddlA ddlA b0381 399053 400147 - (no change) JW0372 399053 400147 - e D-alanine-D-alanine ligase A E 91129242 -!- 92207163 Cytoplasmic 6.3.2.4 COG1181;D-alanine-D-alanine ligase and related ATP-grasp enzymes 52440; Biotin carboxylase N-terminal domain-like -!- 56059; Glutathione synthetase ATP-binding domain-like PF01820;D-ala D-ala ligase N-terminus;1.2e-75;codon 4-139 -!- PF07478;D-ala D-ala ligase C-terminus;2.2e-131;codon 140-348 TIGR01205;D_ala_D_alaTIGR: D-alanine--D-alanine;2.3e-201;codon 5-351 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009252 peptidoglycan biosynthesis CDS ECK0377 yaiB yaiB b0382 400610 400870 + (no change) JW0373 400610 400870 + o predicted protein C Cytoplasmic regulated by attenuation (yaiB) CDS ECK0378 phoA phoA psiA b0383 400971 402386 + (no change) JW0374 400971 402386 + e bacterial alkaline phosphatase E ############################################################################################################################################################################################################################################################### Periplasmic 3.1.3.1 monomeric multimer; alkaline phosphatase (b0383) 471 1EW9 53649; Alkaline phosphatase-like PF00245;Alkaline phosphatase;8.1e-161;codon 58-418 GO:0042597 periplasmic space GO:0006793 phosphorus metabolism CDS ECK0379 psiF psiF b0384 402505 402825 + start codon change JW5054 402505 402825 + o conserved protein member of pho regulon C 90264312 -!- 93163134 -!- 3533724 1-27 regulated by attenuation (psiF) PF07769;psiF repeat;3.7e-19;codon 31-65 -!- PF07769;psiF repeat;1.1e-21;codon 75-109 GO:0006793 phosphorus metabolism -!- GO:0042594 response to starvation CDS ECK0380 yaiC yaiC b0385 402927 404042 + (no change) JW0376 402927 404042 + pr predicted diguanylate cyclase "involved in curli, possibly cellulose, synthesis" C 15716451 -!- 1452311 -!- 3533724 Integral Membrane Protein 5 5 COG2199;FOG: GGDEF domain PF05230;MASE2 domain;6.2e-120;codon 31-200 -!- PF00990;GGDEF domain;3.5e-73;codon 206-366 TIGR00254;GGDEF: putative diguanylate cyclase (GGDEF);7.4e-75;codon 206-371 CDS ECK0381 proC proC Pro2 -!- pro3 -!- pro(3) b0386 404059 404868 - (no change) JW0377 404059 404868 - e "pyrroline-5-carboxylate reductase, NAD(P)-binding" E 6255065 -!- 83116986 1.5.1.2 monomeric multimer; pyrroline-5-carboxylate-reductase (b0386) COG0345;Pyrroline-5-carboxylate reductase 51735; NAD(P)-binding Rossmann-fold domains PF01089;Delta 1-pyrroline-5-carboxylate reductase;7.7e-137;codon 3-251 TIGR00112;proC: pyrroline-5-carboxylate reductase;3.3e-102;codon 5-266 GO:0005737 cytoplasm GO:0006561 proline biosynthesis CDS ECK0382 yaiI yaiI b0387 404988 405446 + start codon change JW0378 404988 405446 + o conserved protein C Cytoplasmic COG1671;Uncharacterized protein conserved in bacteria "PF02639;Uncharacterized BCR, YaiI/YqxD family COG167;3.8e-97;codon 41-186" CDS ECK0383 aroL aroL b0388 405629 406153 + (no change) JW0379 405629 406153 + e shikimate kinase II E 86085675 -!- 92104984 -!- 3001025 -!- 3026317 2.7.1.71 Mg2+ COG0703;Shikimate kinase 52540; P-loop containing nucleotide triphosphate hydrolases PF01202;Shikimate kinase;8.8e-69;codon 11-169 GO:0005737 cytoplasm GO:0009423 chorismate biosynthesis CDS ECK0384 yaiA yaiA b0389 406203 406394 + (no change) JW0380 406203 406394 + o predicted protein C Cytoplasmic CDS ECK0385 aroM aroM b0390 406652 407329 + (no change) JW0381 406652 407329 + o conserved protein member of aroR regulon C 86085675 -!- 3001025 Cytoplasmic PF07302;AroM protein;6.6e-152;codon 4-225 CDS ECK0386 yaiE yaiE b0391 407401 407685 + (no change) JW0382 407401 407685 + o conserved protein C Cytoplasmic COG3123;Uncharacterized protein conserved in bacteria PF06865;Protein of unknown function (DUF1255);3.3e-64;codon 1-94 CDS ECK0387 ykiA ykiA b0392 407893 408174 + (no change) JW0383 407893 408174 + o predicted protein C Cytoplasmic CDS ECK0388 rdgC rdgC yaiD b0393 408332 409243 - (no change) JW0384 408332 409243 - f "DNA-binding protein, non-specific" E 8807285 -!- 99296598 -!- 12554673 Cytoplasmic COG2974;DNA recombination-dependent growth factor C 55895; Ribonuclease Rh-like "PF04381;Putative exonuclease, RdgC;6.6e-225;codon 2-302" GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK0389 mak mak yajF b0394 409368 410276 + start codon change JW0385 409368 410276 + e manno(fructo)kinase E 11742072 -!- 1744033 Cytoplasmic 2.7.1.4 regulated by attenuation (yajF) COG1940;Transcriptional regulator/sugar kinase 53067; Actin-like ATPase domain PF00480;ROK family;2.5e-96;codon 50-239 GO:0016052 carbohydrate catabolism CDS ECK0390 araJ araJ araT b0396 410521 411705 - (no change) JW0386 410521 411705 - pt predicted transporter C 92078081 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in PF07690;Major Facilitator Superfamily;2.1e-49;codon 8-349 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK0391 sbcC sbcC rmuA b0397 411831 414977 - (no change) JW0387 411831 414977 - e "exonuclease, dsDNA, ATP-dependent" E 12826280 -!- 90045931 -!- 93146416 -!- 93214998 -!- 98318595 -!- 9927737 -!- 10886369 -!- 1744033 Cytoplasmic COG0419;ATPase involved in DNA repair 52540; P-loop containing nucleotide triphosphate hydrolases PF02463;RecF/RecN/SMC N terminal domain;5.4e-06;codon 1-179 TIGR00618;sbcc: exonuclease SbcC;0;codon 1-1040 GO:0005737 cytoplasm GO:0006308 DNA catabolism -!- GO:0006308 DNA catabolism CDS ECK0392 sbcD sbcD yajA b0398 414974 416176 - (no change) JW0388 414974 416176 - e "exonuclease, dsDNA, ATP-dependent" metallo-dependent E 12826280 -!- 92138614 -!- 93146416 -!- 93214998 -!- 98318595 -!- 9927737 -!- 2530497 Cytoplasmic regulated by attenuation (sbcD-sbcC) COG0420;DNA repair exonuclease 56300; Metallo-dependent phosphatases PF00149;Calcineurin-like phosphoesterase;1.9e-19;codon 1-226 "TIGR00619;sbcd: nuclease SbcCD, D subunit;9.2e-143;codon 1-254" GO:0005737 cytoplasm GO:0006308 DNA catabolism -!- GO:0006308 DNA catabolism CDS ECK0393 phoB phoB phoRc -!- phoT b0399 416366 417055 + (no change) JW0389 416366 417055 + r DNA-binding response regulator in two-component regulatory system with PhoR (or CreC) activator of pho regulon -!- 2-comp E 90133909 -!- 91100346 Cytoplasmic Two asr -!- iciA -!- phnCDE-f73-phnFGHIJKLMNOP -!- phoA-psiF -!- phoBR -!- phoE -!- phoH -!- psiE -!- pstSCAB-phoU -!- ugpBAECQ COG0745;Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;1.5e-41;codon 3-124 -!- PF00486;Transcriptional regulatory protein, C te;1.9e-25;codon 150-225" TIGR02154;PhoB: Phosphate regulon transcriptional regu;9.4e-189;codon 1-226 GO:0005737 cytoplasm GO:0006793 phosphorus metabolism -!- GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0394 phoR phoR R1pho -!- nmpB -!- phoR1 b0400 417113 418408 + (no change) JW0390 417113 418408 + r sensory histidine kinase in two-component regulatory system with PhoB activator of pho regulon -!- senses Pi E 90133909 -!- 90251245 -!- 93163134 -!- 3550103 -!- 8391104 Membrane Anchored 2.7.3.- monomeric multimer; PhoR (b0400) in COG0642;Signal transduction histidine kinase 47384; Homodimeric domain of signal transducing histidine kinase -!- 55785; PYP-like sensor domain -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF00989;PAS domain;1.4e-09;codon 98-160 -!- PF00512;His Kinase A (phosphoacceptor) domain;1.5e-24;codon 203-269 -!- PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;2.4e-44;codon 313-424" TIGR00229;sensory_box: PAS domain S-box;0.0015;codon 94-204 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006793 phosphorus metabolism -!- GO:0006464 protein modification CDS ECK0395 brnQ brnQ hrbA b0401 418815 420134 + (no change) JW0391 418815 420134 + pt predicted branched chain amino acid transporter (LIV-II) C 6998958 -!- 3550103 -!- 7984428 Integral Membrane Protein 12 12 in COG1114;Branched-chain amino acid permeases PF05525;Branched-chain amino acid transport p;2.5e-238;codon 6-430 TIGR00796;livcs: branched-chain amino acid transport s;1e-245;codon 14-415 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009098 leucine biosynthesis -!- GO:0009063 amino acid catabolism CDS ECK0396 proY proY yajM b0402 420210 421583 + (no change) JW5055 420210 421583 + pt predicted cryptic proline transporter cryptic C Integral Membrane Protein 12 12 in regulated by attenuation (proY) COG1113;Gamma-aminobutyrate permease and related permeases PF00324;Amino acid permease;5.2e-133;codon 15-455 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009063 amino acid catabolism -!- GO:0006526 arginine biosynthesis CDS ECK0397 malZ malZ b0403 421739 423556 + (no change) JW0393 421739 423556 + e maltodextrin glucosidase E 92184757 -!- 1706703 -!- 1918057 Cytoplasmic 3.2.1.20 COG0366;Glycosidases "51011; alpha-Amylases, C-terminal beta-sheet domain -!- 51445; (Trans)glycosidases" "PF00128;Alpha amylase, catalytic domain;8.2e-120;codon 128-522" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0000272 polysaccharide catabolism CDS ECK0398 yajB yajB b0404 423561 424142 - (no change) JW0394 423561 424142 - o conserved protein C Cytoplasmic COG3124;Uncharacterized protein conserved in bacteria "PF04336;Protein of unknown function, DUF479;1.3e-137;codon 19-192" CDS ECK0399 queA queA tsaA b0405 424235 425305 + (no change) JW0395 424235 425305 + e S-adenosylmethionine:tRNA ribosyltransferase-isomerase E 91177815 -!- 93349860 Cytoplasmic -5 COG0809;S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) PF02547;Queuosine biosynthesis protein;3.3e-153;codon 1-217 TIGR00113;queA: S-adenosylmethionine:tRNA ribosyltrans;2.6e-255;codon 1-344 GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK0400 tgt tgt b0406 425361 426488 + (no change) JW0396 425361 426488 + e tRNA-guanine transglycosylase E 11751936 -!- 89155457 -!- 92165719 -!- 9714557 -!- 1706703 -!- 2170107 -!- 7507921 -!- 7893665 -!- 8003468 -!- 8323579 -!- 9055203 Cytoplasmic 2.4.2.29 Zn2+ monomeric multimer; tRNA-guanine transglycosylase (b0406) COG0343;Queuine/archaeosine tRNA-ribosyltransferase 51713; tRNA-guanine transglycosylase PF01702;Queuine tRNA-ribosyltransferase;3.1e-172;codon 125-363 TIGR00430;Q_tRNA_tgt: queuine tRNA-ribosyltransfera;5.1e-298;codon 3-370 -!- TIGR00449;tgt_general: tRNA-guanine transglycosylas;2.5e-188;codon 3-370 GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK0401 yajC yajC b0407 426511 426843 + (no change) JW0397 426511 426843 + t SecYEG protein translocase auxillary subunit E 9305629 -!- 1706703 -!- 2170107 -!- 7507921 -!- 8045893 Membrane Anchored heteromultimer; Sec Protein Secretion Complex (b0098-b0407-b0408-b0409-b3175-b3300-b3609-b3705-b 3981) -!- heteromultimer; SecD-SecF-Yajc-YidC Secretion Complex (b0407-b0408-b0409-b3705) 3.A.5; The General Secretory Pathway (Sec) Family -!- 9.B.18; The SecDF-associated Single Transmembrane Protein (SSTP) Family COG1862;Preprotein translocase subunit YajC PF02699;Preprotein translocase subunit;4e-48;codon 19-102 "TIGR00739;yajC: preprotein translocase, YajC subunit;1.8e-49;codon 19-103" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0402 secD secD b0408 426871 428718 + (no change) JW0398 426871 428718 + t SecYEG protein translocase auxillary subunit E 92210494 -!- 92338228 -!- 94131960 -!- 2170107 -!- 2249673 Integral Membrane Protein heteromultimer; Sec Protein Secretion Complex (b0098-b0407-b0408-b0409-b3175-b3300-b3609-b3705-b 3981) -!- heteromultimer; SecD-SecF-Yajc-YidC Secretion Complex (b0407-b0408-b0409-b3705) 2.A.6; The Resistance-Nodulation-Cell Division (RND) Superfamily -!- 3.A.5; The General Secretory Pathway (Sec) Family 6 6 in COG0342;Preprotein translocase subunit SecD PF07549;SecD/SecF GG Motif;6.3e-05;codon 112-143 -!- PF02355;Protein export membrane protein;2.9e-06;codon 422-603 "TIGR01129;secD: protein-export membrane protein SecD;3e-289;codon 123-601 -!- TIGR00916;2A0604s01: protein-export membrane protein,;1.1e-116;codon 345-594" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0403 secF secF b0409 428729 429700 + (no change) JW0399 428729 429700 + t SecYEG protein translocase auxillary subunit E 92210494 -!- 92338228 -!- 94292431 -!- 2170107 -!- 2249673 Integral Membrane Protein heteromultimer; Sec Protein Secretion Complex (b0098-b0407-b0408-b0409-b3175-b3300-b3609-b3705-b 3981) -!- heteromultimer; SecD-SecF-Yajc-YidC Secretion Complex (b0407-b0408-b0409-b3705) 2.A.6; The Resistance-Nodulation-Cell Division (RND) Superfamily -!- 3.A.5; The General Secretory Pathway (Sec) Family 6 6 in COG0341;Preprotein translocase subunit SecF PF07549;SecD/SecF GG Motif;1.3e-05;codon 40-68 -!- PF02355;Protein export membrane protein;3.8e-95;codon 114-302 "TIGR00966;3a0501s07: protein-export membrane protein;5.8e-144;codon 45-292 -!- TIGR00916;2A0604s01: protein-export membrane protein,;1.6e-78;codon 103-289" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0404 yajD yajD b0410 429829 430176 + (no change) JW0400 429829 430176 + o conserved protein C Cytoplasmic regulated by attenuation (yajD) PF01844;HNH endonuclease;4e-06;codon 25-76 CDS ECK0405 tsx tsx T6rec -!- nupA b0411 430353 431237 - (no change) JW0401 430353 431237 - m "nucleoside channel, receptor of phage T6 and colicin K" E 91092502 -!- 91358319 -!- 93352541 Outer Membrane B-barrel protein 1.B.10; The Nucleoside-specific Channel-forming Outer Membrane Porin (Tsx) Family 1-13 1TLZ COG3248;Nucleoside-binding outer membrane protein PF03502;Nucleoside-specific channel-forming prote;2.3e-121;codon 55-205 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0406 yajI yajI b0412 431536 432075 - start codon change JW5056 431536 432075 - lp predicted lipoprotein C Outer membrane Lipoprotein CDS ECK0407 ybaD ybaD b0413 432226 432675 + (no change) JW0403 432226 432675 + o conserved protein C Cytoplasmic "COG1327;Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains" PF03477;ATP cone domain;2.4e-34;codon 49-139 TIGR00244;TIGR00244: conserved hypothetical protein T;1.2e-79;codon 1-147 CDS ECK0408 ribD ribD ribG -!- ribH -!- nusII -!- ybaE b0414 432679 433782 + (no change) JW0404 432679 433782 + e fused diaminohydroxyphosphoribosylaminopyrimidine deaminase -!- 5-amino-6-(5-phosphoribosylamino) uracil reductase E 9068650 Cytoplasmic 3.5.4.26 -!- 1.1.1.193 NADP fused: diaminohydroxyphosphoribosylaminopyrimidine deaminase (aa 1-143) -!- 5-amino-6-(5-phosphoribosylamino) uracil reductase (aa147-367) "COG0117;Pyrimidine deaminase -!- COG1985;Pyrimidine reductase, riboflavin biosynthesis" 53927; Cytidine deaminase -!- 53927; Cytidine deaminase check -!- 53597; Dihydrofolate reductases PF00383;Cytidine and deoxycytidylate deaminase;1.7e-48;codon 1-100 -!- PF01872;RibD C-terminal domain;1.5e-97;codon 147-362 TIGR00326;eubact_ribD: riboflavin biosynthesis prot;6.6e-289;codon 1-367 -!- TIGR00227;ribD_Cterm: riboflavin-specific deaminase;5.9e-138;codon 145-366 CDS ECK0409 ribE ribE ribH -!- ybaF -!- nusIII b0415 433871 434341 + (no change) JW0405 433871 434341 + e riboflavin synthase beta chain E Cytoplasmic 2.5.1.9 monomeric multimer; lumazine synthase (b0415) COG0054;Riboflavin synthase beta-chain 52121; Lumazine synthase "PF00885;6,7-dimethyl-8-ribityllumazine synthase;1.9e-92;codon 10-154" "TIGR00114;ribH: 6,7-dimethyl-8-ribityllumazine synthas;7.6e-100;codon 1-156" CDS ECK0410 nusB nusB groNB -!- ssaD -!- ssyB b0416 434361 434780 + (no change) JW0406 434361 434780 + f transcription antitermination protein E 91331320 -!- 93024316 -!- 93145327 -!- 99316017 -!- 10881193 -!- 3019094 -!- 6330693 -!- 6330694 -!- 9670024 Cytoplasmic 1EY1 COG0781;Transcription termination factor 48013; Antitermination factor NusB PF01029;NusB family;9.4e-52;codon 7-134 TIGR01951;nusB: transcription antitermination factor N;1.1e-62;codon 6-132 GO:0005737 cytoplasm GO:0006350 transcription CDS ECK0411 thiL thiL thiJ b0417 434858 435835 + (no change) JW0407 434858 435835 + e thiamin-monophosphate kinase E 6284709 Cytoplasmic 2.7.4.16 Mg2+ COG0611;Thiamine monophosphate kinase 55326; Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain "PF02769;AIR synthase related protein, C-terminal dom;4.2e-06;codon 150-305" TIGR01379;thiL: thiamine-monophosphate kinase;1.3e-181;codon 4-322 GO:0009228 thiamin biosynthesis CDS ECK0412 pgpA pgpA yajN b0418 435813 436331 + (no change) JW0408 435813 436331 + e phosphatidylglycerophosphatase A E 89033892 -!- 92104964 Integral Membrane Protein 3.1.3.27 Mg2+ 4 3 out COG1267;Phosphatidylglycerophosphatase A and related proteins 47473; EF-hand PF04608;Phosphatidylglycerophosphatase A;7.3e-97;codon 20-164 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0008654 phospholipid biosynthesis CDS ECK0413 yajO yajO b0419 436385 437359 - start codon change JW0409 436385 437359 - pe "predicted oxidoreductase, NAD(P)-binding" associated with thiamin metabolism C 15292217 Cytoplasmic COG0667;Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) 51430; NAD(P)-linked oxidoreductase PF00248;Aldo/keto reductase family;2.1e-66;codon 31-340 CDS ECK0414 dxs dxs yajP b0420 437539 439401 - (no change) JW0410 437539 439401 - e "1-deoxyxylulose-5-phosphate synthase, thiamine-requiring, FAD-requiring" E 98151473 -!- 10648511 -!- 9371765 2.2.1.7 Mg2+ -!- Mn2+ -!- thiamin diphosphate monomeric multimer; 1-deoxyxylulose-5-phosphate synthase (b0420) COG1154;Deoxyxylulose-5-phosphate synthase 52518; Thiamin diphosphate-binding fold (THDP-binding) -!- 52922; Transketolase C-terminal domain-like "PF02779;Transketolase, pyridine binding domai;6.6e-63;codon 319-483 -!- PF02780;Transketolase, C-terminal domain;8.2e-40;codon 495-611" TIGR00204;dxs: 1-deoxy-D-xylulose-5-phosphate synthase;0;codon 11-620 GO:0008615 pyridoxine biosynthesis -!- GO:0009228 thiamin biosynthesis CDS ECK0415 ispA ispA b0421 439426 440325 - (no change) JW0411 439426 440325 - e geranyltranstransferase E 89291702 -!- 91210228 Cytoplasmic 2.5.1.10 -!- 2.5.1.1 Mg2+ 1RQJ COG0142;Geranylgeranyl pyrophosphate synthase 48576; Terpenoid synthases PF00348;Polyprenyl synthetase;2.9e-137;codon 32-295 GO:0005737 cytoplasm CDS ECK0416 xseB xseB yajE b0422 440325 440567 - (no change) JW0412 440325 440567 - e exonuclease VII small subunit E 21287280 -!- 6284744 -!- 6350262 -!- 2089044 Cytoplasmic 3.1.11.6 COG1722;Exonuclease VII small subunit PF02609;Exonuclease VII small subunit;1.7e-34;codon 9-71 "TIGR01280;xseB: exodeoxyribonuclease VII, small subuni;3.4e-38;codon 7-75" GO:0005737 cytoplasm GO:0006308 DNA catabolism -!- GO:0006281 DNA repair -!- GO:0006308 DNA catabolism CDS ECK0417 thiI thiI nuvC -!- thiJ -!- yajK -!- nuvA -!- yajJ b0423 440773 442221 + (no change) JW0413 440773 442221 + e sulfurtransferase required for thiamine and 4-thiouridine biosynthesis E 20187532 -!- 20206733 -!- 357427 -!- 7007049 Cytoplasmic COG0301;Thiamine biosynthesis ATP pyrophosphatase -!- COG0607;Rhodanese-related sulfurtransferase 52402; Adenine nucleotide alpha hydrolases -!- 52821; Rhodanese/Cell cycle control phosphatase PF02926;THUMP domain;2.9e-28;codon 75-165 -!- PF02568;Thiamine biosynthesis protein (ThiI);1.1e-112;codon 175-369 TIGR00342;TIGR00342: thiamine biosynthesis protein Th;2.4e-233;codon 4-377 GO:0009228 thiamin biosynthesis -!- GO:0009451 RNA modification CDS ECK0418 yajL yajL thiJ b0424 442275 442865 - start codon change JW5057 442275 442865 - d conserved protein C 97039868 -!- 99173753 -!- 99311269 C56 family; non-peptidase homologues (ThiJ protein) 52317; Class I glutamine amidotransferase-like PF01965;DJ-1/PfpI family;1.8e-48;codon 33-175 TIGR01383;not_thiJ: DJ-1 family protein;3.9e-103;codon 6-186 GO:0009102 biotin biosynthesis CDS ECK0419 panE panE apbA b0425 442828 443739 - (no change) JW0415 442828 443739 - e "2-dehydropantoate reductase, NADPH-specific" E 10613889 -!- 20021227 -!- 10736170 -!- 11123955 -!- 11724562 Outer membrane Lipoprotein 1.1.1.169 1KS9 COG1893;Ketopantoate reductase 48179; 6-phosphogluconate dehydrogenase C-terminal domain-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF02558;Ketopantoate reductase PanE/ApbA;4.1e-128;codon 43-290 TIGR00745;apbA_panE: 2-dehydropantoate 2-reductase;7.2e-94;codon 2-292 GO:0006221 pyrimidine nucleotide biosynthesis CDS ECK0420 yajQ yajQ b0426 443907 444398 + start codon change JW5058 443907 444398 + pf predicted nucleotide binding protein C Cytoplasmic regulated by attenuation (yajQ) COG1666;Uncharacterized protein conserved in bacteria PF04461;Protein of unknown function (DUF520);5.3e-119;codon 7-168 CDS ECK0421 yajR yajR b0427 444526 445890 - start codon change JW5059 444526 445890 - pt predicted transporter C Integral Membrane Protein 12 12 in regulated by attenuation (yajR) PF07690;Major Facilitator Superfamily;9.3e-45;codon 19-365 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0422 cyoE cyoE b0428 446039 446929 - (no change) JW0418 446039 446929 - e protoheme IX farnesyltransferase E 90330636 -!- 90366572 -!- 92345252 -!- 9378722 -!- 1336371 -!- 2162835 -!- 8253713 -!- 8262927 Integral Membrane Protein 2.5.1.- Mg2+ 3.D.4; The Proton-translocating Cytochrome Oxidase (COX) Superfamily 9 9 out COG0109;Polyprenyltransferase (cytochrome oxidase assembly factor) PF01040;UbiA prenyltransferase family;1e-86;codon 15-283 TIGR01473;cyoE_ctaB: protoheme IX farnesyltransferase;1.2e-124;codon 4-283 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration CDS ECK0423 cyoD cyoD b0429 446941 447270 - (no change) JW0419 446941 447270 - c cytochrome o ubiquinol oxidase subunit IV E 90330636 -!- 90366572 -!- 92345252 -!- 9378722 -!- 98021084 -!- 11017202 -!- 2162835 Integral Membrane Protein 1.10.3.- heteromultimer; cytochrome bo terminal oxidase (b0429-b0432-b0431-b0430) 3.D.4; The Proton-translocating Cytochrome Oxidase (COX) Superfamily 3 3 out "COG3125;Heme/copper-type cytochrome/quinol oxidase, subunit 4" PF03626;Prokaryotic Cytochrome C oxidase subunit IV;3.9e-53;codon 12-98 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration GO:0009054 electron acceptor activity CDS ECK0424 cyoC cyoC b0430 447270 447884 - (no change) JW0420 447270 447884 - c cytochrome o ubiquinol oxidase subunit III E 90330636 -!- 92345252 -!- 93349845 -!- 9378722 -!- 98021084 -!- 11017202 -!- 2162835 -!- 2168206 Integral Membrane Protein 1.10.3.- heteromultimer; cytochrome bo terminal oxidase (b0429-b0432-b0431-b0430) 3.D.4; The Proton-translocating Cytochrome Oxidase (COX) Superfamily 5 5 out 1FFT "COG1845;Heme/copper-type cytochrome/quinol oxidase, subunit 3" 56869; Membrane all-alpha PF00510;Cytochrome c oxidase subunit III;6.9e-06;codon 1-203 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration GO:0009054 electron acceptor activity CDS ECK0425 cyoB cyoB b0431 447874 449865 - (no change) JW0421 447874 449865 - c cytochrome o ubiquinol oxidase subunit I E 90330636 -!- 92345252 -!- 93349845 -!- 9378722 -!- 98021084 -!- 11017202 -!- 2162835 -!- 2168206 Integral Membrane Protein 1.10.3.- heteromultimer; cytochrome bo terminal oxidase (b0429-b0432-b0431-b0430) 3.D.4; The Proton-translocating Cytochrome Oxidase (COX) Superfamily 14 14 in 1FFT "COG0843;Heme/copper-type cytochrome/quinol oxidases, subunit 1" 56869; Membrane all-alpha PF00115;Cytochrome C and Quinol oxidase polypeptide;4.2e-270;codon 48-505 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration GO:0009054 electron acceptor activity CDS ECK0426 cyoA cyoA b0432 449887 450834 - (no change) JW0422 449887 450834 - c cytochrome o ubiquinol oxidase subunit II E 92112945 -!- 92371427 -!- 9378722 -!- 98021084 -!- 11017202 -!- 1322173 -!- 2162835 -!- 2162837 -!- 2165491 -!- 2168206 -!- 8231804 -!- 8618822 Integral Membrane Protein 1.10.3.- heteromultimer; cytochrome bo terminal oxidase (b0429-b0432-b0431-b0430) 3.D.4; The Proton-translocating Cytochrome Oxidase (COX) Superfamily 3 3 out 1FFT "COG1622;Heme/copper-type cytochrome/quinol oxidases, subunit 2" 49503; Cupredoxins -!- 56869; Membrane all-alpha "PF00116;Cytochrome C oxidase subunit II, periplasmic;4.8e-07;codon 129-225 -!- PF06481;COX Aromatic Rich Motif;8.3e-17;codon 239-286" "TIGR01433;CyoA: ubiquinol oxidase, subunit II;1.5e-200;codon 13-239" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration GO:0009054 electron acceptor activity CDS ECK0427 ampG ampG b0433 451294 452769 - (no change) JW0423 451294 452769 - t muropeptide transporter E 12426329 -!- 94049112 -!- 7773404 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 14 14 in COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;2.1e-30;codon 17-377 TIGR00901;2A0125: AmpG-related permease;2.4e-193;codon 25-363 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0000270 peptidoglycan metabolism CDS ECK0428 yajG yajG b0434 452813 453391 - start codon change JW0424 452813 453391 - lp predicted lipoprotein C Outer membrane Lipoprotein CDS ECK0429 bolA bolA b0435 453696 454013 + start codon change JW5060 453696 454013 + r regulator of penicillin binding proteins and beta lactamase transcription (morphogene) predicted glutaredoxin reductase E 12354237 -!- 90059998 -!- 99291046 -!- 8231804 -!- 15345459 -!- 10361282 -!- 3053647 -!- 2684651 Cytoplasmic BolA PF01722;BolA-like protein;3.8e-41;codon 21-96 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006970 response to osmotic stress CDS ECK0430 tig tig b0436 454357 455655 + (no change) JW0426 454357 455655 + e peptidyl-prolyl cis/trans isomerase (trigger factor) molecular chaperone involved in cell division E 15084258 -!- 15175291 -!- 91008922 -!- 97446330 -!- 99385349 -!- 2197275 -!- 2684651 -!- 2843289 -!- 8521806 -!- 8612805 -!- 9298646 Cytoplasmic COG0544;FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) 54534; FKBP-like PF05697;Bacterial trigger factor protein (TF);1.1e-73;codon 1-151 -!- PF00254;FKBP-type peptidyl-prolyl cis-trans isomera;5.6e-27;codon 152-238 -!- PF05698;Bacterial trigger factor protein (TF) C-ter;6.5e-61;codon 239-408 TIGR00115;tig: trigger factor;1.7e-227;codon 1-430 GO:0005737 cytoplasm GO:0006457 protein folding CDS ECK0431 clpP clpP F21.5 gene -!- LopP -!- lopP -!- wseA b0437 455901 456524 + (no change) JW0427 455901 456524 + e proteolytic subunit of ClpA-ClpP and ClpX-ClpP ATP-dependent serine proteases E 90324245 -!- 90324246 -!- 93015925 -!- 9573050 -!- 9575205 -!- 2211522 -!- 8407953 -!- 8831780 -!- 9390554 3.4.21.92 heteromultimer; ClpAP (b0437-b0882) -!- heteromultimer; ClpAXP (b0437-b0438-b0882) -!- heteromultimer; ClpXP (b0437-b0438) -!- monomeric multimer; ClpP serine protease (b0437) S14 family; endopeptidase Clp (type 1) regulated by attenuation (clpP) 1TYF COG0740;Protease subunit of ATP-dependent Clp proteases 52096; ClpP/crotonase PF00574;Clp protease;1.2e-139;codon 25-206 "TIGR00493;clpP: ATP-dependent Clp protease, proteolyti;3.9e-134;codon 14-205" GO:0005737 cytoplasm GO:0009266 response to temperature GO:0008233 peptidase activity CDS ECK0432 clpX clpX LopC -!- lopC b0438 456650 457924 + (no change) JW0428 456650 457924 + e ATPase and specificity subunit of ClpX-ClpP ATP-dependent serine protease chaperone activity E 12912910 -!- 14525985 -!- 21369885 -!- 94043019 -!- 94043020 -!- 9573050 -!- 9575205 -!- 7743994 Cytoplasmic heteromultimer; ClpAXP (b0437-b0438-b0882) -!- heteromultimer; ClpXP (b0437-b0438) -!- monomeric multimer; ClpX ATP-dependent protease specificity component and chaperone (b0438) "COG1219;ATP-dependent protease Clp, ATPase subunit" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 57903; FYVE/PHD zinc finger PF06689;ClpX C4-type zinc finger;3.1e-26;codon 15-51 -!- PF07724;ATPase family associated with various cell;6.2e-79;codon 110-311 -!- PF00004;ATPase family associated with various cell;1.1e-23;codon 114-373 "TIGR00382;clpX: ATP-dependent Clp protease, ATP-bindin;0;codon 1-412" GO:0005737 cytoplasm GO:0006457 protein folding CDS ECK0433 lon lon capR -!- deg -!- dir -!- muc -!- lopA b0439 458112 460466 + (no change) JW0429 458112 460466 + e DNA-binding ATP-dependent protease La heat shock K-protein E 10094703 -!- 14665623 -!- 8939438 -!- 91072263 -!- 97137085 -!- 2984174 -!- 3042779 -!- 3289547 -!- 7988699 -!- 8226758 -!- 8294008 Cytoplasmic 3.4.21.53 "monomeric multimer; DNA-binding, ATP-dependent protease La (b0439)" S16 family; lon peptidase regulated by attenuation (lon) "COG0466;ATP-dependent Lon protease, bacterial type" 52540; P-loop containing nucleotide triphosphate hydrolases PF02190;ATP-dependent protease La (LON) domain;2.5e-83;codon 10-202 -!- PF00004;ATPase family associated with various cellul;5.6e-42;codon 351-545 -!- PF05362;Lon protease (S16) C-terminal proteolytic do;1.1e-156;codon 569-773 TIGR00763;lon: ATP-dependent protease La;0;codon 12-771 GO:0005737 cytoplasm GO:0008233 peptidase activity CDS ECK0434 hupB hupB dpeA -!- hopD -!- dbhB -!- gsp b0440 460675 460947 + (no change) JW0430 460675 460947 + r "HU, DNA-binding transcriptional regulator, beta subunit" HU-1 E 21150454 -!- 21175605 -!- 91210175 -!- 92380498 -!- 93013008 -!- 9367749 -!- 9683467 -!- 97338083 -!- 215461 -!- 2187099 -!- 2265752 -!- 3003540 -!- 6987059 -!- 9298646 -!- 9868784 Cytoplasmic heteromultimer; HU (b0440-b4000) galETKM -!- micF -!- seqA regulated by attenuation (hupB) COG0776;Bacterial nucleoid DNA-binding protein 47729; IHF-like DNA-binding proteins PF00216;Bacterial DNA-binding protein;2e-47;codon 1-90 GO:0005737 cytoplasm CDS ECK0435 ppiD ppiD ybaU b0441 461139 463010 + (no change) JW0431 461139 463010 + e peptidyl-prolyl cis-trans isomerase (rotamase D) E 9670013 Membrane Anchored 5.2.1.8 regulated by attenuation (ppiD) COG0760;Parvulin-like peptidyl-prolyl isomerase 54534; FKBP-like PF00639;PPIC-type PPIASE domain;2.5e-18;codon 274-355 GO:0006457 protein folding CDS ECK0436 ybaV ybaV b0442 463161 463532 + (no change) JW0432 463161 463532 + d conserved protein C Periplasmic COG1555;DNA uptake protein and related DNA-binding proteins 47781; RuvA domain 2-like PF00633;Helix-hairpin-helix motif;0.26;codon 60-90 -!- PF00633;Helix-hairpin-helix motif;0.92;codon 91-120 TIGR00426;TIGR00426: competence protein ComEA helix-h;1.7e-50;codon 55-123 CDS ECK0437 ybaW ybaW b0443 463626 464024 + (no change) JW0433 463626 464024 + d conserved protein C Cytoplasmic COG0824;Predicted thioesterase 54637; Thioesterase/thiol ester dehydrase-isomerase PF03061;Thioesterase superfamily;3e-13;codon 15-99 TIGR00051;TIGR00051: conserved hypothetical protein;3.5e-59;codon 6-120 CDS ECK0438 ybaX ybaX b0444 464076 464771 - (no change) JW0434 464076 464771 - pr predicted aluminum resistance protein C 9367855 Cytoplasmic COG0603;Predicted PP-loop superfamily ATPase 52402; Adenine nucleotide alpha hydrolases PF06508;ExsB;2.5e-46;codon 69-142 TIGR00364;TIGR00364: exsB protein;6e-140;codon 4-206 GO:0006805 xenobiotic metabolism CDS ECK0439 ybaE ybaE b0445 464836 466536 - (no change) JW0435 464836 466536 - pt predicted transporter subunit: periplasmic-binding component of ABC superfamily C Cytoplasmic "COG4533;ABC-type uncharacterized transport system, periplasmic component" 53850; Periplasmic binding protein-like II PF00496;Bacterial extracellular solute-binding prot;1.5e-23;codon 164-497 GO:0042597 periplasmic space CDS ECK0440 cof cof b0446 466636 467454 + start codon change JW0436 466636 467454 + e thiamin pyrimidine pyrophosphate hydrolase E 15292217 Cytoplasmic COG0561;Predicted hydrolases of the HAD superfamily 56784; HAD-like PF00702;haloacid dehalogenase-like hydrolase;5.8e-13;codon 6-237 "TIGR00099;Cof-subfamily: Cof-like hydrolase;5.3e-87;codon 8-262 -!- TIGR01484;HAD-SF-IIB: HAD-superfamily hydrolase,;9.7e-60;codon 8-233" CDS ECK0441 ybaO ybaO b0447 467607 468065 + start codon change JW0437 467607 468065 + pr predicted DNA-binding transcriptional regulator C 7904973 Cytoplasmic ASNC regulated by attenuation (ybaO-mdlA-mdlB) 46785; Winged helix -!- 69732; Lrp/AsnC-like transcriptional regulator C-terminal domain PF01037;AsnC family;2.7e-55;codon 55-158 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0442 mdlA mdlA mdl b0448 468095 469867 + (no change) JW0438 468095 469867 + pt fused predicted multidrug transporter subunits of ABC superfamily: ATP-binding components C 94124004 Integral Membrane Protein 7 6 in "fused predicted multidrug transport protein, ABC superfamily: membrane component (aa1-310) -!- atp_binding component (aa314-590)" "COG1132;ABC-type multidrug transport system, ATPase and permease components" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00664;ABC transporter transmembrane region;2.9e-64;codon 18-291 -!- PF00005;ABC transporter;3.7e-52;codon 362-546 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0443 mdlB mdlB mdl b0449 469860 471641 + (no change) JW5061 469860 471641 + pt fused predicted multidrug transporter subunits of ABC superfamily: ATP-binding components C 94124004 Integral Membrane Protein 5 4 in "fused predicted multidruge transport protein, ABC superfamily: membrane component (aa1-320) -!- atp_binding component (aa321-593)" "COG1132;ABC-type multidrug transport system, ATPase and permease components" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00664;ABC transporter transmembrane region;1.6e-33;codon 25-298 -!- PF00005;ABC transporter;1.3e-46;codon 367-550 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0444 glnK glnK ybaI b0450 471822 472160 + (no change) JW0440 471822 472160 + r "nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB" E 11847102 -!- 8843440 -!- 9720863 -!- 99248410 -!- 7590157 -!- 7904973 -!- 9733647 Cytoplasmic monomeric multimer; nitrogen regulatory protein GlnK (b0450) 1GNK COG0347;Nitrogen regulatory protein PII 54913; Prokaryotic signal transducing protein PF00543;Nitrogen regulatory protein P-II;9.4e-64;codon 4-105 GO:0006807 nitrogen metabolism CDS ECK0445 amtB amtB ybaG b0451 472190 473476 + (no change) JW0441 472190 473476 + t ammonium transporter E 22020597 -!- 9618533 -!- 10931328 -!- 1645722 -!- 7984428 Integral Membrane Protein 2.A.49; The Ammonium Transporter (Amt) Family 12 12 in COG0004;Ammonia permease PF00909;Ammonium Transporter Family;2.4e-195;codon 33-426 TIGR00836;amt: ammonium transporter;3.3e-218;codon 31-426 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0446 tesB tesB b0452 473525 474385 - (no change) JW0442 473525 474385 - e acyl-CoA thioesterase II E 86139906 -!- 91250410 -!- 10876240 Cytoplasmic 3.1.2.- monomeric multimer; thioesterase II (b0452) 1C8U COG1946;Acyl-CoA thioesterase 54637; Thioesterase/thiol ester dehydrase-isomerase PF02551;Acyl-CoA thioesterase;2e-48;codon 17-115 -!- PF02551;Acyl-CoA thioesterase;7e-80;codon 147-281 TIGR00189;tesB: acyl-CoA thioesterase II;3.2e-111;codon 12-283 CDS ECK0447 ybaY ybaY b0453 474603 475175 + (no change) JW0443 474603 475175 + pm predicted outer membrane lipoprotein glycoprotein/polysaccharide metabolism C Outer membrane Lipoprotein 1-17 GO:0042158 lipoprotein biosynthesis -!- GO:0009101 glycoprotein biosynthesis CDS ECK0448 ybaZ ybaZ b0454 475206 475595 - (no change) JW0444 475206 475595 - pe predicted methyltransferase C Cytoplasmic COG3695;Predicted methylated DNA-protein cysteine methyltransferase "46767; Methylated DNA-protein cysteine methyltransferase, C-terminal domain" PF01035;6-O-methylguanine DNA methyltransferas;2.7e-46;codon 30-115 TIGR00589;ogt: methylated-DNA--protein-cysteine methyl;7.5e-09;codon 33-110 misc_RNA ECK0449 ffs ffs b0455 475672 475785 + (no change) JWR0009 475672 475785 + n 4.5S RNA component of ribonucleoprotein particle E 90040721 -!- 91068003 -!- 92015200 CDS ECK0450 ybaA ybaA b0456 475896 476249 + (no change) JW0445 475896 476249 + o conserved protein C Cytoplasmic PF07237;Protein of unknown function (DUF1428);1.5e-86;codon 2-117 CDS ECK0451 ylaB ylaB b0457 476291 477841 - start codon change JW5062 476291 477841 - pm conserved inner membrane protein C Integral Membrane Protein 3 2 in COG4943;Predicted signal transduction protein containing sensor and EAL domains PF00563;EAL domain;2.6e-106;codon 269-504 CDS ECK0452 ylaC ylaC b0458 478005 478475 - start codon change JW5063 478005 478475 - pm predicted inner membrane protein C Integral Membrane Protein 2 2 in CDS ECK0453 maa maa mac -!- macC -!- ylaD b0459 478591 479142 - (no change) JW0448 478591 479142 - e maltose O-acetyltransferase E 82180540 -!- 91310703 -!- 9600841 Cytoplasmic 2.3.1.79 monomeric multimer; maltose acetyltransferase (b0459) COG0110;Acetyltransferase (isoleucine patch superfamily) 51161; Trimeric LpxA-like enzymes PF00132;Bacterial transferase hexapeptide (three rep;0.039;codon 93-110 -!- PF00132;Bacterial transferase hexapeptide (three rep;0.28;codon 129-146 -!- PF00132;Bacterial transferase hexapeptide (three rep;0.088;codon 147-164 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK0454 hha hha b0460 479314 479532 - (no change) JW0449 479314 479532 - f "modulator of gene expression, with H-NS" E 10322001 -!- 20239026 -!- 92065825 -!- 98193934 -!- 1484495 -!- 8145648 Cytoplasmic 1JW2 68989; Hemolysin expression modulating protein HHA PF05321;Haemolysin expression modulating protein;1.3e-37;codon 13-69 GO:0006350 transcription CDS ECK0455 ybaJ ybaJ b0461 479558 479932 - (no change) JW0450 479558 479932 - o predicted protein C 1956303 -!- 7984428 Cytoplasmic CDS ECK0456 acrB acrB acrE b0462 480478 483627 - (no change) JW0451 480478 483627 - t multidrug efflux system protein E 12351840 -!- 12654283 -!- 15111118 -!- 15155734 -!- 21450803 -!- 94012493 -!- 10920254 -!- 7651136 Integral Membrane Protein heteromultimer; AcrAB-MDR-CPLX (b0462-b0463-b3035) 2.A.6; The Resistance-Nodulation-Cell Division (RND) Superfamily 12 11 in COG0841;Cation/multidrug efflux pump PF00873;AcrB/AcrD/AcrF family;0;codon 1-1030 TIGR00915;2A0602: Hydrophobe/Amphiphile Efflux-1 (HAE1;0;codon 1-1049 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0457 acrA acrA Mb -!- lir -!- mbl -!- mtcA -!- sipB -!- nbsA b0463 483650 484843 - (no change) JW0452 483650 484843 - t multidrug efflux system E 15155734 -!- 21450803 -!- 383699 -!- 390095 -!- 94012493 -!- 10920254 -!- 7651136 Inner membrane Lipoprotein heteromultimer; AcrAB-MDR-CPLX (b0462-b0463-b3035) 8.A.1; The Membrane Fusion Protein (MFP) Family regulated by attenuation (acrA-acrB) COG0845;Membrane-fusion protein 51230; Single hybrid motif PF00529;HlyD family secretion protein;5.7e-95;codon 64-361 "TIGR01730;RND_mfp: efflux transporter, RND family, MFP;2.2e-82;codon 40-376" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0458 acrR acrR ybaH b0464 484985 485632 + (no change) JW0453 484985 485632 + r DNA-binding transcriptional repressor E 96419167 -!- 8407802 -!- 8821940 Cytoplasmic TetR/AcrR acrAB regulated by attenuation (acrR) COG1309;Transcriptional regulator 46689; Homeodomain-like "PF00440;Bacterial regulatory proteins, tetR family;2e-22;codon 16-62" GO:0005737 cytoplasm GO:0006350 transcription -!- GO:0042493 response to drug GO:0016564 transcriptional repressor activity CDS ECK0459 kefA kefA aefA -!- mscK b0465 485760 489122 + (no change) JW0454 485760 489122 + t fused conserved protein -!- mechanosensitive channel protein E 10202137 Outer membrane Lipoprotein 1.A.23; The Small Conductance Mechanosensitive Ion Channel (MscS) Family in fused: conserved protein (1-779) -!- mechanosensitive channel protein (aa780-1120) COG3264;Small-conductance mechanosensitive channel PF00924;Mechanosensitive ion channel;2.3e-85;codon 887-1087 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0460 ybaM ybaM b0466 489334 489495 - (no change) JW0455 489334 489495 - o predicted protein C Cytoplasmic CDS ECK0461 priC priC b0467 489509 490036 - (no change) JW0456 489509 490036 - f primosomal replication protein N'' E 91310687 -!- 93374896 Cytoplasmic COG3923;Primosomal replication protein N'' PF07445;Primosomal replication protein priB and pri;3.4e-103;codon 7-175 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK0462 ybaN ybaN b0468 490106 490483 + (no change) JW0457 490106 490483 + pm conserved inner membrane protein C Integral Membrane Protein 4 4 in COG2832;Uncharacterized protein conserved in bacteria PF04304;Protein of unknown function (DUF454);1.5e-38;codon 43-119 CDS ECK0463 apt apt b0469 490636 491187 + (no change) JW0458 490636 491187 + e adenine phosphoribosyltransferase E 397764 -!- 6787390 -!- 6801015 -!- 3527873 -!- 3534795 -!- 9573169 2.4.2.7 Mg2+ monomeric multimer; adenine phosphoribosyltransferase (b0469) COG0503;Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins 53271; PRTase-like PF00156;Phosphoribosyl transferase domain;4e-52;codon 30-166 TIGR01090;apt: adenine phosphoribosyltransferase;1e-118;codon 11-180 GO:0005737 cytoplasm "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0464 dnaX dnaX dnaZ -!- mutH b0470 491316 493247 + (no change) JW0459 491316 493247 + e "DNA polymerase III/DNA elongation factor III, tau and gamma subunits" two transcripts from one gene E 90036845 -!- 92011792 -!- 92156151 Cytoplasmic 2.7.7.7 "COG2812;DNA polymerase III, gamma/tau subunits" "48019; DNA polymerase III clamp loader subunits, C-terminal domain -!- 52540; P-loop containing nucleotide triphosphate hydrolases" PF00004;ATPase family associated with various cellul;1.5e-10;codon 40-230 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK0465 ybaB ybaB b0471 493300 493629 + (no change) JW0460 493300 493629 + o conserved protein C 15322138 -!- 1698765 -!- 2674903 -!- 3534795 Cytoplasmic COG0718;Uncharacterized protein conserved in bacteria "PF02575;Uncharacterised BCR, YbaB family COG0718;7.8e-53;codon 11-102" TIGR00103;TIGR00103: conserved hypothetical protein T;2.7e-61;codon 1-105 CDS ECK0466 recR recR b0472 493629 494234 + (no change) JW0461 493629 494234 + cp gap repair protein component of RecFOR complex that targets RecA to ssDNA-dsDNA junction E 11743007 -!- 12769856 -!- 89313692 -!- 95166174 -!- 95166183 -!- 98196719 -!- 1698765 -!- 2674903 Cytoplasmic heteromultimer; recfor-cplx (b0472-b2565-b3700) COG0353;Recombinational DNA repair protein (RecF pathway) 56712; Prokaryotic type I DNA topoisomerase PF02132;RecR protein;3.2e-22;codon 38-79 -!- PF01751;Toprim domain;5.7e-24;codon 81-174 TIGR00615;recR: recombination protein RecR;4.8e-137;codon 1-197 GO:0005737 cytoplasm GO:0006281 DNA repair -!- GO:0006310 DNA recombination CDS ECK0467 htpG htpG b0473 494344 496218 + (no change) JW0462 494344 496218 + f molecular chaperone HSP90 family heat shock protein C62.5 E 21134381 -!- 89174688 -!- 91174616 -!- 11606187 -!- 3299380 -!- 8419347 -!- 9298646 Cytoplasmic "monomeric multimer; chaperone HtpG, heat shock protein (b0473)" "COG0326;Molecular chaperone, HSP90 family" 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;1e-17;codon 27-183 -!- PF00183;Hsp90 protein;2.3e-85;codon 186-624" GO:0006457 protein folding CDS ECK0468 adk adk dnaW -!- plsA b0474 496399 497043 + (no change) JW0463 496399 497043 + e adenylate kinase E 89000670 -!- 92084653 -!- 93156056 -!- 99421681 -!- 1548697 -!- 2051480 -!- 2223776 -!- 2997739 -!- 3299380 -!- 8451239 -!- 9298646 -!- 9600841 Cytoplasmic 2.7.4.3 Mg2+ regulated by attenuation (adk) 1AKE COG0563;Adenylate kinase and related kinases "52540; P-loop containing nucleotide triphosphate hydrolases -!- 57774; Microbial and mitochondrial ADK, insert zinc finger domain" "PF00406;Adenylate kinase;7.6e-97;codon 5-187 -!- PF05191;Adenylate kinase, active site lid;1.7e-21;codon 123-158" TIGR01351;adk: adenylate kinases;3.3e-117;codon 2-214 GO:0005737 cytoplasm "GO:0015949 nucleobase, nucleoside and nucleotide interconversion -!- GO:0009152 purine ribonucleotide biosynthesis" CDS ECK0469 hemH hemH popA -!- visA b0475 497279 498241 + (no change) JW0464 497279 498241 + e ferrochelatase E 93011927 -!- 93209964 -!- 2051480 -!- 8056770 Cytoplasmic 4.99.1.1 COG0276;Protoheme ferro-lyase (ferrochelatase) 53800; Chelatase PF00762;Ferrochelatase;2.2e-171;codon 5-320 TIGR00109;hemH: ferrochelatase;3.7e-210;codon 1-320 CDS ECK0470 aes aes ybaC b0476 498238 499197 - (no change) JW0465 498238 499197 - e acetyl esterase regulator of MalT activity E 9401025 -!- 98244813 -!- 2051480 -!- 7721718 3.1.1.- S9C family; unassigned peptidases (acetyl esterase) COG0657;Esterase/lipase 53474; alpha/beta-Hydrolases PF07859;alpha/beta hydrolase fold;8.6e-71;codon 87-296 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK0471 gsk gsk b0477 499349 500653 + (no change) JW0466 499349 500653 + e inosine/guanosine kinase E 90155203 -!- 95238302 -!- 2051480 Cytoplasmic 2.7.1.73 Mg2+ monomeric multimer; guanosine kinase / inosine kinase (b0477) "COG0524;Sugar kinases, ribokinase family" 53613; Ribokinase-like PF00294;pfkB family carbohydrate kinase;1.2e-22;codon 54-423 "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0472 ybaL ybaL ylaA b0478 500786 502462 - (no change) JW0467 500786 502462 - pt predicted transporter with NAD(P)-binding Rossmann-fold domain C Integral Membrane Protein 13 12 in "COG4651;Kef-type K+ transport system, predicted NAD-binding component -!- COG1226;Kef-type K+ transport systems, predicted NAD-binding component" 51735; NAD(P)-binding Rossmann-fold domains PF02254;TrkA-N domain;2.3e-39;codon 419-535 TIGR00932;2a37: potassium efflux system protein;5.7e-112;codon 15-294 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0473 fsr fsr b0479 502700 503920 - (no change) JW0468 502700 503920 - pt predicted fosmidomycin efflux system C 21450803 -!- 97074653 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 10 in COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;2.7e-39;codon 30-375 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0474 ushA ushA b0480 504138 505790 + (no change) JW0469 504138 505790 + e bifunctional UDP-sugar hydrolase and 5'-nucleotidase E 11802543 -!- 86232561 -!- 88268957 -!- 10331872 -!- 9298646 -!- 3012467 Periplasmic 3.6.1.45 Co2+ 1-25 550 2USH "COG0737;5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases" "55816; 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain -!- 56300; Metallo-dependent phosphatases" "PF00149;Calcineurin-like phosphoesterase;4.8e-19;codon 34-256 -!- PF02872;5'-nucleotidase, C-terminal domain;1.6e-56;codon 363-511" GO:0005737 cytoplasm GO:0009226 nucleotide-sugar biosynthesis CDS ECK0475 ybaK ybaK b0481 505827 506306 - (no change) JW0470 505827 506306 - d conserved protein C Cytoplasmic COG2606;Uncharacterized conserved protein 55826; Hypothetical protein HI1434 (YbaK homologue) PF04073;YbaK / prolyl-tRNA synthetases associated do;9.6e-80;codon 10-155 TIGR00011;YbaK_EbsC: ybaK/ebsC protein;7.4e-83;codon 2-156 CDS ECK0476 ybaP ybaP b0482 506510 507304 - (no change) JW0471 506510 507304 - o conserved protein C Cytoplasmic COG3735;Uncharacterized protein conserved in bacteria PF07446;GumN protein;4.6e-09;codon 30-264 CDS ECK0477 ybaQ ybaQ b0483 507442 507783 + start codon change JW0472 507442 507783 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic Unclass 47413; lambda repressor-like DNA-binding domains PF01381;Helix-turn-helix;6e-11;codon 34-88 CDS ECK0478 copA copA ybaR b0484 508099 510603 - (no change) JW0473 508099 510603 - t copper transporter E 12351646 -!- 20105527 -!- 11167016 -!- 11500054 -!- 9868784 Integral Membrane Protein 3.6.3.4 3.A.3; The P-type ATPase (P-ATPase) Superfamily 8 8 in COG2217;Cation transport ATPase 55008; Metal-binding domain -!- 56869; Membrane all-alpha PF00403;Heavy-metal-associated domain;6.5e-11;codon 6-65 -!- PF00403;Heavy-metal-associated domain;1.2e-16;codon 102-163 -!- PF00122;E1-E2 ATPase;1.2e-95;codon 291-513 -!- PF00702;haloacid dehalogenase-like hydrolase;1.7e-40;codon 517-741 "TIGR01511;copper-translocating P-type ATPase;1.5e-296;233-828 -!- TIGR01525; heavy metal translocating P-type ATPase;5.5e-235;252-827 -!- TIGR01494;ATPase, P-type (transporting);5.1e-41;291-541 -!- TIGR01494;ATPase, P-type (transporting);7.2e-49;616-807" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane "GO:0015662 ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism" CDS ECK0479 ybaS ybaS b0485 510865 511797 + (no change) JW0474 510865 511797 + pe predicted glutaminase C 12952533 Cytoplasmic COG2066;Glutaminase 56601; beta-Lactamase/D-ala carboxypeptidase PF04960;Glutaminase;3.8e-175;codon 24-308 GO:0009063 amino acid catabolism CDS ECK0480 ybaT ybaT b0486 511800 513092 + (no change) JW0475 511800 513092 + pt predicted transporter C Integral Membrane Protein 12 12 in COG0531;Amino acid transporters PF00324;Amino acid permease;4.5e-07;codon 17-430 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009063 amino acid catabolism CDS ECK0481 cueR cueR ybbI b0487 513217 513624 + (no change) JW0476 513217 513624 + r DNA-binding transcriptional activator of copper-responsive regulon genes E 21065101 -!- 10915804 -!- 11399769 -!- 12958362 Cytoplasmic MerR copA -!- cueO 1Q07 COG0789;Predicted transcriptional regulators 46955; Putative DNA-binding domain PF00376;MerR family regulatory protein;6.3e-13;codon 2-39 TIGR02044;CueR: Cu(I)-responsive transcriptional regul;3.7e-95;codon 1-127 GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK0482 ybbJ ybbJ b0488 513625 514080 - (no change) JW5065 513625 514080 - pm conserved inner membrane protein C Integral Membrane Protein 2 3 in COG1585;Membrane protein implicated in regulation of membrane protease activity PF01957;Nodulation efficiency protein D (NfeD);2.9e-40;codon 11-150 CDS ECK0483 ybbK ybbK b0489 514080 514997 - (no change) JW0478 514080 514997 - pe "predicted protease, membrane anchored" C Membrane Anchored "COG0330;Membrane protease subunits, stomatin/prohibitin homologs" PF01145;SPFH domain / Band;7.6e-75;codon 20-193 GO:0009274 cell wall (sensu Bacteria) CDS ECK0484 ybbL ybbL b0490 515143 515820 + (no change) JW0479 515143 515820 + pt predicted transporter subunit: ATP-binding component of ABC superfamily C Cytoplasmic "COG4619;ABC-type uncharacterized transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;5.3e-49;codon 33-213 GO:0005737 cytoplasm CDS ECK0485 ybbM ybbM b0491 515807 516586 + start codon change JW5066 515807 516586 + pm predicted inner membrane protein C Integral Membrane Protein 9.B.25; The YbbM (YbbM) Family 7 7 in PF03649;Uncharacterised protein family (UPF0014);5.1e-180;codon 11-256 TIGR00245;TIGR00245: conserved hypothetical protein T;1.8e-115;codon 15-260 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0486 ybbN ybbN b0492 516649 517503 - start codon change JW5067 516649 517503 - pc predicted thioredoxin domain-containing protein C Cytoplasmic 48439; Protein prenylyltransferase -!- 52833; Thioredoxin-like PF00085;Thioredoxin;5.8e-18;codon 17-123 CDS ECK0487 ybbO ybbO b0493 517564 518373 - (no change) JW0482 517564 518373 - pe predicted oxidoreductase with NAD(P)-binding Rossmann-fold domain C Cytoplasmic COG1028;Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) 51735; NAD(P)-binding Rossmann-fold domains PF00106;short chain dehydrogenase;3.1e-36;codon 18-240 CDS ECK0488 tesA tesA apeA -!- pldC b0494 518363 518989 - (no change) JW0483 518363 518989 - e multifunctional acyl-CoA thioesterase I and protease I and lysophospholipase L1 E 91270121 -!- 91324311 -!- 93163029 -!- 93252782 -!- 94179121 -!- 99353977 -!- 1864840 -!- 8432696 -!- 8098033 3.1.2.- -!- 3.1.1.5 1-26 208 1IVN COG2755;Lysophospholipase L1 and related esterases 52266; Esterase/acetylhydrolase PF00657;GDSL-like Lipase/Acylhydrolase;3.4e-37;codon 30-196 GO:0042597 periplasmic space CDS ECK0489 ybbA ybbA b0495 518957 519643 + (no change) JW0484 518957 519643 + pt predicted transporter subunit: ATP-binding component of ABC superfamily C Cytoplasmic heteromultimer; YbbA/YbbP ABC transporter (b0496-b0495) "COG4181;Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;3e-60;codon 36-222 GO:0005737 cytoplasm CDS ECK0490 ybbP ybbP b0496 519640 522054 + (no change) JW0485 519640 522054 + pm predicted inner membrane protein C Integral Membrane Protein heteromultimer; YbbA/YbbP ABC transporter (b0496-b0495) 10 10 "COG3127;Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component" PF02687;Predicted permease;1.9e-12;codon 171-364 -!- PF02687;Predicted permease;1.3e-08;codon 580-798 CDS ECK0491 rhsD rhsD b0497 522485 526765 + (no change) JW0486 522485 526765 + h rhsD element protein C 98361897 -!- 1766878 -!- 2403547 -!- 2644231 -!- 7934896 Cytoplasmic COG3209;Rhs family protein 56935; Porins PF05593;RHS Repeat;0.0016;codon 320-360 -!- PF05593;RHS Repeat;0.71;codon 365-401 -!- PF05593;RHS Repeat;5.8e-07;codon 429-467 -!- PF05593;RHS Repeat;2.6e-06;codon 472-509 -!- PF05593;RHS Repeat;9.8e-06;codon 558-595 -!- PF05593;RHS Repeat;5.1e-05;codon 600-636 -!- PF05593;RHS Repeat;7.9e-05;codon 641-678 -!- PF05593;RHS Repeat;0.026;codon 683-719 -!- PF05593;RHS Repeat;0.00033;codon 724-766 -!- PF05593;RHS Repeat;0.012;codon 870-901 -!- PF05593;RHS Repeat;1.5;codon 950-999 -!- PF03527;RHS protein;3.8e-31;codon 1148-1194 8 of TIGR01643;YD repeat (two copies):0.018;365-406 -!- 0.00038;408-449 -!- 0.023;451-492 -!- 0.0018;493-533 -!- 0.00018;537-577 -!- 9.1e-09;579-620 -!- 7.8e-06;641-682 -!- 0.011;683-723 CDS ECK0492 ybbC ybbC b0498 526805 527173 + (no change) JW0487 526805 527173 + o predicted protein C Outer membrane Lipoprotein CDS ECK0493 ylbH ylbH b0499 527173 527883 + (no change) JW0488 527173 527883 + h "conserved protein, rhs-like" C 1766878 -!- 7934896 Cytoplasmic COG3209;Rhs family protein PF03527;RHS protein;1.1e-05;codon 2-30 CDS ECK0494 ybbD ybbD b0500 527864 528124 + (no change) JW0489 527864 528124 + o predicted protein C Membrane Anchored CDS ECK0495 ylbG ylbG b0502 528869 529240 - start codon change JW5880 528869 529240 - "This ORF is transposase remnant, can be fused with new ORF: complement(528819..528881) on MG, complement(528483..528545) on W, which has no stop & initiation" pr predicted DNA-binding transcriptional regulator C Cytoplasmic Unclass 46689; Homeodomain-like CDS ECK0496 ybbB ybbB b0503 529356 530450 - (no change) JW0491 529356 530450 - e "tRNA 2-selenouridine synthase, selenophosphate-dependent" replaces sulfur of 2-thiouridine in tRNA with selenium -!- required for 5-methylaminomethyl-2-selenouridine synthesis E 14594807 -!- 1766878 Cytoplasmic COG2603;Predicted ATPase 52821; Rhodanese/Cell cycle control phosphatase CDS ECK0497 ybbS ybbS glxA1 -!- allS b0504 530519 531445 - (no change) JW0492 530519 531445 - pr DNA-binding transcriptional activator of the allD operon C 12460564 -!- 10601204 Cytoplasmic LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;3.6e-18;codon 4-63 -!- PF03466;LysR substrate binding domain;1.4e-19;codon 87-294 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0498 allA allA glxA2 -!- ybbT b0505 531675 532157 + (no change) JW0493 531675 532157 + e ureidoglycolate hydrolase utilization of allantoin E 20069628 Cytoplasmic 3.5.3.19 COG3194;Ureidoglycolate hydrolase PF04115;Ureidoglycolate hydrolase;2.6e-105;codon 1-160 GO:0006807 nitrogen metabolism -!- GO:0009442 allantoin assimilation CDS ECK0499 allR allR gclR -!- glxA3 -!- ybbU b0506 532235 533050 + (no change) JW0494 532235 533050 + r DNA-binding transcriptional repressor repressor for allantoin and glyoxylate utilization operons E 12460564 -!- 20069628 IclR COG1414;Transcriptional regulator 46785; Winged helix PF01614;Bacterial transcriptional regulator;1.3e-86;codon 79-264 GO:0005737 cytoplasm GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK0500 gcl gcl b0507 533140 534921 + (no change) JW0495 533140 534921 + e glyoxylate carboligase E 93179387 -!- 14257608 4.1.1.47 monomeric multimer; glyoxylate carboligase (b0507) regulated by attenuation (gcl-hyi) COG3960;Glyoxylate carboligase 52467; DHS-like NAD/FAD-binding domain -!- 52518; Thiamin diphosphate-binding fold (THDP-binding) "PF02776;Thiamine pyrophosphate enzyme, N-termina;5.3e-55;codon 4-175 -!- PF00205;Thiamine pyrophosphate enzyme, central d;3.3e-37;codon 192-352" TIGR01504;glyox_carbo_lig: glyoxylate carboliga;0;codon 2-590 GO:0009441 glycolate metabolism -!- GO:0009442 allantoin assimilation CDS ECK0501 hyi hyi gip -!- ybbG b0508 534934 535710 + (no change) JW0496 534934 535710 + e hydroxypyruvate isomerase E 20029625 -!- 8440684 Cytoplasmic 5.3.1.22 monomeric multimer; hydroxypyruvate isomerase (b0508) COG3622;Hydroxypyruvate isomerase 51658; Xylose isomerase-like PF01261;Xylose isomerase-like TIM barrel;1.6e-50;codon 21-219 GO:0005737 cytoplasm CDS ECK0502 glxR glxR ybbQ -!- glxB1 b0509 535810 536688 + (no change) JW0497 535810 536688 + e "tartronate semialdehyde reductase, NADH-dependent" E 20069628 Cytoplasmic 1.1.1.60 COG2084;3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases 51735; NAD(P)-binding Rossmann-fold domains PF03446;NAD binding domain of 6-phosphogluconat;7.4e-07;codon 2-161 TIGR01505;tartro_sem_red: 2-hydroxy-3-oxopropion;3.8e-233;codon 2-291 GO:0016052 carbohydrate catabolism -!- GO:0009441 glycolate metabolism -!- GO:0009442 allantoin assimilation CDS ECK0503 ybbV ybbV b0510 536720 536998 + (no change) JW0498 536720 536998 + o predicted protein C CDS ECK0504 ybbW ybbW glxB2 -!- ybbW -!- allP b0511 536857 538311 + start codon change JW0499 536857 538311 + pt predicted allantoin transporter C Integral Membrane Protein 12 12 in PF02133;Transp_cyt_pur: Permease for cytosine/purin;2e-186;codon 19-457 TIGR00800;ncs1: NCS1 nucleoside transporter family;2e-194;codon 14-457 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0505 allB allB glxB3 -!- ybbX b0512 538371 539732 + (no change) JW0500 538371 539732 + e allantoinase utilization of allantoin E 20069628 -!- 20545448 Cytoplasmic 3.5.2.5 Co2+ monomeric multimer; allantoinase (b0512) M38 family; non-peptidase homologues (allantoinase) COG0044;Dihydroorotase and related cyclic amidohydrolases 51556; Metallo-dependent hydrolases PF01979;Amidohydrolase family;5.5e-10;codon 50-392 GO:0006807 nitrogen metabolism -!- GO:0009442 allantoin assimilation CDS ECK0506 ybbY ybbY glxB4 b0513 539789 541090 + start codon change JW0501 539789 541090 + pt predicted uracil/xanthine transporter C Integral Membrane Protein 13 12 in PF00860;Permease family;3.2e-129;codon 10-398 CDS ECK0507 glxK glxK ybbZ -!- glxB5 b0514 541112 542257 + (no change) JW0502 541112 542257 + e glycerate kinase II E 20069628 Cytoplasmic 2.7.1.31 Mg2+ COG1929;Glycerate kinase PF02595;Glycerate kinase family;2.9e-285;codon 1-378 TIGR00045;TIGR00045: glycerate kinase;6.4e-223;codon 2-376 GO:0016052 carbohydrate catabolism -!- GO:0009441 glycolate metabolism -!- GO:0009442 allantoin assimilation CDS ECK0508 ylbA ylbA glxB6 b0515 542485 543270 - (no change) JW0503 542485 543270 - d conserved protein C Cytoplasmic "COG3257;Uncharacterized protein, possibly involved in glyoxylate utilization" 51182; RmlC-like PF05899;Protein of unknown function (DUF861);3.1e-17;codon 55-136 -!- PF07883;Cupin domain;0.00015;codon 182-253 CDS ECK0509 allC allC ylbB -!- glxB7 b0516 543281 544516 - (no change) JW0504 543281 544516 - e allantoate amidohydrolase utilization of allantoin E 20069628 Cytoplasmic 3.5.3.4 M20B family; non-peptidase homologues (allantoate amidohydrolase) COG0624;Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases "53187; Zn-dependent exopeptidases -!- 55031; Carboxypeptidase G2, dimerisation domain" PF01546;Peptidase family M20/M25/M40;3.1e-33;codon 77-406 -!- PF07687;Peptidase dimerisation domain;0.004;codon 208-314 "TIGR01879;hydantase: amidase, hydantoinase/carbamoyla;4.3e-301;codon 7-407" GO:0006807 nitrogen metabolism -!- GO:0009442 allantoin assimilation CDS ECK0510 allD allD glxB8 -!- yibC -!- ylbC b0517 544538 545587 - (no change) JW0505 544538 545587 - e ureidoglycolate dehydrogenase utilization of allantoin E 12460564 -!- 20069628 -!- 69151449 1.1.1.154 regulated by attenuation (allD-allC-ylbA) COG2055;Malate/L-lactate dehydrogenases PF02615;Malate/L-lactate dehydrogenase;9.8e-215;codon 1-334 GO:0006807 nitrogen metabolism -!- GO:0009442 allantoin assimilation CDS ECK0511 fdrA fdrA ylbD b0518 545904 547571 + (no change) JW0506 545904 547571 + pe predicted acyl-CoA synthetase with NAD(P)-binding Rossmann-fold domain multicopy suppressor of dominant negative ftsH mutants C 96086937 -!- 3309887 Cytoplasmic "COG0074;Succinyl-CoA synthetase, alpha subunit" 51735; NAD(P)-binding Rossmann-fold domains PF06263;Bacterial FdrA protein;0;codon 1-555 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane ECK0512 ylbE ylbE b4572 547581 548839 + pseudogene; interrupted by frameshift JW0508+JW0507 547581 548839 + ancestral gene su predicted protein (pseudogene) C CDS ECK0512 ylbE ylbE_1 b4507 547581 547841 + pseudogene fragment -!- new JW0507 547581 547841 + pseudogene su "predicted protein, N-ter fragment (pseudogene)" C CDS ECK0512 ylbE ylbE_2 b0519 547838 548839 + pseudogene fragment -!- (no change) JW0508 547838 548839 + pseudogene su "predicted protein, C-ter fragment (pseudogene)" C Cytoplasmic PF06545;Protein of unknown function (DUF1116);3.4e-247;codon 1-332 CDS ECK0513 ylbF ylbF b0520 548850 549665 + (no change) JW0509 548850 549665 + o conserved protein C Cytoplasmic CDS ECK0514 ybcF ybcF arcC b0521 549662 550555 + (no change) JW0510 549662 550555 + pe predicted carbamate kinase C 2464576 -!- 2644189 -!- 7920643 -!- 7940673 -!- 7984428 Cytoplasmic COG0549;Carbamate kinase 53633; Carbamate kinase-like PF00696;Amino acid kinase family;7.9e-88;codon 2-279 TIGR00746;arcC: carbamate kinase;2e-202;codon 2-297 GO:0006526 arginine biosynthesis -!- GO:0006221 pyrimidine nucleotide biosynthesis CDS ECK0515 purK purK purE2 b0522 550750 551817 - (no change) JW0511 550750 551817 - e N5-carboxyaminoimidazole ribonucleotide synthase E 10074353 -!- 8117684 -!- 89123018 -!- 89123019 -!- 92287929 -!- 10569930 Cytoplasmic 4.1.1.21 monomeric multimer; N5-carboxyaminoimidazole ribonucleotide synthase (b0522) 1B6S COG0026;Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) 51246; Rudiment single hybrid motif -!- 52440; Biotin carboxylase N-terminal domain-like -!- 56059; Glutathione synthetase ATP-binding domain-like PF02222;ATP-grasp domain;2.6e-28;codon 30-167 TIGR01161;purK: phosphoribosylaminoimidazole carboxyla;3.9e-197;codon 3-331 GO:0005737 cytoplasm GO:0006164 purine nucleotide biosynthesis CDS ECK0516 purE purE Pur2 -!- ade3 -!- adef -!- ade(f) b0523 551814 552323 - (no change) JW0512 551814 552323 - e N5-carboxyaminoimidazole ribonucleotide mutase E 10074353 -!- 8117684 -!- 89123018 -!- 89123019 -!- 92287929 -!- 10574791 4.1.1.21 monomeric multimer; N5-carboxyaminoimidazole ribonucleotide mutase (b0523) COG0041;Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase 52255; N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) mutase PurE PF00731;AIR carboxylase;7e-109;codon 8-166 TIGR01162;purE: phosphoribosylaminoimidazole carboxyla;1.4e-104;codon 10-167 GO:0005737 cytoplasm GO:0006164 purine nucleotide biosynthesis CDS ECK0517 lpxH lpxH ybbF b0524 552441 553163 - (no change) JW0513 552441 553163 - e "UDP-2,3-diacylglucosamine pyrophosphatase" E "12000770 -!- 12000771 -!- Babinski KJ, Raetz CRH;FASEB J;1998;12:L63 (Abstr. A1288)" Cytoplasmic 3.6.1.- COG2908;Uncharacterized protein conserved in bacteria 56300; Metallo-dependent phosphatases PF00149;Calcineurin-like phosphoesterase;1.7e-14;codon 1-199 "TIGR01854;lipid_A_lpxH: UDP-2,3-diacylglucosamine;2.1e-187;codon 3-233" GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) GO:0009245 lipid A biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0518 ppiB ppiB b0525 553166 553660 - (no change) JW0514 553166 553660 - e peptidyl-prolyl cis-trans isomerase B (rotamase B) E 90272647 -!- 91175755 -!- 1606970 -!- 1864365 -!- 8601841 -!- 9298646 -!- 9600841 Cytoplasmic 5.2.1.8 2NUL COG0652;Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family 50891; Cyclophilin (peptidylprolyl isomerase) PF00160;Cyclophilin type peptidyl-prolyl cis-tr;2.6e-55;codon 1-163 GO:0005737 cytoplasm GO:0006457 protein folding CDS ECK0519 cysS cysS syc b0526 553834 555219 + (no change) JW0515 553834 555219 + e cysteinyl-tRNA synthetase E 92218368 -!- 93332950 -!- 94218236 -!- 10216301 -!- 12032090 -!- 1864365 -!- 1992490 -!- 2014166 Cytoplasmic 6.1.1.16 COG0215;Cysteinyl-tRNA synthetase 52374; Nucleotidylyl transferase PF01406;tRNA synthetases class I (C) catalytic d;4.9e-226;codon 14-314 TIGR00435;cysS: cysteinyl-tRNA synthetase;0;codon 2-461 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK0520 ybcI ybcI b0527 555255 555776 - (no change) JW0516 555255 555776 - pm conserved inner membrane protein C Integral Membrane Protein 4 4 in regulated by attenuation (ybcI) COG1988;Predicted membrane-bound metal-dependent hydrolases PF04307;Predicted membrane-bound metal-dependent hyd;1.8e-34;codon 33-122 CDS ECK0521 ybcJ ybcJ b0528 555884 556096 - start codon change JW5070 555884 556096 - pr predicted RNA-binding protein C 12837795 -!- 1748668 -!- 7567469 Cytoplasmic 1P9K COG2501;Uncharacterized conserved protein 55174; Alpha-L RNA-binding motif CDS ECK0522 folD folD ads b0529 556098 556964 - (no change) JW0518 556098 556964 - e "bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase and 5,10-methylene-tetrahydrofolate cyclohydrolase" E 92084696 Cytoplasmic 1.5.1.5 -!- 3.5.4.9 monomeric multimer; methyleneTHF enzyme / methenyltetrahydrofolate cyclohydrolase / methylenetetrahydrofolate dehydrogenase-(NADP+) (b0529) 1B0A "COG0190;5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase" "51735; NAD(P)-binding Rossmann-fold domains -!- 53223; Aminoacid dehydrogenase-like, N-terminal domain" PF00763;Tetrahydrofolate dehydrogenase/cyclohyd;1.1e-71;codon 4-121 -!- PF02882;Tetrahydrofolate dehydrogenase/cyclohyd;1.5e-104;codon 123-283 GO:0046656 folic acid biosynthesis -!- GO:0009257 10-formyltetrahydrofolate biosynthesis CDS ECK0523 sfmA sfmA b0530 557435 557977 + start codon change JW0519 557435 557977 + ps predicted fimbrial-like adhesin protein C Periplasmic 1-28 49401; Bacterial adhesins PF00419;Fimbrial protein;2.6e-57;codon 39-191 GO:0009289 fimbria CDS ECK0524 sfmC sfmC b0531 558197 558889 + (no change) JW0520 558197 558889 + f "pilin chaperone, periplasmic" E 15372038 -!- 2553674 1-23 "COG3121;P pilus assembly protein, chaperone PapD" 49354; PapD-like -!- 49584; Periplasmic chaperone C-domain PF00345;Gram-negative pili assembly chaperone;8e-57;codon 26-146 -!- PF02753;Gram-negative pili assembly chaperone;3.4e-20;codon 150-226 GO:0006457 protein folding CDS ECK0525 sfmD sfmD b0532 558920 561523 + (no change) JW0521 558920 561523 + pf predicted outer membrane export usher protein C 2553674 Outer Membrane B-barrel protein "COG3188;P pilus assembly protein, porin PapC" PF00577;Fimbrial Usher protein;0;codon 37-847 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0526 sfmH sfmH b0533 561565 562542 + (no change) JW5071 561565 562542 + ps predicted fimbrial-like adhesin protein involved in fimbrial assembly C Periplasmic "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK0527 sfmF sfmF ybcG b0534 562553 563068 + (no change) JW5072 562553 563068 + ps predicted fimbrial-like adhesin protein C Periplasmic "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;1.9e-38;codon 28-171 GO:0009289 fimbria CDS ECK0528 fimZ fimZ ybcA b0535 563071 563703 - (no change) JW5073 563071 563703 - pr predicted DNA-binding transcriptional regulator of fimbrial expression C 90220507 -!- 11911183 Cytoplasmic LuxR/UhpA COG2197;Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;3.6e-37;codon 4-125 -!- PF00196;Bacterial regulatory proteins, luxR fami;4.5e-29;codon 147-204" GO:0009289 fimbria GO:0006350 transcription GO:0016563 transcriptional activator activity tRNA ECK0529 argU argU dnaY -!- pin b0536 563946 564022 + (no change) JWR0010 563946 564022 + n tRNA-Arg(UCU) (Arginine tRNA4) E 3891522 -!- 90236910 -!- 92193285 -!- 93387287 CDS ECK0530 intD intD int b0537 564038 565201 - (no change) JW0525 564038 565201 - h DLP12 prophage; predicted integrase C 90036709 -!- 2183007 Cytoplasmic cryptic prophage DLP12 COG0582;Integrase 56349; DNA breaking-rejoining enzymes PF00589;Phage integrase family;3.4e-60;codon 167-359 CDS ECK0531 ybcC ybcC b0539 565321 565584 - (no change) JW0526 565321 565584 - h DLP12 prophage; predicted exonuclease C Cytoplasmic cryptic prophage DLP12 3.1.11.3 52980; Restriction endonuclease-like CDS ECK0532 ybcD ybcD b4508 565674 565910 + pseudogene fragment -!- new JW0527 565674 565910 + pseudogene -!- prophage h DLP12 prophage; predicted replication protein fragment (pseudogene) phage-like C Cytoplasmic GO:0005737 cytoplasm CDS ECK0533 renD renD ybcE b0542 567285 567470 + start codon change JW0530 567285 567470 + h DLP12 prophage; predicted protein C 6221115 Cytoplasmic cryptic prophage DLP12 CDS ECK0534 emrE emrE mvrC -!- eb -!- mvrB b0543 567538 567870 + (no change) JW0531 567538 567870 + h DLP12 prophage; multidrug resistance protein E 10383465 -!- 14633977 -!- 14755055 -!- 15044024 -!- 15111102 -!- 15175281 -!- 92319648 -!- 1936950 -!- 7896833 -!- 9050242 -!- 9688273 Integral Membrane Protein cryptic prophage DLP12 2.A.7; The Drug/Metabolite Transporter (DMT) Superfamily 4 4 out 1S7B COG2076;Membrane transporters of cations and cationic drugs PF00893;Small Multidrug Resistance protein;3.4e-53;codon 2-94 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0535 ybcK ybcK b0544 568125 569651 + (no change) JW0532 568125 569651 + h DLP12 prophage; predicted recombinase C Cytoplasmic cryptic prophage DLP12 regulated by attenuation (ybcK) "COG1961;Site-specific recombinases, DNA invertase Pin homologs" 53041; Resolvase-like "PF00239;Resolvase, N terminal domain;0.0014;codon 4-163 -!- PF07508;Recombinase;2.3e-26;codon 191-287" CDS ECK0536 ybcL ybcL b0545 570116 570667 + (no change) JW0533 570116 570667 + h DLP12 prophage; predicted kinase inhibitor C 11439028 Periplasmic cryptic prophage DLP12 1-19 183 1FUX COG1881;Phospholipid-binding protein 49777; PEBP-like PF01161;Phosphatidylethanolamine-binding protein;2.9e-15;codon 35-183 TIGR00481;TIGR00481: conserved hypothetical protein T;6.6e-95;codon 39-180 CDS ECK0537 ybcM ybcM b0546 570677 571474 + (no change) JW0534 570677 571474 + h DLP12 prophage; predicted DNA-binding transcriptional regulator C Cytoplasmic cryptic prophage DLP12 COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like PF00165;Bacterial regulatory helix-turn-helix protei;0.53;codon 168-211 -!- PF00165;Bacterial regulatory helix-turn-helix protei;0.00045;codon 217-261 CDS ECK0538 ybcN ybcN b0547 571689 572144 + (no change) JW0535 571689 572144 + h DLP12 prophage; predicted protein C Cytoplasmic cryptic prophage DLP12 CDS ECK0539 ninE ninE b0548 572144 572314 + (no change) JW0536 572144 572314 + h DLP12 prophage; conserved protein C 8648624 Cytoplasmic cryptic prophage DLP12 CDS ECK0540 ybcO ybcO b0549 572307 572597 + (no change) JW0537 572307 572597 + h DLP12 prophage; predicted protein C Cytoplasmic cryptic prophage DLP12 PF07102;Protein of unknown function (DUF1364);2.6e-74;codon 1-94 CDS ECK0541 rusA rusA rus -!- rusA(qsr') -!- ybcP b0550 572594 572956 + (no change) JW0538 572594 572956 + h DLP12 prophage; endonuclease RUS resolves Holliday junctions E 14646089 -!- 93322310 -!- 95112824 -!- 8648624 Cytoplasmic cryptic prophage DLP12 3.1.22 1Q8R COG4570;Holliday junction resolvase PF05866;Endodeoxyribonuclease RusA;1.3e-51;codon 8-117 GO:0005737 cytoplasm GO:0006308 DNA catabolism -!- GO:0006281 DNA repair -!- GO:0006308 DNA catabolism CDS ECK0542 ylcG ylcG b4509 572953 573093 + new JW5076 572953 573093 + h DLP12 prophage; predicted protein C Cytoplasmic GO:0005737 cytoplasm CDS ECK0543 ybcQ ybcQ b0551 573179 573562 + (no change) JW0539 573179 573562 + h DLP12 prophage; predicted antitermination protein C Cytoplasmic cryptic prophage DLP12 regulated by attenuation (ybcQ) PF06530;Phage antitermination protein Q;8.5e-82;codon 1-126 CDS ECK0544 nmpC nmpC phmA b0553 574981 576108 - pseudogene -!- (no change) JW5078 574981 576108 - pseudogene h DLP12 prophage; truncated outer membrane porin (pseudogene) interrupted by IS5B in K-12 E 86304457 -!- 8057841 -!- 8648624 -!- 337109 Outer Membrane B-barrel protein cryptic prophage DLP12 1.B.1; The General Bacterial Porin (GBP) Family 1-43 365 COG3203;Outer membrane protein (porin) 56935; Porins PF00267;Gram-negative porin;2.5e-193;codon 49-373 CDS ECK0545 essD essD ybcR -!- vlyS b0554 576621 576836 + (no change) JW0543 576621 576836 + h DLP12 prophage; predicted phage lysis protein C Integral Membrane Protein cryptic prophage DLP12 2 2 PF04971;Lysis protein S;5.1e-52;codon 4-71 CDS ECK0546 ybcS ybcS lycV b0555 576836 577333 + (no change) JW0544 576836 577333 + h DLP12 prophage; predicted lysozyme C Periplasmic cryptic prophage DLP12 COG3772;Phage-related lysozyme (muraminidase) 53955; Lysozyme-like PF00959;Phage lysozyme;7e-46;codon 48-155 CDS ECK0547 rzpD rzpD ybcT -!- enpP b0556 577330 577791 + (no change) JW5079 577330 577791 + h DLP12 prophage; predicted murein endopeptidase C cryptic prophage DLP12 PF03245;Bacteriophage lysis protein;2e-114;codon 1-153 CDS ECK0548 rzoD rzoD b4510 577550 577732 + new JW5080 577550 577732 + h DLP12 prophage; predicted lipoprotein C Outer membrane Lipoprotein GO:0009279 outer membrane (sensu Gram-negative Bacteria) CDS ECK0549 borD borD ybcU -!- bor -!- iss -!- vboR b0557 577823 578116 - (no change) JW0546 577823 578116 - h DLP12 prophage; predicted lipoprotein implicated in serum resistance C 95173101 Outer membrane Lipoprotein cryptic prophage DLP12 PF06291;Bor protein;8.7e-77;codon 1-97 CDS ECK0550 ybcV ybcV b0558 578407 578817 - start codon change JW5081 578407 578817 - h DLP12 prophage; predicted protein predicted cell envelope protein C Cytoplasmic cryptic prophage DLP12 PF07166;Protein of unknown function (DUF1398);1.1e-94;codon 17-141 CDS ECK0551 ybcW ybcW b0559 579103 579309 + (no change) JW0548 579103 579309 + h DLP12 prophage; predicted protein C Cytoplasmic cryptic prophage DLP12 CDS ECK0552 nohB nohB b0560 580057 580602 + (no change) JW0549 580057 580602 + h DLP12 prophage; DNA packaging protein E 92334985 Cytoplasmic cryptic prophage DLP12 "COG4220;Phage DNA packaging protein, Nu1 subunit of terminase" 46955; Putative DNA-binding domain PF07471;Phage DNA packaging protein Nu1;2.4e-121;codon 1-164 CDS ECK0553 tfaD tfaD yicF -!- ybcX b0561 580757 581320 + pseudogene -!- start codon change JW5815 580757 581320 + "pseudogene, fragment of phage" h DLP12 prophage; predicted tail fiber assembly protein (pseudogene) C Cytoplasmic cryptic prophage DLP12 PF02413;Caudovirales tail fibre assembly protein;2.8e-70;codon 106-245 CDS ECK0554 ybcY ybcY b0562 581375 581959 - (no change) JW0551 581375 581959 - h DLP12 prophage; predicted SAM-dependent methyltransferase C Cytoplasmic cryptic prophage DLP12 53335; S-adenosyl-L-methionine-dependent methyltransferases CDS ECK0555 ylcE ylcE b0563 582098 582283 + (no change) JW0552 582098 582283 + h DLP12 prophage; predicted protein C Cytoplasmic cryptic prophage DLP12 CDS ECK0556 appY appY b0564 582904 583653 + (no change) JW0553 582904 583653 + h DLP12 prophage; DNA-binding transcriptional activator E 89155479 -!- 94350824 -!- 3295784 Cytoplasmic cryptic prophage DLP12 appCBA -!- hyaABCDEF COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like PF00165;Bacterial regulatory helix-turn-helix protei;0.037;codon 144-185 -!- PF00165;Bacterial regulatory helix-turn-helix protei;4.7e-10;codon 191-235 GO:0005737 cytoplasm GO:0006350 transcription -!- GO:0042594 response to starvation GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0557 ompT ompT b0565 583903 584856 - (no change) JW0554 583903 584856 - h DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) E 21460517 -!- 90094263 -!- 92293136 -!- 94117370 -!- 98348467 -!- 10651827 -!- 11566868 -!- 3056908 -!- 3278297 -!- 9629924 Periplasmic cryptic prophage DLP12 3.4.21.87 A26 family; omptin 317 1I78 COG4571;Outer membrane protease 69917; Outer membrane protease OMPT PF01278;Omptin family;2.6e-218;codon 21-317 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0558 envY envY b0566 585370 586131 - (no change) JW0555 585370 586131 - r DNA-binding transcriptional activator of porin biosynthesis E 6317653 -!- 2536924 Cytoplasmic AraC/XylS ompC -!- ompF COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like PF00165;Bacterial regulatory helix-turn-helix protei;4.2e-06;codon 150-195 -!- PF00165;Bacterial regulatory helix-turn-helix protei;1.1e-12;codon 201-245 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0559 ybcH ybcH b0567 586314 587204 - (no change) JW0556 586314 587204 - o predicted protein C 1-20 CDS ECK0560 nfrA nfrA b0568 587205 590177 - (no change) JW0557 587205 590177 - m "bacteriophage N4 receptor, outer membrane subunit" E 89359086 -!- 94042873 -!- 94042874 Periplasmic 1-27 COG0457;FOG: TPR repeat 48452; TPR-like PF00515;Tetratricopeptide repeat;6.4e-06;codon 612-645 -!- PF07719;Tetratricopeptide repeat;2.1e-05;codon 612-645 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0561 nfrB nfrB b0569 590164 592401 - (no change) JW0558 590164 592401 - m "bacteriophage N4 receptor, inner membrane subunit" E 89359086 -!- 94042873 -!- 94042874 Integral Membrane Protein 6 4 53448; Nucleotide-diphospho-sugar transferases PF05157;GSPII_E N-terminal domain;1.6e-36;codon 522-629 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0562 cusS cusS ybcZ b0570 592551 593993 - (no change) JW5082 592551 593993 - r "sensory histidine kinase in two-component regulatory system with CusR, senses copper ions" senses copper ions E 20461235 -!- 11283292 -!- 11399769 Integral Membrane Protein 3 2 in COG0642;Signal transduction histidine kinase 47384; Homodimeric domain of signal transducing histidine kinase -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF00672;HAMP domain;6.5e-13;codon 188-257 -!- PF00512;His Kinase A (phosphoacceptor) domain;9.8e-16;codon 261-327 -!- PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;3.8e-36;codon 371-480" TIGR01386;cztS_silS_copS: heavy metal sensor kin;9.2e-196;codon 9-479 GO:0019866 inner membrane GO:0006464 protein modification CDS ECK0563 cusR cusR ylcA b0571 593983 594666 - (no change) JW0560 593983 594666 - r DNA-binding response regulator in two-component regulatory system with CusS E 20461235 -!- 11283292 -!- 11399769 Cytoplasmic Two cusCFBA COG0745;Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;4.3e-39;codon 1-120 -!- PF00486;Transcriptional regulatory protein, C te;3.2e-24;codon 146-221" TIGR01387;cztR_silR_copR: heavy metal response r;1.5e-130;codon 3-221 GO:0006350 transcription CDS ECK0564 cusC cusC ylcB -!- ibeB b0572 594823 596196 + (no change) JW0561 594823 596196 + t "copper/silver efflux system, outer membrane component" TolC-like outer membrane protein E 20461235 -!- 21125583 -!- 10225861 -!- 10493123 -!- 11283292 -!- 11399769 -!- 12813074 Outer membrane Lipoprotein heteromultimer; Copper Transporting Efflux System (b0572-b0573-b0574-b0575) 1.B.17; The Outer Membrane Factor (OMF) Family -!- 2.A.6; The Resistance-Nodulation-Cell Division (RND) Superfamily regulated by attenuation (cusC) COG1538;Outer membrane protein "56954; Integral outer membrane protein TolC, efflux pump component" PF02321;Outer membrane efflux protein;8.4e-44;codon 63-247 -!- PF02321;Outer membrane efflux protein;6.2e-62;codon 269-455 "TIGR01845;RND_outer_NodT: RND efflux system, out;9.3e-117;codon 9-457" GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0565 cusF cusF cusX -!- ylcC b0573 596354 596686 + (no change) JW0562 596354 596686 + f periplasmic copper-binding protein interacts with CusCBA copper/silver efflux system C 21125583 -!- 11283292 -!- 11399769 -!- 12813074 Periplasmic heteromultimer; Copper Transporting Efflux System (b0572-b0573-b0574-b0575) 2.A.6; The Resistance-Nodulation-Cell Division (RND) Superfamily CDS ECK0566 cusB cusB ylcD b0574 596702 597925 + (no change) JW0563 596702 597925 + t "copper/silver efflux system, membrane fusion protein" E 20461235 -!- 21125583 -!- 11283292 -!- 11399769 -!- 12813074 heteromultimer; Copper Transporting Efflux System (b0572-b0573-b0574-b0575) 2.A.6; The Resistance-Nodulation-Cell Division (RND) Superfamily COG0845;Membrane-fusion protein 51230; Single hybrid motif "TIGR01730;RND_mfp: efflux transporter, RND family, MFP;9.4e-25;codon 96-394" GO:0042493 response to drug CDS ECK0567 cusA cusA ybdE b0575 597937 601080 + (no change) JW0564 597937 601080 + t "copper/silver efflux system, membrane component" E 20461235 -!- 21125583 -!- 21178899 -!- 21450803 -!- 11399769 -!- 12813074 -!- 1711024 -!- 7984428 Integral Membrane Protein heteromultimer; Copper Transporting Efflux System (b0572-b0573-b0574-b0575) 2.A.6; The Resistance-Nodulation-Cell Division (RND) Superfamily 12 12 in COG3696;Putative silver efflux pump PF00873;AcrB/AcrD/AcrF family;0;codon 5-1039 "TIGR00914;2A0601: heavy metal efflux pump, CzcA family;0;codon 1-1047" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0568 pheP pheP b0576 601182 602558 + (no change) JW0565 601182 602558 + t phenylalanine transporter E 91267923 -!- 94042931 -!- 8626334 Integral Membrane Protein 2.A.3; The Amino Acid-Polyamine-Organocation (APC) Family 12 12 in regulated by attenuation (pheP) COG1113;Gamma-aminobutyrate permease and related permeases PF00324;Amino acid permease;1e-145;codon 27-458 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009094 L-phenylalanine biosynthesis -!- GO:0009063 amino acid catabolism CDS ECK0569 ybdG ybdG b0577 602639 603886 - (no change) JW0566 602639 603886 - pt predicted mechanosensitive channel C Integral Membrane Protein 4 5 in COG0668;Small-conductance mechanosensitive channel PF00924;Mechanosensitive ion channel;5.9e-63;codon 143-398 GO:0042597 periplasmic space CDS ECK0570 nfnB nfnB nfsB -!- nfsI -!- ntr -!- dprA b0578 603994 604647 - (no change) JW0567 603994 604647 - e "dihydropteridine reductase, NAD(P)H-dependent, oxygen-insensitive" E 12788749 -!- 338576 -!- 3881084 -!- 89076221 -!- 90245032 -!- 92348377 -!- 94239448 -!- 11020276 -!- 1472094 -!- 7813889 -!- 9298646 1.5.1.34 monomeric multimer; dihydropteridine reductase (b0578) COG0778;Nitroreductase 55469; NADH oxidase/flavin reductase PF00881;Nitroreductase family;5.8e-76;codon 7-193 GO:0042493 response to drug CDS ECK0571 ybdF ybdF b0579 604741 605109 - (no change) JW5083 604741 605109 - o conserved protein C Cytoplasmic COG2315;Uncharacterized protein conserved in bacteria PF04237;Protein of unknown function (DUF419);6.8e-57;codon 7-108 CDS ECK0572 ybdJ ybdJ b0580 605174 605422 - (no change) JW0569 605174 605422 - pm predicted inner membrane protein C Integral Membrane Protein 2 2 PF06643;Protein of unknown function (DUF1158);2.2e-63;codon 1-82 CDS ECK0573 ybdK ybdK b0581 605488 606606 - (no change) JW0570 605488 606606 - e gamma-glutamyl:cysteine ligase E 15211520 Cytoplasmic 6.3.2.2 1R8G COG2170;Uncharacterized conserved protein PF04107;Glutamate-cysteine ligase family 2(GCS2);1.3e-129;codon 13-292 TIGR02050;gshA_cyan_rel: uncharacterized enzyme;4.9e-181;codon 13-297 CDS ECK0574 hokE hokE ybdY b4415 607059 607211 + (no change) JW5084 607059 607211 + f "toxic polypeptide, small" not expressed in K-12 due to upstream IS186 element. E 99291074 Membrane Anchored PF01848;Hok/gef family;1.5e-29;codon 1-50 CDS ECK0575 entD entD b0583 608682 609311 - (no change) JW5085 608682 609311 - e phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex E 89313305 -!- 90132534 -!- 91035252 -!- 8939709 -!- 9214294 Cytoplasmic 2.7.8.- heteromultimer; enterobactin synthase multienzyme complex (b0595-b0583-b0586-b0594) COG2977;Phosphopantetheinyl transferase component of siderophore synthetase 56214; 4'-phosphopantetheinyl transferase; possibly related to the IspF and YjgF-like s PF01648;4'-phosphopantetheinyl transferase superfami;4.2e-13;codon 107-170 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009239 enterobactin biosynthesis CDS ECK0576 fepA fepA cbr -!- cbt -!- fep -!- feuB b0584 609477 611717 - (no change) JW5086 609477 611717 - t iron-enterobactin outer membrane transporter receptor for colicins B and D E 1107801 -!- 12779236 -!- 15150246 -!- 90236939 -!- 94068459 -!- 94198561 -!- 2201687 -!- 2974033 -!- 3015941 -!- 9886293 -!- 10529396 Outer Membrane B-barrel protein heteromultimer; Ferric Enterobactin Transport System (b0584-b0588-b0589-b0590-b0592-b1252-b3005-b3006) -!- heteromultimer; Outer Membrane Ferric Enterobactin Transport System (b0584-b1252-b3005-b3006) 1.B.14; The Outer Membrane Receptor (OMR) Family 746 COG4771;Outer membrane receptor for ferrienterochelin and colicins 56935; Porins PF07715;TonB-dependent Receptor Plug Domain;7.9e-29;codon 43-163 -!- PF00593;TonB dependent receptor;3.6e-32;codon 465-746 TIGR01783;TonB-siderophor: TonB-dependent sider;1.2e-221;codon 27-746 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0006826 iron ion transport CDS ECK0577 fes fes b0585 612038 613162 + (no change) JW0576 612038 613162 + e enterobactin/ferric enterobactin esterase E 92291125 -!- 94198561 -!- 2974033 Cytoplasmic COG2382;Enterochelin esterase and related enzymes 53474; alpha/beta-Hydrolases PF00756;Putative esterase;4.2e-87;codon 138-365 GO:0005737 cytoplasm GO:0006826 iron ion transport CDS ECK0578 ybdZ ybdZ b4511 613165 613383 + new JW0577 613165 613383 + o conserved protein C Cytoplasmic GO:0005737 cytoplasm CDS ECK0579 entF entF b0586 613380 617261 + (no change) JW0578 613380 617261 + e "enterobactin synthase multienzyme complex component, ATP-dependent" possible thiolase activity E 20183918 -!- 87307997 -!- 91035252 -!- 91175738 -!- 9485415 -!- 99307591 -!- 2974033 Cytoplasmic 2.7.7.- Mg2+ heteromultimer; enterobactin synthase multienzyme complex (b0595-b0583-b0586-b0594) COG1020;Non-ribosomal peptide synthetase modules and related proteins -!- COG3319;Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases 53474; alpha/beta-Hydrolases -!- 56801; Firefly luciferase-like PF00668;Condensation domain;2.5e-81;codon 1-301 -!- PF00501;AMP-binding enzyme;1.7e-162;codon 482-887 -!- PF00550;Phosphopantetheine attachment site;4.9e-11;codon 978-1042 -!- PF00975;Thioesterase domain;9.7e-57;codon 1066-1287 TIGR01733;AA-adenyl-dom: amino acid adenylation d;1.3e-162;codon 482-887 GO:0005737 cytoplasm GO:0009239 enterobactin biosynthesis -!- GO:0015937 coenzyme A biosynthesis -!- GO:0019184 nonribosomal peptide biosynthesis -!- GO:0006826 iron ion transport CDS ECK0580 fepE fepE b0587 617477 618610 + (no change) JW0579 617477 618610 + r regulator of length of O-antigen component of lipopolysaccharide chains E 12603743 -!- 87279914 -!- 1826089 Integral Membrane Protein 2 2 in COG3765;Chain length determinant protein PF02706;Chain length determinant protein;2.7e-32;codon 25-175 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006826 iron ion transport CDS ECK0581 fepC fepC b0588 618607 619422 - (no change) JW0580 618607 619422 - t iron-enterobactin transporter subunit -!- ATP-binding component of ABC superfamily E 87279914 -!- 92157868 Cytoplasmic heteromultimer; Ferric Enterobactin Transport System (b0584-b0588-b0589-b0590-b0592-b1252-b3005-b3006) -!- heteromultimer; ferric enterobactin ABC transporter (b0588-b0590-b0589-b0592) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG1120;ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;2.7e-55;codon 33-220 GO:0005737 cytoplasm GO:0006826 iron ion transport CDS ECK0582 fepG fepG b0589 619419 620411 - (no change) JW0581 619419 620411 - t iron-enterobactin transporter subunit -!- membrane component of ABC superfamily E 87279914 -!- 92157868 Integral Membrane Protein heteromultimer; Ferric Enterobactin Transport System (b0584-b0588-b0589-b0590-b0592-b1252-b3005-b3006) -!- heteromultimer; ferric enterobactin ABC transporter (b0588-b0590-b0589-b0592) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 9 8 in "COG4779;ABC-type enterobactin transport system, permease component" PF01032;FecCD transport family;6.2e-131;codon 30-325 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006826 iron ion transport CDS ECK0583 fepD fepD ybdA b0590 620408 621412 - (no change) JW0582 620408 621412 - t iron-enterobactin transporter subunit -!- membrane component of ABC superfamily E 87279914 -!- 92157868 -!- 1787794 Integral Membrane Protein heteromultimer; Ferric Enterobactin Transport System (b0584-b0588-b0589-b0590-b0592-b1252-b3005-b3006) -!- heteromultimer; ferric enterobactin ABC transporter (b0588-b0590-b0589-b0592) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 10 9 in "COG0609;ABC-type Fe3+-siderophore transport system, permease component" PF01032;FecCD transport family;4.2e-135;codon 31-328 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006826 iron ion transport CDS ECK0584 ybdA ybdA ybdA b0591 621523 622773 + (no change) JW0583 621523 622773 + pt predicted transporter C 12068807 -!- 1787794 -!- 1838574 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 11 in COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;8.9e-22;codon 22-372 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0585 fepB fepB b0592 622777 623733 - (no change) JW0584 622777 623733 - t iron-enterobactin transporter subunit -!- periplasmic-binding component of ABC superfamily E 20444181 -!- 87279914 -!- 90008779 -!- 2139473 -!- 7551033 -!- 10986237 Periplasmic heteromultimer; Ferric Enterobactin Transport System (b0584-b0588-b0589-b0590-b0592-b1252-b3005-b3006) -!- heteromultimer; ferric enterobactin ABC transporter (b0588-b0590-b0589-b0592) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-26 318 "COG4592;ABC-type Fe2+-enterobactin transport system, periplasmic component" 53807; Helical backbone PF01497;Periplasmic binding protein;1.2e-63;codon 46-299 GO:0042597 periplasmic space GO:0006826 iron ion transport CDS ECK0586 entC entC fepF b0593 624108 625283 + (no change) JW0585 624108 625283 + e isochorismate synthase 1 E "89123153 -!- 90165423 -!- 90241936 -!- 2110093 -!- 2139473 -!- Elkins, MF, Earhart, CF;FEMS Microbiology Letters;1988;56:35-40" Cytoplasmic 5.4.4.2 Mg2+ COG1169;Isochorismate synthase 56322; ADC synthase PF00425;chorismate binding enzyme;7.9e-123;codon 125-388 TIGR00543;isochor_syn: isochorismate synthases;1.2e-94;codon 72-388 GO:0009239 enterobactin biosynthesis CDS ECK0587 entE entE b0594 625293 626903 + (no change) JW0586 625293 626903 + e "2,3-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex" E 20183918 -!- 87279914 -!- 89290355 -!- 9485415 2.7.7.58 Mg2+ "heteromultimer; enterobactin synthase multienzyme complex (b0595-b0583-b0586-b0594) -!- monomeric multimer; 2,3-dihydroxybenzoate-AMP ligase (b0594)" COG1021;Peptide arylation enzymes 56801; Firefly luciferase-like PF00501;AMP-binding enzyme;4.8e-107;codon 50-462 "TIGR02275;DHB_AMP_lig: 2,3-dihydroxybenzoate-AMP li;0;codon 3-527" GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009239 enterobactin biosynthesis -!- GO:0019184 nonribosomal peptide biosynthesis CDS ECK0588 entB entB entG b0595 626917 627774 + (no change) JW0587 626917 627774 + e isochorismatase E 20183918 -!- 90241937 -!- 91035252 -!- 9485415 -!- 97361959 -!- 2521621 -!- 2521622 Cytoplasmic 3.3.2.1 heteromultimer; enterobactin synthase multienzyme complex (b0595-b0583-b0586-b0594) -!- monomeric multimer; apo-EntB (b0595) COG1535;Isochorismate hydrolase -!- COG3433;Aryl carrier domain 47336; ACP-like -!- 52499; Cysteine hydrolase PF00857;Isochorismatase family;2e-104;codon 26-208 -!- PF00550;Phosphopantetheine attachment site;4.9e-13;codon 216-280 GO:0005737 cytoplasm GO:0009239 enterobactin biosynthesis -!- GO:0019184 nonribosomal peptide biosynthesis CDS ECK0589 entA entA b0596 627774 628520 + (no change) JW0588 627774 628520 + e "2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase" E "89123153 -!- 89123155 -!- 90062192 -!- 2521621 -!- Walsh, CT, Liu, J, Rusnak, F, et al;Chemical Reviews;1990;90:1105-1129" Cytoplasmic 1.3.1.28 "monomeric multimer; 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (b0596)" COG1028;Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) 51735; NAD(P)-binding Rossmann-fold domains PF00106;short chain dehydrogenase;1.7e-64;codon 8-244 GO:0009239 enterobactin biosynthesis CDS ECK0590 ybdB ybdB b0597 628523 628936 + (no change) JW0589 628523 628936 + o conserved protein C 2521621 -!- 2521622 Cytoplasmic "COG2050;Uncharacterized protein, possibly involved in aromatic compounds catabolism" PF03061;Thioesterase superfamily;3.2e-17;codon 50-127 TIGR00369;unchar_dom_1: uncharacterized domain;4.4e-57;codon 19-135 CDS ECK0591 cstA cstA ybdC b0598 629117 631222 + (no change) JW0590 629117 631222 + pf carbon starvation protein predicted to be involved in peptide utilization E 91162636 -!- 2521622 Integral Membrane Protein 9.B.59; The Putative Peptide Transporter Carbon Starvation CstA (CstA) Family 18 18 in "COG1966;Carbon starvation protein, predicted membrane protein" PF02554;Carbon starvation protein CstA;1.3e-297;codon 32-436 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042594 response to starvation CDS ECK0592 ybdD ybdD b4512 631405 631602 + new JW0591 631405 631602 + o conserved protein C Cytoplasmic GO:0005737 cytoplasm CDS ECK0593 ybdH ybdH b0599 631612 632700 - (no change) JW0592 631612 632700 - pe predicted oxidoreductase predicted alcohol dehydrogenase C COG0371;Glycerol dehydrogenase and related enzymes 56796; Dehydroquinate synthase-like PF00465;Iron-containing alcohol dehydrogenase;5.7e-11;codon 12-350 CDS ECK0594 ybdL ybdL b0600 632809 633969 + (no change) JW0593 632809 633969 + e "methionine aminotransferase, PLP-dependent" E 15280032 Cytoplasmic 2.6.1.- 1U08 COG0436;Aspartate/tyrosine/aromatic aminotransferase 53383; PLP-dependent transferases PF00155;Aminotransferase class I and II;3.1e-21;codon 82-386 GO:0008152 metabolism CDS ECK0595 ybdM ybdM b0601 633970 634599 - (no change) JW0594 633970 634599 - o conserved protein C Cytoplasmic COG1475;Predicted transcriptional regulators PF02195;ParB-like nuclease domain;6.3e-21;codon 51-146 CDS ECK0596 ybdN ybdN b0602 634572 635792 - (no change) JW0595 634572 635792 - d conserved protein C Cytoplasmic COG3969;Predicted phosphoadenosine phosphosulfate sulfotransferase 52402; Adenine nucleotide alpha hydrolases CDS ECK0597 ybdO ybdO b0603 635939 636841 - (no change) JW0596 635939 636841 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix protei;1.2e-21;codon 12-71 "GO:0006350 transcription -!- GO:0006355 regulation of transcription, DNA-dependent" CDS ECK0598 dsbG dsbG ybdP b0604 637050 637796 - start codon change JW0597 637050 637796 - e periplasmic disulfide isomerase/thiol-disulphide oxidase E 10075670 -!- 15184683 -!- 20250884 -!- 9383195 -!- 98316716 Periplasmic 5.3.4.1 "monomeric multimer; disulfide isomerase, periplasmic / disulfide oxidoreductase (b0604)" 1-37 248 1V58 COG1651;Protein-disulfide isomerase 52833; Thioredoxin-like GO:0042597 periplasmic space GO:0006457 protein folding CDS ECK0599 ahpC ahpC tpx b0605 638168 638731 + (no change) JW0598 638168 638731 + e "alkyl hydroperoxide reductase, C22 subunit" E 89197774 -!- 1575737 -!- 1592833 -!- 7499381 -!- 8774726 -!- 9298646 -!- 9600841 Cytoplasmic 1.6.4.- heteromultimer; alkylhydroperoxide reductase (b0605-b0606) 1KYG COG0450;Peroxiredoxin 52833; Thioredoxin-like PF00578;AhpC/TSA family;5.6e-68;codon 5-151 GO:0006805 xenobiotic metabolism CDS ECK0600 ahpF ahpF b0606 638976 640541 + start codon change JW0599 638976 640541 + e "alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)-binding" E 89197774 -!- 1592833 Cytoplasmic 1.6.4.- heteromultimer; alkylhydroperoxide reductase (b0605-b0606) regulated by attenuation (ahpF) "COG3634;Alkyl hydroperoxide reductase, large subunit" 51905; FAD/NAD(P)-binding domain -!- 52833; Thioredoxin-like PF00070;Pyridine nucleotide-disulphide oxidoreducta;8.3e-71;codon 224-504 GO:0006805 xenobiotic metabolism CDS ECK0601 uspG uspG ybdQ -!- up12 -!- UP12 -!- yzzU b0607 640662 641090 - (no change) JW0600 640662 641090 - f universal stress protein UP12 E 12732303 -!- 12071968 Cytoplasmic COG0589;Universal stress protein UspA and related nucleotide-binding proteins 52431; ETFP adenine nucleotide-binding domain-like PF00582;Universal stress protein family;1.5e-16;codon 1-142 CDS ECK0602 ybdR ybdR b0608 641311 642549 + (no change) JW0601 641311 642549 + pe "predicted oxidoreductase, Zn-dependent and NAD(P)-binding" C COG1063;Threonine dehydrogenase and related Zn-dependent dehydrogenases 50129; GroES-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF00107;Zinc-binding dehydrogenase;5.7e-82;codon 7-387 CDS ECK0603 rnk rnk b0610 642780 643190 - (no change) JW0602 642780 643190 - r regulator of nucleoside diphosphate kinase E 7565093 Cytoplasmic regulated by attenuation (rnk) COG0782;Transcription elongation factor 54534; FKBP-like "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0604 rna rna rnsA b0611 643420 644226 - (no change) JW0603 643420 644226 - e ribonuclease I E "90151658 -!- 90264307 -!- 2253883 -!- 8188249 -!- Spahr PF, Hollingworth BR;J Biol Chem;1961;236: 823-831" Periplasmic 3.1.27.6 268 regulated by attenuation (rna) COG3719;Ribonuclease I 55895; Ribonuclease Rh-like PF00445;Ribonuclease T2 family;6e-05;codon 34-246 GO:0005737 cytoplasm GO:0006401 RNA catabolism -!- GO:0006401 RNA catabolism CDS ECK0605 citT citT ybdS b0612 644340 645803 - (no change) JW0604 644340 645803 - t citrate:succinate antiporter E 9696764 Integral Membrane Protein 2.A.47; The Divalent Anion:Na+ Symporter (DASS) Family 12 13 COG0471;Di- and tricarboxylate transporters PF00939;Sodium:sulfate symporter transmembrane;1.7e-294;codon 5-486 TIGR00785;dass: anion transporter;4.8e-266;codon 25-480 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK0606 citG citG ybdT b0613 645854 646732 - (no change) JW0605 645854 646732 - e triphosphoribosyl-dephospho-CoA transferase E 20384232 -!- 11042274 Cytoplasmic 2.7.8.25 COG1767;Triphosphoribosyl-dephospho-CoA synthetase PF01874;ATP:dephospho-CoA triphosphoribosyl transfer;1.1e-150;codon 27-287 GO:0006412 protein biosynthesis CDS ECK0607 citX citX ybdU b0614 646707 647258 - (no change) JW0606 646707 647258 - e apo-citrate lyase phosphoribosyl-dephospho-CoA transferase E 20498929 -!- 10924139 -!- 9696764 Cytoplasmic 2.7.7.61 COG3697;Phosphoribosyl-dephospho-CoA transferase (holo-ACP synthetase) PF03802;Apo-citrate lyase phosphoribosyl-dephospho-C;1.2e-110;codon 11-181 GO:0006464 protein modification CDS ECK0608 citF citF ybdV b0615 647262 648794 - (no change) JW5087 647262 648794 - e "citrate lyase, citrate-ACP transferase (alpha) subunit" E 84024606 -!- 87214225 Cytoplasmic 4.1.3.6 -!- 2.8.3.10 Mg2+ "heteromultimer; citrate lyase, inactive (b0615-b0616-b0617) -!- monomeric multimer; citrate-ACP transferase (b0615)" "COG3051;Citrate lyase, alpha subunit" 53316; Glutaconate-CoA transferase subunits "PF04223;Citrate lyase, alpha subunit (CitF);0;codon 44-508" "TIGR01584;citF: citrate lyase, alpha subunit;0;codon 25-510" GO:0005737 cytoplasm CDS ECK0609 citE citE ybdW b0616 648805 649713 - start codon change JW0608 648805 649713 - e "citrate lyase, citryl-ACP lyase (beta) subunit" E 84024606 -!- 87214225 Periplasmic 4.1.3.6 -!- 4.1.3.34 Mg2+ "heteromultimer; citrate lyase, inactive (b0615-b0616-b0617) -!- monomeric multimer; citryl-ACP lyase (b0616)" 51621; Phosphoenolpyruvate/pyruvate domain PF03328;HpcH/HpaI aldolase/citrate lyase family;3e-119;codon 20-239 "TIGR01588;citE: citrate lyase, beta subunit;2.2e-191;codon 17-304" GO:0005737 cytoplasm CDS ECK0610 citD citD ybdX b0617 649710 650006 - (no change) JW0609 649710 650006 - e "citrate lyase, acyl carrier (gamma) subunit" also carries the prosthetic group components E 84024606 -!- 87214225 Cytoplasmic 4.1.3.6 Mg2+ "heteromultimer; citrate lyase, inactive (b0615-b0616-b0617) -!- monomeric multimer; holo-citrate lyase (b0617)" "COG3052;Citrate lyase, gamma subunit" "PF04953;Citrate lyase, gamma subunit;5e-69;codon 1-97" TIGR01608;citD: citrate lyase acyl carrier protein;4.8e-33;codon 1-94 GO:0005737 cytoplasm GO:0042967 acyl-carrier protein biosynthesis CDS ECK0611 citC citC ybeO b0618 650021 651079 - start codon change JW0610 650021 651079 - e citrate lyase synthetase E 84024606 -!- 87214225 Cytoplasmic 6.2.1.22 52374; Nucleotidylyl transferase -!- 55729; Acyl-CoA N-acyltransferases (Nat) PF00583;Acetyltransferase (GNAT) family;7.2e-05;codon 69-140 TIGR00124;cit_ly_ligase: citrate lyase ligase;7.4e-196;codon 36-371 -!- TIGR00125;cyt_tran_rel: cytidyltransferase-relate;1.2e-11;codon 176-234 GO:0005737 cytoplasm GO:0006464 protein modification CDS ECK0612 citA citA dpiB -!- ybeP -!- cit -!- mpdB b0619 651458 653116 + (no change) JW0611 651458 653116 + r sensory histidine kinase in two-component regulatory system with citB senses citrate E 11889485 -!- 21885746 -!- 9701802 Integral Membrane Protein 3 2 in COG3290;Signal transduction histidine kinase regulating citrate/malate metabolism 55785; PYP-like sensor domain -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;8.8e-27;codon 428-540" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006464 protein modification CDS ECK0613 citB citB criR -!- dpiA -!- mpdA b0620 653085 653765 + (no change) JW0612 653085 653765 + r DNA-binding response regulator in two-component regulatory system with citA E 11889485 -!- 7045076 -!- 9701802 Cytoplasmic Two citCDEFXGT -!- appY COG4565;Response regulator of citrate/malate metabolism 52172; CheY-like PF00072;Response regulator receiver domain;9.7e-23;codon 5-126 GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0614 dcuC dcuC b0621 653806 655191 - (no change) JW0616 655299 656390 - pseudogene t anaerobic C4-dicarboxylate transport CDS ECK0614 dcuC dcuC b0621 653806 655191 - (no change) JW0613 653806 654282 - pseudogene t anaerobic C4-dicarboxylate transport CDS ECK0614 dcuC dcuC b0621 653806 655191 - (no change) JW0613+JW0616 653806 656390 - ancestral gene -!- IS is inserted in strain W3110. b0621 is split into JW0613 & JW0616 in strain W -!- intact b0621 is found in strain MG -!- Initiation region of JW0612 overlaps with IS on W genome t anaerobic C4-dicarboxylate transport E 10368146 -!- 99138745 -!- 8955408 Integral Membrane Protein 2.A.61; The C4-dicarboxylate Uptake C (DcuC) Family 14 12 out COG3069;C4-dicarboxylate transporter TIGR00771;DcuC: c4-dicarboxylate anaerobic carrier fam;1e-280;codon 58-441 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK0615 crcA crcA pagP -!- ybeG b0622 655780 656340 + (no change) JW0617 656979 657539 + e palmitoyl transferase for Lipid A "acyl donor is not ACP, rather glycerophospholipids" E 15210985 -!- 20515626 -!- 97001112 2.3.1.- monomeric multimer; PagP homodimer; catalyzes acylation of Lipid A (b0622) 1THQ PF07017;Antimicrobial peptide resistance and lipid A;2.2e-124;codon 36-183 CDS ECK0616 cspE cspE gicA -!- msmC b0623 656515 656724 + (no change) JW0618 657714 657923 + r DNA-binding transcriptional repressor E 10200963 -!- 20345064 -!- 21083396 -!- 21101802 -!- 97001112 -!- 9735283 -!- 12324471 -!- 12071744 -!- 7984109 -!- 8022259 -!- 9921691 Cytoplasmic cspA -!- rpoS -!- uspA COG1278;Cold shock proteins 50249; Nucleic acid-binding proteins PF00313;'Cold-shock' DNA-binding domain;5.7e-44;codon 3-69 GO:0005737 cytoplasm GO:0006350 transcription -!- GO:0009266 response to temperature GO:0016563 transcriptional activator activity CDS ECK0617 crcB crcB ybeI b0624 656778 657161 - (no change) JW0619 657977 658360 - pm predicted inner membrane protein associated with chromosome condensation C 97001112 -!- 12904550 Integral Membrane Protein 4 4 out COG0239;Integral membrane protein possibly involved in chromosome condensation PF02537;CrcB-like protein;1.1e-60;codon 5-121 TIGR00494;crcB: crcB protein;3.5e-70;codon 6-121 GO:0009274 cell wall (sensu Bacteria) CDS ECK0618 ybeH ybeH b0625 657254 657481 + (no change) JW0620 658453 658680 + d predicted protein C Cytoplasmic 56317; Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase CDS ECK0619 ybeM ybeM b0626 657478 658041 + (no change) JW0621 658677 659240 + pe "predicted C-N hydrolase superfamily, NAD(P)-binding amidase/nitrilase" C COG0388;Predicted amidohydrolase 56317; Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase CDS ECK0620 tatE tatE ybeC b0627 658170 658373 + (no change) JW0622 659369 659572 + t TatABCE protein translocation system subunit E 20062812 -!- 98315056 -!- 10652088 -!- 1577793 Membrane Anchored heteromultimer; TatABCE protein export complex (b0627-b3836-b3838-b3839) 2.A.64; The Twin Arginine Targeting (Tat) Family COG1826;Sec-independent protein secretion pathway components PF02416;mttA/Hcf106 family;6.8e-08;codon 4-55 "TIGR01411;tatAE: twin-arginine translocation protein,;1.3e-22;codon 3-49" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0621 lipA lipA lip b0628 658474 659439 - (no change) JW0623 659673 660638 - e lipoate synthase E 12591875 -!- 92250596 -!- 93186699 -!- 99330162 Cytoplasmic 2.8.1.- monomeric multimer; lipoate synthase (b0628) COG0320;Lipoate synthase PF04055;Radical SAM superfamily;1.5e-23;codon 88-252 TIGR00510;lipA: lipoic acid synthetase;8.3e-189;codon 21-321 GO:0005737 cytoplasm GO:0009107 lipoate biosynthesis CDS ECK0622 ybeF ybeF cde b0629 659648 660601 - start codon change JW0624 660847 661800 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic LysR 46785; Winged helix -!- 53850; Periplasmic binding protein-like II "PF00126;HTH_1: transcriptional regulator, LysR famil;3.3e-21;codon 31-90 -!- PF03466;LysR_substrate: LysR substrate binding domai;2.2e-17;codon 112-314" GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0623 lipB lipB lip -!- cde b0630 660860 661501 - start codon change JW5089 662059 662700 - e lipoyl-protein ligase E 12591875 -!- 20525439 -!- 93186699 Cytoplasmic 2.3.1.- COG0321;Lipoate-protein ligase B PF03099;Biotin/lipoate A/B protein ligase famil;1.3e-34;codon 27-140 TIGR00214;lipB: lipoate-protein ligase B;2.3e-85;codon 4-182 GO:0009107 lipoate biosynthesis CDS ECK0624 ybeD ybeD b0631 661602 661865 - (no change) JW0626 662801 663064 - o conserved protein C 8444795 Cytoplasmic COG2921;Uncharacterized conserved protein PF04359;Protein of unknown function (DUF493);2.4e-55;codon 1-87 CDS ECK0625 dacA dacA pbp -!- pfv b0632 661975 663186 - (no change) JW0627 663174 664385 - e D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) E 14555648 -!- 20158889 -!- 89039244 -!- 91072213 -!- 92155204 -!- 1597468 -!- 3279397 -!- 3316191 -!- 6319180 -!- 7042389 -!- 8424800 Periplasmic 3.4.16.4 S11 family; penicillin-binding protein 6 1-29 403 1NZU COG1686;D-alanyl-D-alanine carboxypeptidase "56601; beta-Lactamase/D-ala carboxypeptidase -!- 69189; Penicillin-binding protein 5, C-terminal domain" "PF00768;D-alanyl-D-alanine carboxypeptidase;9.5e-152;codon 35-273 -!- PF07943;Penicillin-binding protein 5, C-termina;5.3e-39;codon 292-383" GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0626 rlpA rlpA b0633 663325 664413 - (no change) JW0628 664524 665612 - lp minor lipoprotein suppressor of prc -!- contains 2 SPOR repeats at its C-terminus. Possible role for these repeats in binding to peptidoglycan E 88058785 -!- 2644207 Outer membrane Lipoprotein 1-16 COG0797;Lipoproteins PF03330;Rare lipoprotein A (RlpA)-like double-psi be;2.7e-27;codon 78-168 -!- PF05036;Sporulation related repeat;1.6e-08;codon 287-323 -!- PF05036;Sporulation related repeat;5.8e-09;codon 324-360 TIGR00413;rlpA: rare lipoprotein A;8.9e-29;codon 81-153 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0627 mrdB mrdB rodA -!- mdrB b0634 664424 665536 - (no change) JW0629 665623 666735 - cp cell wall shape-determining protein cell division protein -!- homologue of FtsW -!- sensitivity to radiation and drugs -!- recruits cognate transpetidase MrdA E 89123070 -!- 90036736 -!- 91072213 -!- 3316191 Integral Membrane Protein 9.B.3; The Putative Bacterial Murein Precursor Exporter (MPE) Family 9 9 in COG0772;Bacterial cell division membrane protein PF01098;Cell cycle protein;1.5e-183;codon 18-365 TIGR02210;rodA_shape: rod shape-determining protein;4.7e-209;codon 17-364 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0628 mrdA mrdA pbpA b0635 665539 667440 - (no change) JW0630 666738 668639 - e transpeptidase involved in peptidoglycan synthesis (penicillin-binding protein 2) E 86196149 -!- 87030266 -!- 89174517 -!- 2644207 Membrane Anchored COG0768;Cell division protein FtsI/penicillin-binding protein 2 "56519; Penicillin-binding protein 2x (pbp-2x), N-terminal domain -!- 56601; beta-Lactamase/D-ala carboxypeptidase" PF03717;Penicillin-binding Protein dimerisatio;5.2e-70;codon 63-240 -!- PF00905;Penicillin binding protein transpeptid;1.2e-106;codon 271-609 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009252 peptidoglycan biosynthesis -!- GO:0042493 response to drug CDS ECK0629 ybeA ybeA b0636 667471 667938 - (no change) JW0631 668670 669137 - o conserved protein C Cytoplasmic 1NS5 COG1576;Uncharacterized conserved protein "PF02590;Uncharacterized ACR, COG1576;2.7e-80;codon 1-153" TIGR00246;TIGR00246: conserved hypothetical protein T;5.1e-90;codon 1-155 CDS ECK0630 ybeB ybeB b0637 667942 668259 - start codon change JW5090 669141 669458 - o predicted protein C Cytoplasmic PF02410;Domain of unknown function DUF143;1.9e-22;codon 1-69 TIGR00090;TIGR00090: iojap-related protein;9.8e-44;codon 1-68 CDS ECK0631 cobC cobC phpB b0638 668519 669130 - (no change) JW0633 669718 670329 - pe predicted alpha-ribazole-5'-P phosphatase C Cytoplasmic "COG0406;Fructose-2,6-bisphosphatase" 53254; Phosphoglycerate mutase-like PF00300;Phosphoglycerate mutase family;1.6e-91;codon 1-191 GO:0009236 vitamin B12 biosynthesis CDS ECK0632 nadD nadD ybeN -!- fusB b0639 669154 669795 - (no change) JW0634 670353 670994 - e "nicotinic acid mononucleotide adenylyltransferase, NAD(P)-dependent" E 20353477 -!- 10493123 -!- 11796112 -!- 13717628 Cytoplasmic 2.7.7.18 Mg2+ 1K4K COG1057;Nicotinic acid mononucleotide adenylyltransferase 52374; Nucleotidylyl transferase PF01467;Cytidylyltransferase;5.5e-65;cod on 7-187 TIGR00125;cyt_tran_rel: cytidyltransferase-related;1.9e-12;codon 5-69 -!- TIGR00482;TIGR00482: nicotinate (nicotinamide) nuc;7.9e-104;codon 7-212 GO:0009435 nicotinamide adenine dinucleotide biosynthesis CDS ECK0633 holA holA b0640 669797 670828 - (no change) JW0635 670996 672027 - e "DNA polymerase III, delta subunit" E 92156151 -!- 93015766 -!- 93280136 -!- 1575709 -!- 3316191 -!- 8505304 Cytoplasmic 2.7.7.7 "COG1466;DNA polymerase III, delta subunit" "48019; DNA polymerase III clamp loader subunits, C-terminal domain -!- 52540; P-loop containing nucleotide triphosphate hydrolases" "PF06144;DNA polymerase III, delta subunit;2.1e-138;codon 21-329" "TIGR01128;holA: DNA polymerase III, delta subunit;2.7e-213;codon 1-332" GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK0634 rlpB rlpB b0641 670828 671409 - (no change) JW0636 672027 672608 - lp minor lipoprotein E 88058785 Membrane Lipoprotein COG2980;Rare lipoprotein B PF04390;Rare lipoprotein B family;3.3e-89;codon 19-165 GO:0019866 inner membrane GO:0042158 lipoprotein biosynthesis CDS ECK0635 leuS leuS syl b0642 671424 674006 - (no change) JW0637 672623 675205 - e leucyl-tRNA synthetase E 90280415 -!- 92412076 -!- 3320963 Cytoplasmic 6.1.1.4 COG0495;Leucyl-tRNA synthetase 47323; Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases -!- 50677; ValRS/IleRS editing domain -!- 52374; Nucleotidylyl transferase "PF00133;tRNA synthetases class I (I, L, M and V);1.7e-301;codon 13-659" TIGR00396;leuS_bact: leucyl-tRNA synthetase;0;codon 5-860 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK0636 ybeL ybeL b0643 674241 674723 + (no change) JW0638 675440 675922 + o conserved protein natural substrate for SsrA-mediated degradation C 11373298 -!- 12105207 -!- 3320963 -!- 7567469 Cytoplasmic PF07295;Protein of unknown function (DUF1451);1.3e-107;codon 11-160 CDS ECK0637 ybeQ ybeQ b0644 674793 675770 - start codon change JW5091 675992 676969 - d conserved protein C Cytoplasmic 48439; Protein prenylyltransferase CDS ECK0638 ybeR ybeR b0645 675934 676641 + (no change) JW0640 677133 677840 + o predicted protein C Cytoplasmic PF06889;Protein of unknown function (DUF1266);9.8e-199;codon 1-235 CDS ECK0639 djlB djlB ybeS b0646 676638 678065 + (no change) JW0641 677837 679264 + pf predicted chaperone DnaJ family -!- non-cognate of nearby HscC C 12183460 Membrane Anchored 46565; Chaperone J-domain PF00226;DnaJ domain;0.00017;codon 3-59 GO:0006457 protein folding CDS ECK0640 ybeT ybeT b0647 678075 678629 - (no change) JW0642 679274 679828 - pm conserved outer membrane protein C Outer membrane Lipoprotein "COG0790;FOG: TPR repeat, SEL1 subfamily" CDS ECK0641 ybeU ybeU b0648 678731 679438 + (no change) JW0643 679930 680637 + pe predicted tRNA ligase C 8940112 Cytoplasmic PF06889;Protein of unknown function (DUF1266);2.4e-199;codon 1-235 CDS ECK0642 djlC djlC hscD -!- ybeV b0649 679435 680886 + (no change) JW0644 680634 682085 + f Hsc56 co-chaperone of HscC E 12183460 -!- 12054669 Cytoplasmic 46565; Chaperone J-domain PF00226;DnaJ domain;0.0039;codon 3-55 CDS ECK0643 hscC hscC ybeW b0650 680946 682616 - (no change) JW0645 682145 683815 - f "Hsp70 family chaperone Hsc62, binds to RpoD and inhibits transcription" binds to RpoD and inhibits transcription -!- mutants are hypersensitivity to Cd(2+) ions and UV irradiation -!- inhibits growth when overexpressed E 12183460 -!- 14734171 -!- 22055095 -!- 9735342 Cytoplasmic COG0443;Molecular chaperone "53067; Actin-like ATPase domain -!- 56778; Heat shock protein 70kD (HSP70), C-terminal, substrate-binding fragment" PF00012;Hsp70 protein;4.2e-91;codon 7-556 GO:0006457 protein folding CDS ECK0644 rihA rihA ybeK b0651 682700 683635 - (no change) JW0646 683899 684834 - e ribonucleoside hydrolase 1 E 21125610 Cytoplasmic 3.2.2.- COG1957;Inosine-uridine nucleoside N-ribohydrolase 53590; Nucleoside hydrolase PF01156;Inosine-uridine preferring nucleoside hy;4.7e-194;codon 2-311 GO:0009226 nucleotide-sugar biosynthesis CDS ECK0645 gltL gltL b0652 683753 684478 - (no change) JW0647 684952 685677 - t glutamate and aspartate transporter subunit -!- ATP-binding component of ABC superfamily E 11121068 Cytoplasmic heteromultimer; glutamate ABC transporter (b0652-b0654-b0653) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG1126;ABC-type polar amino acid transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;5.5e-66;codon 27-212 GO:0005737 cytoplasm GO:0006537 glutamate biosynthesis -!- GO:0006532 aspartate biosynthesis CDS ECK0646 gltK gltK b0653 684478 685152 - (no change) JW0648 685677 686351 - t glutamate and aspartate transporter subunit -!- membrane component of ABC superfamily E 11121068 Integral Membrane Protein heteromultimer; glutamate ABC transporter (b0652-b0654-b0653) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 5 5 in "COG0765;ABC-type amino acid transport system, permease component" PF00528;Binding-protein-dependent transport syst;3.6e-32;codon 16-224 TIGR01726;HEQRo_perm_3TM: amino acid ABC transpo;7.5e-31;codon 12-118 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006537 glutamate biosynthesis -!- GO:0006532 aspartate biosynthesis CDS ECK0647 gltJ gltJ b0654 685152 685892 - (no change) JW0649 686351 687091 - t glutamate and aspartate transporter subunit -!- membrane component of ABC superfamily E 11121068 Integral Membrane Protein heteromultimer; glutamate ABC transporter (b0652-b0654-b0653) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 5 5 in regulated by attenuation (gltJ-gltK-gltL) "COG0765;ABC-type amino acid transport system, permease component" PF00528;Binding-protein-dependent transport syst;3.7e-41;codon 25-239 TIGR01726;HEQRo_perm_3TM: amino acid ABC transpo;3.7e-14;codon 21-132 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006537 glutamate biosynthesis -!- GO:0006532 aspartate biosynthesis CDS ECK0648 gltI gltI ybeJ -!- yzzK b0655 686062 686970 - (no change) JW5092 687261 688169 - t glutamate and aspartate transporter subunit -!- periplasmic-binding component of ABC superfamily E 1091636 -!- 1091635 -!- 10493123 -!- 8740179 -!- 10972807 Periplasmic 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-20 302 "COG0834;ABC-type amino acid transport/signal transduction systems, periplasmic component/domain" 53850; Periplasmic binding protein-like II PF00497;Bacterial extracellular solute-binding prot;1.1e-54;codon 42-272 GO:0042597 periplasmic space GO:0006537 glutamate biosynthesis CDS ECK0649 lnt lnt cutE b0657 688566 690104 - (no change) JW0654 689765 691303 - e apolipoprotein N-acyltransferase E 92041555 -!- 8344936 Integral Membrane Protein 2.3.1.- 7 6 COG0815;Apolipoprotein N-acyltransferase 56317; Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase PF00795;Carbon-nitrogen hydrolase;1.8e-50;codon 223-412 TIGR00546;lnt: apolipoprotein N-acyltransferase;1.9e-169;codon 63-458 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042158 lipoprotein biosynthesis CDS ECK0650 ybeX ybeX b0658 690129 691007 - (no change) JW0655 691328 692206 - pt predicteed ion transport ortholog in Salmonella is involved in Co2+ and Mg2+ efflux C Cytoplasmic COG4535;Putative Mg2+ and Co2+ transporter CorC 54631; CBS-domain PF00571;CBS domain;9.8e-11;codon 73-127 -!- PF00571;CBS domain;1.6e-09;codon 136-189 -!- PF03471;Transporter associated domain;1.2e-29;codon 205-283 GO:0009274 cell wall (sensu Bacteria) CDS ECK0651 ybeY ybeY b0659 691097 691564 - (no change) JW0656 692296 692763 - o conserved protein C Cytoplasmic COG0319;Predicted metal-dependent hydrolase PF02130;Uncharacterized protein family UPF0054;2.7e-53;codon 46-137 TIGR00043;TIGR00043: conserved hypothetical protein T;5.5e-55;codon 39-145 CDS ECK0652 ybeZ ybeZ phoL b0660 691561 692640 - (no change) JW0657 692760 693839 - d predicted protein with nucleoside triphosphate hydrolase domain not a member of Pho regulon C Cytoplasmic regulated by attenuation (ybeZ-ybeY) "COG1702;Phosphate starvation-inducible protein PhoH, predicted ATPase" 52540; P-loop containing nucleotide triphosphate hydrolases PF02562;PhoH-like protein;2.1e-154;codon 130-334 CDS ECK0653 miaB miaB yleA b0661 692754 694178 - (no change) JW0658 693953 695377 - e isopentenyl-adenosine A37 tRNA methylthiolase E 11882645 -!- 20042346 -!- 15339930 Cytoplasmic COG0621;2-methylthioadenine synthetase PF00919;Uncharacterized protein family UPF0004;1.5e-50;codon 4-104 -!- PF04055;Radical SAM superfamily;2.4e-33;codon 151-325 -!- PF01938;TRAM domain;6e-25;codon 378-441 "TIGR00089;TIGR00089: RNA modification enzymes,;2.7e-253;codon 4-437 -!- TIGR01574;miaB-methiolase: tRNA-i(6)A37 thiotra;0;codon 4-440" GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK0654 ubiF ubiF yleB b0662 694324 695499 + (no change) JW0659 695523 696698 + e "2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol oxygenase" E 20263754 1.14.13.- COG0654;2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases 51905; FAD/NAD(P)-binding domain PF01360;Monooxygenase;8.3e-41;codon 157-350 TIGR01988;Ubi-OHases: Ubiquinone biosynthesis hydrox;1.1e-193;codon 7-390 tRNA ECK0655 glnX glnX Su2 -!- Su_II -!- supE -!- glnVbeta b0664 695653 695727 - (no change) JWR0011 696852 696926 - n tRNA-Gln(CUG) (Glutamine tRNA2) E 91312452 -!- 92215850 -!- 94105154 tRNA ECK0656 glnV glnV Su2 -!- Su_II -!- supE -!- glnValpha -!- suII b0665 695765 695839 - (no change) JWR0012 696964 697038 - n tRNA-Gln(CUG) (Glutamine tRNA2) E 91312452 -!- 92215850 -!- 94105154 tRNA ECK0657 metU metU metT(beta) -!- metTbeta b0666 695887 695963 - (no change) JWR0013 697086 697162 - n tRNA-Met(CAU) (Methionine tRNAm) duplicate of metT E 90221808 tRNA ECK0658 glnW glnW glnUbeta -!- sufG b0668 695979 696053 - (no change) JWR0014 697178 697252 - n tRNA-Gln(UUG) (Glutamine tRNA1) E 91312452 -!- 92215850 -!- 94105154 tRNA ECK0659 glnU glnU su_B -!- su_B+ -!- sufG -!- supB -!- glnUalpha -!- trnA b0670 696088 696162 - (no change) JWR0015 697287 697361 - n tRNA-Gln(UUG) (Glutamine tRNA1) E 45219 -!- 91312452 -!- 92215850 -!- 94105154 tRNA ECK0660 leuW leuW feeB b0672 696186 696270 - (no change) JWR0016 697385 697469 - n tRNA-Leu(UAG) (Leucine tRNA3) E 90230300 -!- 93287097 -!- 96386052 tRNA ECK0661 metT metT metTalpha b0673 696280 696356 - (no change) JWR0017 697479 697555 - n tRNA-Met(CAU) (Methionine tRNAm) duplicate of metU E 90221808 CDS ECK0662 asnB asnB b0674 696736 698400 - (no change) JW0660 697935 699599 - e asparagine synthetase B E 6102982 -!- 90330624 Cytoplasmic 6.3.5.4 Mg2+ monomeric multimer; asparagine synthetase B (b0674) C44 family; non-peptidase homologues (asparagine synthetase B) 1CT9 COG0367;Asparagine synthase (glutamine-hydrolyzing) 52402; Adenine nucleotide alpha hydrolases -!- 56235; N-terminal nucleophile aminohydrolases (Ntn hydrolases) PF00310;Glutamine amidotransferases class-II;4.4e-30;codon 2-162 -!- PF00733;Asparagine synthase;1.7e-111;codon 211-450 TIGR01536;asn_synth_AEB: asparagine synthase (glu;3.9e-239;codon 2-453 GO:0005737 cytoplasm GO:0009063 amino acid catabolism -!- GO:0006529 asparagine biosynthesis CDS ECK0663 nagD nagD b0675 698797 699549 - (no change) JW0661 699996 700748 - e UMP phosphatase not essential for N-acetylglucosamine metabolism E 89343637 Cytoplasmic COG0647;Predicted sugar phosphatases of the HAD superfamily 56784; HAD-like PF00702;haloacid dehalogenase-like hydrolase;7.7e-16;codon 3-223 "TIGR01460;HAD-SF-IIA: HAD-superfamily hydrolase, sub;2.1e-100;codon 6-223" GO:0046349 amino sugar biosynthesis CDS ECK0664 nagC nagC nagR b0676 699597 700817 - (no change) JW0662 700796 702016 - r "DNA-binding transcriptional dual regulator, repressor of N-acetylglucosamine" E 15066032 -!- 90136533 -!- 91171292 -!- 92114782 -!- 92356048 -!- 2190615 -!- 2668691 -!- 7545108 Cytoplasmic NagC/XylR celABCDF-ydjC -!- glmUS -!- manXYZ -!- nagBACD -!- nagE -!- nanC COG1940;Transcriptional regulator/sugar kinase 46785; Winged helix -!- 53067; Actin-like ATPase domain PF00480;ROK family;2.5e-92;codon 90-274 GO:0005737 cytoplasm GO:0046349 amino sugar biosynthesis -!- GO:0006350 transcription -!- GO:0009386 translational attenuation GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0665 nagA nagA b0677 700826 701974 - (no change) JW0663 702025 703173 - e N-acetylglucosamine-6-phosphate deacetylase E 89343637 -!- 90136533 -!- 90274974 -!- 92114782 Cytoplasmic 3.5.1.25 monomeric multimer; N-acetylglucosamine-6-phosphate deacetylase (b0677) COG1820;N-acetylglucosamine-6-phosphate deacetylase 51338; Composite domain of metallo-dependent hydrolases PF01979;Amidohydrolase family;5.5e-50;codon 50-364 TIGR00221;nagA: N-acetylglucosamine-6-phosphate deacet;5.6e-189;codon 1-377 GO:0046349 amino sugar biosynthesis CDS ECK0666 nagB nagB glmD b0678 702034 702834 - (no change) JW0664 703233 704033 - e glucosamine-6-phosphate deaminase E 89343637 -!- 90274974 -!- 92114782 -!- 92135199 -!- 10378272 -!- 11513596 -!- 11752775 -!- 12051945 -!- 3284790 -!- 8240271 -!- 8747459 Cytoplasmic 3.5.99.6 monomeric multimer; glucosamine-6-phosphate deaminase (b0678) COG0363;6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase 52512; Glucosamine 6-phosphate deaminase/isomerase PF01182;Glucosamine-6-phosphate isomerases/6-;4.2e-198;codon 15-250 TIGR00502;nagB: glucosamine-6-phosphate isomerase;1.3e-218;codon 1-259 GO:0046349 amino sugar biosynthesis CDS ECK0667 nagE nagE ptsN -!- pstN b0679 703167 705113 + (no change) JW0665 704366 706312 + t fused N-acetyl glucosamine specific PTS enzymes: IIC component -!- IIB component -!- IIA component E 88212176 -!- 90136533 -!- 95020584 -!- 95181483 -!- 3056518 Integral Membrane Protein 2.7.1.69 heteromultimer; EIINag (b2416-b2415-b0679) 4.A.1; The PTS Glucose-Glucoside (Glc) Family 11 10 in "fused PTS family enzyme, N-acetylglucosamine-specific: enzyme IIC (aa1-311) -!- enzyme IIB (aa341-466) -!- enzyme IIA (aa497-648)" "COG1263;Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific -!- COG1264;Phosphotransferase system IIB components -!- COG2190;Phosphotransferase system IIA components" 55604; Glucose permease domain IIB -!- 51261; Duplicated hybrid motif "PF02378;Phosphotransferase system, EIIC;2.9e-100;codon 11-300 -!- PF00367;phosphotransferase system, EIIB;4e-17;codon 393-427 -!- PF00358;phosphoenolpyruvate-dependent sugar phosph;4.8e-69;codon 517-621" "TIGR01998;PTS system, N-acetylglucosamine;0;3-463 -!- TIGR00852;PTS system, maltose/glucose;3.4e-118;45-311 -!- TIGR00826;PTS system, glucose-like IIB component;1.3e-37;360-452 -!- TIGR00830; PTS system, glucose subfamily, IIA component;1.8e-77;501-621" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009310 amine catabolism -!- GO:0046349 amino sugar biosynthesis CDS ECK0668 glnS glnS b0680 705316 706980 + (no change) JW0666 706515 708179 + e glutamyl-tRNA synthetase E 91312452 -!- 93011011 -!- 94105154 -!- 10860750 -!- 1857417 -!- 2464170 -!- 2479982 -!- 6288695 -!- 6389180 -!- 6749844 -!- 9298646 -!- 9562563 Cytoplasmic 6.1.1.18 regulated by attenuation (glnS) 1O0C COG0008;Glutamyl- and glutaminyl-tRNA synthetases 50715; Ribosomal protein L25-like -!- 52374; Nucleotidylyl transferase "PF00749;tRNA synthetases class I (E and Q), ca;5.4e-187;codon 27-338 -!- PF03950;tRNA synthetases class I (E and Q), an;2.1e-110;codon 340-528" TIGR00440;glnS: glutaminyl-tRNA synthetase;0;codon 28-551 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK0669 ybfM ybfM b0681 707557 708963 + (no change) JW0667 708756 710162 + pt predicted outer membrane porin C Outer Membrane B-barrel protein S43 family; non-peptidase homologues (ybfM protein) 1-20 CDS ECK0670 ybfN ybfN b0682 709013 709339 + (no change) JW0668 710212 710538 + lp predicted lipoprotein C Outer membrane Lipoprotein 1-21 CDS ECK0671 fur fur b0683 709423 709869 - (no change) JW0669 710622 711068 - r DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport E 91001360 -!- 92228755 -!- 10387106 -!- 1868094 -!- 2015825 -!- 2823881 -!- 2993806 Cytoplasmic monomeric multimer; Fur transcriptional dual regulator (b0683) Fur cirA -!- entCEBA-ybdB -!- entS -!- exbBD -!- fecABCDE -!- fecIR -!- fepA-entD -!- fepB -!- fepDGC -!- fes-entF-fepE -!- fhuACDB -!- fhuE -!- fiu -!- fumB -!- fur -!- nrdHIEF -!- pgmA -!- sodA -!- tonB -!- ygaC -!- yhhX COG0735;Fe2+/Zn2+ uptake regulation proteins 46785; Winged helix PF01475;Ferric uptake regulator family;1.3e-74;codon 10-130 GO:0005737 cytoplasm GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK0672 fldA fldA b0684 710158 710688 - (no change) JW0671 711357 711887 - c flavodoxin 1 "electron donor for activation of pyruvate formate-lyase, anaerobic ribonucleotide reductase" E 91154129 -!- 94089409 Cytoplasmic 1AHN COG0716;Flavodoxins 52218; Flavoproteins PF00258;Flavodoxin;2e-54;codon 6-160 TIGR01752;flav_long: flavodoxin;2.7e-122;codon 3-169 GO:0009053 electron donor activity CDS ECK0673 ybfE ybfE b0685 710828 711121 - start codon change JW5816 712027 712320 - cp LexA regulated protein E 20223640 -!- 12427949 Cytoplasmic "PF01402;Ribbon-helix-helix protein, copG family;1.3e-09;codon 73-113" GO:0009432 SOS response CDS ECK0674 ybfF ybfF b0686 711261 712025 - (no change) JW0673 712460 713224 - d conserved protein C Cytoplasmic S33 family; non-peptidase homologues (YbfF protein) COG0596;Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) 53474; alpha/beta-Hydrolases PF00561;alpha/beta hydrolase fold;2.8e-17;codon 43-250 CDS ECK0675 seqA seqA b0687 712210 712755 + (no change) JW0674 713409 713954 + cp regulatory protein for replication initiation sequesters hemimethylated oriC origins E 14704346 -!- 21337010 -!- 94236686 -!- 98409620 -!- 99400632 -!- 7553853 -!- 7850437 Cytoplasmic COG3057;Negative regulator of replication initiationR PF03925;SeqA protein;1.4e-149;codon 1-181 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006261 DNA dependent DNA replication CDS ECK0676 pgm pgm blu b0688 712781 714421 + (no change) JW0675 713980 715620 + e phosphoglucomutase E 8083177 -!- 91297199 -!- 99364512 -!- 8011018 -!- 14165931 -!- 14216423 Cytoplasmic 5.4.2.2 Mg2+ COG0033;Phosphoglucomutase "53738; Phosphoglucomutase, first 3 domains" "PF02878;Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I;3.7e-39;codon 39-184 -!- PF02879;Phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain II;8.3e-18;codon 209-319 -!- PF02880;Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III;1.2e-28;codon 320-440 -!- PF00408;Phosphoglucomutase/phosphomannomutase, C-terminal;1.4e-13;codon 455-544" "TIGR01132;pgm: phosphoglucomutase, alpha-D-glucose pho;0;codon 1-544" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0006006 glucose metabolism CDS ECK0677 ybfP ybfP b0689 714635 715129 + (no change) JW0676 715834 716328 + o predicted protein C Outer membrane Lipoprotein 1-24 regulated by attenuation (ybfP) CDS ECK0678 ybfG ybfG ybfH b0690 715170 715580 - start codon change JW5094 716369 716779 - o predicted protein C Cytoplasmic CDS ECK0679 ybfH ybfH ybfI b0691 715611 715820 - start codon change JW5095 716810 717019 - o predicted protein C regulated by attenuation (ybfH) CDS ECK0680 potE potE b0692 716169 717488 - (no change) JW0679 717368 718687 - t putrescine/proton symporter: putrescine/ornithine antiporter E 92041955 -!- 97197801 Integral Membrane Protein 2.A.3; The Amino Acid-Polyamine-Organocation (APC) Family 12 12 in COG0531;Amino acid transporters PF00324;Amino acid permease;3.2e-06;codon 13-438 TIGR00905;2A0302: arginine/ornithine antiporter;1.5e-226;codon 1-439 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009310 amine catabolism -!- GO:0006596 polyamine biosynthesis -!- GO:0006970 response to osmotic stress GO:0015496 putrescine:ornithine antiporter activity CDS ECK0681 speF speF b0693 717485 719683 - (no change) JW0680 718684 720882 - e "ornithine decarboxylase isozyme, inducible" E 92041955 Cytoplasmic 4.1.1.17 "monomeric multimer; ornithine decarboxylase, degradative (b0693)" COG1982;Arginine/lysine/ornithine decarboxylases 53383; PLP-dependent transferases -!- 55904; Ornithine decarboxylase C-terminal domain "PF03709;Orn/Lys/Arg decarboxylase, N-terminal doma;4.8e-44;codon 1-103 -!- PF01276;Orn/Lys/Arg decarboxylase, major domain;0;codon 109-568 -!- PF03711;Orn/Lys/Arg decarboxylase, C-terminal doma;1.5e-87;codon 576-709" GO:0006596 polyamine biosynthesis CDS ECK0682 kdpE kdpE b0694 720279 720956 - (no change) JW5096 721478 722155 - r DNA-binding response regulator in two-component regulatory system with KdpD regulator of potassium transport E 92202140 -!- 92202141 -!- 92334154 Cytoplasmic Two kdpABC COG0745;Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;5.6e-47;codon 2-120 -!- PF00486;Transcriptional regulatory protein, C te;1.6e-19;codon 147-223" GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0683 kdpD kdpD kac b0695 720953 723637 - (no change) JW0683 722152 724836 - r fused sensory histidine kinase in two-component regulatory system with KdpE: signal sensing protein -!- sensory histidine kinase regulator of potassium transport E 14534307 -!- 20287588 -!- 20572080 -!- 92202141 -!- 92334154 -!- 94103190 -!- 9756874 -!- 7499326 Integral Membrane Protein monomeric multimer; KdpD (b0695) 4 4 in fused sensory histidine kinase: signal sensing protein (aa1-373) -!- sensory histidine kinase (aa402-894) COG2205;Osmosensitive K+ channel histidine kinase 52431; ETFP adenine nucleotide-binding domain-like -!- 52540; P-loop containing NTP hydrolases (2) -!- 47384; Homodimeric domain of signal transducing histidine kinase -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF02702;Osmosensitive K+ channel His kinase sensor;6.4e-158;22-230 -!- PF00582;Univ stress prot fam;9.5e-06;249-365 -!- PF00512;His Kinase A (phosphoacceptor);2.5e-15;663-730 -!- PF02518;His kinase-, DNA gyrase B-, and HSP90-like ATPase;1.6e-37;773-882" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006464 protein modification CDS ECK0684 kdpC kdpC kac b0696 723630 724202 - (no change) JW0684 724829 725401 - t "potassium translocating ATPase, subunit C" E 92202140 -!- 93167625 -!- 9858692 Membrane Anchored 3.6.3.12 heteromultimer; potassium ion P-type ATPase transporter (b0696-b0697-b0698) 3.A.3; The P-type ATPase (P-ATPase) Superfamily "COG2156;K+-transporting ATPase, c chain" "PF02669;K+-transporting ATPase, c chain;1.2e-146;codon 1-188" "TIGR00681;kdpC: K+-transporting ATPase, C subunit;5.3e-146;codon 2-188" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane "GO:0015662 ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism" CDS ECK0685 kdpB kdpB kac b0697 724211 726259 - (no change) JW0685 725410 727458 - t "potassium translocating ATPase, subunit B" E 92202140 -!- 93167625 -!- 9858692 -!- 6146979 Integral Membrane Protein 3.6.3.12 heteromultimer; potassium ion P-type ATPase transporter (b0696-b0697-b0698) 3.A.3; The P-type ATPase (P-ATPase) Superfamily 7 7 "COG2216;High-affinity K+ transport system, ATPase chain B" 56869; Membrane all-alpha PF00122;E1-E2 ATPase;8.1e-63;codon 71-297 -!- PF00702;haloacid dehalogenase-like hydrolase;2.2e-35;codon 301-539 "TIGR01497;kdpB: K+-transporting ATPase, B subunit;0;codon 2-677 -!- TIGR01494;ATPase_P-type: ATPase, P-type (transpor;3.6e-44;codon 71-325 -!- TIGR01494;ATPase_P-type: ATPase, P-type (transpor;6.3e-57;codon 374-608" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane "GO:0015662 ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism" CDS ECK0686 kdpA kdpA kac b0698 726282 727955 - (no change) JW0686 727481 729154 - t "potassium translocating ATPase, subunit A" E 92202140 -!- 93167625 -!- 9858692 -!- 6146979 Integral Membrane Protein 3.6.3.12 heteromultimer; potassium ion P-type ATPase transporter (b0696-b0697-b0698) 3.A.3; The P-type ATPase (P-ATPase) Superfamily 12 12 regulated by attenuation (kdpA-kdpB-kdpC-kdpD-kdpE) "COG2060;K+-transporting ATPase, A chain" PF03814;Potassium-transporting ATPase A subunit;0;codon 7-557 "TIGR00680;kdpA: K+-transporting ATPase, A subunit;0;codon 1-557" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane "GO:0015662 ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism" CDS ECK0687 kdpF kdpF b4513 727955 728044 - new JW0687 729154 729243 - f potassium ion accessory transporter subunit stabilizes kdp translocation complex E 10608856 -!- 9858692 -!- 9789555 Membrane Anchored GO:0031225 anchored to membrane CDS ECK0688 ybfA ybfA b0699 728357 728563 + (no change) JW0688 729556 729762 + o predicted protein C Membrane Anchored CDS ECK0689 rhsC rhsC b0700 728806 732999 + (no change) JW0689 730005 734198 + h rhsC element core protein RshC C 98361897 -!- 2403547 -!- 2644231 -!- 7934896 -!- 8387990 Cytoplasmic regulated by attenuation (rhsC1) COG3209;Rhs family protein PF05593;RHS Repeat;3.6;codon 316-356 -!- PF05593;RHS Repeat;0.016;codon 361-397 -!- PF05593;RHS Repeat;3.7e-05;codon 425-463 -!- PF05593;RHS Repeat;2.7e-05;codon 468-505 -!- PF05593;RHS Repeat;0.011;codon 533-570 -!- PF05593;RHS Repeat;1.8e-06;codon 575-612 -!- PF05593;RHS Repeat;4.9e-06;codon 637-674 -!- PF05593;RHS Repeat;0.00014;codon 679-715 -!- PF05593;RHS Repeat;0.0081;codon 720-756 -!- PF05593;RHS Repeat;0.00017;codon 859-895 -!- PF05593;RHS Repeat;0.00013;codon 939-985 -!- PF05593;RHS Repeat;11;codon 994-1042 -!- PF03527;RHS protein;1.7e-32;codon 1137-1183 9 of TIGR01643;YD repeat (two copies): 0.032;aa 361-402 -!- 0.00061;aa 404-445 -!- 1.1e-06;aa 468-509 -!- 0.45;aa 512-553 -!- 4.5e-05;aa 554-595 -!- 0.0026;aa 596-636 -!- 2.1e-06;aa 637-678 -!- 0.0083;aa 679-719 -!- 0.14;aa 859-899 CDS ECK0690 ybfB ybfB b0702 732999 733325 + (no change) JW0691 734198 734524 + pm predicted inner membrane protein C Integral Membrane Protein 3 3 CDS ECK0691 ybfO ybfO b0703 733443 734876 + (no change) JW0692 734642 736075 + h "conserved protein, rhs-like" C Cytoplasmic COG3209;Rhs family protein PF05593;RHS Repeat;0.00013;codon 17-63 -!- PF05593;RHS Repeat;11;codon 72-120 -!- PF03527;RHS protein;1.5e-33;codon 215-261 CDS ECK0692 ybfC ybfC b0704 734873 735442 + (no change) JW0693 736072 736641 + o predicted protein C Periplasmic CDS ECK0693 ybfQ ybfQ b4514 735668 735922 + new JW0694 736867 737121 + ph predicted transposase similarity to H-repeat-like proteins C PF01811;Transposase_18: Transposase;0.055;codon 22-84 CDS ECK0694 ybfL ybfL b0705 736123 737184 + pseudogene -!- start codon change JW0695 737322 738383 + "pseudogene, H repeat" su predicted transposase (pseudogene) C Cytoplasmic PF01609;Transposase DDE domain;1.9e-51;codon 12-250 CDS ECK0695 ybfD ybfD b0706 737315 738076 + (no change) JW0696 738514 739275 + d conserved protein C Cytoplasmic PF01609;Transposase DDE domain;4.1e-14;codon 105-252 CDS ECK0696 ybgA ybgA tkp b0707 738224 738733 + (no change) JW0697 739423 739932 + o conserved protein C 6325460 -!- 8387990 Cytoplasmic COG3272;Uncharacterized conserved protein CDS ECK0697 phr phr phrB b0708 738730 740148 + (no change) JW0698 739929 741347 + e "deoxyribodipyrimidine photolyase, FAD-binding" E 88262577 -!- 94143420 -!- 95311099 -!- 2200511 -!- 6325460 -!- 7604260 Cytoplasmic 4.1.99.3 1DNP COG0415;Deoxyribodipyrimidine photolyase 48173; FAD-binding (C-terminal) domain of DNA photolyase -!- 52425; N-terminal domain of DNA photolyase PF00875;DNA photolyase;4.2e-71;codon 2-177 -!- PF03441;FAD binding domain of DNA photolyase;6.2e-161;codon 202-469 GO:0005737 cytoplasm GO:0006281 DNA repair CDS ECK0698 ybgH ybgH b0709 740298 741779 - (no change) JW0699 741497 742978 - pt predicted transporter C Integral Membrane Protein 14 14 in COG3104;Dipeptide/tripeptide permease PF07690;Major Facilitator Superfamily;2e-11;codon 14-435 -!- PF00854;POT family;8.6e-112;codon 76-426 TIGR00924;yjdL_sub1_fam: amino acid/peptide trans;3.6e-49;codon 6-482 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009063 amino acid catabolism CDS ECK0699 ybgI ybgI b0710 742050 742793 + (no change) JW0700 743249 743992 + d conserved metal-binding protein C 14519207 Cytoplasmic monomeric multimer; putative hydrolase-oxidase (b0710) COG0327;Uncharacterized conserved protein PF01784;NIF3 (NGG1p interacting factor 3);1.1e-116;codon 10-243 TIGR00486;TIGR00486: conserved hypothetical protein T;1.4e-132;codon 1-247 CDS ECK0700 ybgJ ybgJ b0711 742816 743472 + (no change) JW0701 744015 744671 + pe predicted enzyme subunit C Cytoplasmic COG2049;Allophanate hydrolase subunit 1 PF02682;Allophanate hydrolase subunit;1.1e-141;codon 4-202 TIGR00370;TIGR00370: conserved hypothetical protein T;1.5e-162;codon 9-211 CDS ECK0701 ybgK ybgK b0712 743466 744398 + (no change) JW0702 744665 745597 + pe predicted enzyme subunit similarity with RuBisCO small subunit C Cytoplasmic COG1984;Allophanate hydrolase subunit 2 "55239; RuBisCO, small subunit" PF02626;Allophanate hydrolase subunit;1.6e-196;codon 23-298 TIGR00724;urea_amlyse_rel: urea amidolyase-rela;8.5e-222;codon 1-310 CDS ECK0702 ybgL ybgL b0713 744388 745122 + (no change) JW0703 745587 746321 + pe predicted lactam utilization protein low abundance protein C Cytoplasmic "COG1540;Uncharacterized proteins, homologs of lactam utilization protein B" PF03746;LamB/YcsF family;7.7e-161;codon 2-238 GO:0016052 carbohydrate catabolism -!- GO:0042493 response to drug CDS ECK0703 nei nei b0714 745158 745949 + (no change) JW0704 746357 747148 + e endonuclease VIII -!- 5-formyluracil/5-hydroxymethyluracil DNA glycosylase 5-formyluracil/5-hydroxymethyluracil DNA glycosylase E 10515930 -!- 20428684 -!- 20519646 -!- 97315256 -!- 9171429 Cytoplasmic 3.2.-.- COG0266;Formamidopyrimidine-DNA glycosylase 56736; DNA repair protein MutM (Fpg) PF01149;Formamidopyrimidine-DNA glycosylase N-;2.6e-46;codon 1-118 -!- PF06831;Formamidopyrimidine-DNA glycosylase H2;4.2e-36;codon 126-221 GO:0005737 cytoplasm GO:0006281 DNA repair CDS ECK0704 abrB abrB ybgN b0715 745946 746992 - start codon change JW5097 747145 748191 - pr predicted regulator C 8002588 Integral Membrane Protein 11 7 aidB regulated by attenuation (abrB) PF05145;Putative ammonia monooxygenase;2.6e-160;codon 44-359 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0705 ybgO ybgO b0716 747144 748205 - start codon change JW5098 748343 749404 - ps predicted fimbrial-like adhesin protein C Periplasmic 49401; Bacterial adhesins CDS ECK0706 ybgP ybgP b0717 748202 748930 - (no change) JW0707 749401 750129 - pf predicted assembly protein predicted periplasmic pilin assembly protein -!- similarity with PapD C Periplasmic "COG3121;P pilus assembly protein, chaperone PapD" 49354; PapD-like -!- 49584; Periplasmic chaperone C-domain PF00345;Gram-negative pili assembly chaperone;5.4e-41;codon 21-143 -!- PF02753;Gram-negative pili assembly chaperone;1e-11;codon 148-228 GO:0006457 protein folding CDS ECK0707 ybgQ ybgQ b0718 748945 751392 - start codon change JW5099 750144 752591 - pm predicted outer membrane protein C Periplasmic "COG3188;P pilus assembly protein, porin PapC" PF00577;Fimbrial Usher protein;0;codon 25-805 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0708 ybgD ybgD b0719 751452 752018 - (no change) JW0709 752651 753217 - ps predicted fimbrial-like adhesin protein C Periplasmic 1-23 "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;3.4e-67;codon 29-188 GO:0009289 fimbria CDS ECK0709 gltA gltA glut -!- icdB -!- gluT b0720 752408 753691 - (no change) JW0710 753607 754890 - e citrate synthase E 91273907 -!- 92041923 -!- 92082496 -!- 95247701 -!- 9579066 -!- 3309132 -!- 3514304 -!- 6343122 -!- 6380576 -!- 6383359 2.3.3.1 monomeric multimer; citrate synthase (b0720) 1K3P COG0372;Citrate synthase 48256; Citrate synthase PF00285;Citrate synthase;2e-237;codon 46-409 TIGR01798;cit_synth_I: citrate synthase I;1.1e-293;codon 13-421 GO:0006099 tricarboxylic acid cycle -!- GO:0009061 anaerobic respiration CDS ECK0710 sdhC sdhC cybA -!- dhsC b0721 754400 754789 + (no change) JW0711 755599 755988 + m "succinate dehydrogenase, membrane subunit, binds cytochrome b556" cytochrome b556 bound between SdhC and SdhD E 6237244 -!- 89076355 -!- 89123360 -!- 9521736 -!- 99414342 -!- 11259408 -!- 3309132 -!- 6383359 -!- 9822661 -!- Ohnishi T;Current Topics in Bioenergetics;1987;15:37-65 -!- Guest JR;J Gen Microbiol;1981;122:171 Integral Membrane Protein heteromultimer; membrane-bound subcomplex of succinate dehydrogenase (b0721-b0722) -!- heteromultimer; succinate dehydrogenase (b0723-b0724-b0721-b0722) 3 3 out 1NEN "COG2009;Succinate dehydrogenase/fumarate reductase, cytochrome b subunit" 56869; Membrane all-alpha PF01127;Succinate dehydrogenase cytochrome b subunit;1.2e-45;codon 5-122 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006099 tricarboxylic acid cycle -!- GO:0009060 aerobic respiration -!- GO:0017004 cytochrome biogenesis GO:0009053 electron donor activity CDS ECK0711 sdhD sdhD dhsD b0722 754783 755130 + (no change) JW0712 755982 756329 + m "succinate dehydrogenase, membrane subunit, binds cytochrome b556" cytochrome b556 bound bbetween SdhC and SdhD E 82124790 -!- 89076355 -!- 9521736 -!- 99414342 -!- 6383359 -!- Ohnishi T;Current Topics in Bioenergetics;1987;15:37-65 -!- Guest JR;J Gen Microbiol;1981;122:171 Integral Membrane Protein heteromultimer; membrane-bound subcomplex of succinate dehydrogenase (b0721-b0722) -!- heteromultimer; succinate dehydrogenase (b0723-b0724-b0721-b0722) 3 3 out 1NEN "COG2142;Succinate dehydrogenase, hydrophobic anchor subunit" 56869; Membrane all-alpha GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006099 tricarboxylic acid cycle -!- GO:0009060 aerobic respiration GO:0009053 electron donor activity CDS ECK0712 sdhA sdhA dhsA b0723 755130 756896 + (no change) JW0713 756329 758095 + c "succinate dehydrogenase, flavoprotein subunit" E 84307466 -!- 89123360 -!- 89276374 -!- 99414342 -!- 6388571 -!- 9298646 -!- 9600841 -!- Ohnishi T;Current Topics in Bioenergetics;1987;15:37-65 -!- Guest JR;J Gen Microbiol;1981;122:171 Cytoplasmic 1.3.99.1 heteromultimer; catalytic subcomplex of succinate dehydrogenase (b0723-b0724) -!- heteromultimer; succinate dehydrogenase (b0723-b0724-b0721-b0722) 1NEN "COG1053;Succinate dehydrogenase/fumarate reductase, flavoprotein subunit" 46977; Succinate dehydrogenase/fumarate reductase C-terminal domain -!- 51905; FAD/NAD(P)-binding domain -!- 56425; Succinate dehydrogenase/fumarate reductase catalytic domain PF00890;FAD binding domain;1.9e-221;codon 108-440 -!- PF02910;Fumarate reductase/succinate dehydroge;6.6e-69;codon 460-588 "TIGR01816;sdhA_forward: succinate dehydrogenase,;0;codon 6-588 -!- TIGR01812;sdhA_frdA_Gneg: succinate dehydrogenas;0;codon 9-588" GO:0005737 cytoplasm GO:0006099 tricarboxylic acid cycle -!- GO:0009060 aerobic respiration GO:0009053 electron donor activity CDS ECK0713 sdhB sdhB dhsB b0724 756912 757628 + (no change) JW0714 758111 758827 + c "succinate dehydrogenase, FeS subunit" E 85046453 -!- 85261336 -!- 89076355 -!- 99414342 -!- 6376123 -!- 9298646 -!- Ohnishi T;Current Topics in Bioenergetics;1987;15:37-65 -!- Guest JR;J Gen Microbiol;1981;122:171 Cytoplasmic 1.3.99.1 heteromultimer; catalytic subcomplex of succinate dehydrogenase (b0723-b0724) -!- heteromultimer; succinate dehydrogenase (b0723-b0724-b0721-b0722) 1NEN "COG0479;Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit" 46548; alpha-helical ferredoxin -!- 54292; 2Fe-2S ferredoxin-like TIGR00384;dhsB: succinate dehydrogenase and fumarate r;7.9e-108;codon 7-230 GO:0005737 cytoplasm GO:0006099 tricarboxylic acid cycle -!- GO:0009060 aerobic respiration GO:0009053 electron donor activity CDS ECK0714 sucA sucA lys -!- met -!- lys+met b0726 757929 760730 + (no change) JW0715 759128 761929 + e "2-oxoglutarate decarboxylase, thiamin-requiring" E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex E 4904515 -!- 6376123 -!- Reed LJ;Accounts of Chemical Research;1974;7:40-46 Cytoplasmic 1.2.4.2 Mg2+ heteromultimer; 2-oxoglutarate dehydrogenase complex (b0726-b0727-b0116) -!- monomeric multimer; 2-oxoglutarate decarboxylase component of 2-oxoglutarate dehydrogenase complex (b0726) "COG0567;2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, and related enzymes" 52518; Thiamin diphosphate-binding fold (THDP-binding) "PF00676;Dehydrogenase E1 component;9.3e-29;codon 205-528 -!- PF02779;Transketolase, pyridine binding domain;1.3e-75;codon 591-785" "TIGR00239;2oxo_dh_E1: 2-oxoglutarate dehydrogenase,;0;codon 14-930" GO:0006099 tricarboxylic acid cycle CDS ECK0715 sucB sucB lys -!- met b0727 760745 761962 + (no change) JW0716 761944 763161 + e dihydrolipoyltranssuccinase E2 component of the 2-oxoglutarate dehydrogenase multienzyme complex E 4904515 -!- 87005261 -!- 10739245 -!- 1554728 -!- 6376123 -!- 6376124 -!- 8950276 -!- 9298646 -!- 9677295 -!- Reed LJ;Accounts of Chemical Research;1974;7:40-46 Cytoplasmic 2.3.1.61 Mg2+ heteromultimer; 2-oxoglutarate dehydrogenase complex (b0726-b0727-b0116) -!- monomeric multimer; dihydrolipoamide succinate transferase (b0727) "COG0508;Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes" 47005; Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex -!- 51230; Single hybrid motif -!- 52777; CoA-dependent acyltransferases PF00364;Biotin-requiring enzyme;2.3e-21;codon 4-77 -!- PF02817;e3 binding domain;1.6e-17;codon 114-150 -!- PF00198;2-oxoacid dehydrogenases acyltransferas;9.1e-142;codon 173-403 "TIGR01347;sucB: 2-oxoglutarate dehydrogenase, E2 compo;0;codon 4-405" GO:0006099 tricarboxylic acid cycle CDS ECK0716 sucC sucC b0728 762237 763403 + (no change) JW0717 763436 764602 + e "succinyl-CoA synthetase, beta subunit" E 7017725 -!- 91098272 -!- 10625475 -!- 3002435 -!- 8144675 -!- 9298646 -!- 9917402 -!- 6995430 Cytoplasmic 6.2.1.5 heteromultimer; succinyl-CoA synthetase (b0728-b0729) "COG0045;Succinyl-CoA synthetase, beta subunit" 52210; Succinyl-CoA synthetase domains -!- 56059; Glutathione synthetase ATP-binding domain-like PF02222;ATP-grasp domain;1.3e-29;codon 29-198 -!- PF00549;CoA-ligase;7.3e-81;codon 246-382 "TIGR01016;sucCoAbeta: succinyl-CoA synthetase, beta;1e-283;codon 1-386" GO:0006099 tricarboxylic acid cycle CDS ECK0717 sucD sucD b0729 763403 764272 + (no change) JW0718 764602 765471 + e "succinyl-CoA synthetase, NAD(P)-binding, alpha subunit" E 7017725 -!- 91098272 -!- 10625475 -!- 2548486 -!- 3002435 -!- 7783627 -!- 8144675 -!- 9298646 -!- 9917402 -!- 6995430 Cytoplasmic 6.2.1.5 heteromultimer; succinyl-CoA synthetase (b0728-b0729) "COG0074;Succinyl-CoA synthetase, alpha subunit" 51735; NAD(P)-binding Rossmann-fold domains -!- 52210; Succinyl-CoA synthetase domains PF02629;CoA binding domain;1.2e-67;codon 4-115 -!- PF00549;CoA-ligase;4.8e-62;codon 133-274 "TIGR01019;sucCoAalpha: succinyl-CoA synthetase, alp;1.1e-156;codon 3-288" GO:0006099 tricarboxylic acid cycle CDS ECK0718 mngR mngR farR -!- ybgB -!- G30 b0730 764376 765098 - (no change) JW0719 765575 766297 - r "DNA-binding transcriptional dual regulator, fatty-acyl-binding" fatty-acyl responsive E 14645248 -!- 95104410 -!- 12757941 -!- 2548486 -!- 9063979 Cytoplasmic monomeric multimer; MngR transcriptional repressor (b0730) GntR farR -!- mngA COG2188;Transcriptional regulators 46785; Winged helix "PF00392;Bacterial regulatory proteins, gntR family;8.4e-30;codon 6-69 -!- PF07702;UbiC transcription regulator-associated;1.1e-45;codon 90-229" GO:0005737 cytoplasm "GO:0006099 tricarboxylic acid cycle -!- GO:0006350 transcription -!- GO:0006355 regulation of transcription, DNA-dependent" GO:0016564 transcriptional repressor activity CDS ECK0719 mngA mngA hrsA b0731 765207 767183 + (no change) JW0720 766406 768382 + t fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component -!- IIB component -!- IIC component E 14645248 -!- 9063979 Integral Membrane Protein 2.7.1.69 heteromultimer; EIIHrsA (b2416-b2415-b0731) 4.A.2; The PTS Fructose-Mannitol (Fru) Family 9 9 in "fused PTS family enzyme, 2-O-alpha-mannosyl-D-glycerate specific: enzyme IIA (aa1-178) -!- enzyme IIB (aa186-454) -!- enzyme IIB (aa456-628)" "COG1762;Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) -!- COG1445;Phosphotransferase system fructose-specific component IIB -!- COG1299;Phosphotransferase system, fructose-specific IIC component" 55804; Phoshotransferase/anion transport protein -!- 55804; Phoshotransferase/anion transport protein "PF00359;Phosphoenolpyruvate-dependent sugar phos;1e-23;codon 25-171 -!- PF02379;PTS system, Fructose specific IIB subuni;8.1e-60;codon 185-288 -!- PF02378;Phosphotransferase system, EIIC;7.2e-22;codon 311-581" "TIGR00848;fruA: PTS system, fructose subfamily,;1.1e-59;codon 26-155 -!- TIGR00829;FRU: PTS system, fructose-specific, II;2.8e-24;codon 187-271 -!- TIGR01427;PTS_IIC_fructo: PTS system, fructose s;3.5e-83;codon 292-642" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism -!- GO:0006464 protein modification -!- GO:0009266 response to temperature CDS ECK0720 mngB mngB ybgG b0732 767201 769834 + (no change) JW0721 768400 771033 + e alpha-mannosidase 2-O-alpha-mannosyl-D-glycerate utilization E 14645248 -!- 9063979 Cytoplasmic COG0383;Alpha-mannosidase 69898; Golgi alpha-mannosidase II PF01074;Glycosyl hydrolases family;6.6e-34;codon 6-270 -!- PF07748;Glycosyl hydrolases family 38 C-termi;1.4e-07;codon 385-873 GO:0016052 carbohydrate catabolism CDS ECK0721 cydA cydA cyd-1 b0733 770681 772249 + start codon change JW0722 771880 773448 + c "cytochrome d terminal oxidase, subunit I" E 87299685 -!- 89255232 -!- 91035243 -!- 1689724 -!- 1724280 -!- 2843510 -!- 3138232 Integral Membrane Protein 1.9.3.- heteromultimer; cytochrome bd-I terminal oxidase (b0733-b0734) 9 9 in "COG1271;Cytochrome bd-type quinol oxidase, subunit 1" PF01654;Bacterial Cytochrome Ubiquinol Oxidase;0;codon 8-512 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009054 electron acceptor activity CDS ECK0722 cydB cydB cyd-2 b0734 772265 773404 + (no change) JW0723 773464 774603 + c "cytochrome d terminal oxidase, subunit II" E 87299685 -!- 89255232 -!- 91035243 -!- 2843510 -!- 3138232 Integral Membrane Protein 1.9.3.- heteromultimer; cytochrome bd-I terminal oxidase (b0733-b0734) 9 8 in "COG1294;Cytochrome bd-type quinol oxidase, subunit 2" PF02322;Cytochrome oxidase subunit II;1.9e-233;codon 5-367 "TIGR00203;cydB: cytochrome d ubiquinol oxidase, subuni;1.1e-223;codon 1-379" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009054 electron acceptor activity CDS ECK0723 ybgT ybgT b4515 773419 773532 + new JW0724 774618 774731 + o conserved protein "expressed in minicells, in CydAB operon" C Cytoplasmic GO:0005737 cytoplasm CDS ECK0724 ybgE ybgE b0735 773532 773825 + (no change) JW0725 774731 775024 + pm conserved inner membrane protein C Integral Membrane Protein 3 3 COG3790;Predicted membrane protein TIGR02112;cyd_oper_ybgE: cyd operon protein YbgE;3e-63;codon 5-97 CDS ECK0725 ybgC ybgC tol-orf1 b0736 773975 774379 + (no change) JW0726 775174 775578 + pe predicted acyl-CoA thioesterase C 11959124 -!- 10493123 -!- 3294803 Cytoplasmic heteromultimer; Tol-Pal Cell Envelope Complex (b0736-b0737-b0738-b0739-b0740-b0741-b0742) 1S5U COG0824;Predicted thioesterase 54637; Thioesterase/thiol ester dehydrase-isomerase PF03061;Thioesterase superfamily;1e-16;codon 20-105 TIGR00051;TIGR00051: conserved hypothetical protein;4.6e-74;codon 9-125 CDS ECK0726 tolQ tolQ fii -!- tolP b0737 774376 775068 + (no change) JW0727 775575 776267 + m membrane spanning protein in TolA-TolQ-TolR complex E 90036739 -!- 93322327 -!- 94131962 -!- 99403391 -!- 3294803 -!- 8376353 Integral Membrane Protein heteromultimer; Colicin S4 Transport System (b0737-b0738-b0739-b0740-b0741-b0742-b1256) -!- heteromultimer; The Colicin A Import System (b0737-b0738-b0739-b0740-b0741-b0742-b0929-b3966) -!- heteromultimer; The TolA-TolQ-TolR system for energization of outer-membrane receptor-mediated active transport (b0737-b0738-b0739-b0740-b0741-b0742) -!- heteromultimer; Tol-Pal Cell Envelope Complex (b0736-b0737-b0738-b0739-b0740-b0741-b0742) 1.A.30; H+- or Na+-translocating Bacterial Flagellar Motor 1ExbBD Outer Membrane Transport Energizer (Mot/Exb) Superfamily -!- 2.C.1; TonB-ExbB-ExbD/TolA-TolQ-TolR (TonB) Family of Auxiliary Proteins for Energization of OMR-mediated Active Transport 3 3 in COG0811;Biopolymer transport proteins PF01618;MotA/TolQ/ExbB proton channel family;1.6e-64;codon 73-211 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0727 tolR tolR b0738 775072 775500 + (no change) JW0728 776271 776699 + m membrane spanning protein in TolA-TolQ-TolR complex E 89359155 -!- 93322327 -!- 93388543 -!- 99403391 -!- 3294803 Membrane Anchored heteromultimer; Colicin S4 Transport System (b0737-b0738-b0739-b0740-b0741-b0742-b1256) -!- heteromultimer; The Colicin A Import System (b0737-b0738-b0739-b0740-b0741-b0742-b0929-b3966) -!- heteromultimer; The TolA-TolQ-TolR system for energization of outer-membrane receptor-mediated active transport (b0737-b0738-b0739-b0740-b0741-b0742) -!- heteromultimer; Tol-Pal Cell Envelope Complex (b0736-b0737-b0738-b0739-b0740-b0741-b0742) 1.A.30; H+- or Na+-translocating Bacterial Flagellar Motor 1ExbBD Outer Membrane Transport Energizer (Mot/Exb) Superfamily -!- 2.C.1; TonB-ExbB-ExbD/TolA-TolQ-TolR (TonB) Family of Auxiliary Proteins for Energization of OMR-mediated Active Transport COG0848;Biopolymer transport protein PF02472;Biopolymer transport protein ExbD/TolR;3.1e-14;codon 9-142 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0728 tolA tolA cim -!- excC -!- lky -!- tol-2 b0739 775565 776830 + (no change) JW0729 776764 778029 + m membrane anchored protein in TolA-TolQ-TolR complex E 20521929 -!- 91293069 -!- 91296736 -!- 93106959 -!- 99332679 -!- 99403391 -!- 2687247 -!- 8978668 Membrane Anchored heteromultimer; Colicin S4 Transport System (b0737-b0738-b0739-b0740-b0741-b0742-b1256) -!- heteromultimer; The Colicin A Import System (b0737-b0738-b0739-b0740-b0741-b0742-b0929-b3966) -!- heteromultimer; The TolA-TolQ-TolR system for energization of outer-membrane receptor-mediated active transport (b0737-b0738-b0739-b0740-b0741-b0742) -!- heteromultimer; Tol-Pal Cell Envelope Complex (b0736-b0737-b0738-b0739-b0740-b0741-b0742) 2.C.1; The TonB-ExbB-ExbD/TolA-TolQ-TolR (TonB) Family of Auxiliary Proteins for Energization of Outer Membrane Receptor (OMR)-mediated Active Transport COG3064;Membrane protein involved in colicin uptake PF06519;TolA protein;5.4e-209;codon 5-421 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0729 tolB tolB lky -!- lkyA -!- tol-3 b0740 776963 778255 + (no change) JW5100 778162 779454 + cp periplasmic protein "interacts with the TolA-TolQ-TolR complex, required for uptake of group A colicins" E 20015379 -!- 90078104 -!- 9701827 -!- 99403391 -!- 1574003 -!- 7929011 -!- 9740056 Periplasmic heteromultimer; Colicin S4 Transport System (b0737-b0738-b0739-b0740-b0741-b0742-b1256) -!- heteromultimer; The Colicin A Import System (b0737-b0738-b0739-b0740-b0741-b0742-b0929-b3966) -!- heteromultimer; The TolA-TolQ-TolR system for energization of outer-membrane receptor-mediated active transport (b0737-b0738-b0739-b0740-b0741-b0742) -!- heteromultimer; Tol-Pal Cell Envelope Complex (b0736-b0737-b0738-b0739-b0740-b0741-b0742) 2.C.1; The TonB-ExbB-ExbD/TolA-TolQ-TolR (TonB) Family of Auxiliary Proteins for Energization of Outer Membrane Receptor (OMR)-mediated Active Transport 430 regulated by attenuation (tolB-pal-ybgF) 1C5K COG0823;Periplasmic component of the Tol biopolymer transport system "50960; TolB, C-terminal domain -!- 52964; TolB, N-terminal domain" PF04052;TolB amino-terminal domain;1.5e-89;codon 6-173 -!- 5 of PF07676;WD40-like Beta Propeller Repeat: 0.45;codon 192-228 -!- 1.4e-06;codon 237-272 -!- 2.1e-06;codon 280-316 -!- 3.2;codon 324-360 -!- 0.053;codon 368-405 GO:0042597 periplasmic space CDS ECK0730 pal pal excC b0741 778290 778811 + (no change) JW0731 779489 780010 + lp peptidoglycan-associated outer membrane lipoprotein "subunit of the Tol-Pal system -!- required for outer membrane integrity, uptake of group A colicins, and translocation of phage DNA" E 11790745 -!- 87133578 -!- 92244043 -!- 99403391 -!- 11173492 -!- 2687247 Outer membrane Lipoprotein heteromultimer; Colicin S4 Transport System (b0737-b0738-b0739-b0740-b0741-b0742-b1256) -!- heteromultimer; The Colicin A Import System (b0737-b0738-b0739-b0740-b0741-b0742-b0929-b3966) -!- heteromultimer; The TolA-TolQ-TolR system for energization of outer-membrane receptor-mediated active transport (b0737-b0738-b0739-b0740-b0741-b0742) -!- heteromultimer; Tol-Pal Cell Envelope Complex (b0736-b0737-b0738-b0739-b0740-b0741-b0742) 2.C.1; The TonB-ExbB-ExbD/TolA-TolQ-TolR (TonB) Family of Auxiliary Proteins for Energization of Outer Membrane Receptor (OMR)-mediated Active Transport COG2885;Outer membrane protein and related peptidoglycan-associated (lipo)proteins PF00691;OmpA family;2.7e-50;codon 72-167 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0731 ybgF ybgF b0742 778821 779612 + (no change) JW0732 780020 780811 + d predicted protein C 11994151 -!- 1574003 -!- 7567469 Periplasmic heteromultimer; Colicin S4 Transport System (b0737-b0738-b0739-b0740-b0741-b0742-b1256) -!- heteromultimer; The Colicin A Import System (b0737-b0738-b0739-b0740-b0741-b0742-b0929-b3966) -!- heteromultimer; The TolA-TolQ-TolR system for energization of outer-membrane receptor-mediated active transport (b0737-b0738-b0739-b0740-b0741-b0742) -!- heteromultimer; Tol-Pal Cell Envelope Complex (b0736-b0737-b0738-b0739-b0740-b0741-b0742) 2.C.1; The TonB-ExbB-ExbD/TolA-TolQ-TolR (TonB) Family of Auxiliary Proteins for Energization of Outer Membrane Receptor (OMR)-mediated Active Transport 1-23 COG1729;Uncharacterized protein conserved in bacteria 48439; Protein prenylyltransferase PF07719;Tetratricopeptide repeat;0.0029;codon 180-213 -!- PF07719;Tetratricopeptide repeat;0.0035;codon 217-250 GO:0042597 periplasmic space tRNA ECK0732 lysT lysT Su(beta) -!- lysT-alpha -!- su-5 -!- supG -!- supK -!- supL -!- lysTalpha -!- sua b0743 779777 779852 + (no change) JWR0018 780976 781051 + n tRNA-Lys(UUU) (Lysine tRNA) E 90355199 -!- 91067686 -!- 92279029 tRNA ECK0733 valT valT valT-alpha -!- valTalpha b0744 779988 780063 + (no change) JWR0019 781187 781262 + n tRNA-Val(UAC) (Valine tRNA1) duplicate gene with valUXY E 91264822 tRNA ECK0734 lysW lysW lysT-beta -!- lysTbeta -!- su beta -!- su b0745 780066 780141 + (no change) JWR0020 781265 781340 + n tRNA-Lys(UUU) (Lysine tRNA) E 90230300 -!- 91067686 -!- 92279029 tRNA ECK0735 valZ valZ valT-beta -!- valTbeta b0746 780291 780366 + (no change) JWR0021 781490 781565 + n tRNA-Val(UAC) (Valine tRNA1) E 97061202 tRNA ECK0736 lysY lysY lysT-gamma -!- lysTg -!- lysTgamma b0747 780370 780445 + (no change) JWR0022 781569 781644 + n tRNA-Lys(UUU) (Lysine tRNA) E 2184240 -!- 12878731 tRNA ECK0737 lysZ lysZ lysT-gamma b0748 780592 780667 + (no change) JWR0023 781791 781866 + n "tRNA-Lys(UUU), (Lysine tRNA)" E 2184240 -!- 12878731 tRNA ECK0738 lysQ lysQ b0749 780800 780875 + (no change) JWR0024 781999 782074 + n tRNA-Lys(UUU) (Lysine tRNA) E 12878731 CDS ECK0739 nadA nadA nicA b0750 781308 782351 + (no change) JW0733 782507 783550 + e "quinolinate synthase, subunit A" E 88296484 -!- 90253646 Cytoplasmic heteromultimer; quinolinate synthetase (b2574-b0750) COG0379;Quinolinate synthase PF02445;Quinolinate synthetase A protein;1.1e-201;codon 29-341 "TIGR00550;nadA: quinolinate synthetase complex, A subu;1.3e-172;codon 21-342" GO:0005737 cytoplasm GO:0009435 nicotinamide adenine dinucleotide biosynthesis CDS ECK0740 pnuC pnuC b0751 782389 783108 + (no change) JW0734 783588 784307 + pt predicted nicotinamide mononucleotide transporter C 90330519 Integral Membrane Protein 7 6 in COG3201;Nicotinamide mononucleotide transporter PF04973;Nicotinamide mononucleotide transport;4.6e-112;codon 1-194 TIGR01528;NMN_trans_PnuC: nicotinamide mononucle;4.9e-101;codon 22-231 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0741 zitB zitB ybgR b0752 783105 784046 - (no change) JW0735 784304 785245 - t zinc efflux system E 12399046 -!- 14715669 -!- 21336524 Integral Membrane Protein 2.A.4; The Cation Diffusion Facilitator (CDF) Family 5 5 in COG1230;Co/Zn/Cd efflux system component PF01545;Cation efflux family;8.8e-122;codon 21-296 TIGR01297;CDF: cation diffusion facilitator family tra;3.3e-104;codon 17-294 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0742 ybgS ybgS b0753 784160 784540 - (no change) JW0736 785359 785739 - o conserved protein C Periplasmic 1-24 CDS ECK0743 aroG aroG b0754 784856 785908 + (no change) JW0737 786055 787107 + e "3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, phenylalanine repressible" E 2861143 -!- 92210532 -!- 10425687 -!- 6125934 -!- 9298646 Cytoplasmic 2.5.1.54 Fe2+ monomeric multimer; 2-dehydro-3-deoxyphosphoheptonate aldolase (b0754) 1QR7 COG0722;3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase 51569; Aldolase PF00793;DAHP synthetase I family;4.5e-185;codon 25-339 TIGR00034;aroFGH: phospho-2-dehydro-3-deoxyheptonate a;2.2e-285;codon 6-349 GO:0009094 L-phenylalanine biosynthesis CDS ECK0744 gpmA gpmA gpm b0755 786066 786818 - (no change) JW0738 787265 788017 - e phosphoglyceromutase 1 E 71230170 -!- 99364512 Cytoplasmic 5.4.2.1 monomeric multimer; phosphoglycerate mutase 1 (b0755) 1.00E+59 COG0588;Phosphoglycerate mutase 1 53254; Phosphoglycerate mutase-like PF00300;Phosphoglycerate mutase family;2.9e-143;codon 4-228 TIGR01258;pgm_1: phosphoglycerate mutase;1.5e-207;codon 4-248 GO:0006096 glycolysis -!- GO:0006094 gluconeogenesis CDS ECK0745 galM galM b0756 787020 788060 - (no change) JW0739 788219 789259 - e galactose-1-epimerase (mutarotase) E 93023849 -!- 95055764 -!- 9778377 Cytoplasmic 5.1.3.3 COG2017;Galactose mutarotase and related enzymes PF01263;Aldose 1-epimerase;3.6e-133;codon 17-342 GO:0042597 periplasmic space GO:0016052 carbohydrate catabolism CDS ECK0746 galK galK galA b0757 788054 789202 - (no change) JW0740 789253 790401 - e galactokinase E 92338916 -!- 13977183 -!- 200486 -!- 3158881 -!- 7966338 Cytoplasmic 2.7.1.6 Mg2+ COG0153;Galactokinase 54211; Ribosomal protein S5 domain 2-like PF00288;GHMP kinases putative ATP-binding protei;5.5e-51;codon 112-346 TIGR00131;gal_kin: galactokinase;1.1e-267;codon 4-382 GO:0030113 capsule (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006012 galactose metabolism -!- GO:0009242 colanic acid biosynthesis -!- GO:0016052 carbohydrate catabolism -!- GO:0009269 response to dessication "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0747 galT galT galB b0758 789206 790252 - (no change) JW0741 790405 791451 - e galactose-1-phosphate uridylyltransferase E 89247400 -!- 92338916 -!- 14412847 -!- 9698386 -!- 3022232 -!- 3158881 -!- 7669762 -!- 9063869 Cytoplasmic 2.7.7.10 Fe2+ -!- Zn2+ monomeric multimer; UDP-glucose-hexose-1-phosphate uridylyltransferase / galactose-1-phosphate uridylyltransferase (b0758) 1HXQ COG1085;Galactose-1-phosphate uridylyltransferase 54197; HIT-like PF01087;Galactose-1-phosphate uridyl transfer;7.6e-110;codon 2-176 -!- PF02744;Galactose-1-phosphate uridyl transfer;6.4e-107;codon 178-347 TIGR00209;galT_1: galactose-1-phosphate uridylyltransf;1.4e-225;codon 1-348 GO:0030113 capsule (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006012 galactose metabolism -!- GO:0009242 colanic acid biosynthesis -!- GO:0016052 carbohydrate catabolism -!- GO:0009269 response to dessication "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0748 galE galE galD b0759 790262 791278 - (no change) JW0742 791461 792477 - e UDP-galactose-4-epimerase E 89274199 -!- 92253563 -!- 92338916 -!- 3022232 -!- 6301942 -!- 8564363 -!- 8611559 -!- 8931134 -!- 9174344 -!- 9271499 -!- 9708982 Cytoplasmic 5.1.3.2 monomeric multimer; UDP-glucose 4-epimerase (b0759) 2UDP 51735; NAD(P)-binding Rossmann-fold domains PF01370;NAD dependent epimerase/dehydratase family;4e-192;codon 3-333 TIGR01179;galE: UDP-glucose 4-epimerase;1.7e-250;codon 2-336 GO:0030113 capsule (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006012 galactose metabolism -!- GO:0009242 colanic acid biosynthesis -!- GO:0016052 carbohydrate catabolism -!- GO:0009435 nicotinamide adenine dinucleotide biosynthesis -!- GO:0009269 response to dessication "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0749 modF modF phrA -!- chlD b0760 791539 793011 - (no change) JW0743 792738 794210 - t fused molybdate transporter subunits of ABC superfamily: ATP-binding components E 92141226 -!- 92204121 -!- 94143420 -!- 8564363 Cytoplasmic regulated by attenuation (modF) "fused molybdenum transport protein, ABC superfamily: atp_binding component (aa1-260) -!- atp_binding component (aa261-490)" "COG1119;ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;3.1e-20;codon 29-211 -!- PF00005;ABC transporter;3.4e-52;codon 286-479 GO:0005737 cytoplasm GO:0006777 Mo-molybdopterin cofactor biosynthesis GO:0042888 molybdenum ion transporter activity CDS ECK0750 modE modE modR -!- chlD b0761 793079 793867 - (no change) JW0744 794278 795066 - r DNA-binding transcriptional dual regulator repressor of molybdenum transport E 10206709 -!- 8564363 -!- 9466267 -!- 99377070 -!- 10075916 -!- 11421278 -!- 8550508 -!- 9210473 Cytoplasmic monomeric multimer; Molybdate-responsive transcription factor (b0761) dmsABC -!- hycABCDEFGH -!- moaABCDE -!- modABC -!- napFDAGHBC-ccmABCDEFGH -!- narXL COG2005;N-terminal domain of molybdenum-binding protein 46785; Winged helix -!- 50331; MOP-like PF00126;Bacterial regulatory helix-turn-helix protei;3.2e-16;codon 19-83 -!- PF03459;TOBE domain;4.2e-14;codon 125-189 -!- PF03459;TOBE domain;1.9e-11;codon 197-258 TIGR00637;ModE_repress: ModE molybdate transport r;7.3e-51;codon 16-114 -!- TIGR00638;Mop: molybdenum-pterin binding domain;1.3e-30;codon 123-193 -!- TIGR00638;Mop: molybdenum-pterin binding domain;0.00067;codon 195-262 GO:0005737 cytoplasm GO:0006777 Mo-molybdopterin cofactor biosynthesis -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK0751 ybhT ybhT b0762 793996 794145 + (no change) JW5102 795195 795344 + o predicted protein C CDS ECK0752 modA modA b0763 794312 795085 + (no change) JW0746 795511 796284 + t molybdate transporter subunit -!- periplasmic-binding component of ABC superfamily E 90148107 -!- 92011425 -!- 93368423 -!- 7860583 -!- 8564363 -!- 8576221 -!- 9302996 Periplasmic heteromultimer; molybdate ABC transporter (b0765-b0764-b0763) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-67 257 regulated by attenuation (modA-modB-modC) 1WOD "COG0725;ABC-type molybdate transport system, periplasmic component" 53850; Periplasmic binding protein-like II PF01547;Bacterial extracellular solute-binding prot;2.2e-08;codon 5-247 "TIGR01256;modA: molybdate ABC transporter, periplasmic;2.8e-134;codon 34-253" GO:0042597 periplasmic space GO:0006777 Mo-molybdopterin cofactor biosynthesis CDS ECK0753 modB modB chlJ -!- tslJ b0764 795085 795774 + (no change) JW0747 796284 796973 + t molybdate transporter subunit -!- membrane component of ABC superfamily E 89155423 -!- 90148107 -!- 93368423 -!- 3553151 -!- 7665460 -!- 8564363 Integral Membrane Protein heteromultimer; molybdate ABC transporter (b0765-b0764-b0763) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 5 5 in "COG4149;ABC-type molybdate transport system, permease component" PF00528;Binding-protein-dependent transport syst;7.9e-21;codon 7-229 "TIGR02141;modB_ABC: molybdate ABC transporter, permeas;2.1e-95;codon 12-222" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0754 modC modC chlD -!- narD -!- modE b0765 795777 796835 + (no change) JW0748 796976 798034 + t molybdate transporter subunit -!- ATP-binding component of ABC superfamily E 87194564 -!- 89155423 -!- 93368423 -!- 7665460 -!- 8564363 Cytoplasmic 3.6.3.29 heteromultimer; molybdate ABC transporter (b0765-b0764-b0763) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG4148;ABC-type molybdate transport system, ATPase component" 50331; MOP-like -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.9e-68;codon 24-205 -!- PF03459;TOBE domain;6.1e-14;codon 290-352 "TIGR02142;modC_ABC: molybdate ABC transporter, ATP-bin;4.9e-257;codon 2-351 -!- TIGR00638;Mop: molybdenum-pterin binding domain;7.1e-22;codon 288-352" GO:0005737 cytoplasm GO:0006777 Mo-molybdopterin cofactor biosynthesis CDS ECK0755 ybhA ybhA modD b0766 796836 797654 - (no change) JW0749 798035 798853 - pe predicted hydrolase C 89155423 -!- 90148107 -!- 92011425 Cytoplasmic COG0561;Predicted hydrolases of the HAD superfamily 56784; HAD-like PF00702;haloacid dehalogenase-like hydrolase;6.9e-14;codon 3-244 "TIGR00099;Cof-subfamily: Cof-like hydrolase;1.5e-98;codon 5-267 -!- TIGR01484;HAD-SF-IIB: HAD-superfamily hydrolase,;1.3e-08;codon 5-240" CDS ECK0756 ybhE ybhE pgl -!- blu b0767 797809 798804 + (no change) JW0750 799008 800003 + e 6-phosphogluconolactonase E 15576773 -!- 15766779 Cytoplasmic 3.1.1.31 COG2706;3-carboxymuconate cyclase CDS ECK0757 ybhD ybhD b0768 798845 799861 - (no change) JW5896 800044 801060 - pr predicted DNA-binding transcriptional regulator C Membrane Anchored LysR regulated by attenuation (ybhD) 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;7.2e-20;codon 26-85 -!- PF03466;LysR substrate binding domain;4.9e-50;codon 109-316 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0758 ybhH ybhH b0769 799982 801034 + (no change) JW0752 801181 802233 + o conserved protein C Cytoplasmic COG2828;Uncharacterized protein conserved in bacteria PF04303;Protein of unknown function (DUF453);2.9e-238;codon 1-350 CDS ECK0759 ybhI ybhI b0770 801110 802543 + (no change) JW0753 802309 803742 + pt predicted transporter C Integral Membrane Protein 15 15 out COG0471;Di- and tricarboxylate transporters PF00939;Sodium:sulfate symporter transmembrane;1.4e-273;codon 3-474 TIGR00785;dass: anion transporter;2.4e-246;codon 23-468 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0760 ybhJ ybhJ b0771 802726 804987 + start codon change JW5103 803925 806186 + pe predicted hydratase "similarity with AcnA -!- not responsible for the residual aconitase activity in acnA, acnB double mutants" C 11782506 Cytoplasmic COG1048;Aconitase A "52016; Aconitase, C-terminal domain -!- 53732; Aconitase, first 3 domains" PF00330;Aconitase family (aconitate hydratase);1.2e-13;codon 44-479 -!- PF00694;Aconitase C-terminal domain;0.044;codon 579-693 CDS ECK0761 ybhC ybhC b0772 805221 806504 - (no change) JW0755 806420 807703 - pe predicted pectinesterase outer membrane protein C 15130122 -!- 10806384 -!- 331474 -!- 7567469 Outer membrane Lipoprotein 1-68 COG4677;Pectin methylesterase 51126; Pectin lyase-like PF01095;Pectinesterase;1e-06;codon 81-405 -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0008152 metabolism -!- GO:0000272 polysaccharide catabolism CDS ECK0762 ybhB ybhB b0773 806656 807132 - (no change) JW0756 807855 808331 - pf predicted kinase inhibitor C 11439028 -!- 3058702 Cytoplasmic 1VI3 COG1881;Phospholipid-binding protein 49777; PEBP-like PF01161;Phosphatidylethanolamine-binding protein;1.4e-07;codon 6-158 TIGR00481;TIGR00481: conserved hypothetical protein T;6.7e-95;codon 18-157 CDS ECK0763 bioA bioA b0774 807191 808480 - (no change) JW0757 808390 809679 - e "7,8-diaminopelargonic acid synthase, PLP-dependent" E 14756557 -!- 89066784 -!- 94170810 -!- 10452893 Cytoplasmic 2.6.1.62 monomeric multimer; adenosylmethionine-8-amino-7-oxononanoate aminotransferase (b0774) 1QJ5 COG0161;Adenosylmethionine-8-amino-7-oxononanoate aminotransferase 53383; PLP-dependent transferases PF00202;Aminotransferase class-III;1e-162;codon 16-425 TIGR00508;bioA: adenosylmethionine-8-amino-7-oxononano;2e-252;codon 1-424 GO:0009102 biotin biosynthesis CDS ECK0764 bioB bioB b0775 808567 809607 + (no change) JW0758 809766 810806 + e biotin synthase E 11834738 -!- 12475249 -!- 14704425 -!- 14967041 -!- 20250955 -!- 89066784 -!- 94170810 -!- 94190882 -!- 97382445 -!- 11686925 Cytoplasmic 2.8.1.6 monomeric multimer; biotin synthase (b0775) 1R30 COG0502;Biotin synthase and related enzymes PF04055;Radical SAM superfamily;2e-25;codon 47-209 -!- PF06968;Biotin and Thiamin Synthesis associated d;6.2e-54;codon 220-312 TIGR00433;bioB: biotin synthase;2.7e-209;codon 15-310 GO:0009102 biotin biosynthesis CDS ECK0765 bioF bioF b0776 809604 810758 + (no change) JW0759 810803 811957 + e 8-amino-7-oxononanoate synthase E 89066784 -!- 94170810 -!- 9813126 2.3.1.47 monomeric multimer; 8-amino-7-oxononanoate synthase (b0776) COG0156;7-keto-8-aminopelargonate synthetase and related enzymes 53383; PLP-dependent transferases PF00155;Aminotransferase class I and II;8.1e-73;codon 71-381 TIGR00858;bioF: 8-amino-7-oxononanoate synthase;7.1e-231;codon 19-381 GO:0009102 biotin biosynthesis CDS ECK0766 bioC bioC b0777 810745 811500 + (no change) JW0760 811944 812699 + pe "predicted methltransferase, enzyme of biotin synthesis" C 89066784 -!- 94170810 Cytoplasmic COG0500;SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases TIGR02072;BioC: biotin biosynthesis protein BioC;6.6e-121;codon 12-250 GO:0009102 biotin biosynthesis CDS ECK0767 bioD bioD b0778 811493 812170 + (no change) JW0761 812692 813369 + e dethiobiotin synthetase E 89066784 -!- 94118326 -!- 94170810 -!- 10089457 -!- 7881906 -!- 8081756 -!- 9125495 -!- 9576910 -!- 9865950 Cytoplasmic 6.3.3.3 Mg2+ monomeric multimer; dethiobiotin synthetase (b0778) 1-29 COG0132;Dethiobiotin synthetase 52540; P-loop containing nucleotide triphosphate hydrolases PF01656;CobQ/CobB/MinD/ParA nucleotide binding domai;2.4e-29;codon 5-224 TIGR00347;bioD: dethiobiotin synthase;5.4e-107;codon 6-176 GO:0009102 biotin biosynthesis CDS ECK0768 uvrB uvrB dar-1 -!- dar-6 b0779 812749 814770 + (no change) JW0762 813948 815969 + cp "excinulease of nucleotide excision repair, DNA damage recognition component" E 2843804 -!- 89367292 -!- 90237003 -!- 90368795 -!- 99400633 -!- 99419077 -!- 12145219 -!- 11421287 -!- 10946234 -!- 10371161 -!- 10631326 -!- 11689453 -!- 3008099 -!- 3515321 Cytoplasmic heteromultimer; UvrABC Nucleotide Excision Repair Complex (b0779-b1913-b3813-b4058) COG0556;Helicase subunit of the DNA excision repair complex "46600; C-terminal, UvrC-binding domain of UvrB -!- 52540; P-loop containing nucleotide triphosphate hydrolases" "PF04851;Type III restriction enzyme, res subunit;4.3e-06;codon 11-130 -!- PF00271;Helicase conserved C-terminal domain;1.6e-19;codon 465-546 -!- PF02151;UvrB/uvrC motif;1.5e-13;codon 633-668" "TIGR00631;uvrb: excinuclease ABC, B subunit;0;codon 4-666" GO:0005737 cytoplasm GO:0006308 DNA catabolism -!- GO:0006281 DNA repair -!- GO:0006308 DNA catabolism -!- GO:0009314 response to radiation -!- GO:0009432 SOS response CDS ECK0769 ybhK ybhK b0780 814962 815870 - (no change) JW0763 816161 817069 - pe predicted transferase with NAD(P)-binding Rossmann-fold domain CofD-like protein with predicted phosphatase or sulfatase C Cytoplasmic COG0391;Uncharacterized conserved protein 51735; NAD(P)-binding Rossmann-fold domains PF01933;Uncharacterised protein family UPF0052;7.3e-132;codon 12-302 TIGR01826;CofD_related: conserved hypothetical pro;2.6e-168;codon 12-299 CDS ECK0770 moaA moaA bisA -!- chlA -!- chlA1 -!- narA b0781 816267 817256 + (no change) JW0764 817466 818455 + e molybdopterin biosynthesis protein A E 92268047 -!- 93133126 -!- 93368423 Cytoplasmic COG2896;Molybdenum cofactor biosynthesis enzyme PF04055;Radical SAM superfamily;7e-40;codon 18-181 -!- PF06463;Molybdenum Cofactor Synthesis C;1.5e-47;codon 186-313 GO:0006777 Mo-molybdopterin cofactor biosynthesis CDS ECK0771 moaB moaB chlA2 b0782 817278 817790 + (no change) JW0765 818477 818989 + pf molybdopterin biosynthesis protein B E 93368423 Cytoplasmic monomeric multimer; MoaB (b0782) 1R2K COG0521;Molybdopterin biosynthesis enzymes 53218; Molybdenum cofactor biosynthesis proteins PF00994;Probable molybdopterin binding domain;4.4e-52;codon 11-150 TIGR00177;molyb_syn: molybdenum cofactor synthesis do;5.7e-46;codon 10-153 GO:0006777 Mo-molybdopterin cofactor biosynthesis CDS ECK0772 moaC moaC chlA3 b0783 817793 818278 + (no change) JW0766 818992 819477 + pe "molybdopterin biosynthesis, protein C" ferritin-like E 93368423 -!- 10903949 Cytoplasmic 1EKR COG0315;Molybdenum cofactor biosynthesis enzyme "55040; Molybdenum cofactor biosynthesis protein C, MoaC" PF01967;MoaC family;1.2e-95;codon 15-150 TIGR00581;moaC: molybdenum cofactor biosynthesis prote;9.6e-75;codon 4-152 GO:0006777 Mo-molybdopterin cofactor biosynthesis CDS ECK0773 moaD moaD chlM -!- chlA4 b0784 818271 818516 + (no change) JW0767 819470 819715 + e "molybdopterin synthase, small subunit" E 90148107 -!- 92268047 -!- 93293873 -!- 93368423 -!- 12571227 -!- 11135669 Cytoplasmic heteromultimer; molybdoprotein complex (b2203-b2206-b0784) 1JW9 "COG1977;Molybdopterin converting factor, small subunit" 54285; MoaD/ThiS PF02597;ThiS family;3.4e-28;codon 4-81 "TIGR01682;moaD: molybdopterin converting factor, subun;5.8e-37;codon 2-81" GO:0006777 Mo-molybdopterin cofactor biosynthesis CDS ECK0774 moaE moaE chlA5 b0785 818518 818970 + (no change) JW0768 819717 820169 + e "molybdopterin synthase, large subunit" E 93368423 -!- 12571227 -!- 11135669 -!- 8514782 Cytoplasmic monomeric multimer; molybdopterin synthase (b0785) 1NVI "COG0314;Molybdopterin converting factor, large subunit" 54690; Molybdopterin synthase subunit MoaE PF02391;MoaE protein;3.2e-63;codon 5-122 GO:0006777 Mo-molybdopterin cofactor biosynthesis CDS ECK0775 ybhL ybhL b0786 819107 819811 + (no change) JW0769 820306 821010 + pm predicted inner membrane protein C Integral Membrane Protein 9.B.24; The Testis-Enhanced Gene Transfer (TEGT) Family 7 7 in "COG0670;Integral membrane protein, interacts with FtsH" PF01027;Uncharacterised protein family UPF0005;1.1e-66;codon 13-234 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0776 ybhM ybhM b0787 820016 820729 + (no change) JW0770 821215 821928 + pm conserved inner membrane protein C Integral Membrane Protein 7 7 in "COG0670;Integral membrane protein, interacts with FtsH" PF01027;Uncharacterised protein family UPF0005;8.8e-48;codon 9-228 GO:0009274 cell wall (sensu Bacteria) CDS ECK0777 ybhN ybhN b0788 820765 821721 - (no change) JW0771 821964 822920 - pm conserved inner membrane protein C Integral Membrane Protein 8 8 in COG0392;Predicted integral membrane protein CDS ECK0778 ybhO ybhO b0789 821721 822962 - (no change) JW0772 822920 824161 - e cardiolipin synthase 2 E 20102623 -!- 10634942 Cytoplasmic 2.7.8.- COG1502;Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes 56024; Phospholipase D/nuclease PF00614;Phospholipase D Active site motif;7.7e-08;codon 108-135 -!- PF00614;Phospholipase D Active site motif;1.2;codon 285-312 GO:0008654 phospholipid biosynthesis CDS ECK0779 ybhP ybhP b0790 822959 823720 - (no change) JW0773 824158 824919 - pe predicted DNase C Cytoplasmic COG3568;Metal-dependent hydrolase 56219; DNase I-like PF03372;Endonuclease/Exonuclease/phospha tase fa;8.5e-32;codon 10-251 GO:0006308 DNA catabolism CDS ECK0780 ybhQ ybhQ b0791 823853 824263 + (no change) JW0774 825052 825462 + pm predicted inner membrane protein C Integral Membrane Protein 4 4 in CDS ECK0781 ybhR ybhR b0792 824225 825331 - (no change) JW5803 825424 826530 - pt predicted transporter subunit: membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YbhF/YbhR/YbhS ABC transporter (b0793-b0792-b0794) 6 6 in "COG0842;ABC-type multidrug transport system, permease component" PF01061;ABC-2 type transporter;2.4e-44;codon 115-333 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0782 ybhS ybhS b0793 825342 826475 - (no change) JW0777 826541 827674 - pt predicted transporter subunit: membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YbhF/YbhR/YbhS ABC transporter (b0793-b0792-b0794) 6 6 in "COG0842;ABC-type multidrug transport system, permease component" PF01061;ABC-2 type transporter;2e-18;codon 138-342 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0783 ybhF ybhF b0794 826468 828204 - start codon change JW5104 827667 829403 - pt fused predicted transporter subunits of ABC superfamily: ATP-binding components C Cytoplasmic heteromultimer; YbhF/YbhR/YbhS ABC transporter (b0793-b0792-b0794) "fused predicted transport protein, ABC superfamily: atp_binding component (aa1-292) -!- atp_binding component (aa293-583)" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;5.4e-46;codon 38-218 -!- PF00005;ABC transporter;8.8e-51;codon 360-540 GO:0005737 cytoplasm CDS ECK0784 ybhG ybhG b0795 828197 829195 - (no change) JW0779 829396 830394 - pt "predicted membrane fusion protein (MFP) component of efflux pump, membrane anchor" C Membrane Anchored COG0845;Membrane-fusion protein 51230; Single hybrid motif PF00529;HlyD family secretion protein;2.2e-17;codon 43-327 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0785 ybiH ybiH b0796 829195 829866 - start codon change JW0780 830394 831065 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic TetR/AcrR COG1309;Transcriptional regulator 46689; Homeodomain-like "PF00440;Bacterial regulatory proteins, tetR family;4.4e-15;codon 21-66" GO:0005737 cytoplasm GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK0786 rhlE rhlE b0797 830095 831459 + (no change) JW0781 831294 832658 + e RNA helicase member of DEAD box family E 94312114 -!- 14731278 -!- 15554979 -!- 15196029 -!- 10361280 -!- 1931833 Cytoplasmic COG0513;Superfamily II DNA and RNA helicases 52540; P-loop containing nucleotide triphosphate hydrolases PF00270;DEAD/DEAH box helicase;1.9e-70;codon 24-197 -!- PF00271;Helicase conserved C-terminal domain;2e-33;codon 264-340 GO:0009451 RNA modification CDS ECK0787 ybiA ybiA b0798 831691 832173 - (no change) JW0783 832890 833372 - o conserved protein C Cytoplasmic COG3236;Uncharacterized protein conserved in bacteria CDS ECK0788 dinG dinG rarB b0799 832293 834443 + (no change) JW0784 833492 835642 + e ATP-dependent DNA helicase E 12748189 -!- 92250435 -!- 93219138 -!- 1629168 -!- 8037924 Cytoplasmic COG1199;Rad3-related DNA helicases 52540; P-loop containing nucleotide triphosphate hydrolases GO:0005737 cytoplasm GO:0006281 DNA repair -!- GO:0009432 SOS response CDS ECK0789 ybiB ybiB b0800 834471 835433 + (no change) JW0785 835670 836632 + pe predicted transferase/phosphorylase C Cytoplasmic COG0547;Anthranilate phosphoribosyltransferase 47648; Pyrimidine nucleoside phosphorylase N-terminal domain -!- 52418; Pyrimidine nucleoside phosphorylase central domain "PF02885;Glycosyl transferase family, helical;1.8e-24;codon 3-71 -!- PF00591;Glycosyl transferase family, a/b doma;5.5e-65;codon 77-320" CDS ECK0790 ybiC ybiC b0801 835574 836659 + (no change) JW0786 836773 837858 + pe predicted dehydrogenase C COG2055;Malate/L-lactate dehydrogenases PF02615;Malate/L-lactate dehydrogenase;1.3e-217;codon 5-341 CDS ECK0791 ybiJ ybiJ b0802 836888 837148 - (no change) JW0787 838087 838347 - o predicted protein C 1-22 PF07338;Protein of unknown function (DUF1471);1.4e-41;codon 1-86 CDS ECK0792 ybiI ybiI b0803 837413 837679 - (no change) JW0788 838612 838878 - o conserved protein C Cytoplasmic COG1734;DnaK suppressor protein PF01258;Prokaryotic dksA/traR C4-type zinc finge;8e-38;codon 1-71 CDS ECK0793 ybiX ybiX b0804 837753 838430 - start codon change JW5105 838952 839629 - o conserved protein C Cytoplasmic PF03171;2OG-Fe(II) oxygenase superfamily;7.4e-10;codon 90-189 CDS ECK0794 fiu fiu ybiL b0805 838472 840754 - (no change) JW0790 839671 841953 - pt predicted iron outer membrane transporter C 20267815 Outer Membrane B-barrel protein 1-33 COG4774;Outer membrane receptor for monomeric catechols 56935; Porins PF07715;TonB-dependent Receptor Plug Domain;3.6e-21;codon 67-169 -!- PF00593;TonB dependent receptor;1.9e-32;codon 514-760 TIGR01783;TonB-siderophor: TonB-dependent sider;2.4e-54;codon 70-760 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0006826 iron ion transport CDS ECK0795 ybiM ybiM b0806 841019 841279 - start codon change JW5106 842218 842478 - o predicted protein C PF07338;Protein of unknown function (DUF1471);7.5e-18;codon 49-134 CDS ECK0796 ybiN ybiN b0807 841555 842481 + start codon change JW5107 842754 843680 + pe predicted SAM-dependent methyltransferase C Cytoplasmic COG3129;Predicted SAM-dependent methyltransferase 53335; S-adenosyl-L-methionine-dependent methyltransferases PF05971;Protein of unknown function (DUF890);1.8e-228;codon 29-323 CDS ECK0797 ybiO ybiO b0808 842478 844703 - start codon change JW5108 843677 845902 - pt predicted mechanosensitive channel C Integral Membrane Protein 10 11 in "82861; Mechanosensitive channel protein MscS (YggB), transmembrane region -!- 50182; Sm-like ribonucleoproteins -!- 82689; Mechanosensitive channel protein MscS (YggB), C-terminal domain" PF00924;Mechanosensitive ion channel;1.5e-63;codon 514-716 CDS ECK0798 glnQ glnQ b0809 844964 845686 - (no change) JW0794 846163 846885 - t glutamine transporter subunit -!- ATP-binding component of ABC superfamily E 87115160 Cytoplasmic heteromultimer; glutamine ABC transporter (b0809-b0810-b0811) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG1126;ABC-type polar amino acid transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;4.5e-74;codon 27-212 GO:0005737 cytoplasm GO:0006542 glutamine biosynthesis CDS ECK0799 glnP glnP b0810 845683 846342 - (no change) JW0795 846882 847541 - t glutamine transporter subunit -!- membrane component of ABC superfamily E 87115160 Integral Membrane Protein heteromultimer; glutamine ABC transporter (b0809-b0810-b0811) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 5 3 in "COG0765;ABC-type amino acid transport system, permease component" PF00528;Binding-protein-dependent transport syst;3.2e-40;codon 15-218 TIGR01726;HEQRo_perm_3TM: amino acid ABC transpo;1.9e-46;codon 11-111 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006542 glutamine biosynthesis CDS ECK0800 glnH glnH b0811 846481 847227 - (no change) JW0796 847680 848426 - t glutamine transporter subunit -!- periplasmic binding component of ABC superfamily E 87115160 -!- 8831790 -!- 9298646 -!- 9571045 -!- 3027504 -!- 9740056 Periplasmic heteromultimer; glutamine ABC transporter (b0809-b0810-b0811) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-22 248 regulated by attenuation (glnH) 1WDN "COG0834;ABC-type amino acid transport/signal transduction systems, periplasmic component/domain" 53850; Periplasmic binding protein-like II PF00497;Bacterial extracellular solute-binding prot;2.8e-93;codon 27-245 TIGR01096;3A0103s03R: lysine-arginine-ornithine-bind;2.5e-115;codon 2-243 GO:0042597 periplasmic space GO:0006542 glutamine biosynthesis CDS ECK0801 dps dps pexB -!- vtm b0812 847631 848134 - (no change) JW0797 848830 849333 - c Fe-binding and storage protein binds and protects DNA against oxidative damage mediated by H(2)O(2) -!- induced by oxidative or nutritional stress E 1340475 -!- 12016214 -!- 12163499 -!- 3027504 -!- 7984106 -!- 8021175 -!- 8354462 -!- 9298646 -!- 9546221 -!- 9694902 Cytoplasmic monomeric multimer; Dps complex; stationary phase nucleoid component that sequesters iron and protects DNA from damage (b0812) 1F33 COG0783;DNA-binding ferritin-like protein (oxidative damage protectant) 47240; Ferritin-like PF00210;Ferritin-like domain;2.5e-28;codon 26-167 GO:0005737 cytoplasm GO:0042594 response to starvation CDS ECK0802 rhtA rhtA ybiF b0813 848433 849320 - (no change) JW0798 849632 850519 - t threonine and homoserine efflux system E 12648727 -!- 8021175 Integral Membrane Protein 2.A.7; The Drug/Metabolite Transporter (DMT) Superfamily 10 10 in "COG5006;Predicted permease, DMT superfamily" PF00892;Integral membrane protein DUF6;5.1e-21;codon 158-281 GO:0009274 cell wall (sensu Bacteria) CDS ECK0803 ompX ompX ompP -!- ybiG b0814 849673 850188 + (no change) JW0799 850872 851387 + m outer membrane protein receptor for phage OX2 E 14679242 -!- 15037080 -!- 94117370 -!- 95138044 -!- 99339953 -!- 10545325 -!- 9629924 1-23 171 1Q9F COG3637;Opacity protein and related surface antigens 56925; Outer membrane protein PF06316;Enterobacterial Ail/Lom protein;6e-18;codon 1-171 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0804 ybiP ybiP b0815 850237 851820 - (no change) JW0800 851436 853019 - pe "predicted hydrolase, inner membrane" C Integral Membrane Protein 4 4 out "COG2194;Predicted membrane-associated, metal-dependent hydrolase" 53649; Alkaline phosphatase-like PF00884;Sulfatase;7.3e-98;codon 215-517 GO:0009274 cell wall (sensu Bacteria) CDS ECK0805 yliL yliL b0816 851894 852163 + (no change) JW5969 853093 853362 + GeneMark cannot predict -!- similar to hypothetical protein of O157 o predicted protein C 15690043 misc_RNA ECK0806 rybA rybA b4416 852175 852263 - (no change) JWR0226 853374 853462 - n small RNA E 11445539 CDS ECK0807 mntR mntR ybiQ b0817 852406 852873 + (no change) JW0801 853605 854072 + r DNA-binding transcriptional regulator of mntH Mn(2+) responsive E 21359323 Cytoplasmic COG1321;Mn-dependent transcriptional regulator "46785; Winged helix -!- 47979; Iron-dependent represor protein, dimerization domain" "PF02742;Iron dependent repressor, metal binding;3.4e-07;codon 95-153" CDS ECK0808 ybiR ybiR b0818 852870 853988 + (no change) JW0802 854069 855187 + pt predicted transporter closer to citB than arsB family C Integral Membrane Protein 10 9 out COG0471;Di- and tricarboxylate transporters GO:0009274 cell wall (sensu Bacteria) CDS ECK0809 ybiS ybiS b0819 854047 854967 - (no change) JW0803 855246 856166 - o conserved protein C 10493123 -!- 9298646 306 COG1376;Uncharacterized protein conserved in bacteria PF03734;ErfK/YbiS/YcfS/YnhG;8.6e-67;codo n 96-233 CDS ECK0810 ybiT ybiT b0820 855186 856778 + (no change) JW0804 856385 857977 + pt fused predicted transporter subunits of ABC superfamily: ATP-binding components C Cytoplasmic "fused predicted transport protein, ABC superfamily: atp_binding component (aa1-280) -!- atp_binding component (aa293-583)" COG0488;ATPase components of ABC transporters with duplicated ATPase domains 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;2.3e-40;codon 27-228 -!- PF00005;ABC transporter;1.4e-41;codon 345-511 GO:0005737 cytoplasm CDS ECK0811 ybiU ybiU b0821 857019 858284 - (no change) JW0805 858218 859483 - o predicted protein C Cytoplasmic PF07350;Protein of unknown function (DUF1479);0;codon 2-421 CDS ECK0812 ybiV ybiV b0822 858436 859251 - (no change) JW0806 859635 860450 - pe predicted hydrolase C 15657928 Cytoplasmic COG0561;Predicted hydrolases of the HAD superfamily 56784; HAD-like PF00702;haloacid dehalogenase-like hydrolase;4.8e-05;codon 3-236 "TIGR00099;Cof-subfamily: Cof-like hydrolase;4.6e-89;codon 5-259 -!- TIGR01484;HAD-SF-IIB: HAD-superfamily hydrolase,;1.2e-12;codon 5-232" CDS ECK0813 ybiW ybiW pflF b0823 859397 861829 - (no change) JW0807 860596 863028 - pe predicted pyruvate formate lyase C Cytoplasmic COG1882;Pyruvate-formate lyase 51998; PFL-like glycyl radical enzymes PF02901;Pyruvate formate lyase;0;codon 9-671 -!- PF01228;Glycine radical;3.1e-23;codon 687-792 TIGR01774;PFL2-3: pyruvate formate-lyase;0;codon 1-810 GO:0006113 fermentation CDS ECK0814 ybiY ybiY pflE b0824 861835 862761 - (no change) JW0808 863034 863960 - pe predicted pyruvate formate lyase activating enzyme predicted 4Fe-4S ferredoxin protein C Cytoplasmic COG1180;Pyruvate-formate lyase-activating enzyme 54862; 4Fe-4S ferredoxins PF04055;Radical SAM superfamily;1.8e-09;codon 28-244 GO:0009061 anaerobic respiration -!- GO:0006464 protein modification CDS ECK0815 fsaA fsaA fsa -!- mipB -!- ybiZ b0825 862865 863527 + start codon change JW5109 864064 864726 + e fructose-6-phosphate aldolase 1 E 21179155 Cytoplasmic 4.1.2.- monomeric multimer; fructose 6-phosphate aldolase 1 (b0825) 51569; Aldolase PF00923;Transaldolase;2.6e-99;codon 26-242 "TIGR00875;talC: transaldolase, putative;2e-113;codon 25-239" CDS ECK0816 moeB moeB chlN b0826 863603 864352 - (no change) JW0810 864802 865551 - e molybdopterin synthase sulfurylase E 21433988 -!- 88314906 -!- 90148107 -!- 93293873 -!- 93368423 COG0476;Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 69572; Molybdenum cofactor biosynthesis protein MoeB PF00899;ThiF family;6.7e-58;codon 30-164 -!- PF05237;MoeZ/MoeB domain;4.1e-37;codon 168-249 GO:0006777 Mo-molybdopterin cofactor biosynthesis CDS ECK0817 moeA moeA bisB -!- chlE -!- narE b0827 864352 865587 - (no change) JW0811 865551 866786 - f molybdopterin biosynthesis protein adds molybdenum to dithiolene of molybdopterin E 12006571 -!- 21322584 -!- 88314906 -!- 90148107 -!- 93368423 -!- 9515915 Cytoplasmic regulated by attenuation (moeA-moeB) COG0303;Molybdopterin biosynthesis enzyme "53218; Molybdenum cofactor biosynthesis proteins -!- 63882; Molybdenum cofactor biosynthesis protein MoeA, N-terminal and linker domains" PF03453;MoeA N-terminal region (domain I and II;1.5e-86;codon 7-168 -!- PF00994;Probable molybdopterin binding domain;4.7e-59;codon 178-311 -!- PF03454;MoeA C-terminal region (domain IV);3.5e-26;codon 332-405 TIGR00177;molyb_syn: molybdenum cofactor synthesis do;1.6e-48;codon 177-314 GO:0006777 Mo-molybdopterin cofactor biosynthesis CDS ECK0818 iaaA iaaA spt -!- ybiK b0828 865791 866756 + (no change) JW0812 866990 867955 + e L-asparaginase E 20508248 -!- 3045084 -!- 7984428 Cytoplasmic 3.5.1.1 monomeric multimer; asparaginase III (b0828) -!- monomeric multimer; asparaginase III alpha-beta complex (b0828) T2 family; asparaginase COG1446;Asparaginase 56235; N-terminal nucleophile aminohydrolases (Ntn hydrolases) PF01112;Asparaginase;3e-190;codon 2-317 GO:0009063 amino acid catabolism CDS ECK0819 yliA yliA b0829 866776 868614 + (no change) JW5897 867975 869813 + pt fused predicted peptide transport subunits of ABC superfamily: ATP-binding components C Cytoplasmic heteromultimer; YliA/YliB/YliC/YliD ABC transporter (b0829-b0830-b0832-b0831) "fused predicted peptide transport protein, ABC superfamily: atp_binding component (aa1-279) -!- atp_binding component (aa281-612)" "COG1123;ATPase components of various ABC-type transport systems, contain duplicated ATPase" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 53795; PEP carboxykinase-like -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;4.5e-58;codon 31-234 -!- PF00005;ABC transporter;6.6e-62;codon 339-529 GO:0005737 cytoplasm CDS ECK0820 yliB yliB b0830 868634 870172 + (no change) JW5111 869833 871371 + pt predicted peptide transporter subunit: periplasmic-binding component of ABC superfamily C Periplasmic heteromultimer; YliA/YliB/YliC/YliD ABC transporter (b0829-b0830-b0832-b0831) 1UQW "COG0747;ABC-type dipeptide transport system, periplasmic component" 53850; Periplasmic binding protein-like II PF00496;Bacterial extracellular solute-binding prot;1.8e-87;codon 70-431 GO:0042597 periplasmic space CDS ECK0821 yliC yliC b0831 870190 871110 + (no change) JW0815 871389 872309 + pt predicted peptide transporter subunit: membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YliA/YliB/YliC/YliD ABC transporter (b0829-b0830-b0832-b0831) 6 6 in "COG0601;ABC-type dipeptide/oligopeptide/nickel transport systems, permease components" PF00528;Binding-protein-dependent transport syst;8.3e-56;codon 95-305 GO:0019866 inner membrane CDS ECK0822 yliD yliD b0832 871113 872024 + (no change) JW0816 872312 873223 + pt predicted peptide transporter subunit: membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YliA/YliB/YliC/YliD ABC transporter (b0829-b0830-b0832-b0831) 6 6 in "COG1173;ABC-type dipeptide/oligopeptide/nickel transport systems, permease components" PF00528;Binding-protein-dependent transport syst;7.9e-47;codon 101-303 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0823 yliE yliE b0833 872202 874550 + (no change) JW0817 873401 875749 + pm conserved inner membrane protein C Integral Membrane Protein 3 2 in COG2200;FOG: EAL domain 51412; Inosine monophosphate dehydrogenase (IMPDH) PF00563;EAL domain;3.8e-103;codon 526-767 CDS ECK0824 yliF yliF b0834 874558 875886 + (no change) JW0818 875757 877085 + pr predicted diguanylate cyclase C Integral Membrane Protein 3 2 in COG2199;FOG: GGDEF domain PF00990;GGDEF domain;3.7e-26;codon 291-438 TIGR00254;GGDEF: putative diguanylate cyclase (GGDEF);2.6e-17;codon 291-442 CDS ECK0825 yliG yliG b0835 875933 877258 - (no change) JW0819 877132 878457 - pe predicted SAM-dependent methyltransferase C Cytoplasmic COG0621;2-methylthioadenine synthetase 53335; S-adenosyl-L-methionine-dependent methyltransferases PF00919;Uncharacterized protein family UPF0004;1.1e-42;codon 9-102 -!- PF04055;Radical SAM superfamily;2.4e-29;codon 144-323 "TIGR00089;TIGR00089: RNA modification enzymes, MiaB-f;6.7e-138;codon 9-438 -!- TIGR01125;TIGR01125: MiaB-like tRNA modifying enzyme;0;codon 9-438" CDS ECK0826 yliH yliH b0836 877471 877854 + (no change) JW0820 878670 879053 + o conserved protein induced in stationary phase C 14727089 Cytoplasmic CDS ECK0827 yliI yliI b0837 877965 879080 + (no change) JW0821 879164 880279 + pe predicted dehydrogenase RpoS regulon member -!- similarity with glucose dehydrogenase B C Periplasmic 1-22 regulated by attenuation (yliI) COG2133;Glucose/sorbosone dehydrogenases 50952; Soluble quinoprotein glucose dehydrogenase CDS ECK0828 yliJ yliJ b0838 879077 879703 - start codon change JW0822 880276 880902 - pe predicted glutathione S-transferase C "47616; Glutathione S-transferases, C-terminal domain -!- 52833; Thioredoxin-like" "PF02798;Glutathione S-transferase, N-terminal domain;2.5e-15;codon 4-79 -!- PF00043;Glutathione S-transferase, C-terminal domain;6.6e-14;codon 92-199" CDS ECK0829 dacC dacC pbp b0839 879950 881152 + (no change) JW0823 881149 882351 + e D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 6a) E 88157719 -!- 7042389 Periplasmic 3.4.16.4 S11 family; penicillin-binding protein 6 1-27 400 COG1686;D-alanyl-D-alanine carboxypeptidase "56601; beta-Lactamase/D-ala carboxypeptidase -!- 69189; Penicillin-binding protein 5, C-terminal domain" "PF00768;D-alanyl-D-alanine carboxypeptidase;2.5e-152;codon 28-266 -!- PF07943;Penicillin-binding protein 5, C-termina;5.1e-39;codon 285-376" GO:0042597 periplasmic space GO:0042493 response to drug CDS ECK0830 deoR deoR nucR b0840 881199 881957 - (no change) JW0824 882398 883156 - r DNA-binding transcriptional repressor deoxyribose-5-phosphate responsive E 89231635 -!- 89336786 -!- 92231401 -!- 2994018 Cytoplasmic DeoR deoCABD -!- nupG -!- tsx COG1349;Transcriptional regulators of sugar metabolism 47413; lambda repressor-like DNA-binding domains "PF00455;Bacterial regulatory proteins, deoR family;2.3e-108;codon 8-232" GO:0005737 cytoplasm "GO:0015949 nucleobase, nucleoside and nucleotide interconversion -!- GO:0006350 transcription" GO:0016564 transcriptional repressor activity CDS ECK0831 ybjG ybjG b0841 882015 882611 - (no change) JW5112 883214 883810 - e undecaprenyl pyrophosphate phosphatase E 15778224 Integral Membrane Protein 4 4 in COG0671;Membrane-associated phospholipid phosphatase 48317; Acid phosphatase/Vanadium-dependent haloperoxidase PF01569;PAP2 superfamily;6.5e-33;codon 41-173 GO:0009274 cell wall (sensu Bacteria) CDS ECK0832 cmr cmr cmlA -!- mdfA b0842 882896 884128 + (no change) JW0826 884095 885327 + t multidrug efflux system protein E 10022825 -!- 12578981 -!- 14688269 -!- 21217867 -!- 21450803 -!- 9079913 -!- 9644262 -!- 99030337 -!- 8655497 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;7.9e-28;codon 22-400 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK0833 ybjH ybjH b0843 884169 884453 - (no change) JW0827 885368 885652 - o predicted protein C 1-22 CDS ECK0834 ybjI ybjI b0844 884539 885354 - start codon change JW5113 885738 886553 - d conserved protein C Cytoplasmic 56784; HAD-like PF00702;haloacid dehalogenase-like hydrolase;0.00046;codon 1-227 "TIGR00099;Cof-subfamily: Cof-like hydrolase;5.7e-63;codon 1-250 -!- TIGR01484;HAD-SF-IIB: HAD-superfamily hydrolase,;1.7e-07;codon 1-223" CDS ECK0835 ybjJ ybjJ b0845 885354 886562 - (no change) JW0829 886553 887761 - pt predicted transporter C Integral Membrane Protein 12 12 in COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;1.2e-24;codon 16-363 CDS ECK0836 ybjK ybjK b0846 886646 887182 + (no change) JW5114 887845 888381 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic COG3226;Uncharacterized protein conserved in bacteria 46689; Homeodomain-like "PF00440;Bacterial regulatory proteins, tetR family;6.2e-09;codon 13-59" misc_RNA ECK0837 rybB rybB p25 b4417 887199 887277 - (no change) JWR0227 888398 888476 - n small RNA interacts with Hfq E 11445539 CDS ECK0838 ybjL ybjL b0847 887357 889042 - (no change) JW0831 888556 890241 - pt predicted transporter C Integral Membrane Protein 11 9 COG2985;Predicted permease PF06826;Predicted Permease Membrane Region;1e-68;codon 16-183 -!- PF02080;TrkA-C domain;2.5e-11;codon 217-287 -!- PF02080;TrkA-C domain;2e-12;codon 303-372 -!- PF06826;Predicted Permease Membrane Region;1.4e-63;codon 385-555 TIGR01625;YidE_YbjL_dupl: YidE/YbjL duplication;1.8e-65;codon 21-169 -!- TIGR01625;YidE_YbjL_dupl: YidE/YbjL duplication;5.3e-64;codon 390-541 CDS ECK0839 ybjM ybjM b0848 889312 889689 + (no change) JW0832 890511 890888 + pm predicted inner membrane protein C Integral Membrane Protein 4 4 in CDS ECK0840 grxA grxA grx b0849 889719 889976 - (no change) JW0833 890918 891175 - c "glutaredoxin 1, redox coenzyme for ribonucleotide reductase (RNR1a)" E 91242463 -!- 93003075 -!- 95024051 -!- 99175138 -!- 1304339 -!- 1889405 -!- 1942053 -!- 3530878 -!- 6352262 -!- 9125525 Cytoplasmic 1EGR COG0695;Glutaredoxin and related proteins 52833; Thioredoxin-like PF00462;Glutaredoxin;4.1e-26;codon 2-85 "TIGR02183;GRXA: Glutaredoxin, GrxA family;2.5e-54;codon 2-85" CDS ECK0841 ybjC ybjC b0850 890136 890423 + (no change) JW0834 891335 891622 + pm predicted inner membrane protein C 3530878 -!- 7567469 Integral Membrane Protein 2 2 PF07214;Protein of unknown function (DUF1418);1.1e-71;codon 1-95 CDS ECK0842 nfsA nfsA mdaA -!- ybjB -!- mda18 b0851 890407 891129 + (no change) JW0835 891606 892328 + e "nitroreductase A, NADPH-dependent, FMN-dependent" E 12788749 -!- 338576 -!- 94239448 -!- 96004656 -!- 96345615 -!- 99199218 -!- 2570347 -!- 9440535 Cytoplasmic -1 monomeric multimer; NADPH nitroreductase (b0851) COG0778;Nitroreductase 55469; NADH oxidase/flavin reductase PF00881;Nitroreductase family;1.7e-36;codon 8-159 GO:0009061 anaerobic respiration CDS ECK0843 rimK rimK nek b0852 891190 892092 + (no change) JW0836 892389 893291 + s ribosomal protein S6 modification protein E 76239710 -!- 89364710 Cytoplasmic COG0189;Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) 56059; Glutathione synthetase ATP-binding domain-like PF02222;ATP-grasp domain;7.4e-29;codon 27-193 "TIGR00768;rimK_fam: alpha-L-glutamate ligases, RimK fa;1.1e-161;codon 2-286" GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006412 protein biosynthesis GO:0003735 structural constituent of ribosome CDS ECK0844 ybjN ybjN b0853 892180 892656 + (no change) JW0837 893379 893855 + d predicted oxidoreductase glutaredoxin/thioredoxin family C Cytoplasmic 55008; Metal-binding domain CDS ECK0845 potF potF b0854 893007 894119 + (no change) JW0838 894206 895318 + t putrescine transporter subunit: periplasmic-binding component of ABC superfamily E 93106992 -!- 9651355 -!- 9298646 -!- 8416922 Periplasmic heteromultimer; putrescine ABC transporter (b0855-b0856-b0857-b0854) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-26 370 1A99 COG0687;Spermidine/putrescine-binding periplasmic protein 53850; Periplasmic binding protein-like II PF01547;Bacterial extracellular solute-binding prot;2.9e-11;codon 9-306 GO:0042597 periplasmic space GO:0006596 polyamine biosynthesis -!- GO:0009310 amine catabolism -!- GO:0015847 putrescine transport CDS ECK0846 potG potG b0855 894214 895347 + start codon change JW5818 895413 896546 + t putrescine transporter subunit: ATP-binding component of ABC superfamily E 93106992 Cytoplasmic heteromultimer; putrescine ABC transporter (b0855-b0856-b0857-b0854) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;3e-69;codon 72-253 "TIGR01187;potA: polyamine ABC transporter, ATP-binding;2.5e-243;codon 77-402" GO:0005737 cytoplasm GO:0006596 polyamine biosynthesis -!- GO:0009310 amine catabolism -!- GO:0015847 putrescine transport CDS ECK0847 potH potH b0856 895357 896310 + (no change) JW0840 896556 897509 + t putrescine transporter subunit: membrane component of ABC superfamily E 93106992 Integral Membrane Protein heteromultimer; putrescine ABC transporter (b0855-b0856-b0857-b0854) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 6 6 in "COG1176;ABC-type spermidine/putrescine transport system, permease component I" PF00528;Binding-protein-dependent transport syst;2.6e-33;codon 99-315 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006596 polyamine biosynthesis -!- GO:0009310 amine catabolism -!- GO:0015847 putrescine transport CDS ECK0848 potI potI b0857 896307 897152 + (no change) JW0841 897506 898351 + t putrescine transporter subunit: membrane component of ABC superfamily E 93106992 Integral Membrane Protein heteromultimer; putrescine ABC transporter (b0855-b0856-b0857-b0854) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 6 6 in "COG1177;ABC-type spermidine/putrescine transport system, permease component II" PF00528;Binding-protein-dependent transport syst;0.00043;codon 61-273 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006596 polyamine biosynthesis -!- GO:0009310 amine catabolism -!- GO:0015847 putrescine transport CDS ECK0849 ybjO ybjO b0858 897212 897700 + (no change) JW0842 898411 898899 + pm predicted inner membrane protein C Integral Membrane Protein 4 4 in CDS ECK0850 rumB rumB ybjF b0859 897741 898868 + (no change) JW0843 898940 900067 + e 23S rRNA m(5)U747 methyltransferase "responsible for modification of U747 iin 23S rRNA, SAM-dependent" E 12907714 Cytoplasmic 2.1.1.- COG2265;SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase 53335; S-adenosyl-L-methionine-dependent methyltransferases PF05958;tRNA (Uracil-5-)-methyltransferase;8.9e-06;codon 23-375 TIGR02085;meth_trns_rumB: 23S rRNA (uracil-5-)-m;0;codon 2-374 GO:0009451 RNA modification CDS ECK0851 artJ artJ b0860 899067 899798 - (no change) JW0844 900266 900997 - t arginine transporter subunit -!- periplasmic-binding component of ABC superfamily E 93273744 -!- 9298646 -!- 9600841 -!- 8801422 Periplasmic heteromultimer; arginine ABC transporter (b0864-b0861-b0862-b0863-b0860) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-19 243 regulated by attenuation (artJ) "COG0834;ABC-type amino acid transport/signal transduction systems, periplasmic component/domain" 53850; Periplasmic binding protein-like II PF00497;Bacterial extracellular solute-binding prot;1.7e-106;codon 23-243 TIGR01096;3A0103s03R: lysine-arginine-ornithine-bind;4.6e-138;codon 2-241 GO:0042597 periplasmic space GO:0006526 arginine biosynthesis CDS ECK0852 artM artM b0861 900089 900757 - (no change) JW0845 901288 901956 - t arginine transporter subunit -!- membrane component of ABC superfamily E 93273744 Integral Membrane Protein heteromultimer; arginine ABC transporter (b0864-b0861-b0862-b0863-b0860) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 5 5 in "COG4160;ABC-type arginine/histidine transport system, permease component" PF00528;Binding-protein-dependent transport syst;1.9e-10;codon 12-217 TIGR01726;HEQRo_perm_3TM: amino acid ABC transpo;8e-19;codon 4-112 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006526 arginine biosynthesis -!- GO:0009063 amino acid catabolism CDS ECK0853 artQ artQ b0862 900757 901473 - (no change) JW0846 901956 902672 - t arginine transporter subunit -!-membrane component of ABC superfamily E 93273744 Integral Membrane Protein heteromultimer; arginine ABC transporter (b0864-b0861-b0862-b0863-b0860) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 5 4 in "COG4215;ABC-type arginine transport system, permease component" PF00528;Binding-protein-dependent transport syst;8.6e-18;codon 7-232 TIGR01726;HEQRo_perm_3TM: amino acid ABC transpo;2.9e-10;codon 3-125 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006526 arginine biosynthesis CDS ECK0854 artI artI b0863 901480 902211 - (no change) JW0847 902679 903410 - t arginine transporter subunit -!- periplasmic-binding component of ABC superfamily E 93273744 -!- 9298646 -!- 9600841 -!- 8801422 -!- 9740056 Periplasmic heteromultimer; arginine ABC transporter (b0864-b0861-b0862-b0863-b0860) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-19 243 "COG0834;ABC-type amino acid transport/signal transduction systems, periplasmic component/domain" 53850; Periplasmic binding protein-like II PF00497;Bacterial extracellular solute-binding prot;5.7e-93;codon 23-243 TIGR01096;3A0103s03R: lysine-arginine-ornithine-bind;2.8e-139;codon 2-241 GO:0042597 periplasmic space GO:0006542 glutamine biosynthesis CDS ECK0855 artP artP b0864 902229 902957 - (no change) JW0848 903428 904156 - t arginine transporter subunit -!- ATP-binding component of ABC superfamily E 93273744 Cytoplasmic heteromultimer; arginine ABC transporter (b0864-b0861-b0862-b0863-b0860) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG4161;ABC-type arginine transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.5e-74;codon 28-217 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006526 arginine biosynthesis CDS ECK0856 ybjP ybjP b0865 903175 903690 - (no change) JW0849 904374 904889 - lp predicted lipoprotein C Outer membrane Lipoprotein CDS ECK0857 ybjQ ybjQ b0866 903816 904139 + (no change) JW0850 905015 905338 + o conserved protein C Cytoplasmic COG0393;Uncharacterized conserved protein PF01906;Domain of unknown function DUF74;3.7e-61;codon 1-106 CDS ECK0858 ybjR ybjR b0867 904136 904966 + (no change) JW0851 905335 906165 + pe predicted amidase and lipoprotein similarity with AmpD N-acetyl-anhydromuranmyl-L-alanine amidase C Outer membrane Lipoprotein COG3023;Negative regulator of beta-lactamase expression PF01510;N-acetylmuramoyl-L-alanine amidase;1.2e-45;codon 33-194 CDS ECK0859 ybjS ybjS b0868 904963 905976 - start codon change JW5819 906162 907175 - pe predicted NAD(P)H-binding oxidoreductase with NAD(P)-binding Rossmann-fold domain C Cytoplasmic regulated by attenuation (ybjS) COG0451;Nucleoside-diphosphate-sugar epimerases 51735; NAD(P)-binding Rossmann-fold domains CDS ECK0860 ybjT ybjT b0869 906075 907505 - start codon change JW5116 907274 908704 - d conserved protein with NAD(P)-binding Rossmann-fold domain C Membrane Anchored 51735; NAD(P)-binding Rossmann-fold domains CDS ECK0861 ltaE ltaE ybjU -!- ltaA b0870 907516 908517 - (no change) JW0854 908715 909716 - e "L-allo-threonine aldolase, PLP-dependent" E 98355671 Cytoplasmic 4.1.2.5 monomeric multimer; L-allo-threonine aldolase (b0870) COG2008;Threonine aldolase 53383; PLP-dependent transferases PF01212;Beta-eliminating lyase;5.7e-158;codon 3-286 GO:0005737 cytoplasm GO:0006545 glycine biosynthesis CDS ECK0862 poxB poxB b0871 908554 910272 - (no change) JW0855 909753 911471 - e "pyruvate dehydrogenase (pyruvate oxidase), thiamin-dependent, FAD-binding" E 20558080 -!- 89308683 -!- 91250398 Cytoplasmic 1.2.2.2 Mg2+ monomeric multimer; acetoin synthesis / pyruvate oxidase (b0871) "COG0028;Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]" 52467; DHS-like NAD/FAD-binding domain -!- 52518; Thiamin diphosphate-binding fold (THDP-binding) "PF02776;Thiamine pyrophosphate enzyme, N-termina;2.7e-81;codon 3-172 -!- PF00205;Thiamine pyrophosphate enzyme, central d;6e-55;codon 190-336" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0042867 pyruvate catabolism GO:0009053 electron donor activity CDS ECK0863 hcr hcr ybjV b0872 910405 911373 - (no change) JW5117 911604 912572 - e "HCP oxidoreductase, NADH-dependent" E 20117674 Cytoplasmic -1 COG1018;Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 "52343; Ferredoxin reductase-like, C-terminal NADP-linked domain -!- 54292; 2Fe-2S ferredoxin-like -!- 63380; Riboflavin synthase domain-like" PF00970;Oxidoreductase FAD-binding domain;2e-07;codon 11-106 -!- PF00175;Oxidoreductase NAD-binding domain;4.1e-05;codon 111-213 -!- PF00111;2Fe-2S iron-sulfur cluster binding doma;1.4e-20;codon 241-317 CDS ECK0864 hcp hcp ybjW -!- priS b0873 911385 913037 - start codon change JW0857 912584 914236 - c hybrid-cluster [4Fe-2S-2O] protein in anaerobic terminal reductases expressed anaerobically with nitrate or nitrite as terminal electron acceptors E 99310594 -!- 10651802 -!- 12374823 Cytoplasmic 56821; Prismane protein-like PF03063;Prismane/CO dehydrogenase family;1.7e-259;codon 3-550 TIGR01703;hybrid_clust: hybrid cluster protein;0;codon 3-550 CDS ECK0865 ybjE ybjE b0874 913181 914080 - start codon change JW0858 914380 915279 - pt predicted transporter C Integral Membrane Protein 9 8 COG2431;Predicted membrane protein PF03956;Membrane protein of unknown function (DUF340;3.7e-89;codon 125-315 CDS ECK0866 aqpZ aqpZ bniP b0875 914575 915270 - (no change) JW0859 915774 916469 - t aquaporin water channel E 96094287 -!- 99328963 -!- 99448397 Integral Membrane Protein 1.A.8; The Major Intrinsic Protein (MIP) Family 6 6 in COG0580;Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family) 56869; Membrane all-alpha PF00230;Major intrinsic protein;2.4e-51;codon 1-223 TIGR00861;MIP: MIP family channel proteins;4.9e-97;codon 7-223 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006970 response to osmotic stress CDS ECK0867 ybjD ybjD b0876 915696 917354 + (no change) JW0860 916895 918553 + d conserved protein with nucleoside triphosphate hydrolase domain C Cytoplasmic COG3593;Predicted ATP-dependent endonuclease of the OLD family 52540; P-loop containing nucleotide triphosphate hydrolases CDS ECK0868 ybjX ybjX b0877 917351 918343 - (no change) JW0861 918550 919542 - o conserved protein similarity with SomA and VirK C Cytoplasmic COG2990;Uncharacterized protein conserved in bacteria PF04393;Protein of unknown function (DUF535);2.4e-155;codon 40-328 CDS ECK0869 macA macA ybjY b0878 918458 919573 + start codon change JW0862 919657 920772 + t "macrolide transporter subunit, membrane fusion protein (MFP) component" E 21429237 -!- 21450803 Membrane Anchored heteromultimer; MacAB macrolide efflux transporter complex (b3035-b0879-b0878) 51230; Single hybrid motif PF00529;HlyD family secretion protein;0.00015;codon 69-371 "TIGR01730;RND_mfp: efflux transporter, RND family, MFP;2e-41;codon 45-380" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0870 macB macB ybjZ b0879 919570 921516 + (no change) JW0863 920769 922715 + t fused macrolide transporter subunits of ABC superfamily: ATP-binding component -!- membrane component E 21429237 -!- 21450803 Integral Membrane Protein heteromultimer; MacAB macrolide efflux transporter complex (b3035-b0879-b0878) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 4 4 "fused macrolide transport protein, ABC superfamily: atp_binding component (aa1-253) -!- membrane component (aa254-648)" "COG1136;ABC-type antimicrobial peptide transport system, ATPase component -!- COG0577;ABC-type antimicrobial peptide transport system, permease component" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;7.8e-59;codon 34-219 -!- PF02687;Predicted permease;1.7e-54;codon 469-641 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0871 cspD cspD cspH -!- ybjA b0880 921589 921813 - (no change) JW0864 922788 923012 - f cold shock protein homolog induced during the stationary phase E 21160192 -!- 94293754 -!- 97405911 -!- 1622933 -!- 2186030 -!- 9868784 Cytoplasmic monomeric multimer; CspD dimer (b0880) COG1278;Cold shock proteins 50249; Nucleic acid-binding proteins PF00313;'Cold-shock' DNA-binding domain;9.8e-40;codon 1-67 GO:0005737 cytoplasm CDS ECK0872 clpS clpS yljA b0881 922136 922456 + (no change) JW0865 923335 923655 + r regulatory protein for ClpA substrate specificity E 11931773 -!- 12576022 Cytoplasmic 1MBX COG2127;Uncharacterized conserved protein PF02617;ATP-dependent Clp protease adaptor protein C;1.6e-49;codon 22-103 CDS ECK0873 clpA clpA lopD b0882 922487 924763 + (no change) JW0866 923686 925962 + e "ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease, chaperone activity" E 21243159 -!- 21369885 -!- 90239044 -!- 90243657 -!- 9573050 -!- 9575205 -!- 12205096 -!- 12235156 -!- 12426582 -!- 3049606 Cytoplasmic heteromultimer; ClpAP (b0437-b0882) -!- heteromultimer; ClpAXP (b0437-b0438-b0882) -!- monomeric multimer; ClpA ATP-dependent protease specificity component and chaperone (b0882) 1R6B "COG0542;ATPases with chaperone activity, ATP-binding subunit" 52540; P-loop containing nucleotide triphosphate hydrolases PF02861;Clp amino terminal domain;8.2e-17;codon 13-63 -!- PF00004;ATPase family associated with various cellul;1.9e-20;codon 209-403 -!- PF07724;ATPase family associated with various cellul;1.1e-88;codon 486-647 GO:0005737 cytoplasm tRNA ECK0874 serW serW b0883 925107 925194 - (no change) JWR0025 926306 926393 - n tRNA-Ser(GGA) (Serine tRNA5) E 88320491 -!- 91088251 -!- 92302305 regulated by attenuation (serW) CDS ECK0875 infA infA bypA1 b0884 925448 925666 - (no change) JW0867 926647 926865 - f translation initiation factor IF-1 E 91358434 -!- 94110226 -!- 3037488 -!- 376343 -!- 8331068 -!- 9135158 -!- 9868784 Cytoplasmic 1AH9 COG0361;Translation initiation factor 1 (IF-1) 50249; Nucleic acid-binding proteins PF00575;S1 RNA binding domain;1.2e-10;codon 2-72 TIGR00008;infA: translation initiation factor IF-1;9.1e-47;codon 3-71 GO:0005737 cytoplasm GO:0006412 protein biosynthesis CDS ECK0876 aat aat ycaA b0885 925951 926655 - (no change) JW0868 927150 927854 - e leucyl/phenylalanyl-tRNA-protein transferase E 90352297 -!- 91177849 -!- 92304971 -!- 93322314 -!- 1909328 -!- 7657641 Cytoplasmic 2.3.2.6 COG2360;Leu/Phe-tRNA-protein transferase PF03588;Leucyl/phenylalanyl-tRNA protein transf;3.9e-120;codon 34-204 TIGR00667;aat: leucyl/phenylalanyl-tRNA--protein trans;7e-116;codon 32-232 GO:0005737 cytoplasm GO:0006508 proteolysis and peptidolysis CDS ECK0877 cydC cydC mdrA -!- mdrH -!- surB -!- ycaB b0886 926697 928418 - (no change) JW0869 927896 929617 - t fused cysteine transporter subunits of ABC superfamily: membrane component -!- ATP-binding component E 12393891 -!- 93296240 -!- 94010227 -!- 95020541 -!- 1909328 -!- 8276245 -!- 8331068 Integral Membrane Protein heteromultimer; abc-6-cplx (b0887-b0886) 6 6 in "fused cysteine transport protein, ABC superfamily: membrane component (aa1-318) -!- atp_binding component (aa319-573)" "COG4987;ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components" 52540; P-loop containing nucleotide triphosphate hydrolases PF00664;ABC transporter transmembrane region;0.00064;codon 22-293 -!- PF00005;ABC transporter;3.8e-61;codon 366-548 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0878 cydD cydD htrD b0887 928419 930185 - (no change) JW0870 929618 931384 - t fused cysteine transporter subunits of ABC superfamily: membrane component -!- ATP-binding component E 12393891 -!- 93296240 -!- 94010227 -!- 95020541 -!- 1310500 -!- 8276245 -!- 8380150 Integral Membrane Protein heteromultimer; abc-6-cplx (b0887-b0886) 6 5 in regulated by attenuation (cydD-cydC) "fused cysteine transport protein, ABC superfamily: membrane component (aa1-318) -!- atp_binding component (aa319-588)" "COG4988;ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components" 52540; P-loop containing nucleotide triphosphate hydrolases PF00664;ABC transporter transmembrane region;9.5e-47;codon 24-299 -!- PF00005;ABC transporter;1.1e-68;codon 376-559 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0879 trxB trxB b0888 930308 931273 - (no change) JW0871 931507 932472 - e "thioredoxin reductase, FAD/NAD(P)-binding" E 89123358 -!- 89327225 -!- 93348217 -!- 99175138 -!- 10595539 -!- 10947986 -!- 1575737 -!- 2067578 -!- 3288628 -!- 7934832 -!- 8114095 -!- 8380150 -!- 14245401 Periplasmic 1.8.1.9 monomeric multimer; thioredoxin reductase (b0888) 1CL0 COG0492;Thioredoxin reductase 51905; FAD/NAD(P)-binding domain PF00070;Pyridine nucleotide-disulphide oxidoreducta;1.4e-73;codon 8-293 TIGR01292;TRX_reduct: thioredoxin-disulfide reductas;2.4e-204;codon 7-314 GO:0005737 cytoplasm CDS ECK0880 lrp lrp ihb -!- livR -!- lrs -!- lss -!- lstR -!- mbf -!- oppI -!- rblA -!- alsB b0889 931818 932312 + (no change) JW0872 933017 933511 + r "DNA-binding transcriptional dual regulator, leucine-binding" global regulator -!- leucine responsive E 10217490 -!- 7022128 -!- 92138602 -!- 92193284 -!- 93285120 -!- 99445490 -!- 12054800 -!- 1729203 -!- 2040596 -!- 2115869 -!- 7883720 -!- 8212136 Cytoplasmic AsnC aidB -!- csiD-ygaF-gabDTP -!- dadAX -!- fimEAICDFGH -!- gcvTHP -!- gltBDF -!- ilvIH -!- ilvLG_1G_2MEDA -!- kbl-tdh -!- leuLABCD -!- livJ -!- livKHMGF -!- lrp -!- lysU -!- malT -!- micF -!- ompC -!- ompF -!- oppABCDF -!- osmC -!- osmY -!- sd COG1522;Transcriptional regulators 46785; Winged helix -!- 69732; Lrp/AsnC-like transcriptional regulator C-terminal domain PF01037;AsnC family;8e-57;codon 36-139 GO:0005737 cytoplasm GO:0009098 leucine biosynthesis -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0881 ftsK ftsK dinH b0890 932447 936436 + (no change) JW0873 933646 937635 + cp DNA-binding membrane protein required for chromosome resolution and partitioning localized to division septal ring E 10027974 -!- 11864592 -!- 12034757 -!- 99047597 -!- 10922461 -!- 11703663 -!- 11832210 -!- 11948172 -!- 7592387 Integral Membrane Protein 3.A.12; The Septal DNA Translocator (S-DNA-T) Family 4 5 in COG1674;DNA segregation ATPase FtsK/SpoIIIE and related proteins 52540; P-loop containing nucleotide triphosphate hydrolases PF01580;FtsK/SpoIIIE family;1.2e-105;codon 947-1161 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009432 SOS response CDS ECK0882 lolA lolA lplA -!- yzzV b0891 936592 937206 + (no change) JW0874 937791 938405 + f chaperone for lipoproteins "with LolB; required for sorting, positioning and membrane localization of lipoproteins" E 12839983 -!- 94266793 -!- 95095954 -!- 95366962 -!- 99453001 -!- 7628437 -!- 9298646 Periplasmic 1-22 203 1UA8 COG2834;Outer membrane lipoprotein-sorting protein PF03548;Outer membrane lipoprotein carrier protein L;5.4e-116;codon 9-202 TIGR00547;lolA: outer membrane lipoprotein carrier pro;6.4e-128;codon 2-204 GO:0042597 periplasmic space CDS ECK0883 ycaJ ycaJ b0892 937217 938560 + (no change) JW0875 938416 939759 + cp recombination protein "involved in processing recombination intermediates at replication forks, affecting dimer formation -!- grows poorly when combined with xer or dif mutations -!- homologous to dnaX and ruvB" E 7567469 -!- 7628437 -!- 11459952 -!- 11029431 Cytoplasmic COG2256;ATPase related to the helicase subunit of the Holliday junction resolvase 52540; P-loop containing nucleotide triphosphate hydrolases PF00004;ATPase family associated with various cellul;1.2e-22;codon 52-225 CDS ECK0884 serS serS b0893 938651 939943 + (no change) JW0876 939850 941142 + e "seryl-tRNA synthetase, also charges selenocysteinyl-tRNA with serine" E 90384563 -!- 91296775 -!- 94157910 -!- 1859832 -!- 3029694 -!- 3062312 -!- 7537870 Cytoplasmic 6.1.1.11 monomeric multimer; seryl-tRNA synthetase (b0893) COG0172;Seryl-tRNA synthetase 46589; A class II aminoacyl-tRNA synthetase N-domain -!- 55681; Class II aaRS and biotin synthetases "PF02403;Seryl-tRNA synthetase N-terminal domain;2.6e-48;codon 1-107 -!- PF00587;tRNA synthetase class II core domain (G,;1.8e-57;codon 161-323" TIGR00414;serS: seryl-tRNA synthetase;5.2e-208;codon 1-423 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK0885 dmsA dmsA b0894 940182 942626 + start codon change JW5118 941381 943825 + e "dimethyl sulfoxide reductase, anaerobic, subunit A" E 91008971 -!- 92011349 -!- 94171715 -!- 10801884 -!- 3062312 Periplasmic 1.8.99.- heteromultimer; dimethyl sulfoxide reductase (b0894-b0895-b0896) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3" PF04879;Molybdopterin oxidoreductase Fe4S4 do;4.8e-19;codon 27-87 -!- PF00384;Molybdopterin oxidoreductase;9.2e-191;codon 90-547 -!- PF01568;Molydopterin dinucleotide binding dom;2.9e-48;codon 666-779 TIGR02166;dmsA_ynfE: anaerobic dimethyl sulfoxide red;0;codon 1-785 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration GO:0009054 electron acceptor activity CDS ECK0886 dmsB dmsB b0895 942637 943254 + (no change) JW0878 943836 944453 + e "dimethyl sulfoxide reductase, anaerobic, subunit B" E 91070067 -!- 91355180 -!- 92011349 -!- 3062312 Cytoplasmic 1.8.99.- heteromultimer; dimethyl sulfoxide reductase (b0894-b0895-b0896) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family COG0437;Fe-S-cluster-containing hydrogenase components 1 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;1.4e-07;codon 92-115 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration GO:0009054 electron acceptor activity CDS ECK0887 dmsC dmsC b0896 943256 944119 + (no change) JW0879 944455 945318 + e "dimethyl sulfoxide reductase, anaerobic, subunit C" E 91008971 -!- 92011349 -!- 3062312 -!- 8429002 Integral Membrane Protein 1.8.99.- heteromultimer; dimethyl sulfoxide reductase (b0894-b0895-b0896) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 8 8 out COG3302;DMSO reductase anchor subunit PF04976;DMSO reductase anchor subunit (DmsC);6.9e-175;codon 1-277 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration GO:0009054 electron acceptor activity CDS ECK0888 ycaC ycaC b0897 944154 944780 - (no change) JW0880 945353 945979 - pe predicted hydrolase C 9782055 -!- 3062312 Cytoplasmic monomeric multimer; putative cysteine hydrolase (b0897) 1YAC COG1335;Amidases related to nicotinamidase 52499; Cysteine hydrolase PF00857;Isochorismatase family;5.1e-62;codon 8-171 GO:0009063 amino acid catabolism CDS ECK0889 ycaD ycaD b0898 945094 946242 + (no change) JW0881 946293 947441 + pt predicted transporter C Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;9.2e-28;codon 11-346 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0890 ycaM ycaM b0899 946452 947882 + start codon change JW5119 947651 949081 + pt predicted transporter C Integral Membrane Protein 12 12 in COG0531;Amino acid transporters PF00324;aa_permeases: Amino acid permease;0.052;codon 6-471 TIGR00909;2A0306: amino acid transporter;0.014;codon 7-461 -!- TIGR00910;2A0307: Glutamate:g-aminobutyrate antiporte;0.01;codon 1-476 -!- TIGR00905;2A0302: arginine/ornithine antiporter;0.32;codon 1-465 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0891 ycaN ycaN b0900 947883 948791 - (no change) JW0883 949082 949990 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;3.8e-21;codon 5-64 -!- PF03466;LysR substrate binding domain;7.8e-37;codon 88-293 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK0892 ycaK ycaK b0901 948891 949481 + (no change) JW0884 950090 950680 + d conserved protein C 3053170 -!- 7567469 Cytoplasmic COG2249;Putative NADPH-quinone reductase (modulator of drug activity B) 52218; Flavoproteins PF02525;Flavodoxin-like fold;4.6e-68;codon 4-194 GO:0009055 electron carrier activity CDS ECK0893 pflA pflA act b0902 949563 950303 - (no change) JW0885 950762 951502 - e pyruvate formate lyase activating enzyme 1 E "89030680 -!- 90286913 -!- 94083413 -!- Broderick JB, Duderstadt RE, Fernandez DC, et al;J Am Chem Soc;1997;119:7396-7397" Cytoplasmic 1.97.1.4 Fe4S4 iron-sulfur center regulated by attenuation (pflA) COG1180;Pyruvate-formate lyase-activating enzyme PF04055;Radical SAM superfamily;3.8e-27;codon 24-185 GO:0005737 cytoplasm GO:0009061 anaerobic respiration -!- GO:0006464 protein modification CDS ECK0894 pflB pflB pfl b0903 950495 952777 - (no change) JW0886 951694 953976 - e pyruvate formate lyase I E 91064082 -!- 92276323 -!- 10504733 -!- 1310545 -!- 2651404 -!- 3053170 -!- 9629924 Cytoplasmic 2.3.1.54 OXYGEN-SENSITIVE FREE RADICAL monomeric multimer; pyruvate formate-lyase (inactive) (b0903) 1MZO COG1882;Pyruvate-formate lyase 51998; PFL-like glycyl radical enzymes PF02901;Pyruvate formate lyase;0;codon 11-614 -!- PF01228;Glycine radical;1e-68;codon 630-741 TIGR01255;pyr_form_ly_1: formate acetyltransferas;0;codon 11-760 GO:0005737 cytoplasm GO:0009061 anaerobic respiration -!- GO:0009063 amino acid catabolism CDS ECK0895 focA focA ycaE b0904 952832 953689 - (no change) JW0887 954031 954888 - t formate transporter formate channel 1 E 94293770 -!- 2651404 Integral Membrane Protein 2.A.44; The Formate-Nitrite Transporter (FNT) Family 6 6 in COG2116;Formate/nitrite family of transporters PF01226;Formate/nitrite transporter;1.3e-179;codon 8-283 TIGR00790;fnt: formate/nitrite transporter;9.3e-155;codon 26-280 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK0896 ycaO ycaO b0905 954095 955855 - start codon change JW0888 955294 957054 - o conserved protein C Cytoplasmic PF02624;YcaO-like family;1.3e-166;codon 24-395 TIGR00702;TIGR00702: uncharacterized domain;7.2e-184;codon 14-407 CDS ECK0897 ycaP ycaP b0906 955985 956677 + (no change) JW0889 957184 957876 + pm conserved inner membrane protein C Integral Membrane Protein 2 3 COG2323;Predicted membrane protein PF04239;Protein of unknown function (DUF421);2.6e-36;codon 101-203 CDS ECK0898 serC serC pdxC -!- pdxF b0907 956876 957964 + (no change) JW0890 958075 959163 + e 3-phosphoserine/phosphohydroxythreonine aminotransferase E 86215119 -!- 91035267 -!- 10024454 -!- 2682527 -!- 9298646 Cytoplasmic 2.6.1.52 monomeric multimer; phosphohydroxythreonine transaminase / phosphoserine transaminase (b0907) 1BJO COG1932;Phosphoserine aminotransferase 53383; PLP-dependent transferases PF00266;Aminotransferase class-V;2.3e-138;codon 14-350 TIGR01364;serC_1: phosphoserine aminotransferase;5.8e-225;codon 4-361 GO:0005737 cytoplasm GO:0006564 L-serine biosynthesis CDS ECK0899 aroA aroA b0908 958035 959318 + (no change) JW0891 959234 960517 + e 5-enolpyruvylshikimate-3-phosphate synthetase E "90202793 -!- 92042175 -!- 92390338 -!- 11607190 -!- 1899181 -!- 8452542 -!- 3276677 -!- Duncan K, Lewendon A, Coggins JR;FEBS Lett;1984;170:59-63" Cytoplasmic 2.5.1.19 regulated by attenuation (aroA) COG0128;5-enolpyruvylshikimate-3-phosphate synthase 55205; EPT/RTPC-like PF00275;EPSP synthase (3-phosphoshikimate 1-car;1.5e-220;codon 8-420 TIGR01356;aroA: 3-phosphoshikimate 1-carboxyvinyltrans;8.7e-174;codon 14-426 GO:0009423 chorismate biosynthesis CDS ECK0900 ycaL ycaL b0909 959487 960251 + start codon change JW0892 960686 961450 + pf predicted peptidase with chaperone function C Outer membrane Lipoprotein M48X family; unassigned peptidases (YcaL protein) 1-22 regulated by attenuation (ycaL) COG0501;Zn-dependent protease with chaperone function PF01435;Peptidase family M48;1.2e-27;codon 88-259 GO:0009266 response to temperature CDS ECK0901 cmk cmk mssA -!- ycaG -!- ycaF b0910 960424 961107 + (no change) JW0893 961623 962306 + e cytidylate kinase E 95138007 -!- 6281725 -!- 6384724 -!- 8190075 -!- 9126287 -!- 9862805 Cytoplasmic 2.7.4.14 Mg2+ COG0283;Cytidylate kinase 52540; P-loop containing nucleotide triphosphate hydrolases PF02224;Cytidylate kinase;1.3e-94;codon 61-218 TIGR00017;cmk: cytidylate kinase;3.3e-145;codon 4-220 GO:0005737 cytoplasm "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK0902 rpsA rpsA ssyF -!- rps b0911 961218 962891 + (no change) JW0894 962417 964090 + s 30S ribosomal subunit protein S1 E 92075656 -!- 93011980 -!- 93038753 -!- 1712292 -!- 3159903 -!- 6281725 -!- 6384724 -!- 7041110 -!- 7783627 -!- 9298646 -!- 9716382 Cytoplasmic COG0539;Ribosomal protein S1 50249; Nucleic acid-binding proteins 6 of PF00575;S1 RNA binding domain: 1.4e-12;codon 17-87 -!- 1.2e-17;codon 101-171 -!- 7.1e-32;codon 188-260 -!- 4e-30;codon 273-347 -!- 5.5e-26;codon 360-434 -!- 4e-27;codon 447-520 TIGR00717;rpsA: ribosomal protein S1;0;codon 3-520 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006412 protein biosynthesis GO:0003735 structural constituent of ribosome CDS ECK0903 ihfB ihfB himD -!- hip b0912 963051 963335 + (no change) JW0895 964250 964534 + r "integration host factor (IHF), DNA-binding protein, beta subunit" E 92021785 -!- 92155171 -!- 93078609 -!- 1917861 -!- 3159903 -!- 8980235 -!- 9868784 Cytoplasmic heteromultimer; IHF transcriptional dual regulator (b0912-b1712) aceBAK -!- acs-yjcHG -!- adiA -!- amiA-hemF -!- caiTABCDE -!- carAB -!- dmsABC -!- dppABCDF -!- dps -!- dusB-fis -!- ecpD-htrE -!- fimAICDFGH -!- focA-pflB -!- gcd -!- glcDEFGBA -!- glnHPQ -!- gltA -!- hemA -!- himA -!- himD -!- hpt -!- hyc regulated by attenuation (himD) 1OWG COG0776;Bacterial nucleoid DNA-binding protein 47729; IHF-like DNA-binding proteins PF00216;Bacterial DNA-binding protein;9.3e-47;codon 1-91 "TIGR00988;hip: integration host factor, beta subunit;1e-75;codon 1-94" GO:0005737 cytoplasm GO:0006310 DNA recombination CDS ECK0904 ycaI ycaI b0913 963543 965807 + start codon change JW5120 964742 967006 + pm conserved inner membrane protein C Integral Membrane Protein 10 7 regulated by attenuation (ycaI-msbA-lpxK-ycaQ-ycaR-kdsB) COG0658;Predicted membrane metal-binding protein -!- COG2333;Predicted hydrolase (metallo-beta-lactamase superfamily) 56281; Metallo-hydrolase/oxidoreductase PF03772;Competence protein;9.2e-95;codon 226-496 -!- PF00753;Metallo-beta-lactamase superfamily;1.3e-12;codon 534-715 TIGR00361;ComEC_Rec2: DNA internalization-related;0;codon 91-744 -!- TIGR00360;ComEC_N-term: ComEC/Rec2-related protein;4.2e-73;codon 247-431 CDS ECK0905 msbA msbA b0914 965844 967592 + (no change) JW0897 967043 968791 + t fused lipid transporter subunits of ABC superfamily: membrane component -!- ATP-binding component E 22229348 -!- 93172962 -!- 94124004 -!- 9575204 Integral Membrane Protein 3.A.1; The ATP-binding Cassette (ABC) Superfamily 5 5 in "fused lipid transport protein (flippase), ABC superfamily: membrane component (aa1-321) -!- atp_binding component (aa322-582)" "COG1132;ABC-type multidrug transport system, ATPase and permease components" 52540; P-loop containing nucleotide triphosphate hydrolases PF00664;ABC transporter transmembrane region;9.7e-70;codon 23-298 -!- PF00005;ABC transporter;5.6e-67;codon 369-554 TIGR02203;MsbA_lipidA: lipid A export ATP-binding/p;0;codon 12-582 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0906 lpxK lpxK ycaH b0915 967589 968575 + (no change) JW0898 968788 969774 + e lipid A 4'kinase E 9268317 -!- 98241618 -!- 9883892 -!- 8094880 2.7.1.130 Mg2+ COG1663;Tetraacyldisaccharide-1-P 4'-kinase 52540; P-loop containing nucleotide triphosphate hydrolases PF02606;Tetraacyldisaccharide-1-P 4'-kinase;4.6e-192;codon 11-326 TIGR00682;lpxK: tetraacyldisaccharide 4'-kinase;8.7e-157;codon 19-326 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0030113 capsule (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009244 lipopolysaccharide core region biosynthesis -!- GO:0009245 lipid A biosynthesis -!- GO:0009248 K antigen biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0907 ycaQ ycaQ b0916 968612 969844 + (no change) JW0899 969811 971043 + o conserved protein C Cytoplasmic COG3214;Uncharacterized protein conserved in bacteria PF06224;Protein of unknown function (DUF1006);1.4e-262;codon 4-397 CDS ECK0908 ycaR ycaR b0917 969896 970078 + (no change) JW0900 971095 971277 + o conserved protein C Cytoplasmic COG2835;Uncharacterized conserved protein PF03966;Protein of unknown function (DUF343);9.7e-24;codon 2-52 CDS ECK0909 kdsB kdsB b0918 970075 970821 + (no change) JW0901 971274 972020 + e 3-deoxy-manno-octulosonate cytidylyltransferase E 89193678 -!- 3023327 Cytoplasmic 2.7.7.38 Mg2+ COG1212;CMP-2-keto-3-deoxyoctulosonic acid synthetase 53448; Nucleotide-diphospho-sugar transferases PF02348;Cytidylyltransferase;3.2e-99;cod on 4-221 TIGR00466;kdsB: 3-deoxy-D-manno-octulosonate cytidylyl;3.8e-191;codon 1-241 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0030113 capsule (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009244 lipopolysaccharide core region biosynthesis -!- GO:0009245 lipid A biosynthesis -!- GO:0009248 K antigen biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK0910 ycbJ ycbJ b0919 970975 971868 + (no change) JW0902 972174 973067 + d conserved protein C Cytoplasmic regulated by attenuation (ycbJ) 56112; Protein kinase-like (PK-like) CDS ECK0911 ycbC ycbC b0920 971845 972624 - (no change) JW0903 973044 973823 - pm conserved inner membrane protein C Integral Membrane Protein 2 2 COG1434;Uncharacterized conserved protein PF02698;DUF218 domain;7.1e-47;codon 78-244 CDS ECK0912 smtA smtA ycbD b0921 972760 973545 + (no change) JW0904 973959 974744 + e predicted S-adenosyl-L-methionine-dependent methyltransferase C 8566713 -!- 7513784 Cytoplasmic COG0500;SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases GO:0006071 glycerol metabolism CDS ECK0913 mukF mukF kicB b0922 973542 974864 + (no change) JW0905 974741 976063 + cp "Involved in chromosome partioning, Ca2+ binding protein" E 15178751 -!- 94232180 -!- 8602138 Cytoplasmic heteromultimer; MukB-MukE-MukF complex (b0922-b0923-b0924) COG3006;Uncharacterized protein involved in chromosome partitioning PF03882;KicB killing factor;0;codon 1-440 CDS ECK0914 mukE mukE kicA -!- ycbA b0923 974872 975549 + (no change) JW0906 976071 976748 + cp protein involved in chromosome partitioning C 15178751 -!- 94232180 -!- 1989883 -!- 8602138 Cytoplasmic heteromultimer; MukB-MukE-MukF complex (b0922-b0923-b0924) COG3095;Uncharacterized protein involved in chromosome partitioning PF04288;MukE-like family;1.5e-166;codon 1-225 CDS ECK0915 mukB mukB b0924 975549 980009 + (no change) JW0907 976748 981208 + f fused chromosome partitioning protein: predicted nucleotide hydrolase -!- conserved protein -!- conserved protein E 1497312 -!- 15178751 -!- 20012898 -!- 91114703 -!- 92021778 -!- 9688555 -!- 10545328 -!- 7513784 -!- 7988894 Cytoplasmic heteromultimer; MukB-MukE-MukF complex (b0922-b0923-b0924) fused chromosome partitioning protein: predicted nucleotide hydrolase (aa1-454) -!- conserved protein (aa455-783) -!- conserved protein (aa784-1486) COG3096;Uncharacterized protein involved in chromosome partitioning 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF04310;MukB N-terminal;4e-189;codon 1-227 CDS ECK0916 ycbB ycbB b0925 980270 982117 + (no change) JW0908 981469 983316 + pe predicted carboxypeptidase C Periplasmic COG2989;Uncharacterized protein conserved in bacteria 47090; PGBD-like CDS ECK0917 ycbK ycbK b0926 982298 982846 + (no change) JW0909 983497 984045 + d conserved protein C COG3108;Uncharacterized protein conserved in bacteria 55166; Hedgehog/DD-pepidase PF05951;Bacterial protein of unknown function (DUF88;1.1e-104;codon 32-182 TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.12;codon 6-30 CDS ECK0918 ycbL ycbL b0927 982873 983520 + (no change) JW0910 984072 984719 + pe predicted metal-binding enzyme C 14529289 Cytoplasmic "COG0491;Zn-dependent hydrolases, including glyoxylases" 56281; Metallo-hydrolase/oxidoreductase PF00753;Metallo-beta-lactamase superfamily;4.3e-38;codon 12-192 CDS ECK0919 aspC aspC b0928 983742 984932 - (no change) JW0911 984941 986131 - e "aspartate aminotransferase, PLP-dependent" E 90352297 -!- 91177849 -!- 92304971 -!- 1868057 -!- 1993208 -!- 2513875 -!- 3298240 -!- 3521591 -!- 3897210 -!- 6378205 -!- 9298646 -!- 9891001 Cytoplasmic 2.6.1.1 monomeric multimer; aspartate transaminase (b0928) 1CQ8 COG1448;Aspartate/tyrosine/aromatic aminotransferase 53383; PLP-dependent transferases PF00155;Aminotransferase class I and II;7.4e-118;codon 80-396 GO:0005737 cytoplasm GO:0009063 amino acid catabolism -!- GO:0006532 aspartate biosynthesis CDS ECK0920 ompF ompF cmlB -!- coa -!- cry -!- tolF b0929 985117 986205 - (no change) JW0912 986316 987404 - t outer membrane porin 1a (Ia;b;F) E 91008984 -!- 91250447 -!- 91285367 -!- 1380671 -!- 2997131 -!- 6294623 -!- 7037455 -!- 7049161 -!- 7524100 -!- 9298646 -!- 9629924 -!- 9843370 Outer Membrane B-barrel protein heteromultimer; The Colicin A Import System (b0737-b0738-b0739-b0740-b0741-b0742-b0929-b3966) 1.B.1; The General Bacterial Porin (GBP) Family 1-22 362 1OPF COG3203;Outer membrane protein (porin) 56935; Porins PF00267;Gram-negative porin;2.9e-191;codon 28-362 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0921 asnS asnS lcs -!- tss b0930 986808 988208 - (no change) JW0913 988007 989407 - e asparaginyl tRNA synthetase E 92112640 -!- 92183913 -!- 1425658 -!- 2009959 -!- 2693216 -!- 9298646 Cytoplasmic 6.1.1.22 monomeric multimer; asparaginyl-tRNA synthetase (b0930) regulated by attenuation (asnS) COG0017;Aspartyl/asparaginyl-tRNA synthetases 50249; Nucleic acid-binding proteins -!- 55681; Class II aaRS and biotin synthetases "PF01336;OB-fold nucleic acid binding domain;4.6e-19;codon 20-100 -!- PF00152;tRNA synthetases class II (D, K and N);3.6e-178;codon 117-462" TIGR00457;asnS: asparaginyl-tRNA synthetase;0;codon 3-466 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK0922 pncB pncB b0931 988377 989579 - (no change) JW0914 989576 990778 - e nicotinate phosphoribosyltransferase E 91009224 Cytoplasmic 2.4.2.11 COG1488;Nicotinic acid phosphoribosyltransferase PF04095;Nicotinate phosphoribosyltransferase (NAPRTa;6.4e-212;codon 10-395 TIGR01514;NAPRTase: nicotinate phosphoribosyltransfera;1.8e-292;codon 8-394 GO:0042597 periplasmic space GO:0009435 nicotinamide adenine dinucleotide biosynthesis CDS ECK0923 pepN pepN b0932 989845 992457 + (no change) JW0915 991044 993656 + e aminopeptidase N E 21101837 -!- 86164315 -!- 87163509 -!- 2436977 -!- 3018440 Cytoplasmic 3.4.11.2 M1 family; alanyl aminopeptidase (proteobacteria) COG0308;Aminopeptidase N "55486; Metalloproteases (zincins), catalytic domain -!- 63737; Leukotriene A4 hydrolase N-terminal domain" PF01433;Peptidase family M1;2.2e-72;codon 14-384 CDS ECK0924 ssuB ssuB ycbE b0933 992500 993267 - (no change) JW0916 993699 994466 - t alkanesulfonate transporter subunit -!- ATP-binding component of ABC superfamily E 20245523 -!- 99410391 -!- 99436146 -!- 3549459 -!- 7984428 Cytoplasmic heteromultimer; YcbE/YcbM ABC transporter (b0936-b0934-b0933) "COG1116;ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.9e-57;codon 37-209 GO:0005737 cytoplasm GO:0006790 sulfur metabolism CDS ECK0925 ssuC ssuC ycbM b0934 993264 994055 - start codon change JW5121 994463 995254 - t alkanesulfonate transporter subunit -!- membrane component of ABC superfamily E 20245523 -!- 99410391 -!- 99436146 Integral Membrane Protein heteromultimer; YcbE/YcbM ABC transporter (b0936-b0934-b0933) 6 7 in PF00528;Binding-protein-dependent transport syst;8.4e-38;codon 73-266 GO:0009274 cell wall (sensu Bacteria) -!- GO:0042597 periplasmic space GO:0006793 phosphorus metabolism CDS ECK0926 ssuD ssuD ycbM -!- ycbN -!- ssi6 b0935 994066 995211 - (no change) JW0918 995265 996410 - e "alkanesulfonate monooxygenase, FMNH(2)-dependent" E 20245523 -!- 99410391 -!- 99436146 -!- 12445781 -!- 8774726 Cytoplasmic 1.14.14.5 monomeric multimer; alkanesulfonate monooxygenase (b0935) 1NQK "COG2141;Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases" 51679; Bacterial luciferase-like PF00296;Luciferase-like monooxygenase;0.00018;codon 1-290 GO:0006790 sulfur metabolism CDS ECK0927 ssuA ssuA ycbO b0936 995208 996167 - start codon change JW0919 996407 997366 - t alkanesulfonate transporter subunit -!- periplasmic-binding component of ABC superfamily E 20245523 -!- 99410391 -!- 99436146 Periplasmic heteromultimer; YcbE/YcbM ABC transporter (b0936-b0934-b0933) 1-36 53850; Periplasmic binding protein-like II "TIGR01728;SsuA_fam: ABC transporter, substrate-binding;1.1e-92;codon 43-328" GO:0042597 periplasmic space GO:0006793 phosphorus metabolism CDS ECK0928 ssuE ssuE ycbE -!- ycbP -!- ssi4 b0937 996160 996735 - (no change) JW0920 997359 997934 - e NAD(P)H-dependent FMN reductase E 20245523 -!- 99410391 -!- 99436146 -!- 8774726 Cytoplasmic 1.5.1.29 monomeric multimer; NAD(P)H-dependent FMN reductase (b0937) COG0431;Predicted flavoprotein 52218; Flavoproteins PF03358;NADPH-dependent FMN reductase;1.7e-60;codon 1-173 GO:0006790 sulfur metabolism -!- GO:0042594 response to starvation GO:0009055 electron carrier activity CDS ECK0929 ycbQ ycbQ b0938 997091 997630 + start codon change JW5122 998290 998829 + ps predicted fimbrial-like adhesin protein C Periplasmic 1-24 "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;7.1e-26;codon 33-182 GO:0009289 fimbria CDS ECK0930 ycbR ycbR b0939 997713 998414 + (no change) JW0922 998912 999613 + pf predicted periplasmic pilin chaperone similar to PapD -!- induced by autoinducer 2 C Periplasmic 1-26 regulated by attenuation (ycbR-ycbS-ycbT-ycbU-ycbV-ycbF) "COG3121;P pilus assembly protein, chaperone PapD" 49354; PapD-like -!- 49584; Periplasmic chaperone C-domain PF00345;Gram-negative pili assembly chaperone;3.5e-37;codon 31-149 -!- PF02753;Gram-negative pili assembly chaperone;9.6e-17;codon 153-230 GO:0006457 protein folding CDS ECK0931 ycbS ycbS b0940 998439 1001039 + (no change) JW0923 999638 1002238 + pf predicted outer membrane usher protein predicted pilin assembly function C Outer Membrane B-barrel protein 1-32 "COG3188;P pilus assembly protein, porin PapC" PF00577;Fimbrial Usher protein;0;codon 37-850 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0932 ycbT ycbT b0941 1001030 1002100 + (no change) JW0924 1002229 1003299 + ps predicted fimbrial-like adhesin protein C 1-30 "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;0.0036;codon 213-356 GO:0009289 fimbria CDS ECK0933 ycbU ycbU b0942 1002112 1002654 + (no change) JW0925 1003311 1003853 + ps predicted fimbrial-like adhesin protein C "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;1.3e-27;codon 29-180 GO:0009289 fimbria CDS ECK0934 ycbV ycbV b0943 1002662 1003177 + start codon change JW5123 1003861 1004376 + ps predicted fimbrial-like adhesin protein C Periplasmic "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;6.4e-32;codon 41-187 GO:0009289 fimbria CDS ECK0935 ycbF ycbF b0944 1003170 1003880 + start codon change JW5124 1004369 1005079 + pf predicted periplasmic pilini chaperone similarity with PapD C 49354; PapD-like -!- 49584; Periplasmic chaperone C-domain PF00345;Gram-negative pili assembly chaperone;2.1e-22;codon 36-159 -!- PF02753;Gram-negative pili assembly chaperone;1.4e-19;codon 163-241 GO:0006457 protein folding CDS ECK0936 pyrD pyrD b0945 1003991 1005001 + (no change) JW0928 1005190 1006200 + e "dihydro-orotate oxidase, FMN-linked" E 12824540 -!- 90264314 -!- 2992959 Cytoplasmic 1.3.3.1 monomeric multimer; dihydroorotate oxidase (b0945) COG0167;Dihydroorotate dehydrogenase 51395; FMN-linked oxidoreductases PF01180;Dihydroorotate dehydrogenase;7.1e-172;codon 46-336 TIGR01036;pyrD_sub2: dihydroorotate dehydrogenase;5.9e-252;codon 3-336 GO:0005737 cytoplasm GO:0006221 pyrimidine nucleotide biosynthesis CDS ECK0937 ycbW ycbW b0946 1005175 1005717 + start codon change JW5125 1006374 1006916 + o predicted protein C Cytoplasmic regulated by attenuation (ycbW) PF07126;Protein of unknown function (DUF1379);3.7e-130;codon 13-192 CDS ECK0938 ycbX ycbX b0947 1005714 1006823 - (no change) JW5126 1006913 1008022 - pc predicted 2Fe-2S cluster-containing protein C Cytoplasmic COG3217;Uncharacterized Fe-S protein -!- COG0633;Ferredoxin "52343; Ferredoxin reductase-like, C-terminal NADP-linked domain -!- 54292; 2Fe-2S ferredoxin-like" PF03476;MOSC N-terminal beta barrel domain;1.4e-49;codon 1-117 -!- PF03473;MOSC domain;1.4e-59;codon 128-263 -!- PF00111;2Fe-2S iron-sulfur cluster binding domain;1.1e-17;codon 291-363 GO:0009055 electron carrier activity CDS ECK0939 ycbY ycbY b0948 1007067 1009175 + (no change) JW0931 1008266 1010374 + pe predicted methyltransferase C Cytoplasmic COG0116;Predicted N6-adenine-specific DNA methylase -!- COG1092;Predicted SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases PF02926;THUMP domain;1.1e-22;codon 56-154 -!- PF01170;Putative RNA methylase family UPF0020;1.2e-106;codon 162-376 CDS ECK0940 uup uup ycbH -!- ycbI b0949 1009187 1011094 + (no change) JW0932 1010386 1012293 + pt fused predicted transporter subunits of ABC superfamily: ATP-binding components C 6294054 -!- 7751275 -!- 9139905 Cytoplasmic "fused predicted transport protein, ABC superfamily: atp_binding component (aa1-290) -!- atp_binding component (aa292-635)" COG0488;ATPase components of ABC transporters with duplicated ATPase domains 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;3e-44;codon 29-229 -!- PF00005;ABC transporter;2.9e-40;codon 345-513 GO:0005737 cytoplasm CDS ECK0941 pqiA pqiA pqi5A -!- pqi5 b0950 1011224 1012477 + (no change) JW0933 1012423 1013676 + cp paraquat-inducible membrane protein A part of superoxide reductase response (soxRS) E 95270582 Integral Membrane Protein 8 8 in COG2995;Uncharacterized paraquat-inducible protein A PF04403;Paraquat-inducible protein A;1.1e-95;codon 2-204 -!- PF04403;Paraquat-inducible protein A;1.6e-106;codon 213-413 "TIGR00155;pqiA_fam: integral membrane protein, PqiA fa;2.2e-213;codon 1-408" CDS ECK0942 pqiB pqiB pqi5B -!- pqi5 b0951 1012482 1014122 + (no change) JW0934 1013681 1015321 + cp paraquat-inducible protein B part of superoxide reductase response (soxRS) E 95270582 Membrane Anchored COG3008;Paraquat-inducible protein B CDS ECK0943 ymbA ymbA b0952 1014134 1014682 + (no change) JW5127 1015333 1015881 + o conserved protein C Cytoplasmic COG3009;Uncharacterized protein conserved in bacteria PF03886;Protein of unknown function (DUF330);1.3e-108;codon 1-176 CDS ECK0944 rmf rmf ramB -!- rimF -!- rimG -!- res b0953 1014938 1015105 + (no change) JW0936 1016137 1016304 + f ribosome modulation factor inactivates ribosome function by dimerization during stationary phase E 1101029 -!- 90207255 -!- 2832401 -!- 8440252 Cytoplasmic regulated by attenuation (rmf) COG3130;Ribosome modulation factor PF04957;Ribosome modulation factor;1.5e-44;codon 1-55 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006457 protein folding CDS ECK0945 fabA fabA b0954 1015175 1015693 - (no change) JW0937 1016374 1016892 - e beta-hydroxydecanoyl thioester dehydrase E 84104816 -!- 88169574 -!- 8910376 -!- 90202993 -!- 1505031 -!- 8805534 -!- 8808925 4.2.1.60 monomeric multimer; beta-hydroxyacyl-ACP dehydrase / beta-hydroxydecanoyl-ACP dehydrase / trans-2-decenoyl-ACP isomerase (b0954) 1MKB COG0764;3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases 54637; Thioesterase/thiol ester dehydrase-isomerase TIGR01749;fabA: beta-hydroxyacyl-(acyl-carrier-protein;1.8e-118;codon 4-172 CDS ECK0946 ycbZ ycbZ b0955 1015762 1017522 - (no change) JW0938 1016961 1018721 - pe predicted peptidase C Cytoplasmic COG1067;Predicted ATP-dependent protease GO:0006508 proteolysis and peptidolysis CDS ECK0947 ycbG ycbG b0956 1017708 1018160 + (no change) JW0939 1018907 1019359 + o conserved protein C Cytoplasmic COG3120;Uncharacterized protein conserved in bacteria PF06303;Protein of unknown function (DUF1047);5.1e-123;codon 1-149 CDS ECK0948 ompA ompA con -!- tolG -!- tut b0957 1018236 1019276 - (no change) JW0940 1019435 1020475 - m outer membrane protein A (3a;II*;G;d) involved in stability of cell envelope E 14644420 -!- 88330834 -!- 91035411 -!- 93257455 -!- 98440126 -!- 10368142 -!- 10757971 -!- 10764596 -!- 1370823 -!- 3902787 -!- 6086577 -!- 6253901 -!- 6260961 -!- 7001461 -!- 8106193 -!- 9298646 -!- 9629924 -!- 9808047 -!- 340230 -!- 8740179 Periplasmic 1.B.6; The OmpA-OmpF Porin (OOP) Family 346 regulated by attenuation (ompA) COG2885;Outer membrane protein and related peptidoglycan-associated (lipo)proteins 56925; Outer membrane protein PF01389;OmpA-like transmembrane domain;3.9e-123;codon 6-195 -!- PF00691;OmpA family;1e-49;codon 222-319 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0949 sulA sulA sfiA -!- suf b0958 1019633 1020142 - (no change) JW0941 1020832 1021341 - cp SOS cell division inhibitor inhibits FtsZ ring formation upon DNA damage/inhibition E 10368140 -!- 91072263 -!- 93163041 -!- 98348458 -!- 3297925 -!- 6253901 -!- 6306396 Cytoplasmic "COG5404;SOS-response cell division inhibitor, blocks FtsZ ring formation" PF03846;Cell division inhibitor SulA;3.9e-97;codon 2-120 TIGR00623;sula: cell division inhibitor SulA;2.7e-140;codon 2-169 GO:0042597 periplasmic space GO:0006281 DNA repair -!- GO:0009432 SOS response CDS ECK0950 yccR yccR b0959 1020361 1020990 + (no change) JW0942 1021560 1022189 + o conserved protein C Cytoplasmic COG3070;Regulator of competence-specific genes PF04993;TfoX N-terminal domain;6.3e-08;codon 8-108 -!- PF04994;TfoX C-terminal domain;7.5e-49;codon 115-195 CDS ECK0951 yccS yccS b0960 1020953 1023106 - start codon change JW5128 1022152 1024305 - pm predicted inner membrane protein C Integral Membrane Protein 2.A.85; The Aromatic Acid Exporter (ArAE) Family 12 9 in COG1289;Predicted membrane protein PF05976;Bacterial membrane protein of unknown functi;0;codon 10-708 "TIGR01666;YCCS: hypothetical membrane protein, TIGR01;0;codon 11-709 -!- TIGR01667;YCCS_YHJK: integral membrane protein, YccS/;0;codon 11-709" CDS ECK0952 yccF yccF b0961 1023125 1023571 - (no change) JW0944 1024324 1024770 - pm conserved inner membrane protein C Integral Membrane Protein 3 3 in COG3304;Predicted membrane protein PF03733;Domain of unknown function (DUF307);3.3e-19;codon 3-59 -!- PF03733;Domain of unknown function (DUF307);9.1e-32;codon 76-132 CDS ECK0953 helD helD srjB b0962 1023694 1025748 + (no change) JW0945 1024893 1026947 + e DNA helicase IV E 89255269 -!- 93328668 -!- 95058623 Cytoplasmic 3.6.1.- COG0210;Superfamily I DNA and RNA helicases 52540; P-loop containing nucleotide triphosphate hydrolases PF00580;UvrD/REP helicase;2.7e-19;codon 197-676 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK0954 mgsA mgsA yccG -!- mgs b0963 1025780 1026238 - start codon change JW5129 1026979 1027437 - e methylglyoxal synthase E 73035308 -!- 9665712 -!- 10368300 -!- 10715115 -!- 2542273 -!- 7984428 -!- 9489667 Cytoplasmic 4.2.3.3 monomeric multimer; methylglyoxal synthase (b0963) regulated by attenuation (mgsA) 1IK4 COG1803;Methylglyoxal synthase 52335; Methylglyoxal synthase-like PF02142;MGS-like domain;1.1e-26;codon 28-121 TIGR00160;MGSA: methylglyoxal synthase;1.6e-116;codon 13-155 GO:0005737 cytoplasm GO:0009438 methylglyoxal metabolism CDS ECK0955 yccT yccT b0964 1026334 1026996 - (no change) JW0947 1027533 1028195 - o conserved protein C Periplasmic COG3110;Uncharacterized protein conserved in bacteria CDS ECK0956 yccU yccU b0965 1027169 1027582 + start codon change JW5130 1028368 1028781 + d predicted CoA-binding protein with NAD(P)-binding Rossmann-fold domain member of the widespread CoA subfamily C Cytoplasmic 51735; NAD(P)-binding Rossmann-fold domains PF02629;CoA binding domain;3.5e-32;codon 37-146 CDS ECK0957 yccV yccV b0966 1027627 1027944 - (no change) JW5970 1028826 1029143 - f "DNA-binding protein, hemimethylated" E 12700277 -!- 15569148 Cytoplasmic TIGR02097;yccV: hemimethylated DNA binding domain;3.4e-50;codon 20-119 CDS ECK0958 yccW yccW b0967 1028002 1029105 - (no change) JW5898 1029201 1030304 - pe predicted methyltransferase C Cytoplasmic 48371; ARM repeat -!- 53335; S-adenosyl-L-methionine-dependent methyltransferases CDS ECK0959 yccX yccX b0968 1029287 1029565 + (no change) JW5131 1030486 1030764 + pe predicted acylphosphatase C 15159579 Cytoplasmic COG1254;Acylphosphatases 54975; Acylphosphatase PF00708;Acylphosphatase;1.4e-11;codon 1-88 CDS ECK0960 yccK yccK b0969 1029562 1029891 - start codon change JW0952 1030761 1031090 - pe predicted sulfite reductase subunit C Cytoplasmic "69721; DsrC, the gamma subunit of dissimilatory sulfite reductase" PF04358;DsrC like protein;1.3e-80;codon 20-128 CDS ECK0961 yccA yccA b0970 1029982 1030641 - (no change) JW0953 1031181 1031840 - m inner membrane protein degraded by FtsH protease C 6376117 Integral Membrane Protein 9.B.24; The Testis-Enhanced Gene Transfer (TEGT) Family 7 7 in regulated by attenuation (yccA-yccK) "COG0670;Integral membrane protein, interacts with FtsH" PF01027;Uncharacterised protein family UPF0005;1.1e-61;codon 13-217 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm tRNA ECK0962 serT serT divE b0971 1030848 1030935 - (no change) JWR0026 1032047 1032134 - n tRNA-Ser(UGA) (Serine tRNA1) E 374381 -!- 6376117 -!- 88320491 -!- 91088251 -!- 92302305 CDS ECK0963 hyaA hyaA b0972 1031362 1032480 + (no change) JW0954 1032561 1033679 + e "hydrogenase 1, small subunit" E 86192450 -!- 90202716 -!- 92215587 Integral Membrane Protein 1.12.99.6 "heteromultimer; hydrogenase I (b0972-b0973-b0974) -!- monomeric multimer; hydrogenase I, small subunit (b0972)" 1-35 3 2 in "COG1740;Ni,Fe-hydrogenase I small subunit" "56770; Nickel-iron hydrogenase, small subunit" "PF01058;NADH ubiquinone oxidoreductase, 20 Kd sub;1.6e-18;codon 106-209" TIGR00391;hydA: hydrogenase (NiFe) small subunit;4.3e-214;codon 2-360 -!- TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;1.1e-06;codon 16-45 GO:0019866 inner membrane GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK0964 hyaB hyaB b0973 1032477 1034270 + (no change) JW0955 1033676 1035469 + e "hydrogenase 1, large subunit" E 86192450 -!- 90202716 -!- 92215587 Cytoplasmic 1.12.99.6 "heteromultimer; hydrogenase I (b0972-b0973-b0974) -!- monomeric multimer; hydrogenase I, large subunit (b0973)" "COG0374;Ni,Fe-hydrogenase I large subunit" "56762; Nickel-iron hydrogenase, large subunit" PF00374;Nickel-dependent hydrogenase;0;codon 54-582 GO:0019866 inner membrane GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK0965 hyaC hyaC cybH b0974 1034289 1034996 + (no change) JW0956 1035488 1036195 + c "hydrogenase 1, b-type cytochrome subunit" Ni/Fe hydrogenase E 90202716 -!- 91310595 -!- 92215587 Integral Membrane Protein heteromultimer; hydrogenase I (b0972-b0973-b0974) 4 4 in "COG1969;Ni,Fe-hydrogenase I cytochrome b subunit" PF01292;Cytochrome b561 family;3.2e-86;codon 11-220 "TIGR02125;CytB-hydogenase: Ni/Fe-hydrogenase, b;6.5e-136;codon 12-226" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration -!- GO:0017004 cytochrome biogenesis GO:0009053 electron donor activity CDS ECK0966 hyaD hyaD b0975 1034993 1035580 + (no change) JW0957 1036192 1036779 + f protein involved in processing of HyaA and HyaB proteins E 90202716 -!- 91310595 -!- 92215587 Cytoplasmic M52 family; HyaD endopeptidase (HyaD protein) "COG0680;Ni,Fe-hydrogenase maturation factor" 53163; HybD-like PF01750;Hydrogenase maturation protease;2.1e-59;codon 23-152 TIGR00072;hydrog_prot: hydrogenase maturation pr;6.5e-78;codon 3-163 -!- TIGR00140;hupD: hydrogenase expression/formation;6.6e-96;codon 6-157 -!- TIGR00141;hupD_frhD_pept: hydrogenase maturation;1e-53;codon 6-157 GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration -!- GO:0006457 protein folding CDS ECK0967 hyaE hyaE b0976 1035577 1035975 + (no change) JW0958 1036776 1037174 + f protein involved in processing of HyaA and HyaB proteins E 90202716 -!- 91310595 -!- 92215587 Cytoplasmic 52833; Thioredoxin-like PF07449;Hydrogenase-1 expression protein HyaE;3e-63;codon 10-116 GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration -!- GO:0006457 protein folding CDS ECK0968 hyaF hyaF b0977 1035972 1036829 + (no change) JW0959 1037171 1038028 + f protein involved in nickel incorporation into hydrogenase-1 proteins E 90202716 -!- 91310595 -!- 92215587 Cytoplasmic "PF04809;HupH hydrogenase expression protein, C-termi;3.8e-72;codon 163-280" GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration -!- GO:0006457 protein folding CDS ECK0969 appC appC cyxA -!- cbdA b0978 1036963 1038507 + (no change) JW0960 1038162 1039706 + c "cytochrome bd-II oxidase, subunit I" E 92049231 -!- 96198179 Integral Membrane Protein 1.10.3.- heteromultimer; cytochrome bd-II terminal oxidase (b0978-b0979) 9 9 in "COG1271;Cytochrome bd-type quinol oxidase, subunit 1" PF01654;Bacterial Cytochrome Ubiquinol Oxidase;0;codon 7-511 GO:0019866 inner membrane GO:0009054 electron acceptor activity CDS ECK0970 appB appB cyxB -!- cbdB b0979 1038519 1039655 + (no change) JW0961 1039718 1040854 + c "cytochrome bd-II oxidase, subunit II" E 92049231 -!- 96198179 Integral Membrane Protein 1.10.3.- heteromultimer; cytochrome bd-II terminal oxidase (b0978-b0979) 9 8 in "COG1294;Cytochrome bd-type quinol oxidase, subunit 2" PF02322;Cytochrome oxidase subunit II;8.5e-217;codon 5-366 "TIGR00203;cydB: cytochrome d ubiquinol oxidase, subuni;1.1e-212;codon 1-378" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009054 electron acceptor activity CDS ECK0971 appA appA b0980 1039840 1041138 + (no change) JW0963 1041039 1042337 + e phosphoanhydride phosphorylase E "20122624 -!- 92049231 -!- 93054596 -!- 10696472 -!- 2168385 -!- 3038201 -!- 8387749 -!- Greiner R, Jany KD;Biol Chem Hoppe-Seyler;1991;372:664-665" Periplasmic 3.1.3.26 -!- 3.1.3.2 monomeric multimer; 6-phytase / pH 2.5 acid phosphatase (b0980) 1-22 432 1DKL 53254; Phosphoglycerate mutase-like PF00328;Histidine acid phosphatase;5.9e-156;codon 28-407 GO:0042597 periplasmic space GO:0006793 phosphorus metabolism -!- GO:0042594 response to starvation CDS ECK0972 yccC yccC etk b0981 1041253 1043433 - (no change) JW0964 1042452 1044632 - e cryptic autophosphorylating protein tyrosine kinase Etk E 10369665 -!- 11090276 -!- 2168385 -!- 7984428 Integral Membrane Protein 2.7.1.112 8.A.3; The Cytoplasmic Membrane-Periplasmic Auxiliary-1 (MPA1) Protein with Cytoplasmic (C) Domain (MPA1-C or MPA1+C) Family 2 2 in COG3206;Uncharacterized protein involved in exopolysaccharide biosynthesis -!- COG0489;ATPases involved in chromosome partitioning 52540; P-loop containing nucleotide triphosphate hydrolases PF02706;Chain length determinant protein;5.3e-96;codon 16-252 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006464 protein modification CDS ECK0973 etp etp yccY -!- epd b0982 1043453 1043899 - start codon change JW5132 1044652 1045098 - e phosphotyrosine-protein phosphatase responsible for dephosphorylating phospho-Etk autokinase E 11090276 Cytoplasmic 52788; Phosphotyrosine protein phosphatases I PF01451;Low molecular weight phosphotyrosine protein;2.4e-65;codon 11-149 GO:0006464 protein modification CDS ECK0974 yccZ yccZ b0983 1043887 1045026 - (no change) JW0966 1045086 1046225 - pt predicted exopolysaccharide export protein C Outer membrane Lipoprotein COG1596;Periplasmic protein involved in polysaccharide export PF02563;Polysaccharide biosynthesis/export protei;1.7e-65;codon 74-205 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK0975 ymcA ymcA b0984 1045072 1047168 - (no change) JW0967 1046271 1048367 - o conserved protein C Periplasmic PF06082;Bacterial putative lipoprotein (DUF940);0;codon 7-697 CDS ECK0976 ymcB ymcB b0985 1047168 1047914 - (no change) JW0968 1048367 1049113 - o conserved protein C Periplasmic PF06251;Protein of unknown function (DUF1017);1.3e-148;codon 4-248 CDS ECK0977 ymcC ymcC b0986 1047911 1048555 - (no change) JW0969 1049110 1049754 - pm predicted outer membrane lipoprotein C Outer membrane Lipoprotein CDS ECK0978 ymcD ymcD b0987 1048662 1048967 - start codon change JW5133 1049861 1050166 - o predicted protein C out GO:0009274 cell wall (sensu Bacteria) CDS ECK0979 cspH cspH cspK b0989 1050186 1050398 - (no change) JW5134 1051385 1051597 - f "stress protein, member of the CspA-family" C 9484881 -!- 9439003 Cytoplasmic regulated by attenuation (cspH) COG1278;Cold shock proteins 50249; Nucleic acid-binding proteins PF00313;'Cold-shock' DNA-binding domain;1.3e-27;codon 4-70 GO:0009266 response to temperature CDS ECK0980 cspG cspG cspI b0990 1050684 1050896 + (no change) JW0974 1051883 1052095 + r DNA-binding transcriptional regulator E 9484881 -!- 15466053 -!- 8631696 -!- 9439003 Cytoplasmic COG1278;Cold shock proteins 50249; Nucleic acid-binding proteins PF00313;'Cold-shock' DNA-binding domain;3.6e-44;codon 4-70 GO:0009266 response to temperature CDS ECK0981 ymcE ymcE gnsA -!- sfa -!- yccL b0991 1051070 1051300 + (no change) JW0975 1052269 1052499 + f cold shock gene suppresses fabA and ts growth mutation E 96404784 -!- 11544213 Membrane Anchored CDS ECK0982 gnsA gnsA b4517 1051290 1051463 + new JW0976 1052489 1052662 + pr predicted regulator of phosphatidylethanolamine synthesis overproduction specifically increases the acidic phospholipid contents at low temperatures C Cytoplasmic GO:0005737 cytoplasm CDS ECK0983 yccM yccM b0992 1051512 1052585 - (no change) JW0977 1052711 1053784 - pc predicted 4Fe-4S membrane protein C Integral Membrane Protein 7 5 out COG0348;Polyferredoxin 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;7.5e-05;codon 244-267 -!- PF00037;4Fe-4S binding domain;0.00066;codon 271-294 CDS ECK0984 torS torS yccI b0993 1052657 1055401 - start codon change JW5135 1053856 1056600 - r hybrid sensory histidine kinase in two-component regulatory system with TorR senses TMAO E 9135110 -!- 99340208 -!- 11274133 -!- 8083154 -!- 8809780 Integral Membrane Protein monomeric multimer; TorS (b0993) 2 2 fused hybrid sensory histidine kinase: sensory histidine kinase (aa1-665) -!- response regulator (aa669-904) COG0642;Signal transduction histidine kinase -!- COG2198;FOG: HPt domain "47384; Homodimeric domain of signal transducing histidine kinase -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase -!- 47226; Histidine-containing phosphotransfer domain, HPT domain -!- 52172; CheY-like" "PF00672;HAMP;3.2e-10;324-394 -!- PF00512;His Kinase A (phosphoacceptor);1.1e-21;433-498 -!- PF02518; His kinase-, DNA gyrase B-, and HSP90-like ATPase;2.2e-42;547-653 -!- PF00072;Response reg receiver;6.2e-14;672-792 -!- PF01627;Hpt;8.2e-14;817-895" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration -!- GO:0006464 protein modification CDS ECK0985 torT torT yccH b0994 1055484 1056512 + (no change) JW0979 1056683 1057711 + r periplasmic sensory protein associated with the TorRS two-component regulatory system E 8576063 -!- 8809780 -!- 8083154 Periplasmic 1-18 342 "COG1879;ABC-type sugar transport system, periplasmic component" 53822; Periplasmic binding protein-like I PF00532;Periplasmic binding proteins and sugar b;9e-115;codon 44-337 GO:0042597 periplasmic space GO:0009061 anaerobic respiration -!- GO:0006464 protein modification CDS ECK0986 torR torR b0995 1056485 1057177 - (no change) JW0980 1057684 1058376 - r DNA-binding response regulator in two-component regulatory system with TorS E 91250102 -!- 95095983 -!- 10648521 -!- 8083154 -!- 8596446 -!- 9135110 Cytoplasmic monomeric multimer; TorR transcriptional dual regulator (b0995) Two gadAX -!- hdeAB -!- tnaCAB -!- torCAD -!- torR COG0745;Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;2.7e-41;codon 3-121 -!- PF00486;Transcriptional regulatory protein, C te;2.5e-18;codon 153-225" GO:0005737 cytoplasm GO:0009061 anaerobic respiration -!- GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK0987 torC torC b0996 1057307 1058479 + (no change) JW0981 1058506 1059678 + c "trimethylamine N-oxide (TMAO) reductase I, cytochrome c-type subunit" also functions with TorA as a negative regulator of the tor operon E 94293785 -!- 94314186 -!- 99340208 -!- 11056172 -!- 11562502 heteromultimer; trimethylamine N-oxide reductase I (b0996-b0997) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family "COG3005;Nitrate/TMAO reductases, membrane-bound tetraheme cytochrome c subunit" 48695; Multiheme cytochromes "PF03264;NapC/NirT cytochrome c family, N-termin;2.8e-122;codon 10-184" TIGR02162;torC: trimethylamine-N-oxide reductase c-typ;0;codon 2-383 GO:0042597 periplasmic space GO:0009061 anaerobic respiration -!- GO:0017004 cytochrome biogenesis -!- GO:0006350 transcription GO:0009055 electron carrier activity -!- GO:0016564 transcriptional repressor activity CDS ECK0988 torA torA b0997 1058479 1061025 + (no change) JW0982 1059678 1062224 + e "trimethylamine N-oxide (TMAO) reductase I, catalytic subunit" E 88193091 -!- 90089471 -!- 94293785 -!- 8302830 -!- 8022286 Periplasmic 1.6.6.9 heteromultimer; trimethylamine N-oxide reductase I (b0996-b0997) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 1-45 848 "COG0243;Anaerobic dehydrogenases, typically selenocysteine-containing" "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3" PF00384;Molybdopterin oxidoreductase;2e-200;codon 99-573 -!- PF01568;Molydopterin dinucleotide binding dom;1.1e-47;codon 690-812 TIGR02164;torA: trimethylamine-N-oxide reductase;0;codon 1-836 -!- TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.04;codon 9-39 -!- TIGR00509;bisC_fam: molybdopterin guanine dinucl;0;codon 56-836 GO:0042597 periplasmic space GO:0009061 anaerobic respiration GO:0009054 electron acceptor activity CDS ECK0989 torD torD b0998 1061022 1061621 + (no change) JW0983 1062221 1062820 + f chaperone involved in maturation of TorA subunit of trimethylamine N-oxide reductase system I E 12766163 -!- 94293785 -!- 9632735 -!- 8302830 Cytoplasmic 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family COG3381;Uncharacterized component of anaerobic dehydrogenases PF06192;Cytoplasmic chaperone TorD;1.5e-51;codon 37-172 GO:0005737 cytoplasm GO:0006457 protein folding CDS ECK0990 cbpM cbpM yccD b0999 1061773 1062078 - (no change) JW0984 1062972 1063277 - f modulator of CbpA co-chaperone E 15184371 Cytoplasmic CDS ECK0991 cbpA cbpA b1000 1062078 1062998 - (no change) JW0985 1063277 1064197 - f "curved DNA-binding protein, DnaJ homologue that functions as a co-chaperone of DnaK" E 94134696 -!- 15184371 Cytoplasmic monomeric multimer; chaperone with DnaK; curved DNA-binding protein (b1000) COG2214;DnaJ-class molecular chaperone 46565; Chaperone J-domain -!- 49493; HSP40/DnaJ peptide-binding domain PF00226;DnaJ domain;3.9e-34;codon 5-69 -!- PF01556;DnaJ C terminal region;1.4e-35;codon 172-291 GO:0005737 cytoplasm GO:0006457 protein folding CDS ECK0992 yccE yccE b1001 1063259 1064515 + (no change) JW0986 1064458 1065714 + o predicted protein C 8302830 Cytoplasmic CDS ECK0993 agp agp b1002 1064808 1066049 + (no change) JW0987 1066007 1067248 + e glucose-1-phosphatase/inositol phosphatase E 12455612 -!- 90368616 -!- 91297199 -!- 2153660 -!- 9298646 Periplasmic 3.1.3.10 monomeric multimer; 3-phytase / glucose-1-phosphatase (b1002) 1-22 413 regulated by attenuation (agp) 1NT4 53254; Phosphoglycerate mutase-like PF00328;Histidine acid phosphatase;1.5e-159;codon 29-393 GO:0042597 periplasmic space GO:0006006 glucose metabolism CDS ECK0994 yccJ yccJ b1003 1066087 1066314 - (no change) JW0988 1067286 1067513 - o predicted protein C Cytoplasmic CDS ECK0995 wrbA wrbA b1004 1066335 1066931 - (no change) JW0989 1067534 1068130 - pr predicted flavoprotein in Trp regulation modifies association between Trp repressor and operator in stationary phase C 93296226 -!- 9694845 Cytoplasmic COG0655;Multimeric flavodoxin WrbA 52218; Flavoproteins PF00258;Flavodoxin;2e-26;codon 6-135 TIGR01755;flav_wrbA: flavoprotein WrbA;8.7e-165;codon 2-196 GO:0005737 cytoplasm GO:0000162 tryptophan biosynthesis CDS ECK0996 ymdF ymdF b4518 1067304 1067477 + new JW5136 1068503 1068676 + o conserved protein C Cytoplasmic GO:0005737 cytoplasm CDS ECK0997 ycdG ycdG b1006 1067734 1069062 - start codon change JW5137 1068933 1070261 - pt predicted transporter C Integral Membrane Protein 14 11 in PF00860;Permease family;1e-140;codon 52-426 TIGR00801;ncs2: uracil-xanthine permease;8.6e-185;codon 48-446 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK0998 ycdH ycdH b1007 1069083 1069577 - start codon change JW5138 1070282 1070776 - pc "predicted oxidoreductase, flavin:NADH component" C Cytoplasmic 50475; FMN-binding split barrel PF01613;Flavin reductase like domain;6.6e-70;codon 1-148 CDS ECK0999 ycdI ycdI b1008 1069588 1070178 - (no change) JW0993 1070787 1071377 - pe predicted oxidoreductase predicted NADH dehydrogenase -!- NAD(P)H nitroreductase C Cytoplasmic COG0778;Nitroreductase 55469; NADH oxidase/flavin reductase PF00881;Nitroreductase family;4.7e-07;codon 14-174 CDS ECK1000 rarA rarA ycdJ b1009 1070188 1070988 - (no change) JW0994 1071387 1072187 - pe predicted hydrolase C S33 family; non-peptidase homologues (YcdJ protein) COG0596;Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) 53474; alpha/beta-Hydrolases PF00561;alpha/beta hydrolase fold;1.7e-19;codon 40-253 CDS ECK1001 ycdK ycdK b1010 1070996 1071382 - (no change) JW0995 1072195 1072581 - d conserved protein C Periplasmic "COG0251;Putative translation initiation inhibitor, yjgF family" 55298; YjgF-like PF01042;Endoribonuclease L-PSP;1.1e-48;codon 10-126 CDS ECK1002 ycdL ycdL b1011 1071394 1072086 - start codon change JW5139 1072593 1073285 - pe predicted enzyme C Cytoplasmic COG1335;Amidases related to nicotinamidase 52499; Cysteine hydrolase PF00857;Isochorismatase family;1.5e-101;codon 27-233 CDS ECK1003 ycdM ycdM b1012 1072086 1073234 - (no change) JW0997 1073285 1074433 - pe predicted monooxygenase C Cytoplasmic 51679; Bacterial luciferase-like PF00296;Luciferase-like monooxygenase;0.00022;codon 20-341 CDS ECK1004 ycdC ycdC b1013 1073465 1074103 + (no change) JW0998 1074664 1075302 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic TetR/AcrR regulated by attenuation (ycdC) COG1309;Transcriptional regulator 46689; Homeodomain-like "PF00440;Bacterial regulatory proteins, tetR family;5e-18;codon 23-69" GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1005 putA putA poaA -!- putC b1014 1074143 1078105 - (no change) JW0999 1075342 1079304 - e fused DNA-binding transcriptional regulator -!- proline dehydrogenase -!- pyrroline-5-carboxylate dehydrogenase E 12514740 -!- 87092411 -!- 93232060 -!- 95055736 -!- 3325781 Cytoplasmic 1.5.99.8 -!- 1.5.1.12 monomeric multimer; proline dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase (b1014) putA "fused: bifunctional transcriptional repressor (N-terminal) and proline dehydrogenase, FAD-binding (C-terminal) (aa1-569) -!- pyrroline-5-carboxylate dehydrogenase (aa618-1320)" COG0506;Proline dehydrogenase -!- COG4230;Delta 1-pyrroline-5-carboxylate dehydrogenase 53720; ALDH-like PF01619;Proline dehydrogenase;4.3e-193;codon 228-574 -!- PF00171;Aldehyde dehydrogenase family;3.4e-92;codon 655-1119 TIGR01238;D1pyr5carbox3: delta-1-pyrroline-5-carb;0;codon 610-1114 GO:0005737 cytoplasm GO:0009063 amino acid catabolism -!- GO:0006350 transcription GO:0009053 electron donor activity -!- GO:0016564 transcriptional repressor activity CDS ECK1006 putP putP putC b1015 1078528 1080036 + (no change) JW1001 1079727 1081235 + t proline:sodium symporter E 12923181 -!- 88213396 -!- 91227628 -!- 93132799 -!- 98359785 -!- 1400239 -!- 1567896 -!- 3053649 -!- 3053687 -!- 3302614 -!- 3325781 -!- 8119910 Integral Membrane Protein 2.A.21; The Solute:Sodium Symporter (SSS) Family 13 12 in COG0591;Na+/proline symporter PF00474;Sodium:solute symporter family;8.8e-223;codon 35-437 TIGR02121;Na_Pro_sym: sodium/proline symporter;0;codon 5-492 -!- TIGR00813;sss: SSS sodium solute transporter superfa;7e-179;codon 35-437 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006561 proline biosynthesis GO:0005298 proline:sodium symporter activity ECK1007 ycdN ycdN b4490 1080570 1081408 + pseudogene; interrupted by frameshift JW5141+JW1002 1081778 1082607 + ancestral gene su predicted membrane protein (pseudogene) C CDS ECK1007 ycdN ycdN_2 ycdN_frag2 b1017 1080677 1081408 + pseudogene fragment -!- (no change) JW1002 1081876 1082607 + "pseudogene, split by frameshift (ycdN)" su "predicted protein, C-ter fragment (pseudogene)" C CDS ECK1007 ycdN ycdN_1 ycdN_frag1 b1016 1080579 1080689 + pseudogene fragment -!- start codon change JW5141 1081778 1081888 + "pseudogene, split by frameshift (ycdN)" su "predicted protein, N-ter fragment (pseudogene)" C CDS ECK1008 ycdO ycdO b1018 1081466 1082593 + (no change) JW1003 1082665 1083792 + o conserved protein C 10493123 Periplasmic 1-24 COG2822;Predicted periplasmic lipoprotein involved in iron transport PF04302;Protein of unknown function (DUF451);1.1e-181;codon 119-372 CDS ECK1009 ycdB ycdB b1019 1082599 1083870 + (no change) JW1004 1083798 1085069 + o conserved protein C 15375152 Periplasmic 1-35 COG2837;Predicted iron-dependent peroxidase PF04261;Dyp-type peroxidase family;1.1e-198;codon 61-411 TIGR01412;tat_substr_1: Tat-translocated enzyme;3.4e-296;codon 5-422 -!- TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.011;codon 12-35 -!- TIGR01413;Dyp_perox_fam: Dyp-type peroxidase fam;7.2e-124;codon 61-411 CDS ECK1010 phoH phoH psiH b1020 1084215 1085279 + (no change) JW1005 1085414 1086478 + d conserved protein with nucleoside triphosphate hydrolase domain pho regulon component E 90264312 -!- 93186698 Cytoplasmic "COG1702;Phosphate starvation-inducible protein PhoH, predicted ATPase" 52540; P-loop containing nucleotide triphosphate hydrolases PF02562;PhoH-like protein;2.3e-143;codon 148-354 GO:0005737 cytoplasm GO:0006793 phosphorus metabolism -!- GO:0042594 response to starvation CDS ECK1011 ycdP ycdP hmsS -!- pgaD b1021 1085329 1085742 - (no change) JW1006 1086528 1086941 - pm predicted inner membrane protein associated with biofilm formation C 15090514 -!- 99392474 Integral Membrane Protein 2 2 in GO:0009274 cell wall (sensu Bacteria) CDS ECK1012 ycdQ ycdQ hmsR -!- pgaC b1022 1085744 1087069 - (no change) JW1007 1086943 1088268 - pe predicted glycosyl transferase C 15090514 -!- 99392474 Integral Membrane Protein 9.B.32; The Putative Vectorial Glycosyl Polymerization (VGP) Family 5 5 in "COG1215;Glycosyltransferases, probably involved in cell wall biogenesis" 53448; Nucleotide-diphospho-sugar transferases PF00535;Glycosyl transferase;5.1e-41;codon 78-246 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1013 ycdR ycdR hmsF -!- pgaB b1023 1087062 1089080 - (no change) JW5142 1088261 1090279 - pe predicted enzyme associated with biofilm formation C 15090514 -!- 99392474 Outer membrane Lipoprotein COG0726;Predicted xylanase/chitin deacetylase PF01522;Polysaccharide deacetylase;1.7e-37;codon 102-271 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1014 ycdS ycdS hmsH -!- pgaA b1024 1089089 1091512 - (no change) JW1010 1090288 1092711 - pm predicted outer membrane protein role in biofilm formation C 15090514 -!- 99392474 Periplasmic 1-29 48439; Protein prenylyltransferase PF07719;Tetratricopeptide repeat;1.6e-05;codon 98-131 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK1015 ycdT ycdT b1025 1092099 1093457 + (no change) JW5143 1093298 1094656 + pr predicted diguanylate cyclase C 99392474 Integral Membrane Protein 7 8 in COG2199;FOG: GGDEF domain PF00990;GGDEF domain;1.5e-71;codon 278-439 TIGR00254;GGDEF: putative diguanylate cyclase (GGDEF);3.1e-43;codon 278-444 CDS ECK1016 ymdE ymdE b1028 1094767 1095069 + pseudogene -!- start codon change JW5145 1095966 1096268 + pseudogene su predicted protein (pseudogene) C Cytoplasmic 52151; Catalytic domain of malonyl-CoA ACP transacylase CDS ECK1017 ycdU ycdU b1029 1095066 1096052 + (no change) JW1015 1096265 1097251 + pm predicted inner membrane protein C Integral Membrane Protein 8 8 tRNA ECK1018 serX serX b1032 1096788 1096875 - (no change) JWR0027 1097806 1097893 - n tRNA-Ser(GGA) (Serine tRNA5) E 88320491 -!- 91088251 -!- 92302305 CDS ECK1019 ycdW ycdW b1033 1097109 1098047 + start codon change JW5146 1098127 1099065 + e 2-ketoacid reductase E 11237876 -!- 10493123 Cytoplasmic 1.1.1.79 COG0111;Phosphoglycerate dehydrogenase and related dehydrogenases 51735; NAD(P)-binding Rossmann-fold domains PF02826;D-isomer specific 2-hydroxyacid dehydrog;4.6e-16;codon 114-288 CDS ECK1020 ycdX ycdX b1034 1098102 1098839 + (no change) JW1017 1099120 1099857 + pe predicted zinc-binding hydrolase C 12661000 Cytoplasmic COG1387;Histidinol phosphatase and related hydrolases of the PHP family PF02231;PHP domain N-terminal region;2.2e-23;codon 4-76 -!- PF02811;PHP domain C-terminal region;3.9e-15;codon 98-200 GO:0006261 DNA dependent DNA replication CDS ECK1021 ycdY ycdY b1035 1098863 1099417 + (no change) JW1018 1099881 1100435 + o conserved protein predicted oxidoreductase component C Cytoplasmic COG3381;Uncharacterized component of anaerobic dehydrogenases PF06192;Cytoplasmic chaperone TorD;1.9e-48;codon 23-151 CDS ECK1022 ycdZ ycdZ b1036 1099519 1100010 + start codon change JW5147 1100537 1101028 + pm predicted inner membrane protein C Integral Membrane Protein 4 5 in PF06496;Protein of unknown function (DUF1097);7.2e-96;codon 17-168 CDS ECK1023 csgG csgG b1037 1100074 1100907 - (no change) JW1020 1101092 1101925 - lp outer membrane lipoprotein involved in curli assembly/transport -!- 2nd curli operon C 98043534 -!- 8817489 Outer membrane Lipoprotein COG1462;Uncharacterized protein involved in formation of curli polymers PF03783;Curli production assembly/transport componen;7.3e-118;codon 7-252 GO:0009289 fimbria -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK1024 csgF csgF b1038 1100934 1101350 - (no change) JW1021 1101952 1102368 - pt predicted transport protein involved in curli assembly/transport -!- 2nd curli operon C 9457880 -!- 8817489 1-47 GO:0009289 fimbria CDS ECK1025 csgE csgE b1039 1101375 1101764 - (no change) JW1022 1102393 1102782 - pt predicted transport protein involved in curli assembly/transport -!- 2nd curli operon C 9457880 -!- 8817489 Periplasmic GO:0009289 fimbria CDS ECK1026 csgD csgD b1040 1101769 1102419 - (no change) JW1023 1102787 1103437 - r DNA-binding transcriptional activator in two-component regulatory system "activates csgD which mediates production of allosteric activator of cyclic di-GMP, which stimulates rdar morphotype (aggregation, cellulose & curli synthesis)" E 15818467 -!- 14523117 -!- 9457880 -!- 8817489 Cytoplasmic LuxR/UhpA csgBA -!- csgDEFG COG2771;DNA-binding HTH domain-containing proteins "46894; C-terminal, effector domain of the bipartite response regulators" "PF00196;Bacterial regulatory proteins, luxR family;5.3e-21;codon 153-210" GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1027 csgB csgB b1041 1103174 1103629 + (no change) JW1024 1104192 1104647 + f "curlin nucleator protein, minor subunit in curli complex" "present as minor subunit in wild-type curli -!- homology with major curlin, CsgA" E 97459968 -!- 7854117 -!- 8817489 Periplasmic 1-21 PF07012;Curlin associated repeat;4.6e-12;codon 53-86 -!- PF07012;Curlin associated repeat;3.7e-09;codon 97-130 GO:0009289 fimbria -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0009101 glycoprotein biosynthesis CDS ECK1028 csgA csgA b1042 1103670 1104125 + (no change) JW1025 1104688 1105143 + s cryptic curlin major subunit E 89201357 -!- 93023873 -!- 1677357 -!- 8459772 -!- 8817489 -!- 1357528 Periplasmic 1-20 151 PF07012;Curlin associated repeat;4e-13;codon 40-74 -!- PF07012;Curlin associated repeat;1.1e-13;codon 85-119 -!- PF07012;Curlin associated repeat;1.4;codon 120-141 GO:0009289 fimbria -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0009101 glycoprotein biosynthesis CDS ECK1029 csgC csgC ycdE b1043 1104184 1104516 + (no change) JW1026 1105202 1105534 + pf predicted curli production protein C 9457880 Periplasmic GO:0009289 fimbria CDS ECK1030 ymdA ymdA b1044 1104637 1104948 + (no change) JW1031 1106991 1107302 + o predicted protein C CDS ECK1031 ymdB ymdB b1045 1105043 1105576 + (no change) JW1032 1107397 1107930 + o conserved protein C Cytoplasmic 1SPV COG2110;Predicted phosphatase homologous to the C-terminal domain of histone macroH2A1 PF01661;Appr-1-p processing enzyme family;7.4e-66;codon 21-138 CDS ECK1032 ymdC ymdC b1046 1105578 1106999 + start codon change JW5150 1107932 1109353 + pe predicted hydrolase C Cytoplasmic COG1502;Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes 56024; Phospholipase D/nuclease PF00614;Phospholipase D Active site motif;0.045;codon 145-172 -!- PF00614;Phospholipase D Active site motif;8.1e-05;codon 384-411 CDS ECK1033 mdoC mdoC ymdD b1047 1107007 1108164 - (no change) JW1034 1109361 1110518 - m membrane protein required for modification of periplasmic glucan succinyl substitution of glucan backbone of osmoregulated periplasmic glucan E 99296569 Integral Membrane Protein 10 10 PF01757;Acyltransferase family;9.9e-68;codon 9-366 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009250 glucan biosynthesis -!- GO:0006970 response to osmotic stress CDS ECK1034 mdoG mdoG opgG -!- mdoA b1048 1108558 1110093 + (no change) JW1035 1110912 1112447 + e "glucan biosynthesis protein, periplasmic" "determines glucose backbone length, osmoregulated" E 15175282 -!- 92048494 -!- 7934824 -!- 9298646 Periplasmic 511 COG3131;Periplasmic glucans biosynthesis protein "PF04349;Periplasmic glucan biosynthesis protein, Mdo;0;codon 23-509" GO:0042597 periplasmic space GO:0009250 glucan biosynthesis -!- GO:0006970 response to osmotic stress CDS ECK1035 mdoH mdoH mdoA b1049 1110086 1112629 + (no change) JW1037 1112440 1114983 + e glucan biosynthesis: glycosyl transferase "determines glucose backbone length, osmoregulated" E 92048494 -!- 12798996 -!- 15175282 Integral Membrane Protein 6 6 in COG2943;Membrane glycosyltransferase 53448; Nucleotide-diphospho-sugar transferases PF00535;Glycosyl transferase;1.9e-11;codon 245-430 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006970 response to osmotic stress CDS ECK1036 yceK yceK b1050 1112802 1113029 + (no change) JW5151 1115156 1115383 + lp predicted lipoprotein C Membrane Lipoprotein regulated by attenuation (yceK) PF07119;Protein of unknown function (DUF1375);1.7e-40;codon 2-70 CDS ECK1037 msyB msyB b1051 1113030 1113404 - start codon change JW1039 1115384 1115758 - o predicted protein suppresses mutants in protein secretion machinery C 92165719 Cytoplasmic CDS ECK1038 mdtG mdtG yceE b1053 1113487 1114713 - (no change) JW1040 1115841 1117067 - pt predicted drug efflux system C 21450803 -!- 1537791 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 10 regulated by attenuation (yceE-b1052-msyB) COG0477;Permeases of the major facilitator superfamily PF00083;Sugar (and other) transporter;3.7e-05;codon 14-407 -!- PF07690;Major Facilitator Superfamily;5.4e-48;codon 19-372 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1039 lpxL lpxL htrB -!- waaM b1054 1114885 1115805 - (no change) JW1041 1117239 1118159 - e lauryl-acyl carrier protein (ACP)-dependent acyltransferase lipid A biosynthesis E 11830595 -!- 12591892 -!- 92021792 -!- 92114808 -!- 92121107 -!- 1846149 -!- 2203778 Membrane Anchored 2.3.1.- COG1560;Lauroyl/myristoyl acyltransferase PF03279;Bacterial lipid A biosynthesis acyltr;6e-169;codon 4-297 TIGR02207;lipid_A_htrB: lipid A biosynthesis lauro;1.3e-241;codon 5-306 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009245 lipid A biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK1040 yceA yceA b1055 1116030 1117082 + (no change) JW1042 1118384 1119436 + d conserved protein C 1840644 Cytoplasmic COG1054;Predicted sulfurtransferase 52821; Rhodanese/Cell cycle control phosphatase PF00581;Rhodanese-like domain;1.5e-29;codon 137-234 GO:0007049 cell cycle CDS ECK1041 yceI yceI b1056 1117124 1117699 - (no change) JW1043 1119478 1120053 - o predicted protein C 1840644 -!- 9298646 Periplasmic 1-22 191 COG2353;Uncharacterized conserved protein PF04264;YceI like family;6.9e-86;codon 22-190 CDS ECK1042 yceJ yceJ b1057 1117703 1118269 - (no change) JW1044 1120057 1120623 - pc predicted cytochrome b561 C Integral Membrane Protein 4 4 in COG3038;Cytochrome B561 PF01292;Cytochrome b561 family;1.4e-73;codon 7-181 GO:0017004 cytochrome biogenesis CDS ECK1043 yceO yceO b1058 1118530 1118670 - (no change) JW1045 1120884 1121024 - o predicted protein C Membrane Anchored CDS ECK1044 solA solA b1059 1118691 1119809 - (no change) JW1046 1121045 1122163 - e "N-methyltryptophan oxidase, FAD-binding" E "11170472 -!- 11170473 -!- 97128788 -!- 10220347 -!- Khanna P, Jorns MS;Biochemistry;2001;40:1441-1450 -!- Khanna P, Jorns MS;Biochemistry;2001;40:1451-1459" Cytoplasmic 1.5.3.2 regulated by attenuation (solA-yceO) COG0665;Glycine/D-amino acid oxidases (deaminating) "51905; FAD/NAD(P)-binding domain -!- 54373; FAD-linked reductases, C-terminal domain" PF01266;FAD dependent oxidoreductase;1.5e-64;codon 4-353 CDS ECK1045 yceP yceP b1060 1119924 1120178 - (no change) JW5152 1122278 1122532 - o predicted protein C 14727089 Cytoplasmic CDS ECK1046 dinI dinI b1061 1120465 1120710 - (no change) JW1048 1122819 1123064 - f DNA damage-inducible protein I inhibits the co-protease activity of RecA E 9606202 -!- 11152126 -!- 11230150 -!- 8682790 Cytoplasmic 1GHH 54857; DNA damage-inducible protein DinI PF06183;DinI-like family;5.6e-38;codon 13-79 GO:0005737 cytoplasm GO:0006281 DNA repair -!- GO:0009432 SOS response CDS ECK1047 pyrC pyrC b1062 1120784 1121830 - (no change) JW1049 1123138 1124184 - e dihydro-orotase E 90264313 -!- 90264314 -!- 91107654 -!- 11401542 -!- 2876892 -!- 2885307 -!- 9298646 Cytoplasmic 3.5.2.3 monomeric multimer; dihydroorotase (b1062) regulated by attenuation (pyrC) COG0418;Dihydroorotase 51556; Metallo-dependent hydrolases PF01979;Amidohydrolase family;5.5e-80;codon 5-348 "TIGR00856;pyrC_dimer: dihydroorotase, homodimeric ty;3.2e-259;codon 7-347" GO:0005737 cytoplasm GO:0006221 pyrimidine nucleotide biosynthesis CDS ECK1048 yceB yceB b1063 1121936 1122496 - (no change) JW1050 1124290 1124850 - lp predicted lipoprotein C Outer membrane Lipoprotein PF07273;Protein of unknown function (DUF1439);4.9e-137;codon 1-186 CDS ECK1049 grxB grxB b1064 1122630 1123277 - (no change) JW1051 1124984 1125631 - c glutaredoxin 2 (Grx2) regulated by RpoS and ppGpp E 95024051 -!- 99175138 -!- 9111025 Cytoplasmic 1G7O COG2999;Glutaredoxin 2 "47616; Glutathione S-transferases, C-terminal domain -!- 52833; Thioredoxin-like" "PF02798;Glutathione S-transferase, N-terminal;8.7e-05;codon 1-71 -!- PF04399;Glutaredoxin 2, C terminal domain;5.3e-90;codon 84-215" "TIGR02182;GRXB: Glutaredoxin, GrxB family;4.8e-161;codon 2-210" CDS ECK1050 mdtH mdtH yceL b1065 1123341 1124549 - start codon change JW1052 1125695 1126903 - pt predicted drug efflux system C 21450803 -!- 9111025 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 10 in PF07690;Major Facilitator Superfamily;4.4e-44;codon 25-368 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1051 rimJ rimJ tcp b1066 1124785 1125369 + (no change) JW1053 1127139 1127723 + e ribosomal-protein-S5-alanine N-acetyltransferase E 88121676 -!- 90136529 -!- 1356970 Cytoplasmic 2.3.1.128 "COG1670;Acetyltransferases, including N-acetylases of ribosomal proteins" 55729; Acyl-CoA N-acyltransferases (Nat) PF00583;Acetyltransferase (GNAT) family;1.3e-12;codon 80-162 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006464 protein modification CDS ECK1052 yceH yceH b1067 1125380 1126027 + (no change) JW1054 1127734 1128381 + o conserved protein C 1356970 -!- 2828880 Cytoplasmic COG3132;Uncharacterized protein conserved in bacteria "PF04337;Protein of unknown function, DUF480;7.3e-139;codon 5-175" CDS ECK1053 mviM mviM yceM b1068 1126029 1126952 + (no change) JW1055 1128383 1129306 + pe predicted oxidoreductase with NAD(P)-binding Rossmann-fold domain C Periplasmic 1-26 COG0673;Predicted dehydrogenases and related proteins 51735; NAD(P)-binding Rossmann-fold domains "PF01408;Oxidoreductase family, NAD-binding Ros;2.1e-37;codon 4-121 -!- PF02894;Oxidoreductase family, C-terminal alph;1.4e-09;codon 133-227" CDS ECK1054 mviN mviN yceN b1069 1127062 1128597 + (no change) JW1056 1129416 1130951 + pm predicted inner membrane protein similar to MviN virulence factor of Salmonella C Integral Membrane Protein 13 13 "COG0728;Uncharacterized membrane protein, putative virulence factor" PF03023;MviN-like protein;9.4e-225;codon 28-482 TIGR01695;mviN: integral membrane protein MviN;1.9e-256;codon 2-509 CDS ECK1055 flgN flgN b1070 1128637 1129053 - (no change) JW1057 1130991 1131407 - f export chaperone for FlgK and FlgL believed to be export chaperone for FlgK and FlgL flagellar biosynthesis protein E 10320579 Cytoplasmic COG3418;Flagellar biosynthesis/type III secretory pathway chaperone PF05130;FlgN protein;6.2e-78;codon 1-138 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0006457 protein folding -!- GO:0042330 taxis CDS ECK1056 flgM flgM b1071 1129058 1129351 - (no change) JW1058 1131412 1131705 - f anti-sigma factor for FliA (sigma 28) E 1482109 -!- 89181349 -!- 9095196 Cytoplasmic COG2747;Negative regulator of flagellin synthesis (anti-sigma28 factor) "PF04316;Anti-sigma-28 factor, FlgM;2e-30;codon 10-91" GO:0019861 flagellum -!- GO:0005737 cytoplasm GO:0006350 transcription -!- GO:0042330 taxis CDS ECK1057 flgA flgA flaU b1072 1129427 1130086 - (no change) JW1059 1131781 1132440 - s assembly protein for flagellar basal-body periplasmic P ring E 1482109 -!- 87165754 -!- 89181349 Periplasmic COG1261;Flagellar basal body P-ring biosynthesis protein PF03240;FlgA family;8.9e-81;codon 54-219 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1058 flgB flgB flbA -!- fla FII b1073 1130241 1130657 + (no change) JW1060 1132595 1133011 + s flagellar component of cell-proximal portion of basal-body rod E 1482109 -!- 89181349 Cytoplasmic heteromultimer; Flagellar Motor Complex (b1073-b1074-b1077-b1078-b1080-b1889-b1890-b1938-b 1945) COG1815;Flagellar basal body protein PF00460;Flagella basal body rod protein;1e-12;codon 9-39 TIGR01396;FlgB: flagellar basal-body rod protein FlgB;3.8e-48;codon 5-135 GO:0019861 flagellum -!- GO:0042597 periplasmic space GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1059 flgC flgC flaW -!- fla FIII b1074 1130661 1131065 + (no change) JW1061 1133015 1133419 + s flagellar component of cell-proximal portion of basal-body rod E 1482109 -!- 89181349 Cytoplasmic heteromultimer; Flagellar Motor Complex (b1073-b1074-b1077-b1078-b1080-b1889-b1890-b1938-b 1945) COG1558;Flagellar basal body rod protein PF00460;Flagella basal body rod protein;1.1e-11;codon 7-38 -!- PF06429;Domain of unknown function (DUF1078);1e-07;codon 94-132 TIGR01395;FlgC: flagellar basal-body rod protein FlgC;6e-82;codon 4-134 GO:0019861 flagellum -!- GO:0042597 periplasmic space GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1060 flgD flgD flaV -!- fla FIV -!- fla FVI b1075 1131077 1131772 + (no change) JW1062 1133431 1134126 + s flagellar hook assembly protein E 1482109 -!- 89181349 Periplasmic COG1843;Flagellar hook capping protein PF03963;Flagellar hook capping protein;6.7e-61;codon 2-151 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1061 flgE flgE flaK -!- fla FV b1076 1131797 1133005 + (no change) JW1063 1134151 1135359 + s flagellar hook protein E 1482109 -!- 89181349 Cytoplasmic COG1749;Flagellar hook protein FlgE PF00460;Flagella basal body rod protein;8e-13;codon 3-33 -!- PF07559;Flagellar basal body protein FlaE;4.7e-30;codon 170-283 -!- PF06429;Domain of unknown function (DUF1078);6.3e-20;codon 363-401 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1062 flgF flgF flaX -!- fla FVI b1077 1133025 1133780 + (no change) JW1064 1135379 1136134 + s flagellar component of cell-proximal portion of basal-body rod E 1482109 -!- 89181349 Cytoplasmic heteromultimer; Flagellar Motor Complex (b1073-b1074-b1077-b1078-b1080-b1889-b1890-b1938-b 1945) COG4787;Flagellar basal body rod protein PF00460;Flagella basal body rod protein;3.5e-11;codon 5-35 -!- PF06429;Domain of unknown function (DUF1078);0.00062;codon 209-247 GO:0019861 flagellum -!- GO:0042597 periplasmic space GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1063 flgG flgG flaL -!- fla FVII b1078 1133952 1134734 + (no change) JW1065 1136306 1137088 + s flagellar component of cell-distal portion of basal-body rod E 1482109 -!- 89181349 Cytoplasmic heteromultimer; Flagellar Motor Complex (b1073-b1074-b1077-b1078-b1080-b1889-b1890-b1938-b 1945) COG4786;Flagellar basal body rod protein PF00460;Flagella basal body rod protein;5e-15;codon 5-35 -!- PF06429;Domain of unknown function (DUF1078);1.5e-19;codon 222-260 GO:0019861 flagellum -!- GO:0042597 periplasmic space GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1064 flgH flgH flaY -!- fla FVIII b1079 1134787 1135485 + (no change) JW5153 1137141 1137839 + s flagellar protein of basal-body outer-membrane L ring E 1482109 -!- 87165755 -!- 89181349 Outer membrane Lipoprotein 1-37 COG2063;Flagellar basal body L-ring protein PF02107;Flagellar L-ring protein;4.5e-111;codon 22-231 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019861 flagellum -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1065 flgI flgI flaM -!- fla FIX b1080 1135497 1136594 + (no change) JW1067 1137851 1138948 + ps predicted flagellar basal body protein C 87165754 Periplasmic heteromultimer; Flagellar Motor Complex (b1073-b1074-b1077-b1078-b1080-b1889-b1890-b1938-b 1945) PF02119;Flagellar P-ring protein;2.5e-235;codon 21-365 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1066 flgJ flgJ flaZ -!- fla FX b1081 1136594 1137535 + (no change) JW1068 1138948 1139889 + e muramidase involved in flagellar biosynthesis in S. typhimurium E 11554792 -!- 1482109 -!- 89181349 Cytoplasmic COG3951;Rod binding protein -!- COG1705;Muramidase (flagellum-specific) 53955; Lysozyme-like PF01832;Mannosyl-glycoprotein endo-beta-N-ace;2.2e-71;codon 156-296 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1067 flgK flgK flaS b1082 1137601 1139244 + (no change) JW1069 1139955 1141598 + s flagellar hook-filament junction protein 1 E 1482109 -!- 89181349 -!- 8158647 Cytoplasmic COG1256;Flagellar hook-associated protein PF00460;Flagella basal body rod protein;2.1e-06;codon 5-35 -!- PF06429;Domain of unknown function (DUF1078);6.1e-16;codon 508-546 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0006457 protein folding -!- GO:0042330 taxis CDS ECK1068 flgL flgL flaT b1083 1139256 1140209 + (no change) JW1070 1141610 1142563 + s flagellar hook-filament junction protein E 1482109 -!- 89181349 -!- 1447789 -!- 8158647 Cytoplasmic COG1344;Flagellin and related hook-associated proteins 64518; F41 fragment of flagellin PF00669;Bacterial flagellin N-terminus;3.5e-52;codon 27-167 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0006457 protein folding -!- GO:0042330 taxis CDS ECK1069 rne rne ams -!- hmp1 -!- rne_1 -!- smbB b1084 1140405 1143590 - (no change) JW1071 1142759 1145944 - e fused ribonucleaseE: endoribonuclease -!- RNA-binding protein -!-RNA degradosome binding protein scaffold for formation of degradosome E 10329633 -!- 10411735 -!- 12000793 -!- 12207692 -!- 21065205 -!- 92112032 -!- 92126069 -!- 94022304 -!- 1447789 -!- 1704367 -!- 2011493 Cytoplasmic 3.1.4.- heteromultimer; degradosome (b1084-b3164-b3780) fused RNase E: endoribonuclease (aa1-509) -!- RNA-binding protein (aa511-849) -!- RNA degradosome binding protein (aa851-1061) COG1530;Ribonucleases G and E 50249; Nucleic acid-binding proteins PF00575;S1 RNA binding domain;6.3e-19;codon 35-119 "TIGR00757;RNaseEG: ribonuclease, Rne/Rng family;1.4e-265;codon 13-425" GO:0005737 cytoplasm GO:0006401 RNA catabolism -!- GO:0006401 RNA catabolism CDS ECK1070 yceQ yceQ b1085 1143725 1144045 + start codon change JW5154 1146079 1146399 + o predicted protein C CDS ECK1071 rluC rluC yceC b1086 1144163 1145122 + (no change) JW1072 1146517 1147476 + e 23S rRNA pseudouridylate synthase E 98325071 -!- 99190868 -!- 1447160 -!- 1704367 Cytoplasmic 4.2.1.70 "COG0564;Pseudouridylate synthases, 23S RNA-specific" 55174; Alpha-L RNA-binding motif PF01479;S4 domain;3.3e-11;codon 20-66 -!- PF00849;RNA pseudouridylate synthase;4.4e-61;codon 101-250 TIGR00005;rluD_subfam: ribosomal large subunit pseu;1.4e-155;codon 15-316 GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK1072 yceF yceF b1087 1145234 1145818 - start codon change JW5155 1147588 1148172 - d predicted protein predicted nucleotide-binding C Cytoplasmic regulated by attenuation (yceF) COG0424;Nucleotide-binding protein implicated in inhibition of septum formation 52972; Maf/Ham1 PF02545;Maf-like protein;2.7e-100;codon 15-205 TIGR00172;maf: maf protein;2.5e-115;codon 14-198 misc_RNA ECK1073 sraB sraB pke20 -!- psrA4 b4418 1145812 1145980 + (no change) JWR0228 1148166 1148334 + n small RNA E 21341747 CDS ECK1074 yceD yceD g30K b1088 1146017 1146538 + (no change) JW1074 1148371 1148892 + o conserved protein C 90008815 -!- 1447160 Cytoplasmic "COG1399;Predicted metal-binding, possibly nucleic acid-binding protein" "PF02620;Uncharacterized ACR, COG1399;1.4e-57;codon 15-172" CDS ECK1075 rpmF rpmF b1089 1146590 1146763 + (no change) JW1075 1148944 1149117 + s 50S ribosomal subunit protein L32 E 90008815 -!- 10094780 -!- 12809609 -!- 765258 -!- 9642179 Cytoplasmic 1P86 COG0333;Ribosomal protein L32 PF01783;Ribosomal L32p protein family;5.9e-20;codon 2-57 TIGR01031;rpmF_bact: ribosomal protein L32;8.3e-23;codon 2-56 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006412 protein biosynthesis GO:0003735 structural constituent of ribosome CDS ECK1076 plsX plsX b1090 1146844 1147914 + start codon change JW5156 1149198 1150268 + pe fatty acid/phospholipid synthesis protein E 6094487 -!- 1447160 Cytoplasmic COG0416;Fatty acid/phospholipid biosynthesis enzyme PF02504;Fatty acid synthesis protein;4e-184;codon 1-321 TIGR00182;plsX: fatty acid/phospholipid synthesis prot;7.2e-226;codon 1-336 GO:0008654 phospholipid biosynthesis CDS ECK1077 fabH fabH b1091 1147982 1148935 + (no change) JW1077 1150336 1151289 + e 3-oxoacyl-[acyl-carrier-protein] synthase III E 14523010 -!- 92202232 -!- 10593943 -!- 10673437 -!- 11078736 -!- 11243824 -!- 11375394 -!- 1314802 -!- 1447160 -!- 8631920 2.3.1.41 monomeric multimer; beta-ketoacyl-ACP synthase III / acetyl-CoA:ACP transacylase (b1091) 1HNK COG0332;3-oxoacyl-[acyl-carrier-protein] synthase III 53901; Thiolase-like TIGR00747;fabH: 3-oxoacyl-(acyl-carrier-protein) synth;2e-231;codon 1-317 GO:0005737 cytoplasm CDS ECK1078 fabD fabD tpfA -!- tfpA b1092 1148951 1149880 + (no change) JW1078 1151305 1152234 + e malonyl-CoA-[acyl-carrier-protein] transacylase E 92052166 -!- 92183950 -!- 92210530 -!- 92234941 -!- 7700236 -!- 7768883 -!- 9298646 Cytoplasmic 2.3.1.39 COG0331;(acyl-carrier-protein) S-malonyltransferase 52151; Catalytic domain of malonyl-CoA ACP transacylase -!- 55048; Probable ACP-binding domain of malonyl-CoA ACP transacylase PF00698;Acyl transferase domain;1.2e-12;codon 5-309 TIGR00128;fabD: malonyl CoA-acyl carrier protein trans;3.6e-204;codon 2-292 GO:0005737 cytoplasm CDS ECK1079 fabG fabG b1093 1149893 1150627 + (no change) JW1079 1152247 1152981 + e 3-oxoacyl-[acyl-carrier-protein] reductase E 92052166 -!- 92183950 -!- 92210530 -!- 92234941 Cytoplasmic 1.1.1.100 1Q7B COG1028;Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) 51735; NAD(P)-binding Rossmann-fold domains PF00106;short chain dehydrogenase;2.8e-93;codon 8-241 TIGR01830;3oxo_ACP_reduc: 3-oxoacyl-(acyl-carrie;2e-157;codon 8-242 GO:0005737 cytoplasm CDS ECK1080 acpP acpP b1094 1150838 1151074 + (no change) JW1080 1153192 1153428 + c acyl carrier protein (ACP) E "88296479 -!- 89050961 -!- 92210530 -!- 2062368 -!- 2091027 -!- 3549687 -!- 4882206 -!- 4882207 -!- 7673201 -!- 7972002 -!- 8359454 -!- Mathews CK, van Holde KE;Biochemistry.;1990;The Benjamin/Cummings Publishing Company, Inc., Redwood City" Cytoplasmic COG0236;Acyl carrier protein 47336; ACP-like PF00550;Phosphopantetheine attachment site;4.5e-24;codon 6-73 TIGR00517;acyl_carrier: acyl carrier protein;3.9e-39;codon 1-77 GO:0042967 acyl-carrier protein biosynthesis CDS ECK1081 fabF fabF cvc -!- fabJ -!- vtr -!- vtrB b1095 1151162 1152403 + (no change) JW1081 1153516 1154757 + e 3-oxoacyl-[acyl-carrier-protein] synthase II E 80159932 -!- 87165751 -!- 89351281 -!- 10037680 -!- 7768872 -!- 7972002 -!- 9013860 -!- 9482715 Periplasmic 2.3.1.41 monomeric multimer; beta-ketoacyl-ACP synthase II (b1095) regulated by attenuation (fabF) COG0304;3-oxoacyl-(acyl-carrier-protein) synthase 53901; Thiolase-like "PF00109;Beta-ketoacyl synthase, N-terminal do;4.1e-84;codon 4-247 -!- PF02801;Beta-ketoacyl synthase, C-terminal do;4.4e-73;codon 255-412" GO:0005737 cytoplasm CDS ECK1082 pabC pabC b1096 1152523 1153332 + (no change) JW1082 1154877 1155686 + e 4-amino-4-deoxychorismate lyase component of para-aminobenzoate synthase multienzyme complex E 91067712 -!- 91302313 -!- 92355506 -!- 10876155 Cytoplasmic 4.1.3.38 heteromultimer; para-aminobenzoate synthase multi-enzyme complex / para-aminobenzoate synthase (b1812-b3360-b1096) -!- monomeric multimer; aminodeoxychorismate lyase (b1096) 1I2L COG0115;Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase 56752; D-amino acid aminotransferase-like PLP-dependent enzymes PF01063;Aminotransferase class IV;1e-91;codon 1-262 GO:0046656 folic acid biosynthesis CDS ECK1083 yceG yceG b1097 1153335 1154357 + (no change) JW1083 1155689 1156711 + pe predicted aminodeoxychorismate lyase C Membrane Anchored COG1559;Predicted periplasmic solute-binding protein PF02618;Aminodeoxychorismate lyase;2.1e-156;codon 40-333 TIGR00247;TIGR00247: conserved hypothetical protein T;1.2e-238;codon 1-340 CDS ECK1084 tmk tmk ycfG b1098 1154347 1154988 + (no change) JW1084 1156701 1157342 + e thymidylate kinase E 91251767 -!- 8505303 -!- 8509334 -!- 8631667 -!- 9826650 Cytoplasmic 2.7.4.9 Mg2+ 5TMP COG0125;Thymidylate kinase 52540; P-loop containing nucleotide triphosphate hydrolases PF02223;Thymidylate kinase;5.1e-86;codon 8-200 TIGR00041;DTMP_kinase: thymidylate kinase;1.1e-107;codon 1-200 "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK1085 holB holB b1099 1154985 1155989 + (no change) JW1085 1157339 1158343 + e "DNA polymerase III, delta prime subunit" E 12819857 -!- 93280136 -!- 93285995 -!- 93341937 -!- 1575709 -!- 8505304 -!- 9363942 Cytoplasmic 2.7.7.7 COG0470;ATPase involved in DNA replication "48019; DNA polymerase III clamp loader subunits, C-terminal domain -!- 52540; P-loop containing nucleotide triphosphate hydrolases" "TIGR00678;holB: DNA polymerase III, delta prime subuni;5.1e-102;codon 24-190" GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK1086 ycfH ycfH b1100 1156000 1156797 + (no change) JW1086 1158354 1159151 + pe predicted metallodependent hydrolase C 8505303 -!- 8509334 Cytoplasmic COG0084;Mg-dependent DNase 51556; Metallo-dependent hydrolases PF01026;TatD related DNase;2.8e-122;codon 1-255 "TIGR00010;TIGR00010: hydrolase, TatD family;3.1e-155;codon 3-256" CDS ECK1087 ptsG ptsG CR -!- car -!- cat -!- gptA -!- umg -!- catB2 -!- glcA -!- tgl -!- umgC b1101 1157092 1158525 + (no change) JW1087 1159446 1160879 + t fused glucose-specific PTS enzymes: IIBcomponent -!- IIC component E 10318813 -!- 15059634 -!- 339828 -!- 6787390 -!- 6801015 -!- 92011381 -!- 92156123 -!- 92234940 -!- 9851989 -!- 99353964 -!- 3023349 -!- 8112346 -!- 8505292 -!- 8784182 -!- 9200688 Integral Membrane Protein 2.7.1.69 heteromultimer; EIIGlc (b2416-b2415-b2417-b1101) 4.A.1; The PTS Glucose-Glucoside (Glc) Family 10 10 in "fused PTS family enzyme, glucose-specific: enzyme IIC (aa1-330) -!- enzyme IIB (aa360-477)" "COG1263;Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific -!- COG1264;Phosphotransferase system IIB components" 55604; Glucose permease domain IIB "PF02378;Phosphotransferase system, EIIC;1.2e-106;codon 13-320 -!- PF00367;phosphotransferase system, EIIB;1.4e-18;codon 402-436" "TIGR02002;PTS-II-BC-glcB: PTS system, glucose-sp;0;codon 2-476 -!- TIGR00852;pts-Glc: PTS system, maltose and gluco;2.1e-130;codon 52-331 -!- TIGR00826;EIIB_glc: PTS system, glucose-like IIB;3.8e-34;codon 377-460" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism -!- GO:0006464 protein modification CDS ECK1088 fhuE fhuE b1102 1158585 1160774 - (no change) JW1088 1160939 1163128 - t ferric-rhodotorulic acid outer membrane transporter E 90286919 -!- 3032906 -!- 10529396 Periplasmic 1.B.14; The Outer Membrane Receptor (OMR) Family 1-36 729 COG4773;Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid 56935; Porins PF07715;TonB-dependent Receptor Plug Domain;6e-19;codon 74-177 -!- PF00593;TonB dependent receptor;4.2e-27;codon 493-729 TIGR01783;TonB-siderophor: TonB-dependent sider;6.1e-238;codon 77-729 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0006826 iron ion transport CDS ECK1089 hinT hinT ycfF b1103 1161108 1161467 + (no change) JW1089 1163462 1163821 + e purine nucleoside phosphoramidase E 15703176 -!- 10493123 -!- 2162465 Cytoplasmic 54197; HIT-like PF01230;HIT domain;4.3e-56;codon 5-110 GO:0006412 protein biosynthesis CDS ECK1090 ycfL ycfL b1104 1161470 1161847 + (no change) JW1090 1163824 1164201 + o predicted protein C Outer membrane Lipoprotein PF07233;Protein of unknown function (DUF1425);3.5e-71;codon 6-125 CDS ECK1091 ycfM ycfM b1105 1161861 1162502 + (no change) JW5157 1164215 1164856 + pm predicted outer membrane lipoprotein C Outer membrane Lipoprotein COG3417;Collagen-binding surface adhesin SpaP (antigen I/II family) CDS ECK1092 ycfN ycfN b1106 1162483 1163307 + (no change) JW1092 1164837 1165661 + e thiamin kinase E 15150256 Cytoplasmic 2.7.1.89 Mg2+ COG0510;Predicted choline kinase involved in LPS biosynthesis 56112; Protein kinase-like (PK-like) PF01636;Phosphotransferase enzyme family;3.6e-26;codon 24-235 CDS ECK1093 nagZ nagZ ycfO b1107 1163318 1164343 + (no change) JW1093 1165672 1166697 + e beta N-acetyl-glucosaminidase E 20564261 -!- 10940025 -!- 1377 Cytoplasmic 3.2.1.52 COG1472;Beta-glucosidase-related glycosidases 51445; (Trans)glycosidases PF00933;Glycosyl hydrolase family 3 N terminal;3.7e-90;codon 52-278 GO:0000270 peptidoglycan metabolism CDS ECK1094 ycfP ycfP b1108 1164366 1164908 + start codon change JW5158 1166720 1167262 + o conserved protein C Cytoplasmic 53474; alpha/beta-Hydrolases PF05728;Uncharacterised protein family (UPF0227);7.9e-103;codon 20-197 CDS ECK1095 ndh ndh b1109 1165308 1166612 + (no change) JW1095 1167662 1168966 + e respiratory NADH dehydrogenase 2/cupric reductase E 14766919 -!- 20130027 -!- 81256452 -!- 92296775 -!- 94042945 -!- 99441207 -!- 6265208 1.16.1.- -!- 1.6.99.3 "COG1252;NADH dehydrogenase, FAD-containing subunit" 51905; FAD/NAD(P)-binding domain PF00070;Pyridine nucleotide-disulphide oxidoreducta;5.9e-61;codon 7-320 GO:0005737 cytoplasm GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK1096 ycfJ ycfJ b1110 1166822 1167361 + (no change) JW1096 1169176 1169715 + o predicted protein C 6265208 -!- 7984428 Membrane Anchored COG3134;Predicted outer membrane lipoprotein PF05433;Rickettsia 17 kDa surface antigen;4e-15;codon 70-113 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK1097 ycfQ ycfQ b1111 1167423 1168055 - start codon change JW5159 1169777 1170409 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic regulated by attenuation (ycfQ) 46689; Homeodomain-like "PF00440;Bacterial regulatory proteins, tetR family;8.3e-15;codon 50-96" "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1098 ycfR ycfR b1112 1168296 1168553 + (no change) JW1098 1170650 1170907 + o predicted protein C 14727089 Periplasmic 1-22 PF07338;Protein of unknown function (DUF1471);3.5e-23;codon 1-85 CDS ECK1099 ycfS ycfS b1113 1168635 1169597 - (no change) JW5820 1170989 1171951 - d conserved protein C 1-25 COG1376;Uncharacterized protein conserved in bacteria 54106; LysM domain PF01476;LysM domain;9.8e-08;codon 46-91 -!- PF03734;ErfK/YbiS/YcfS/YnhG;8.6e-67;codo n 99-240 CDS ECK1100 mfd mfd b1114 1169741 1173187 - (no change) JW1100 1172095 1175541 - f transcription-repair coupling factor mediates repair of DNA damage in the template strand during transcription -!- mutation frequency decline -!- member of DEAD box family E 14602898 -!- 90158497 -!- 92107993 -!- 8465200 Cytoplasmic COG1197;Transcription-repair coupling factor (superfamily II helicase) 52540; P-loop containing nucleotide triphosphate hydrolases "PF02559;CarD-like/TRCF;1.2e-49;476-573 -!- PF04851;Type III restriction enzyme, res subunit;8.5e-08;599-761 -!- PF00270;DEAD/DEAH box helicase;4.1e-43;601-766 -!- PF00271;Helicase conserved C-term;4e-20;830-907 -!- PF03461;TRCF;3.2e-57;1005-1113" TIGR00580;mfd: transcription-repair coupling factor;0;codon 145-1079 GO:0005737 cytoplasm GO:0006350 transcription CDS ECK1101 ycfT ycfT b1115 1173315 1174388 - (no change) JW1101 1175669 1176742 - pm predicted inner membrane protein C Integral Membrane Protein 9 8 in COG4763;Predicted membrane protein PF01757;Acyltransferase family;2.8e-60;codon 5-338 CDS ECK1102 lolC lolC ycfU b1116 1174650 1175849 + (no change) JW5161 1177004 1178203 + t outer membrane-specific lipoprotein transporter subunit -!- membrane component of ABC superfamily inner membrane transporter transfers nascent outer membrane lipoproteins to periplasm E 11844772 -!- 20245870 Integral Membrane Protein heteromultimer; LolCDE ABC lipoprotein transporter (b1118-b1117-b1116) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 4 4 "COG4591;ABC-type transport system, involved in lipoprotein release, permease component" PF02687;Predicted permease;1.4e-46;codon 219-392 "TIGR02212;lolCE: lipoprotein releasing system, transme;2.5e-234;codon 4-399" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1103 lolD lolD ycfV b1117 1175842 1176543 + start codon change JW5162 1178196 1178897 + t outer membrane-specific lipoprotein transporter subunit -!- ATP-binding component of ABC superfamily ABC transporter transfers nascent outer membrane lipoproteins to periplasm E 20245870 Cytoplasmic heteromultimer; LolCDE ABC lipoprotein transporter (b1118-b1117-b1116) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;4.2e-66;codon 30-216 TIGR02211;LolD_lipo_ex: lipoprotein releasing syst;2.6e-178;codon 1-220 GO:0005737 cytoplasm CDS ECK1104 lolE lolE ycfW b1118 1176543 1177787 + (no change) JW1104 1178897 1180141 + t outer membrane-specific lipoprotein transporter subunit -!- membrane component of ABC superfamily inner membrane transporter transfers nascent outer membrane lipoproteins to periplasm E 11844772 -!- 20245870 Integral Membrane Protein heteromultimer; LolCDE ABC lipoprotein transporter (b1118-b1117-b1116) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 4 4 "COG4591;ABC-type transport system, involved in lipoprotein release, permease component" PF02687;Predicted permease;3.3e-54;codon 221-407 "TIGR02212;lolCE: lipoprotein releasing system, tra;9.8e-253;codon 4-414 -!- TIGR02213;lolE_release: lipoprotein releasing syst;0;codon 4-414" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1105 ycfX nagK ycfX b1119 1177816 1178727 + (no change) JW1105 1180170 1181081 + e N-acetyl-D-glucosamine kinase E 15489439 -!- 15157072 2.7.1.59 COG1940;Transcriptional regulator/sugar kinase 53067; Actin-like ATPase domain PF00480;ROK family;4.6e-55;codon 4-194 "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1106 cobB cobB ycfY b1120 1178743 1179582 + (no change) JW1106 1181097 1181936 + e "deacetylase of acetyl-CoA synthetase, NAD-dependent" E 15019790 -!- 22586414 -!- 8955330 -!- 9822644 -!- 10381378 -!- 10811920 1S5P "COG0846;NAD-dependent protein deacetylases, SIR2 family" 52467; DHS-like NAD/FAD-binding domain PF02146;Sir2 family;1.4e-83;codon 48-221 "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1107 ycfZ ycfZ b1121 1179702 1180490 - (no change) JW1107 1182056 1182844 - pm predicted inner membrane protein C Integral Membrane Protein 1-18 4 4 in CDS ECK1108 ymfA ymfA b1122 1180487 1180948 - start codon change JW5164 1182841 1183302 - pm predicted inner membrane protein C Integral Membrane Protein 2 2 in regulated by attenuation (ymfA-ycfZ) CDS ECK1109 potD potD b1123 1181006 1182052 - (no change) JW1109 1183360 1184406 - t polyamine transporter subunit -!- periplasmic-binding component of ABC superfamily E 92041956 -!- 93374918 -!- 8194593 -!- 8621624 -!- 8897598 -!- 9298646 -!- 1939142 -!- 8740179 Periplasmic heteromultimer; putrescine/spermidine ABC transporter (b1126-b1125-b1124-b1123) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-23 348 1POT COG0687;Spermidine/putrescine-binding periplasmic protein 53850; Periplasmic binding protein-like II PF01547;Bacterial extracellular solute-binding prot;1.3e-13;codon 9-285 GO:0042597 periplasmic space GO:0006596 polyamine biosynthesis -!- GO:0009310 amine catabolism CDS ECK1110 potC potC b1124 1182049 1182843 - (no change) JW1110 1184403 1185197 - t polyamine transporter subunit -!- membrane component of ABC superfamily E 92041956 Integral Membrane Protein heteromultimer; putrescine/spermidine ABC transporter (b1126-b1125-b1124-b1123) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 6 6 in "COG1177;ABC-type spermidine/putrescine transport system, permease component II" PF00528;Binding-protein-dependent transport syst;1.1e-14;codon 56-257 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006596 polyamine biosynthesis -!- GO:0009310 amine catabolism CDS ECK1111 potB potB b1125 1182840 1183667 - (no change) JW1111 1185194 1186021 - t polyamine transporter subunit -!- membrane component of ABC superfamily E 92041956 Integral Membrane Protein heteromultimer; putrescine/spermidine ABC transporter (b1126-b1125-b1124-b1123) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 6 6 in "COG1176;ABC-type spermidine/putrescine transport system, permease component I" PF00528;Binding-protein-dependent transport syst;3.4e-14;codon 55-274 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006596 polyamine biosynthesis -!- GO:0009310 amine catabolism CDS ECK1112 potA potA b1126 1183681 1184817 - (no change) JW1112 1186035 1187171 - t polyamine transporter subunit -!- ATP-binding component of ABC superfamily E 11976340 -!- 92041956 -!- 93374918 Cytoplasmic heteromultimer; putrescine/spermidine ABC transporter (b1126-b1125-b1124-b1123) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG3842;ABC-type spermidine/putrescine transport systems, ATPase components" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.7e-68;codon 43-224 "TIGR01187;potA: polyamine ABC transporter, ATP-binding;2.7e-246;codon 48-372" GO:0005737 cytoplasm GO:0006596 polyamine biosynthesis -!- GO:0009310 amine catabolism CDS ECK1113 pepT pepT b1127 1185067 1186293 + (no change) JW1113 1187421 1188647 + e peptidase T "aminotripeptidase -!- anaerobically induced, biofilm-induced, cell-density induced" E 94064578 -!- 1939142 Cytoplasmic monomeric multimer; peptidase T (b1127) M20B family; peptidase T 1VIX COG2195;Di- and tripeptidases 53187; Zn-dependent exopeptidases PF07687;Peptidase dimerisation domain;2.3e-26;codon 205-309 TIGR01882;peptidase-T: peptidase T;5.3e-191;codon 2-408 CDS ECK1114 ycfD ycfD b1128 1186342 1187463 - start codon change JW1114 1188696 1189817 - d conserved protein C Cytoplasmic 51182; RmlC-like CDS ECK1115 phoQ phoQ b1129 1187539 1188999 - (no change) JW1115 1189893 1191353 - r sensory histidine kinase in two-compoent regulatory system with PhoP senses magnesium ions E 92105017 Integral Membrane Protein 2 2 in COG0642;Signal transduction histidine kinase 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF00672;HAMP domain;3.7e-07;codon 195-263 -!- PF00512;His Kinase A (phosphoacceptor) domain;0.00034;codon 267-330 -!- PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;3.8e-27;codon 374-479" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006464 protein modification CDS ECK1116 phoP phoP b1130 1188999 1189670 - (no change) JW1116 1191353 1192024 - r DNA-binding response regulator in two-component regulatory system with PhoQ E 92105016 -!- 92105017 -!- 1729205 Cytoplasmic Two mgrB -!- mgtA -!- phoPQ -!- treR COG0745;Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;3.6e-33;codon 1-120 -!- PF00486;Transcriptional regulatory protein, C te;6.1e-16;codon 144-220" GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1117 purB purB ade(h) -!- adeh b1131 1189839 1191209 - (no change) JW1117 1192193 1193563 - e adenylosuccinate lyase E 92104952 -!- 97124206 Cytoplasmic 4.3.2.2 COG0015;Adenylosuccinate lyase 48557; L-aspartase-like PF00206;Lyase;7.4e-118;codon 14-321 TIGR00928;purB: adenylosuccinate lyase;1.4e-249;codon 12-456 GO:0005737 cytoplasm GO:0006164 purine nucleotide biosynthesis CDS ECK1118 hflD hflD ycfC -!- hslZ b1132 1191213 1191854 - (no change) JW5165 1193567 1194208 - pr predicted lysogenization regulator C 97124206 -!- 11278968 -!- 1729205 Cytoplasmic 1SDI COG2915;Uncharacterized protein involved in purine metabolism PF04356;Protein of unknown function (DUF489);4.9e-148;codon 2-207 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1119 trmU trmU asuE -!- mnmA -!- ycfB b1133 1191890 1192996 - start codon change JW1119 1194244 1195350 - e tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase E 12549933 -!- 99030459 -!- 1729205 Cytoplasmic 2.1.1.61 52402; Adenine nucleotide alpha hydrolases PF03054;tRNA methyl transferase;1.9e-235;codon 21-375 TIGR00420;trmU: tRNA (5-methylaminomethyl-2-thiouridyl;5.7e-251;codon 21-375 GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK1120 ymfB ymfB b1134 1193050 1193511 - (no change) JW1120 1195404 1195865 - e bifunctional thiamin pyrimidine pyrophosphate hydrolase and thiamin pyrophosphate hydrolase E 15292217 Cytoplasmic COG0494;NTP pyrophosphohydrolases including oxidative damage repair enzymes 55811; Nudix PF00293;NUDIX domain;6.4e-28;codon 4-133 CDS ECK1121 ymfC ymfC rluE b1135 1193521 1194174 - start codon change JW1121 1195875 1196528 - e 23S rRNA pseudouridine synthase E 21577312 Cytoplasmic 4.2.1.70 regulated by attenuation (ymfC-ymfB-trmU-ycfC-purB) COG1187;16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases PF00849;RNA pseudouridylate synthase;2.9e-22;codon 30-176 TIGR00093;TIGR00093: conserved hypothetical protein;1.9e-109;codon 35-207 GO:0009451 RNA modification CDS ECK1122 icd icd icdA -!- icdE -!- icdR -!- icdC b1136 1194346 1195596 + (no change) JW1122 1196700 1197950 + h "e14 prophage; isocitrate dehydrogenase, specific for NADP+" E "90046847 -!- 91363356 -!- 93106417 -!- 10623532 -!- 2204109 -!- 3112144 -!- 9298646 -!- 9352899 -!- Apostolakos D, Menter PA, Rampsch BJ, et al;Current Microbiology;1982;7:45-47" Cytoplasmic cryptic prophage e14 1.1.1.42 Mn2+ monomeric multimer; isocitrate dehydrogenase (b1136) 1PB3 COG0538;Isocitrate dehydrogenases 53659; Isocitrate & isopropylmalate dehydrogenases PF00180;Isocitrate/isopropylmalate dehydrogenase;6.3e-161;codon 28-412 TIGR00183;prok_nadp_idh: isocitrate dehydrogenase;5.4e-253;codon 1-416 GO:0006099 tricarboxylic acid cycle -!- GO:0009061 anaerobic respiration CDS ECK1123 ymfD ymfD b1137 1196090 1196755 - (no change) JW1123 1198444 1199109 - h e14 prophage; predicted SAM-dependent methyltransferase C Cytoplasmic cryptic prophage e14 COG0500;SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases CDS ECK1124 ymfE ymfE b1138 1196756 1197460 - (no change) JW5166 1199110 1199814 - h e14 prophage; predicted inner membrane protein C Integral Membrane Protein cryptic prophage e14 4 4 CDS ECK1125 lit lit b1139 1197918 1198811 + (no change) JW1125 1200272 1201165 + h "e14 prophage; cell death peptidase, inhibitor of T4 late gene expression" E 15196039 -!- 88197991 -!- 89291767 cryptic prophage e14 U49 family; Lit peptidase (Escherichia coli) CDS ECK1126 intE intE int(Lambda) -!- ycfI b1140 1198902 1200029 - (no change) JW1126 1201256 1202383 - h e14 prophage; predicted integrase C Cytoplasmic cryptic prophage e14 COG0582;Integrase 56349; DNA breaking-rejoining enzymes PF00589;Phage integrase family;1.2e-06;codon 194-372 CDS ECK1127 ymfG ymfG b1141 1200010 1200255 - (no change) JW1127 1202364 1202609 - h e14 prophage; predicted excisionase C Cytoplasmic cryptic prophage e14 PF07825;Excisionase-like protein;2.2e-07;codon 3-79 CDS ECK1128 ymfH ymfH b1142 1200292 1200603 - (no change) JW1128 1202646 1202957 - h e14 prophage; predicted protein C cryptic prophage e14 CDS ECK1129 ymfI ymfI b1143 1200720 1201061 + start codon change JW5168 1203074 1203415 + h e14 prophage; predicted protein C Cytoplasmic cryptic prophage e14 CDS ECK1130 ymfJ ymfJ b1144 1200999 1201307 - start codon change JW1130 1203353 1203661 - h e14 prophage; predicted protein C cryptic prophage e14 CDS ECK1131 ymfK ymfK b1145 1201482 1202156 - (no change) JW1131 1203836 1204510 - h e14 prophage; repressor protein phage e14 E 12878731 -!- 13129938 -!- 9689094 Cytoplasmic cryptic prophage e14 S24 family; phage lambda repressor protein COG1974;SOS-response transcriptional repressors (RecA-mediated autopeptidases) 51306; LexA/Signal peptidase PF00717;Peptidase S24-like;3.7e-19;codon 133-202 CDS ECK1132 ymfT ymfT b1146 1202247 1202447 + start codon change JW5169 1204601 1204801 + h e14 prophage; predicted DNA-binding transcriptional regulator C cryptic prophage e14 47413; lambda repressor-like DNA-binding domains CDS ECK1133 ymfL ymfL b1147 1202479 1203048 + (no change) JW1133 1204833 1205402 + h e14 prophage; predicted DNA-binding transcriptional regulator C Cytoplasmic cryptic prophage e14 CDS ECK1134 ymfM ymfM b1148 1203045 1203383 + (no change) JW1134 1205399 1205737 + h e14 prophage; predicted protein C Cytoplasmic cryptic prophage e14 CDS ECK1135 ymfN ymfN b1149 1203393 1204760 + (no change) JW1135 1205747 1207114 + h e14 prophage; predicted DNA-binding transcriptional regulator C Cytoplasmic cryptic prophage e14 "COG4626;Phage terminase-like protein, large subunit" 46785; Winged helix PF03354;Phage Terminase;5e-31;codon 1-439 CDS ECK1136 ymfR ymfR b1150 1204772 1204954 + (no change) JW1136 1207126 1207308 + h e14 prophage; predicted protein C cryptic prophage e14 CDS ECK1137 ymfO ymfO b1151 1204954 1205427 + (no change) JW1137 1207308 1207781 + h e14 prophage; conserved protein C Cytoplasmic cryptic prophage e14 COG4695;Phage-related protein CDS ECK1138 ymfP ymfP b1152 1205483 1206145 + start codon change JW5170 1207837 1208499 + h e14 prophage; conserved protein C Cytoplasmic cryptic prophage e14 COG3299;Uncharacterized homolog of phage Mu protein gp47 PF04865;Baseplate J-like protein;1.4e-34;codon 3-228 CDS ECK1139 ymfQ ymfQ b1153 1206136 1206720 + (no change) JW1139 1208490 1209074 + h e14 prophage; conserved protein C Cytoplasmic cryptic prophage e14 COG3778;Uncharacterized protein conserved in bacteria CDS ECK1140 ycfK ycfK b1154 1206724 1207353 + (no change) JW1140 1209078 1209707 + h e14 prophage; predicted protein C cryptic prophage e14 CDS ECK1141 ymfS ymfS b1155 1207355 1207768 + (no change) JW5171 1209709 1210122 + h e14 prophage; predicted protein C Cytoplasmic cryptic prophage e14 PF02413;Caudovirales tail fibre assembly protein;2e-46;codon 1-133 CDS ECK1142 tfaE tfaE ycfA b1156 1207740 1208342 - (no change) JW1142 1210094 1210696 - h e14 prophage; predicted tail fiber assembly protein C Cytoplasmic cryptic prophage e14 PF02413;Caudovirales tail fibre assembly protein;4.8e-66;codon 59-199 CDS ECK1143 stfE stfE ycfE b1157 1208342 1208878 - pseudogene -!- start codon change JW5172 1210696 1211232 - pseudogene h e14 prophage; predicted side tail fiber protein fragment (pseudogene) C 3894006 Cytoplasmic cryptic prophage e14 69349; Phage fibre proteins PF07484;Phage Tail Collar Domain;7.5e-25;codon 25-72 CDS ECK1144 pin pin b1158 1208908 1209462 + (no change) JW1144 1211262 1211816 + h e14 prophage; site-specific DNA recombinase encoded in phage tail fibre region E 3891522 -!- 3894006 -!- 6310572 Cytoplasmic cryptic prophage e14 "COG1961;Site-specific recombinases, DNA invertase Pin homologs" 46689; Homeodomain-like -!- 53041; Resolvase-like "PF00239;Resolvase, N terminal domain;9.5e-79;codon 2-136 -!- PF02796;Helix-turn-helix domain of resolvase;9.9e-15;codon 138-182" CDS ECK1145 mcrA mcrA rglA b1159 1209569 1210402 + (no change) JW1145 1211923 1212756 + h e14 prophage; 5-methylcytosine-specific restriction endonuclease B E 88157715 -!- 89357443 -!- 1938927 Cytoplasmic cryptic prophage e14 3.1.21.- COG1403;Restriction endonuclease PF01844;HNH endonuclease;3.3e-10;codon 205-259 CDS ECK1146 icdC icdC b4519 1210648 1210800 + pseudogene -!- new JW5173 1213002 1213154 + pseudogene su conserved protein (pseudogene) C Cytoplasmic 53659; Isocitrate/Isopropylmalate dehydrogenase-like "TIGR00183;prok_nadp_idh: isocitrate dehydrogenase, NA;9.9e-21; codon 1-50" GO:0005737 cytoplasm CDS ECK1147 elbA elbA ycgW -!- elb1 b1160 1210903 1211226 - (no change) JW1147 1213257 1213580 - o predicted protein associated with lycopene formation C 9603997 Cytoplasmic CDS ECK1148 ycgX ycgX b1161 1211926 1212330 - (no change) JW1148 1214280 1214684 - o predicted protein C Cytoplasmic PF07166;Protein of unknown function (DUF1398);3.1e-99;codon 3-127 CDS ECK1149 ycgE ycgE b1162 1212551 1213282 - (no change) JW1149 1214905 1215636 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic MerR COG0789;Predicted transcriptional regulators 46955; Putative DNA-binding domain PF00376;MerR family regulatory protein;3.5e-11;codon 5-42 GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1150 ycgF ycgF b1163 1213487 1214698 - (no change) JW1150 1215841 1217052 - pe predicted FAD-binding phosphodiesterase C 15453820 COG2200;FOG: EAL domain 51395; FMN-linked oxidoreductases PF04940;Sensors of blue-light using FAD;2.4e-68;codon 2-94 -!- PF00563;EAL domain;3e-62;codon 158-389 CDS ECK1151 ycgZ ycgZ b1164 1215012 1215248 + (no change) JW1151 1217366 1217602 + o predicted protein C Cytoplasmic CDS ECK1152 ymgA ymgA b1165 1215291 1215563 + (no change) JW1152 1217645 1217917 + o predicted protein C Cytoplasmic CDS ECK1153 ymgB ymgB b1166 1215592 1215858 + (no change) JW1153 1217946 1218212 + o predicted protein C Cytoplasmic CDS ECK1154 ymgC ymgC b1167 1215971 1216219 + (no change) JW1154 1218325 1218573 + o predicted protein C Cytoplasmic CDS ECK1155 ycgG ycgG b1168 1216551 1218074 + start codon change JW5174 1218905 1220428 + pm conserved inner membrane protein C Integral Membrane Protein 3 2 in COG2200;FOG: EAL domain PF00563;EAL domain;2.1e-111;codon 259-500 CDS ECK1156 ymgF ymgF b4520 1218206 1218424 + new JW1156 1220560 1220778 + pseudogene o predicted protein C Integral Membrane Protein GO:0016021 integral to membrane ECK1157 ycgH ycgH b4491 1218824 1221445 + pseudogene; interrupted by frameshift and in-frame stop JW5901+JW5176 1222378 1223799 + ancestral gene su predicted protein (pseudogene) C Periplasmic CDS ECK1157 ycgH ycgH_2 b1170 1220429 1221445 + pseudogene fragment -!- (no change) JW5176 1222783 1223799 + pseudogene su "predicted protein, C-ter fragment (pseudogene)" C CDS ECK1157 ycgH ycgH_1 b1169 1220024 1220344 + pseudogene fragment -!- start codon change JW5901 1222378 1222698 + pseudogene su "predicted protein, N-ter fragment (pseudogene)" C CDS ECK1158 ymgD ymgD b1171 1221528 1221857 - start codon change JW5177 1223882 1224211 - o predicted protein C Periplasmic 1-21 CDS ECK1159 ymgG ymgG b1172 1221867 1222142 - start codon change JW5178 1224221 1224496 - o predicted protein C CDS ECK1160 ymgH ymgH b4521 1222688 1222909 + new JW5179 1225042 1225263 + o predicted protein part of ycgI pseudogene C CDS ECK1161 ycgI ycgI b1173 1222918 1223130 + (no change) JW1162 1225272 1225484 + o predicted protein C Cytoplasmic CDS ECK1162 minE minE minB b1174 1223502 1223768 - (no change) JW1163 1225856 1226122 - cp cell division topological specificity factor blocks MinCD inhibition of FtsZ polymerization -!- forms membrane-associated coiled arrays in a ring at the cell center E 10096083 -!- 11703919 -!- 12897015 -!- 90138951 -!- 92104991 -!- 94079315 -!- 99248411 -!- 2645057 Cytoplasmic COG0851;Septum formation topological specificity factor 55229; Cell division protein MinE topological specificity domain PF03776;Septum formation topological specificity fac;1.2e-53;codon 1-83 TIGR01215;minE: cell division topological specificity;2.6e-53;codon 1-83 GO:0005737 cytoplasm CDS ECK1163 minD minD minB b1175 1223772 1224584 - (no change) JW1164 1226126 1226938 - f membrane ATPase of the MinC-MinD-MinE system regulates septum placement E 10096083 -!- 11248256 -!- 12519187 -!- 90138951 -!- 92097557 -!- 92104991 -!- 99248411 -!- 10220403 -!- 2645057 -!- 9298646 Cytoplasmic COG2894;Septum formation inhibitor-activating ATPase 52540; P-loop containing nucleotide triphosphate hydrolases PF01656;CobQ/CobB/MinD/ParA nucleotide binding domai;5.3e-27;codon 5-219 TIGR01968;minD_bact: septum site-determining protein;4.2e-163;codon 2-268 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1164 minC minC minB b1176 1224608 1225303 - (no change) JW1165 1226962 1227657 - cp cell division inhibitor inhibition of FtsZ ring polymerization -!- forms membrane-associated coiled arrays E 10096083 -!- 20079565 -!- 21528844 -!- 90138951 -!- 92104991 -!- 93163041 -!- 98083073 -!- 99248411 -!- 99445473 -!- 10869074 -!- 2645057 Cytoplasmic COG0850;Septum formation inhibitor "63848; Cell-division inhibitor MinC, C-terminal domain" "PF05209;Septum formation inhibitor MinC, N-terminal;6.2e-58;codon 1-104 -!- PF03775;Septum formation inhibitor MinC, C-terminal;1e-65;codon 122-230" TIGR01222;minC: septum site-determining protein MinC;2.7e-65;codon 5-230 GO:0005737 cytoplasm CDS ECK1165 ycgJ ycgJ b1177 1225823 1226191 + (no change) JW1166 1228177 1228545 + o predicted protein C Periplasmic 1-24 PF05666;Fels-1 Prophage Protein-like;1.8e-30;codon 19-62 -!- PF05666;Fels-1 Prophage Protein-like;2.3e-31;codon 66-121 CDS ECK1166 ycgK ycgK b1178 1226294 1226695 - (no change) JW1167 1228648 1229049 - o predicted protein C Periplasmic 1-22 PF04151;Bacterial pre-peptidase C-terminal domain;5.8e-13;codon 48-130 CDS ECK1167 ycgL ycgL b1179 1226904 1227230 + (no change) JW1168 1229258 1229584 + o conserved protein C Cytoplasmic PF05166;Family of unknown function (DUF709);3.3e-60;codon 13-94 CDS ECK1168 ycgM ycgM b1180 1227302 1227961 + (no change) JW1169 1229656 1230315 + pe predicted isomerase/hydrolase C Cytoplasmic 1NR9 "COG0179;2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)" 56529; FAH PF01557;Fumarylacetoacetate (FAA) hydrolase fam;2.1e-92;codon 33-201 CDS ECK1169 ycgN ycgN b1181 1228053 1228499 + start codon change JW5180 1230407 1230853 + o conserved protein C Cytoplasmic PF05779;Bacterial protein of unknown function (DUF83;6.4e-109;codon 13-154 CDS ECK1170 hlyE hlyE clyA -!- sheA -!- ycgD -!- hpr b1182 1228706 1229617 - start codon change JW5181 1231060 1231971 - c hemolysin E only expressed in an fnr mutant E 10027972 -!- 11902713 -!- 14525984 -!- 14532000 -!- 14996792 -!- 99028910 -!- 10383763 -!- 10660049 -!- 11006277 -!- 11053378 -!- 12057949 -!- 12949101 Membrane Anchored 1.C.10; The Pore-forming Haemolysin E (HlyE) Family PF06109;Haemolysin E (HlyE);6.2e-244;codon 6-304 GO:0005576 extracellular CDS ECK1171 umuD umuD uvm b1183 1229990 1230409 + (no change) JW1172 1232344 1232763 + e "DNA polymerase V, subunit D" E 92002333 -!- 92318898 -!- 93376765 -!- 9734356 -!- 9864328 -!- 99362686 Cytoplasmic 3.4.21.- S24 family; UmuD protein COG1974;SOS-response transcriptional repressors (RecA-mediated autopeptidases) 51306; LexA/Signal peptidase PF00717;Peptidase S24-like;2.4e-18;codon 55-122 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication -!- GO:0006281 DNA repair -!- GO:0006350 transcription -!- GO:0009432 SOS response CDS ECK1172 umuC umuC uvm b1184 1230409 1231677 + (no change) JW1173 1232763 1234031 + e "DNA polymerase V, subunit C" E 90017467 -!- 92318898 -!- 93287979 -!- 9734356 -!- 99362686 -!- 2989816 -!- 2989817 Cytoplasmic COG0389;Nucleotidyltransferase/DNA polymerase involved in DNA repair 56672; DNA/RNA polymerases PF00817;impB/mucB/samB family;3.1e-175;codon 5-352 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication -!- GO:0006281 DNA repair -!- GO:0009432 SOS response CDS ECK1173 dsbB dsbB iarB -!- roxB -!- dsbX -!- ycgA b1185 1231723 1232253 - (no change) JW5182 1234077 1234607 - e oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I E 12853466 -!- 93157338 -!- 93348217 -!- 10064586 -!- 1317851 -!- 7957076 Integral Membrane Protein 5.A.2; The Disulfide Bond Oxidoreductase B (DsbB) Family 4 4 in PF02600;Disulfide bond formation protein DsbB;8.9e-89;codon 4-164 GO:0019861 flagellum -!- GO:0009289 fimbria -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009296 flagella biogenesis -!- GO:0006457 protein folding -!- GO:0042330 taxis CDS ECK1174 nhaB nhaB b1186 1232399 1233940 - (no change) JW1175 1234753 1236294 - t sodium:proton antiporter E 92011431 -!- 92283803 -!- 93131914 -!- 93157338 -!- 93348217 Integral Membrane Protein 2.A.34; The NhaB Na+:H+ Antiporter (NhaB) Family 12 12 COG3067;Na+/H+ antiporter PF06450;Bacterial Na+/H+ antiporter B (NhaB);0;codon 1-512 TIGR00774;NhaB: Na+/H+ antiporter NhaB;0;codon 1-513 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009268 response to pH CDS ECK1175 fadR fadR dec -!- ole -!- thdB -!- oleR b1187 1234161 1234880 + (no change) JW1176 1236515 1237234 + r DNA-binding transcriptional dual regulator of fatty acid metabolism E 21192039 -!- 21264500 -!- 21450824 -!- 92235103 -!- 92370687 -!- 93094273 -!- 9388199 -!- 2843809 GntR fabA -!- fabB -!- fadBA -!- fadD -!- fadIJ -!- fadL -!- iclR -!- uspA 1HW2 COG2186;Transcriptional regulators "46785; Winged helix -!- 48008; Fatty acid responsive transcription factor FadR, C-terminal domain" "PF00392;Bacterial regulatory proteins, gntR family;5.6e-24;codon 8-71 -!- PF07840;FadR C-terminal domain;3.2e-122;codon 72-239" GO:0005737 cytoplasm GO:0019395 fatty acid oxidation -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK1176 ycgB ycgB b1188 1234932 1236464 - (no change) JW1177 1237286 1238818 - o conserved protein C Cytoplasmic COG2719;Uncharacterized conserved protein PF04293;SpoVR like protein;0;codon 17-453 CDS ECK1177 dadA dadA dadR b1189 1236794 1238092 + (no change) JW1178 1239148 1240446 + e D-amino acid dehydrogenase E 80182101 -!- 83012214 -!- 94156858 Cytoplasmic 1.4.99.1 monomeric multimer; D-amino acid dehydrogenase (b1189) COG0665;Glycine/D-amino acid oxidases (deaminating) "51971; Nucleotide-binding domain -!- 54373; FAD-linked reductases, C-terminal domain" PF01266;FAD dependent oxidoreductase;8.1e-107;codon 2-397 GO:0009063 amino acid catabolism CDS ECK1178 dadX dadX alnA -!- alnB -!- dadB b1190 1238102 1239172 + (no change) JW1179 1240456 1241526 + e "alanine racemase 2, PLP-binding" E "85152992 -!- 89075905 -!- 94156858 -!- 98269038 -!- Thornberry NA, Bull HG, Taub D, et al;J Am Chem Soc;1987;109:7543-7544" Cytoplasmic 5.1.1.1 COG0787;Alanine racemase "50621; Alanine racemase-like, C-terminal domain -!- 51419; PLP-binding barrel" "PF01168;Alanine racemase, N-terminal domain;1.7e-87;codon 4-218 -!- PF00842;Alanine racemase, C-terminal domain;1.4e-66;codon 232-356" TIGR00492;alr: alanine racemase;4.8e-222;codon 3-356 GO:0009063 amino acid catabolism -!- GO:0006523 alanine biosynthesis CDS ECK1179 cvrA cvrA ycgO b1191 1239558 1241294 - start codon change JW5184 1241912 1243648 - pt predicted cation/proton antiporter C 21557160 Integral Membrane Protein 13 11 COG3263;NhaP-type Na+/H+ and K+/H+ antiporters with a unique C-terminal domain PF00999;Na_H_Exchanger: Sodium/hydrogen exchanger f;6.4e-97;codon 9-394 -!- PF02080;TrkA-C: TrkA potassium uptake protein;8.1e-21;codon 401-487 TIGR00831;a_cpa1: Na+/H+ antiporter;3.3e-06;codon 4-484 -!- TIGR00840;b_cpa1: sodium/hydrogen exchanger 3;0.00054;codon 6-543 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1180 ldcA ldcA ycgQ b1192 1241389 1242303 - (no change) JW1181 1243743 1244657 - e "L,D-carboxypeptidase A" E 99359339 Cytoplasmic 3.4.17.13 U61 family; muramoyl-tetrape "COG1619;Uncharacterized proteins, homologs of microcin C7 resistance protein MccF" PF02016;LD-carboxypeptidase;1.1e-21;codo n 72-147 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0000270 peptidoglycan metabolism CDS ECK1181 emtA emtA mltE -!- sltZ -!- ycgP b1193 1242403 1243014 + start codon change JW5821 1244757 1245368 + e lytic murein endotransglycosylase E E 98317285 Outer membrane Lipoprotein 3.2.1.- COG0741;Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) 53955; Lysozyme-like PF01464;Transglycosylase SLT domain;1.7e-40;codon 79-207 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009252 peptidoglycan biosynthesis CDS ECK1182 ycgR ycgR b1194 1243016 1243750 - (no change) JW1183 1245370 1246104 - cp protein involved in flagellar function C 11031114 Cytoplasmic PF07317;YcgR protein;2.3e-197;codon 4-244 "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1183 ymgE ymgE tag1 -!- tag b1195 1243951 1244205 + (no change) JW1184 1246305 1246559 + pm predicted inner membrane protein C Integral Membrane Protein 3 3 COG2261;Predicted membrane protein PF04226;Transglycosylase associated protein;8.4e-20;codon 33-83 CDS ECK1184 ycgY ycgY b1196 1244383 1244823 + (no change) JW1185 1246737 1247177 + o predicted protein C Cytoplasmic CDS ECK1185 treA treA tre -!- osmA b1197 1244902 1246599 - (no change) JW1186 1247256 1248953 - e periplasmic trehalase E 89364718 -!- 92078100 -!- 93302496 -!- 1710760 -!- 2820965 -!- 2671658 Periplasmic 3.2.1.28 1-30 565 COG1626;Neutral trehalase PF01204;Trehalase;2.1e-279;codon 55-533 GO:0042597 periplasmic space GO:0006006 glucose metabolism -!- GO:0006970 response to osmotic stress CDS ECK1186 dhaH dhaH dhaM -!- ycgC -!- ptsD b1198 1246919 1248337 - start codon change JW5185 1249273 1250691 - pt fused predicted dihydroxyacetone-specific PTS enzymes: HPr component -!- EI component C 20476408 -!- 21248583 -!- 2671658 -!- 7984428 -!- 11021910 Cytoplasmic heteromultimer; dihydroxyacetone kinase (b1198-b1199-b1200) "fused predicted PTS family enzyme, dihydroxyacetone-specific: HPr component (aa1-259) -!- enzymeI (aa260-473)" COG3412;Uncharacterized protein conserved in bacteria -!- COG1080;Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) 53901; Thiolase-like -!- 47831; Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain -!- 52009; Phosphohistidine domain -!- 53901; Thiolase-like -!- 55594; HPr-like "PF03610;PTS system fructose IIA component;1.9e-34;3-122 -!- PF00381;PTS HPr component phosphorylation site;7.5e-09;156-239 -!- PF05524;PEP-utilising enzyme, N-terminal;1.4e-44;251-370 -!- PF00391;PEP-utilising enzyme, mobile domain;1.4e-22;375-467" TIGR01003;PTS_HPr_family: phosphocarrier protein;4.3e-09;codon 158-237 CDS ECK1187 dhaL dhaL ycgS -!- dhaK2 -!- ptsD b1199 1248348 1248980 - (no change) JW5186 1250702 1251334 - e "dihydroxyacetone kinase, C-terminal domain" "phosphoryl donor is DhaH, not ATP" E 20476408 -!- 10493123 -!- 11021910 heteromultimer; dihydroxyacetone kinase (b1198-b1199-b1200) COG2376;Dihydroxyacetone kinase PF02734;DAK2 domain;4.6e-84;codon 32-206 CDS ECK1188 dhaK dhaK ycgT -!- dhaK1 -!- ptsD b1200 1248991 1250061 - start codon change JW5187 1251345 1252415 - e "dihydroxyacetone kinase, N-terminal domain" "phosphoryl donor is DhaH, not ATP" E 20476408 -!- 11021910 Cytoplasmic heteromultimer; dihydroxyacetone kinase (b1198-b1199-b1200) PF02733;Dak1 domain;2.1e-227;codon 26-366 CDS ECK1189 dhaR dhaR ptsD -!- ycgU b1201 1250289 1252208 + start codon change JW5188 1252643 1254562 + pr "predicted DNA-binding transcriptional regulator, dihydroxyacetone" C 20476408 -!- 11021910 Cytoplasmic EBP COG3284;Transcriptional activator of acetoin/glycerol metabolism 48283; FIS-like -!- 52540; P-loop containing nucleotide triphosphate hydrolases -!- 55785; PYP-like sensor domain "PF01590;GAF domain;5.3e-14;codon 55-192 -!- PF00989;PAS domain;4.5e-08;codon 206-268 -!- PF00158;Sigma-54 interaction domain;1.7e-33;codon 330-547 -!- PF02954;Bacterial regulatory protein, Fis fam;9.8e-15;codon 591-631" "TIGR01199;HTH_fis: Helix-turn-helix domain, fis-type;5.5e-14;codon 591-633" GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1190 ycgV ycgV b1202 1252308 1255175 - (no change) JW1193 1254662 1257529 - pf predicted adhesin "overexpression increases adhesion and biofilm formation, possible adhesin" C 15659678 Cytoplasmic j "COG3468;Type V secretory pathway, adhesin AidA" 51126; Pectin lyase-like PF03212;Pertactin;4.3e-67;codon 494-616 -!- PF03797;Autotransporter beta-domain;1e-31;codon 688-942 TIGR01414;autotrans_barl: outer membrane autotra;9.8e-100;codon 512-955 GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK1191 ychF ychF gtp1 b1203 1255944 1257035 - (no change) JW1194 1258298 1259389 - pf predicted GTP-binding protein C 94068503 -!- 1833189 -!- 7828865 -!- 9298646 Cytoplasmic "COG0012;Predicted GTPase, probable translation factor" 52540; P-loop containing nucleotide triphosphate hydrolases PF01926;GTPase of unknown function;2.4e-32;codon 3-138 -!- PF06071;Protein of unknown function (DUF933);8e-61;codon 279-362 TIGR00092;TIGR00092: GTP-binding protein YchF;4e-275;codon 1-363 CDS ECK1192 pth pth rap b1204 1257152 1257736 - (no change) JW1195 1259506 1260090 - e peptidyl-tRNA hydrolase E 91073389 -!- 92007806 -!- 92215859 -!- 9144799 -!- 9303320 Periplasmic 3.1.1.29 COG0193;Peptidyl-tRNA hydrolase 53178; Peptidyl-tRNA hydrolase PF01195;Peptidyl-tRNA hydrolase;2e-114;codon 5-189 TIGR00447;pth: peptidyl-tRNA hydrolase;9.1e-118;codon 3-190 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK1193 ychH ychH b1205 1258014 1258292 + (no change) JW1196 1260368 1260646 + pm predicted inner membrane protein C 1833189 -!- 7828865 Integral Membrane Protein 2 2 regulated by attenuation (ychH) CDS ECK1194 ychM ychM b1206 1258347 1260026 - start codon change JW5189 1260701 1262380 - pt predicted transporter C 3009477 -!- 7984428 -!- 8140616 Integral Membrane Protein 10 11 in regulated by attenuation (ychM) COG0659;Sulfate permease and related transporters (MFS superfamily) 52091; Anti-sigma factor antagonist SpoIIaa PF00916;Sulfate transporter family;9.2e-108;codon 110-433 -!- PF01740;STAS domain;5e-22;codon 441-546 TIGR00815;sulP: sulfate permease;5.8e-198;codon 7-546 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1195 prsA prsA dnaR -!- prs b1207 1260151 1261098 - (no change) JW1198 1262505 1263452 - e phosphoribosylpyrophosphate synthase synonym PRPP synthase E 88139171 -!- 89255522 -!- 3009477 -!- 9298646 Cytoplasmic 2.7.6.1 Mg2+ -!- phosphate COG0462;Phosphoribosylpyrophosphate synthetase 53271; PRTase-like PF00156;Phosphoribosyl transferase domain;1.9e-37;codon 140-270 TIGR01251;ribP_PPkin: ribose-phosphate pyrophosphoki;1.3e-140;codon 4-314 GO:0009152 purine ribonucleotide biosynthesis CDS ECK1196 ispE ispE IPK -!- ychB -!- ipk b1208 1261249 1262100 - (no change) JW1199 1263603 1264454 - e 4-diphosphocytidyl-2-C-methylerythritol kinase E 12878729 -!- 20122571 Cytoplasmic 2.7.1.148 COG1947;4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate synthase 54211; Ribosomal protein S5 domain 2-like PF00288;GHMP kinases putative ATP-binding protei;8.4e-37;codon 89-252 TIGR00154;ispE: 4-diphosphocytidyl-2C-methyl-D-erythri;9.3e-188;codon 1-283 GO:0005737 cytoplasm CDS ECK1197 lolB lolB hemM -!- ychC b1209 1262100 1262723 - (no change) JW1200 1264454 1265077 - f chaperone for lipoproteins "with LolA; required for sorting, positioning and membrane localization of lipoproteins" E 12839983 -!- 93051347 -!- 9384574 -!- 97369828 -!- 99453001 Outer membrane Lipoprotein 1IWN COG3017;Outer membrane lipoprotein involved in outer membrane biogenesis PF03550;Outer membrane lipoprotein LolB;4.7e-95;codon 7-194 TIGR00548;lolB: outer membrane lipoprotein LolB;2e-103;codon 5-206 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK1198 hemA hemA gtrA b1210 1262937 1264193 + (no change) JW1201 1265291 1266547 + e glutamyl tRNA reductase E 90060810 -!- 92235044 -!- 93051347 -!- 2548996 -!- 2664455 -!- 7543480 1.2.1.- COG0373;Glutamyl-tRNA reductase "51735; NAD(P)-binding Rossmann-fold domains -!- 69075; Glutamyl tRNA-reductase dimerization domain -!- 69742; Glutamyl tRNA-reductase catalytic, N-terminal domain" "PF05201;Glutamyl-tRNAGlu reductase, N-terminal;8.2e-90;codon 6-157 -!- PF05200;Glutamyl-tRNAGlu reductase, NAD(P) bin;2.6e-86;codon 161-315 -!- PF00745;Glutamyl-tRNAGlu reductase, dimerisati;6.4e-38;codon 319-418" TIGR01035;hemA: glutamyl-tRNA reductase;3.2e-260;codon 3-418 GO:0005737 cytoplasm GO:0042493 response to drug CDS ECK1199 prfA prfA sueB -!- uar b1211 1264235 1265317 + (no change) JW1202 1266589 1267671 + f peptide chain release factor RF-1 E 88163791 -!- 91310602 -!- 11118225 -!- 2548996 -!- 3049538 -!- 3889910 -!- 7543480 -!- 7883187 Cytoplasmic COG0216;Protein chain release factor A PF03462;PCRF domain;6.6e-75;codon 63-178 -!- PF00472;Peptidyl-tRNA hydrolase domain;7.8e-74;codon 210-321 TIGR00019;prfA: peptide chain release factor;6e-274;codon 1-359 GO:0005737 cytoplasm GO:0006412 protein biosynthesis CDS ECK1200 prmC prmC hemK b1212 1265317 1266150 + (no change) JW1203 1267671 1268504 + e "N5-glutamine methyltransferase, modifies release factors RF-1 and RF-2" E 11805295 -!- 11847124 -!- 95189105 Cytoplasmic 2.1.1.- COG2890;Methylase of polypeptide chain release factors 53335; S-adenosyl-L-methionine-dependent methyltransferases "TIGR00536;hemK_fam: modification methylase, HemK famil;2.4e-100;codon 1-277" CDS ECK1201 ychQ ychQ b1213 1266147 1266539 + (no change) JW1204 1268501 1268893 + pr predicted transcriptional regulator C Integral Membrane Protein 4 4 out COG3094;Uncharacterized protein conserved in bacteria "PF04247;Invasion gene expression up-regulator, SirB;4.6e-77;codon 3-129" "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1202 ychA ychA b1214 1266543 1267352 + (no change) JW1205 1268897 1269706 + pr predicted transcriptional regulator C Cytoplasmic COG2912;Uncharacterized conserved protein 48452; TPR-like "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1203 kdsA kdsA b1215 1267388 1268242 + (no change) JW1206 1269742 1270596 + e 3-deoxy-D-manno-octulosonate 8-phosphate synthase E 87286380 -!- 10926505 -!- 11371194 -!- 7543480 -!- 7775423 -!- 9298646 Cytoplasmic 2.5.1.55 monomeric multimer; 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase (b1215) 1PL9 COG2877;3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase 51569; Aldolase PF00793;DAHP synthetase I family;8.2e-120;codon 10-276 TIGR01362;KDO8P_synth: 3-deoxy-8-phosphooctulonate;1e-177;codon 17-276 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0030113 capsule (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009244 lipopolysaccharide core region biosynthesis -!- GO:0009248 K antigen biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK1204 ldrA ldrA b4419 1268391 1268498 - (no change) JW5957 1270745 1270852 - f "toxic polypeptide, small" E misc_RNA ECK1205 rdlA rdlA b4420 1268546 1268612 + (no change) JWR0229 1270900 1270966 + n "regulatory, antisense RNA" trans-acting regulator of ldrA translation E CDS ECK1206 ldrB ldrB b4421 1268926 1269033 - (no change) JW5958 1271280 1271387 - f "toxic polypeptide, small" E misc_RNA ECK1207 rdlB rdlB b4422 1269081 1269146 + (no change) JWR0230 1271435 1271500 + n "regulatory, antisense sRNA" trans-acting regulator of ldrB translation E CDS ECK1208 ldrC ldrC b4423 1269461 1269568 - (no change) JW5959 1271815 1271922 - f "toxic polypeptide, small" E misc_RNA ECK1209 rdlC rdlC b4424 1269616 1269683 + (no change) JWR0231 1271970 1272037 + n "regulatory, antisense sRNA" trans-acting regulator of ldrC translation E CDS ECK1210 chaA chaA b1216 1269972 1271072 - (no change) JW1207 1272326 1273426 - t calcium/sodium:proton antiporter E 93266586 -!- 94193576 -!- 94292460 Integral Membrane Protein 2.A.19; The Ca2+:Cation Antiporter (CaCA) Family 11 11 out COG0387;Ca2+/H+ antiporter PF01699;Sodium/calcium exchanger protein;7e-16;codon 232-364 TIGR00846;caca2: calcium/proton exchanger;2.1e-199;codon 1-365 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1211 chaB chaB b1217 1271342 1271572 + (no change) JW1208 1273696 1273926 + pr predicted cation regulator predicted to regulate membrane ion antiporter ChaA C Cytoplasmic COG4572;Putative cation transport regulator PF06150;ChaB;2.7e-13;codon 8-76 GO:0005737 cytoplasm GO:0006350 transcription CDS ECK1212 chaC chaC b1218 1271709 1272425 + (no change) JW1209 1274063 1274779 + r regulatory protein for cation transport E Cytoplasmic COG3703;Uncharacterized protein involved in cation transport PF04752;ChaC-like protein;1.9e-99;codon 54-223 GO:0005737 cytoplasm GO:0006350 transcription CDS ECK1213 ychN ychN b1219 1272469 1272822 - (no change) JW1210 1274823 1275176 - d conserved protein sulfur reduction like C Cytoplasmic 1JX7 COG1553;Uncharacterized conserved protein involved in intracellular sulfur reduction PF02635;DsrE/DsrF-like family;6.2e-40;codon 2-117 CDS ECK1214 ychP ychP ychO b1220 1273148 1274401 + (no change) JW1211 1275502 1276755 + pf predicted invasin C Periplasmic CDS ECK1215 narL narL frdR -!- narR b1221 1274402 1275052 - (no change) JW1212 1276756 1277406 - r DNA-binding response regulator in two-component regulatory system with NarX (or NarQ) regulator of nitrate/nitrite response E 89263708 -!- 91058381 -!- 91294187 -!- 2648330 -!- 2649492 -!- 8780507 -!- 9521685 Cytoplasmic LuxR/UhpA adhE -!- caiF -!- cydDC -!- dcuB-fumB -!- dmsABC -!- fdhF -!- fdnGHI -!- focA-pflB -!- frdABCD -!- hcp -!- hyaABCDEF -!- hybOABCDEFG -!- moeAB -!- napFDAGHBC-ccmABCDEFGH -!- narGHJI -!- narK -!- nirBDC-cysG -!- norVW -!- nrfABCDEFG -!- nuoA COG2197;Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;1.3e-44;codon 7-128 -!- PF00196;Bacterial regulatory proteins, luxR fami;3.1e-27;codon 153-210" GO:0005737 cytoplasm GO:0009061 anaerobic respiration -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK1216 narX narX frdR -!- narR -!- frd1 b1222 1275045 1276841 - (no change) JW1213 1277399 1279195 - r sensory histidine kinase in two-component regulatory system with NarL regulator of nitrate/nitrite response -!- senses nitrate/nitrite E 92276349 -!- 92374842 -!- 94083940 -!- 2649492 -!- 2657652 -!- 2668029 Integral Membrane Protein monomeric multimer; NarX (b1222) 2 2 "COG3850;Signal transduction histidine kinase, nitrate/nitrite-specific" 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF00672;HAMP domain;4e-12;codon 157-225 -!- PF07730;Histidine kinase;2.5e-22;codon 390-458 -!- PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;3.6e-23;codon 494-586" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration -!- GO:0006464 protein modification CDS ECK1217 narK narK b1223 1277180 1278571 + (no change) JW1214 1279534 1280925 + t nitrate/nitrite transporter E 91258310 -!- 2657652 -!- 2668029 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG2223;Nitrate/nitrite transporter PF07690;Major Facilitator Superfamily;1.7e-15;codon 44-430 TIGR00886;2A0108: nitrate transporter;1.1e-189;codon 36-418 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006807 nitrogen metabolism CDS ECK1218 narG narG chlC -!- narC b1224 1279087 1282830 + (no change) JW1215 1281441 1285184 + e "nitrate reductase 1, alpha subunit" E 74167294 -!- 89384449 -!- 92121125 -!- 2233673 -!- 2668029 -!- 2995309 -!- 3053688 -!- 3308846 -!- 6094247 Cytoplasmic 1.7.99.4 heteromultimer; NarGH catalytic dimer of nitrate reductase A (b1224-b1225) -!- heteromultimer; nitrate reductase A (b1224-b1225-b1227) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 1Q16 COG5013;Nitrate reductase alpha subunit "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3" PF00384;Molybdopterin oxidoreductase;1.6e-187;codon 108-833 -!- PF01568;Molydopterin dinucleotide binding dom;3.6e-43;codon 1087-1208 "TIGR01580;narG: nitrate reductase, alpha subunit;0;codon 2-1235" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration GO:0009054 electron acceptor activity CDS ECK1219 narH narH chlC b1225 1282827 1284365 + (no change) JW1216 1285181 1286719 + c "nitrate reductase 1, beta (Fe-S) subunit" E 74167294 -!- 89384449 -!- 92121125 -!- 1321049 -!- 2832376 -!- 3053688 -!- 8383531 -!- 8388253 -!- 8664273 -!- 9516445 Cytoplasmic 1.7.99.4 heteromultimer; NarGH catalytic dimer of nitrate reductase A (b1224-b1225) -!- heteromultimer; nitrate reductase A (b1224-b1225-b1227) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 1SIW COG1140;Nitrate reductase beta subunit 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;0.01;codon 9-32 -!- PF00037;4Fe-4S binding domain;0.011;codon 177-202 "TIGR01660;narH: nitrate reductase, beta subunit;0;codon 1-494" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration GO:0009054 electron acceptor activity CDS ECK1220 narJ narJ b1226 1284362 1285072 + (no change) JW1217 1286716 1287426 + f molybdenum-cofactor-assembly chaperone subunit (delta subunit) of nitrate reductase 1 E 89384449 -!- 92121125 -!- 9632249 -!- 2832376 Cytoplasmic 1.7.99.4 COG2180;Nitrate reductase delta subunit PF02613;Nitrate reductase delta subunit;5.5e-104;codon 3-166 TIGR00684;narJ: nitrate reductase molybdenum cofactor;3.4e-65;codon 8-161 GO:0009061 anaerobic respiration -!- GO:0006457 protein folding CDS ECK1221 narI narI chlI b1227 1285072 1285749 + (no change) JW1218 1287426 1288103 + c "nitrate reductase 1, gamma (cytochrome b(NR)) subunit" E 75114694 -!- 89384449 -!- 92121125 -!- 2832376 -!- 3053688 Integral Membrane Protein 1.7.99.4 heteromultimer; nitrate reductase A (b1224-b1225-b1227) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 5 5 in COG2181;Nitrate reductase gamma subunit PF02665;Nitrate reductase gamma subunit;2.6e-124;codon 3-225 "TIGR00351;narI: respiratory nitrate reductase, gamma s;1.1e-131;codon 1-225" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration -!- GO:0017004 cytochrome biogenesis GO:0009054 electron acceptor activity CDS ECK1222 ychS ychS b1228 1285932 1286207 + (no change) JW5881 1288286 1288561 + GeneMark can predict -!- similar to corresponding hypothetical protein of O157 o predicted protein C misc_RNA ECK1223 rttR rtT rtV1 b4425 1286289 1286459 - (no change) JWR0232 1288643 1288813 - n regulatory sRNA may modulate the stringent response E 92051373 CDS ECK1224 tpr tpr b1229 1286310 1286411 - (no change) JW1219 1288664 1288765 - pf predicted protamine-like protein encoded within tyrT transcript C 92051373 -!- 7034959 -!- 7034960 Cytoplasmic GO:0005737 cytoplasm tRNA ECK1225 tyrV tyrV tyrT -!- tyrTbeta b1230 1286467 1286551 - (no change) JWR0028 1288821 1288905 - n tRNA-Tyr(GUA) (Tyrosine tRNA1) tandemly duplicated E 91088251 tRNA ECK1226 tyrT tyrT Su-3 -!- Su-4 -!- suI_III -!- su_III -!- supC -!- supF -!- supO -!- tyrTalpha -!- su(c) -!- suIII b1231 1286761 1286845 - (no change) JWR0029 1289115 1289199 - n tRNA-Tyr(GUA) (Tyrosine tRNA1) tandemly duplicated E 90036683 -!- 91088251 -!- 92051373 CDS ECK1227 purU purU tgs -!- ychI b1232 1287005 1287847 - (no change) JW1220 1289359 1290201 - e formyltetrahydrofolate hydrolase E 94042872 -!- 7868604 -!- 8282700 Cytoplasmic 3.5.1.10 monomeric multimer; formyltetrahydrofolate deformylase (b1232) COG0788;Formyltetrahydrofolate hydrolase 53328; Formyltransferase -!- 55021; Regulatory domain in the aminoacid metabolism PF01842;ACT domain;2.2e-08;codon 7-79 -!- PF00551;Formyl transferase;1.9e-82;codon 85-262 TIGR00655;PurU: formyltetrahydrofolate deformylase;7.2e-209;codon 7-280 GO:0005737 cytoplasm GO:0009257 10-formyltetrahydrofolate biosynthesis -!- GO:0009152 purine ribonucleotide biosynthesis CDS ECK1228 ychJ ychJ b1233 1287897 1288355 - (no change) JW1221 1290251 1290709 - o conserved protein C Cytoplasmic COG3012;Uncharacterized protein conserved in bacteria PF02810;SEC-C motif;1.6e-06;codon 1-21 -!- PF02810;SEC-C motif;6.6e-06;codon 134-152 CDS ECK1229 rssA rssA ychK b1234 1288429 1289373 + (no change) JW1222 1290783 1291727 + o conserved protein C Cytoplasmic COG1752;Predicted esterase of the alpha-beta hydrolase superfamily PF01734;Patatin-like phospholipase;3.3e-57;codon 21-181 GO:0009274 cell wall (sensu Bacteria) CDS ECK1230 rssB rssB hnr -!- mviA -!- sprE -!- ychI -!- ychL b1235 1289465 1290478 + (no change) JW1223 1291819 1292832 + r response regulator of RpoS part of regulation of RpoS in response to carbon starvtion E 10339606 -!- 12912910 -!- 9495753 Cytoplasmic COG0784;FOG: CheY-like receiver 52172; CheY-like PF00072;Response regulator receiver domain;3e-38;codon 8-127 GO:0005737 cytoplasm GO:0006350 transcription CDS ECK1231 galU galU ychD -!- verA b1236 1290680 1291588 + (no change) JW1224 1293034 1293942 + e glucose-1-phosphate uridylyltransferase E 94222839 -!- 14253441 -!- 1537791 -!- 7528731 -!- 7961613 -!- 9298646 Cytoplasmic 2.7.7.9 Mg2+ monomeric multimer; UTP-glucose-1-phosphate uridylyltransferase (b1236) COG1210;UDP-glucose pyrophosphorylase 53448; Nucleotide-diphospho-sugar transferases PF00483;Nucleotidyl transferase;2.3e-12;codon 10-282 TIGR01099;galU: UTP-glucose-1-phosphate uridylyltransf;8.3e-194;codon 8-275 GO:0030113 capsule (sensu Bacteria) GO:0006012 galactose metabolism -!- GO:0006006 glucose metabolism -!- GO:0009242 colanic acid biosynthesis -!- GO:0016052 carbohydrate catabolism -!- GO:0009269 response to dessication CDS ECK1232 hns hns bglY -!- cur -!- drc -!- drdX -!- drs -!- fimG -!- irk -!- mssyA -!- msyA -!- osmZ -!- pilG -!- topX -!- virR -!- hnsA -!- topS -!- B1 -!- H1 b1237 1291732 1292145 - (no change) JW1225 1294086 1294499 - r global DNA-binding transcriptional dual regulator H-NS E 89056689 -!- 92394896 -!- 93209204 -!- 94335643 -!- 95267838 -!- 95286558 -!- 99355427 -!- 1406252 -!- 2668687 Cytoplasmic adiA -!- bglGFB -!- bolA -!- cadBA -!- chiA -!- csiD-ygaF-gabDTP -!- csiE -!- cspD -!- cydAB -!- fimEAICDFGH -!- flhDC -!- fliAZY -!- fliC -!- gadAX -!- galETKM -!- hlyE -!- hns -!- lacZYA -!- micF -!- nhaA -!- nirBDC-cysG -!- proU -!- rcsA COG2916;DNA-binding protein H-NS 47729; IHF-like DNA-binding proteins PF00816;H-NS histone family;1.5e-49;codon 21-130 GO:0019861 flagellum -!- GO:0005737 cytoplasm "GO:0006350 transcription -!- GO:0006355 regulation of transcription, DNA-dependent -!- GO:0042330 taxis" CDS ECK1233 tdk tdk b1238 1292750 1293367 + (no change) JW1226 1295104 1295721 + e thymidine kinase/deoxyuridine kinase E 91251767 -!- 2060797 -!- 7773397 -!- 14114853 -!- 14114854 Cytoplasmic 2.7.1.21 Mg2+ COG1435;Thymidine kinase 52540; P-loop containing nucleotide triphosphate hydrolases PF00265;Thymidine kinase;1.8e-106;codon 2-186 "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" ECK1234 ychG ychG b4573 1293794 1294545 - pseudogene; interrupted by frameshift and C-ter deletion JW5883+JW1227 1296003 1296775 - ancestral gene su predicted protein (pseudogene) C CDS ECK1234 ychG ychG_1 b1240 1294191 1294421 - pseudogene fragment -!- (no change) JW5883 1296545 1296775 - "pseudogene -!- frameshift in three ORFs; b1239: complement(1293649..1294239), pseudo" su "predicted protein, N-ter fragment (pseudogene)" C CDS ECK1234 ychG ychG_2 b1239 1293649 1294239 - pseudogene fragment -!- (no change) JW1227 1296003 1296593 - "pseudogene -!- frameshift in three ORFs; b1239: complement(1293649..1294239), pseudo; b1240: complement(1294191..1294421), pseudo; new: complement(1294360..1294545), pseudo -!- split transposase, N-terminal -!- GeneMark can predict" su "predicted protein, C-ter fragment (pseudogene)" C Cytoplasmic PF01609;Transposase DDE domain;1.4e-15;codon 25-195 CDS ECK1235 adhE adhE adhC -!- ana b1241 1294669 1297344 - (no change) JW1228 1297023 1299698 - e fused acetaldehyde-CoA dehydrogenase -!- iron-dependent alcohol dehydrogenase -!- pyruvate-formate lyase deactivase E 12783863 -!- 4301680 -!- 89291706 -!- 91200315 Cytoplasmic 1.2.1.10 -!- 1.1.1.1 Fe2+ -!- NAD -!- coenzyme A monomeric multimer; PFL-deactivase / alcohol dehydrogenase / acetaldehyde dehydrogenase (b1241) fused: acetaldehyde-CoA dehydrogenase (aa1-400) -!- iron-dependent alcohol dehydrogenase (aa449-891) "COG1012;NAD-dependent aldehyde dehydrogenases -!- COG1454;Alcohol dehydrogenase, class IV" 53720; ALDH-like -!- 56796; Dehydroquinate synthase-like PF00465;Iron-containing alcohol dehydrogenase;7e-237;codon 457-854 GO:0006113 fermentation CDS ECK1236 ychE ychE b1242 1297821 1298468 + (no change) JW1229 1300175 1300822 + pm predicted inner membrane protein C Integral Membrane Protein 6 6 out regulated by attenuation (ychE) COG2095;Multiple antibiotic transporter PF01914;MarC family integral membrane protein;2.4e-110;codon 8-210 TIGR00427;TIGR00427: conserved hypothetical protein T;2.3e-137;codon 2-206 GO:0009274 cell wall (sensu Bacteria) CDS ECK1237 oppA oppA b1243 1299206 1300837 + (no change) JW1235 1302896 1304527 + t oligopeptide transporter subunit -!- periplasmic-binding component of ABC superfamily E 20256410 -!- 86111605 -!- 90256748 -!- 92325017 -!- 2015910 -!- 9298646 -!- 9600841 -!- 2187863 -!- 8740179 -!- 9740056 -!- 10972807 heteromultimer; oligopeptide ABC transporter (b1245-b1246-b1247-b1244-b1243) 543 "COG4166;ABC-type oligopeptide transport system, periplasmic component" 53850; Periplasmic binding protein-like II PF00496;Bacterial extracellular solute-binding prot;5.7e-82;codon 81-464 GO:0009274 cell wall (sensu Bacteria) -!- GO:0042597 periplasmic space GO:0000270 peptidoglycan metabolism -!- GO:0006457 protein folding CDS ECK1238 oppB oppB b1244 1300923 1301843 + (no change) JW1236 1304613 1305533 + t oligopeptide transporter subunit -!- membrane component of ABC superfamily E 86111606 -!- 93106975 -!- 2187863 Integral Membrane Protein heteromultimer; oligopeptide ABC transporter (b1245-b1246-b1247-b1244-b1243) 6 6 in regulated by attenuation (oppB-oppC-oppD-oppF) "COG0601;ABC-type dipeptide/oligopeptide/nickel transport systems, permease components" PF00528;Binding-protein-dependent transport syst;6.9e-56;codon 94-306 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0000270 peptidoglycan metabolism CDS ECK1239 oppC oppC b1245 1301858 1302766 + (no change) JW1237 1305548 1306456 + t oligopeptide transporter subunit -!- membrane component of ABC superfamily E 86111606 Integral Membrane Protein heteromultimer; oligopeptide ABC transporter (b1245-b1246-b1247-b1244-b1243) 6 6 in "COG1173;ABC-type dipeptide/oligopeptide/nickel transport systems, permease components" PF00528;Binding-protein-dependent transport syst;2e-40;codon 101-302 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0000270 peptidoglycan metabolism CDS ECK1240 oppD oppD b1246 1302778 1303791 + (no change) JW1238 1306468 1307481 + t oligopeptide transporter subunit -!- ATP-binding component of ABC superfamily E 86111606 Cytoplasmic heteromultimer; oligopeptide ABC transporter (b1245-b1246-b1247-b1244-b1243) 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;5.3e-59;codon 49-245 TIGR01727;oligo_HPY: oligopeptide/dipeptide ABC trans;2.2e-31;codon 246-331 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0000270 peptidoglycan metabolism CDS ECK1241 oppF oppF b1247 1303788 1304792 + (no change) JW1239 1307478 1308482 + t oligopeptide transporter subunit -!- ATP-binding component of ABC superfamily E 86111606 Cytoplasmic heteromultimer; oligopeptide ABC transporter (b1245-b1246-b1247-b1244-b1243) "COG4608;ABC-type oligopeptide transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.8e-64;codon 50-241 TIGR01727;oligo_HPY: oligopeptide/dipeptide ABC trans;1.7e-45;codon 242-330 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0000270 peptidoglycan metabolism CDS ECK1242 yciU yciU b1248 1304845 1305174 - start codon change JW1240 1308535 1308864 - o predicted protein C Cytoplasmic "PF04269;Protein of unknown function, DUF440;4.1e-40;codon 29-135" CDS ECK1243 cls cls nov -!- yciJ b1249 1305209 1306669 - (no change) JW1241 1308899 1310359 - e cardiolipin synthase 1 E 88115179 -!- 92121165 -!- 92356877 -!- 7665497 -!- 7896699 -!- 8170937 -!- 9370333 Integral Membrane Protein 2.7.8.- 2 2 COG1502;Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes 56024; Phospholipase D/nuclease PF00614;Phospholipase D Active site motif;2.7e-07;codon 219-246 -!- PF00614;Phospholipase D Active site motif;5.2e-08;codon 399-426 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0008654 phospholipid biosynthesis -!- GO:0042493 response to drug CDS ECK1244 kch kch b1250 1307040 1308293 - (no change) JW1242 1310730 1311983 - t voltage-gated potassium channel E 12220501 -!- 12912904 -!- 94224769 -!- 98319474 Integral Membrane Protein 1.A.1; The Voltage-gated Ion Channel (VIC) Superfamily 7 7 in regulated by attenuation (kch) "COG1226;Kef-type K+ transport systems, predicted NAD-binding component" 51735; NAD(P)-binding Rossmann-fold domains -!- 56869; Membrane all-alpha PF07885;Ion channel;2.4e-19;codon 148-226 -!- PF02254;TrkA-N domain;4.5e-38;codon 245-365 GO:0019866 inner membrane GO:0005244 voltage-gated ion channel activity CDS ECK1245 yciI yciI b1251 1308593 1308889 - start codon change JW1243 1312283 1312579 - pe predicted enzyme C 15779043 Cytoplasmic COG2350;Uncharacterized protein conserved in bacteria PF03795;YCII-related domain;8e-48;codon 41-130 CDS ECK1246 tonB tonB T1rec -!- exbA b1252 1309113 1309832 + (no change) JW5195 1312803 1313522 + m membrane spanning protein in TonB-ExbB-ExbD complex E 91307892 -!- 93346371 -!- 94209234 -!- 11328822 -!- 1885532 -!- 6310567 -!- 8316087 Cytoplasmic heteromultimer; Ferric Enterobactin Transport System (b0584-b0588-b0589-b0590-b0592-b1252-b3005-b3006) -!- heteromultimer; Outer Membrane Ferric Citrate Transport System (b1252-b3005-b3006-b4291) -!- heteromultimer; Outer Membrane Ferric Enterobactin Transport System (b0584-b1252-b3005-b3006) -!- heteromultimer; Outer Membrane Ferrichrome Transport System (b0150-b1252-b3005-b3006) -!- heteromultimer; TonB energy transducing system (b1252-b3005-b3006) -!- heteromultimer; ferric dicitrate uptake system (b1252-b3005-b3006-b4287-b4288-b4289-b4290-b4291) -!- heteromultimer; ferrichrome uptake system (b0150-b0151-b0152-b0153-b1252-b3005-b3006) -!- heteromultimer; vitamin B12 outer membrane transport complex (b1252-b3005-b3006-b3966) -!- heteromultimer; vitamin B12 transport system (b0158-b1252-b1709-b1710-b1711-b3005-b3006-b3966) 2.C.1; The TonB-ExbB-ExbD/TolA-TolQ-TolR (TonB) Family of Auxiliary Proteins for Energization of Outer Membrane Receptor (OMR)-mediated Active Transport "COG0810;Periplasmic protein TonB, links inner and outer membranes" PF03544;Gram-negative bacterial tonB protein;2.6e-18;codon 160-194 TIGR01352;tonB_Cterm: TonB family C-terminal domain;1.9e-25;codon 161-233 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1247 yciA yciA b1253 1309872 1310270 - (no change) JW1245 1313562 1313960 - pe predicted hydrolase C 2985285 Cytoplasmic COG1607;Acyl-CoA hydrolase 54637; Thioesterase/thiol ester dehydrase-isomerase PF03061;Thioesterase superfamily;3e-18;codon 26-103 CDS ECK1248 yciB yciB b1254 1310375 1310914 - (no change) JW1246 1314065 1314604 - pm predicted inner membrane protein similar to Shigella IspA virulence factor C Integral Membrane Protein 5 5 in COG2917;Intracellular septation protein A PF04279;Intracellular septation protein A;2.3e-119;codon 1-176 TIGR00997;ispZ: intracellular septation protein A;4.2e-118;codon 1-178 CDS ECK1249 yciC yciC b1255 1310944 1311687 - (no change) JW1247 1314634 1315377 - pm predicted inner membrane protein C Integral Membrane Protein 6 6 PF06790;Uncharacterised protein family (UPF0259);4.6e-164;codon 1-247 GO:0009274 cell wall (sensu Bacteria) CDS ECK1250 ompW ompW yciD b1256 1312044 1312682 + (no change) JW1248 1315734 1316372 + m outer membrane protein W colicin S4 receptor E 99287842 -!- 3058546 -!- 9629924 Outer Membrane B-barrel protein heteromultimer; Colicin S4 Transport System (b0737-b0738-b0739-b0740-b0741-b0742-b1256) 1-21 212 COG3047;Outer membrane protein W 56925; Outer membrane protein PF03922;OmpW family;3.4e-116;codon 23-212 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK1251 yciE yciE b1257 1312742 1313248 - (no change) JW1249 1316432 1316938 - d conserved protein C 15388941 -!- 3058546 -!- 8455549 Cytoplasmic COG3685;Uncharacterized protein conserved in bacteria 47240; Ferritin-like PF05974;Protein of unknown function (DUF892);7e-71;codon 2-157 CDS ECK1252 yciF yciF b1258 1313294 1313794 - (no change) JW1250 1316984 1317484 - o conserved protein H-NS repressed C 3058546 -!- 8455549 Cytoplasmic COG3685;Uncharacterized protein conserved in bacteria PF05974;Protein of unknown function (DUF892);1.4e-89;codon 5-163 CDS ECK1253 yciG yciG b1259 1313880 1314059 - start codon change JW1251 1317570 1317749 - o predicted protein C Cytoplasmic CDS ECK1254 trpA trpA try -!- tryp b1260 1314440 1315246 - (no change) JW1252 1318130 1318936 - e "tryptophan synthase, alpha subunit" E 92183935 -!- 92184769 -!- 92232675 -!- 2502189 -!- 388433 -!- 4863752 -!- 7038627 -!- 8095913 -!- 9298646 Cytoplasmic 4.2.1.20 heteromultimer; tryptophan synthase (b1260-b1261) COG0159;Tryptophan synthase alpha chain 51366; Ribulose-phoshate binding barrel PF00290;Tryptophan synthase alpha chain;4.2e-156;codon 8-267 "TIGR00262;trpA: tryptophan synthase, alpha subunit;3.9e-120;codon 8-263" GO:0005737 cytoplasm GO:0000162 tryptophan biosynthesis CDS ECK1255 trpB trpB b1261 1315246 1316439 - (no change) JW1253 1318936 1320129 - e "tryptophan synthase, beta subunit" E 91104752 -!- 92183935 -!- 92232675 -!- 1309752 -!- 4552018 -!- 4943677 -!- 6985892 -!- 7007651 -!- 7038627 -!- 8095913 -!- 9298646 Cytoplasmic 4.2.1.20 "heteromultimer; tryptophan synthase (b1260-b1261) -!- monomeric multimer; tryptophan synthase, beta subunit dimer (b1261)" COG0133;Tryptophan synthase beta chain 53686; Tryptophan synthase beta subunit-like PLP-dependent enzymes PF00291;Pyridoxal-phosphate dependent enzyme;6.2e-117;codon 50-379 "TIGR00263;trpB: tryptophan synthase, beta subunit;1.5e-282;codon 7-391" GO:0005737 cytoplasm GO:0000162 tryptophan biosynthesis CDS ECK1256 trpC trpC b1262 1316451 1317809 - start codon change JW1254 1320141 1321499 - e fused indole-3-glycerolphosphate synthetase -!- N-(5-phosphoribosyl)anthranilate isomerase E "92148832 -!- 2184433 -!- 6355484 -!- 7007653 -!- 7038627 -!- White JL, Grutter MG, Wilson E,et al;FEBS Lett;1982;148:87-90 -!- Smith OH, Yanofsky C;Methods in Enzymology;1962;V:794-806" Cytoplasmic 5.3.1.24 -!- 4.1.1.48 fused: indole-3-glycerolphosphate synthetase (aa1-257) -!- N-(5-phosphoribosyl)anthranilate isomerase (aa258-453) 1PII COG0134;Indole-3-glycerol phosphate synthase -!- COG0135;Phosphoribosylanthranilate isomerase 51366; Ribulose-phoshate binding barrel -!- 51366; Ribulose-phoshate binding barrel PF00218;Indole-3-glycerol phosphate synthase;2.9e-157;codon 5-253 -!- PF00697;N-(5'phosphoribosyl)anthranilate (PRA) isome;7.7e-88;codon 258-449 GO:0005737 cytoplasm GO:0000162 tryptophan biosynthesis CDS ECK1257 trpD trpD trpGD b1263 1317813 1319408 - (no change) JW1255 1321503 1323098 - e fused glutamine amidotransferase (component II) of anthranilate synthase -!- anthranilate phosphoribosyl transferase E 7320769 -!- 82216842 -!- 4594441 -!- 7038627 -!- 4886289 Cytoplasmic 4.1.3.27 -!- 2.4.2.18 Mg2+ heteromultimer; anthranilate synthase (b1264-b1263) -!- monomeric multimer; anthranilate phosphoribosyl transferase (b1263) fused: glutamine amidotransferase (aa1-193) -!- anthranilate phosphoribosyltransferase (aa198-531) COG0512;Anthranilate/para-aminobenzoate synthases component II -!- COG0547;Anthranilate phosphoribosyltransferase 52317; Class I glutamine amidotransferase-like -!- 47648; Pyrimidine nucleoside phosphorylase N-terminal domain -!- 52418; Pyrimidine nucleoside phosphorylase central domain "PF00117;Glutamine amidotransferase class-I;4.3e-71;codon 5-190 -!- PF02885;Glycosyl transferase family, helical;1.3e-26;codon 200-264 -!- PF00591;Glycosyl transferase family, a/b doma;9.2e-146;codon 270-521" TIGR00566;trpG_papA: glutamine amidotransferase of an;1.9e-58;codon 3-189 -!- TIGR01245;trpD: anthranilate phosphoribosyltransferas;5.2e-201;codon 204-530 GO:0005737 cytoplasm GO:0000162 tryptophan biosynthesis CDS ECK1258 trpE trpE anth -!- tryD -!- tryp-4 b1264 1319408 1320970 - (no change) JW1256 1323098 1324660 - e component I of anthranilate synthase E 7320769 -!- 88142543 -!- 351195 -!- 4598537 -!- 7021857 -!- 7038627 -!- 4886289 Cytoplasmic 4.1.3.27 Mg2+ heteromultimer; anthranilate synthase (b1264-b1263) regulated by attenuation (trpE-trpD-trpC-trpB-trpA) COG0147;Anthranilate/para-aminobenzoate synthases component I 56322; ADC synthase "PF04715;Anthranilate synthase component I, N;3.1e-33;codon 42-193 -!- PF00425;chorismate binding enzyme;3e-158;codon 241-510" TIGR00565;trpE_proteo: anthranilate synthase compon;0;codon 17-515 GO:0000162 tryptophan biosynthesis CDS ECK1259 trpL trpL trpEE b1265 1321062 1321106 - (no change) JW1257 1324752 1324796 - l trp operon leader peptide E 2991886 -!- 91204432 Cytoplasmic GO:0005737 cytoplasm GO:0000162 tryptophan biosynthesis CDS ECK1260 yciV yciV trpH b1266 1321244 1322125 + (no change) JW1258 1324934 1325815 + o conserved protein TrpR-regulated C Cytoplasmic COG0613;Predicted metal-dependent phosphoesterases (PHP family) PF02231;PHP domain N-terminal region;5.3e-22;codon 10-75 -!- PF02811;PHP domain C-terminal region;2.1e-20;codon 140-265 CDS ECK1261 yciO yciO b1267 1322122 1322742 + start codon change JW5196 1325812 1326432 + o conserved protein C Cytoplasmic 1KK9 55821; YrdC/RibB PF01300;yrdC domain;3e-82;codon 34-210 TIGR00057;TIGR00057: Sua5/YciO/YrdC/YwlC family prote;2.3e-116;codon 19-218 CDS ECK1262 yciQ yciQ yciP b1268 1322770 1324665 + (no change) JW5197 1326460 1328355 + pm predicted inner membrane protein C Integral Membrane Protein 6 5 CDS ECK1263 rluB rluB yciL b1269 1324876 1325751 + (no change) JW1261 1328566 1329441 + e 23S rRNA pseudouridylate synthase E 21577312 -!- 2644187 -!- 7984428 Cytoplasmic 4.2.1.70 COG1187;16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases 55174; Alpha-L RNA-binding motif PF01479;S4 domain;1.1e-08;codon 3-50 -!- PF00849;RNA pseudouridylate synthase;5.8e-13;codon 68-202 TIGR00093;TIGR00093: conserved hypothetical protein;8.4e-96;codon 73-234 GO:0009451 RNA modification CDS ECK1264 btuR btuR cobA b1270 1325791 1326381 - (no change) JW1262 1329481 1330071 - e cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase E 90094228 -!- 2644187 Cytoplasmic 2.5.1.- -!- 2.5.1.17 COG2109;ATP:corrinoid adenosyltransferase 52540; P-loop containing nucleotide triphosphate hydrolases PF02572;ATP:corrinoid adenosyltransferase BtuR;3.7e-139;codon 22-196 TIGR00708;cobA: cob(I)alamin adenosyltransferase;2.3e-131;codon 24-196 GO:0005737 cytoplasm GO:0009236 vitamin B12 biosynthesis CDS ECK1265 yciK yciK b1271 1326378 1327136 - (no change) JW1263 1330068 1330826 - pe "predicted oxoacyl-(acyl carrier protein) reductase, EmrKY-TolC system" C Cytoplasmic COG1028;Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) 51735; NAD(P)-binding Rossmann-fold domains PF00106;short chain dehydrogenase;3.2e-75;codon 15-246 CDS ECK1266 sohB sohB b1272 1327356 1328405 + (no change) JW1264 1331046 1332095 + pe predicted inner membrane peptidase predicted endopeptidase -!- multicopy suppressor of the HtrA (DegP) null phenotype -!- similarity with inner membrane protease IV for cleavage of signal peptides C 91358368 Integral Membrane Protein S49 family; sohB endopeptidase 2 2 in COG0616;Periplasmic serine proteases (ClpP class) PF01343;Peptidase family S49;6.6e-70;codon 160-311 CDS ECK1267 yciN yciN b1273 1328441 1328692 - (no change) JW1265 1332131 1332382 - o predicted protein C 3029379 -!- 7567469 -!- 9868784 Cytoplasmic CDS ECK1268 topA topA supX b1274 1329072 1331669 + (no change) JW1266 1332762 1335359 + e "DNA topoisomerase I, omega subunit" E 10209756 -!- 87141164 -!- 91205604 -!- 94124564 -!- 3029379 -!- 3032952 -!- 7779808 -!- 8114910 Cytoplasmic 5.99.1.2 COG0550;Topoisomerase IA -!- COG0551;Zn-finger domain associated with topoisomerase type I 56712; Prokaryotic type I DNA topoisomerase -!- 57783; Zinc beta-ribbon PF01751;Toprim domain;9.8e-40;codon 3-140 -!- PF01131;DNA topoisomerase;1.1e-204;codon 154-553 -!- PF01396;Topoisomerase DNA binding C4 zinc fing;1e-13;codon 596-639 -!- PF01396;Topoisomerase DNA binding C4 zinc fing;6e-15;codon 708-745 TIGR01051;topA_bact: DNA topoisomerase I;0;codon 5-637 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication -!- GO:0006350 transcription CDS ECK1269 cysB cysB b1275 1331879 1332853 + (no change) JW1267 1335569 1336543 + r "DNA-binding transcriptional dual regulator, O-acetyl-L-serine-binding" E 14663078 -!- 21371682 -!- 90236288 -!- 91072242 -!- 1541275 -!- 2182030 -!- 3032952 Cytoplasmic monomeric multimer; CysB transcriptional dual regulator (b1275) LysR cbl -!- cysB -!- cysDNC -!- cysJIH -!- cysK -!- cysPUWAM -!- tauABCD regulated by attenuation (cysB) 1AL3 COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;2.5e-15;codon 3-64 -!- PF03466;LysR substrate binding domain;6.1e-47;codon 88-296 GO:0005737 cytoplasm GO:0019344 cysteine biosynthesis -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity ECK1270 yciX yciX b4574 1333184 1333482 + pseudogene; interrupted by frameshift JW5198+JW5199 1336874 1337172 + ancestral gene su predicted protein (pseudogene) C Cytoplasmic GO:0005737 cytoplasm CDS ECK1270 yciX yciX_2 b4523 1333294 1333482 + pseudogene fragment -!- new JW5199 1336984 1337172 + pseudogene su "predicted protein, C-ter fragment (pseudogene)" C CDS ECK1270 yciX yciX_1 b4522 1333184 1333312 + pseudogene fragment -!- new JW5198 1336874 1337002 + pseudogene su "predicted protein, N-ter fragment (pseudogene)" C CDS ECK1271 acnA acnA acn b1276 1333855 1336530 + (no change) JW1268 1337545 1340220 + e aconitate hydratase 1 E 20053887 -!- 92148368 -!- 92174916 -!- 9421904 Cytoplasmic 4.2.1.3 COG1048;Aconitase A "52016; Aconitase, C-terminal domain -!- 53732; Aconitase, first 3 domains" PF00330;Aconitase family (aconitate hydratase);0;codon 57-562 -!- PF00694;Aconitase C-terminal domain;2.6e-67;codon 689-819 TIGR01341;aconitase_1: aconitate hydratase;0;codon 18-890 GO:0006099 tricarboxylic acid cycle -!- GO:0009061 anaerobic respiration CDS ECK1272 ribA ribA b1277 1336594 1337184 - (no change) JW1269 1340284 1340874 - e GTP cyclohydrolase II E 92041545 -!- 93308083 -!- 94193559 -!- 1541275 Cytoplasmic 3.5.4.25 Mg2+ monomeric multimer; GTP cyclohydrolase II (b1277) COG0807;GTP cyclohydrolase II PF00925;GTP cyclohydrolase II;3.7e-119;codon 1-171 TIGR00505;ribA: GTP cyclohydrolase II;6e-145;codon 4-194 CDS ECK1273 pgpB pgpB b1278 1337354 1338118 + (no change) JW1270 1341044 1341808 + e phosphatidylglycerophosphatase B E 89033893 -!- 92104964 Integral Membrane Protein 3.1.3.27 6 6 in COG0671;Membrane-associated phospholipid phosphatase 48317; Acid phosphatase/Vanadium-dependent haloperoxidase PF01569;PAP2 superfamily;5.3e-24;codon 102-235 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0008654 phospholipid biosynthesis CDS ECK1274 yciS yciS b1279 1338267 1338575 + (no change) JW1271 1341957 1342265 + pm conserved inner membrane protein C Integral Membrane Protein 2 2 in COG3771;Predicted membrane protein PF06305;Protein of unknown function (DUF1049);2.8e-58;codon 1-89 CDS ECK1275 yciM yciM b1280 1338582 1339751 + (no change) JW1272 1342272 1343441 + d conserved protein heat shock related protein C Periplasmic COG2956;Predicted N-acetylglucosaminyl transferase 48452; TPR-like PF07719;Tetratricopeptide repeat;0.36;codon 180-213 -!- PF07719;Tetratricopeptide repeat;0.0028;codon 214-247 CDS ECK1276 pyrF pyrF URA-3 b1281 1339945 1340682 + (no change) JW1273 1343635 1344372 + e orotidine-5'-phosphate decarboxylase E 87280048 -!- 3052852 Membrane Anchored 4.1.1.23 monomeric multimer; orotidine-5'-phosphate-decarboxylase (b1281) 1EIX COG0284;Orotidine-5'-phosphate decarboxylase 51366; Ribulose-phoshate binding barrel PF00215;Orotidine 5'-phosphate decarboxylase / HUMP;4.7e-92;codon 15-237 TIGR01740;pyrF: orotidine 5'-phosphate decarboxylase;4.2e-68;codon 17-238 "GO:0006221 pyrimidine nucleotide biosynthesis -!- GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK1277 yciH yciH b1282 1340682 1341008 + start codon change JW1274 1344372 1344698 + d conserved protein C Cytoplasmic COG0023;Translation initiation factor 1 (eIF-1/SUI1) and related proteins 55159; eIF1-like PF01253;Translation initiation factor SUI1;7.1e-34;codon 28-106 "TIGR01158;SUI1_rel: translation initation factor SUI1,;3.9e-58;codon 9-109" CDS ECK1278 osmB osmB b1283 1341134 1341352 - (no change) JW1275 1344824 1345042 - lp lipoprotein induced by hyperosmolarity and during stationary phase E 92078100 -!- 2644204 Outer membrane Lipoprotein 1-22 GO:0006970 response to osmotic stress CDS ECK1279 yciT yciT b1284 1341621 1342370 - (no change) JW1276 1345311 1346060 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic DeoR COG1349;Transcriptional regulators of sugar metabolism 46785; Winged helix "PF00455;Bacterial regulatory proteins, deoR family;2e-52;codon 4-226" GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1280 gmr gmr yciR -!- gem b1285 1342781 1344766 - (no change) JW1278 1346471 1348456 - pf modulator of Rnase II stability E 11260472 Cytoplasmic regulated by attenuation (yciR) COG2202;FOG: PAS/PAC domain -!- COG2200;FOG: EAL domain 55785; PYP-like sensor domain PF00990;GGDEF domain;1.2e-66;codon 233-391 -!- PF00563;EAL domain;1.6e-118;codon 405-644 TIGR00229;sensory_box: PAS domain S-box;4.2e-11;codon 107-233 -!- TIGR00254;GGDEF: putative diguanylate cyclase (GGDE;5.4e-32;codon 233-396 CDS ECK1281 rnb rnb b1286 1345002 1346936 - (no change) JW1279 1348692 1350626 - e ribonuclease II E 20397813 -!- 86094326 -!- 93015723 -!- 93268098 -!- 99376595 Cytoplasmic 3.1.13.1 K+ -!- Mg2+ -!- Mn2+ -!- NH4+ COG4776;Exoribonuclease II 50249; Nucleic acid-binding proteins PF00773;RNB-like protein;5.2e-131;codon 118-474 -!- PF00575;S1 RNA binding domain;1.5e-10;codon 557-636 TIGR02062;RNase_B: exoribonuclease II;0;codon 1-642 -!- TIGR00358;3_prime_RNase: VacB and RNase II family;8.4e-283;codon 6-643 GO:0006401 RNA catabolism -!- GO:0006401 RNA catabolism CDS ECK1282 yciW yciW b1287 1347004 1348131 - start codon change JW5200 1350694 1351821 - pe predicted oxidoreductase C Cytoplasmic COG4950;Uncharacterized protein conserved in bacteria -!- COG2128;Uncharacterized conserved protein CDS ECK1283 fabI fabI envM -!- gts -!- qmeA b1288 1348275 1349063 - (no change) JW1281 1351965 1352753 - e "enoyl-[acyl-carrier-protein] reductase, NADH-dependent" E 4594014 -!- 93123967 -!- 94164884 -!- 10201369 -!- 10398587 -!- 10493822 -!- 8075395 -!- 8953047 -!- 9298646 Cytoplasmic 1.3.1.9 1MFP COG0623;Enoyl-[acyl-carrier-protein] reductase (NADH) 51735; NAD(P)-binding Rossmann-fold domains PF00106;short chain dehydrogenase;3.6e-15;codon 9-251 GO:0005737 cytoplasm CDS ECK1284 ycjD ycjD b1289 1349431 1349784 - (no change) JW1282 1353121 1353474 - d conserved protein C Cytoplasmic COG2852;Uncharacterized protein conserved in bacteria 52980; Restriction endonuclease-like PF04480;Protein of unknown function (DUF559);1.4e-77;codon 3-111 CDS ECK1285 sapF sapF b1290 1349852 1350658 - (no change) JW1283 1353542 1354348 - pt predicted antimicrobial peptide transporter subunit -!- ATP-binding component of ABC superfamily C 8332529 Cytoplasmic heteromultimer; peptide uptake ABC transporter (b1290-b1291-b1293-b1292-b1294) "COG4167;ABC-type antimicrobial peptide transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.6e-67;codon 40-227 GO:0005737 cytoplasm GO:0009063 amino acid catabolism CDS ECK1286 sapD sapD trkE b1291 1350660 1351652 - (no change) JW1284 1354350 1355342 - pt predicted antimicrobial peptide transporter subunit -!- ATP-binding component of ABC superfamily confers ATP dependence to the potassium-uptake systems TrkH and TrkG C 91100357 Cytoplasmic heteromultimer; peptide uptake ABC transporter (b1290-b1291-b1293-b1292-b1294) "COG4170;ABC-type antimicrobial peptide transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;3.2e-61;codon 33-235 TIGR01727;oligo_HPY: oligopeptide/dipeptide ABC trans;4.3e-23;codon 236-323 GO:0005737 cytoplasm GO:0009063 amino acid catabolism CDS ECK1287 sapC sapC b1292 1351652 1352542 - (no change) JW1285 1355342 1356232 - pt predicted antimicrobial peptide transporter subunit -!- membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; peptide uptake ABC transporter (b1290-b1291-b1293-b1292-b1294) 6 5 in "COG4171;ABC-type antimicrobial peptide transport system, permease component" PF00528;Binding-protein-dependent transport syst;3.8e-27;codon 99-296 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1288 sapB sapB b1293 1352529 1353494 - (no change) JW1286 1356219 1357184 - pt predicted antimicrobial peptide transporter subunit -!- membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; peptide uptake ABC transporter (b1290-b1291-b1293-b1292-b1294) 6 5 in "COG4168;ABC-type antimicrobial peptide transport system, permease component" PF00528;Binding-protein-dependent transport syst;1.2e-52;codon 74-315 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1289 sapA sapA b1294 1353491 1355134 - (no change) JW1287 1357181 1358824 - pt predicted antimicrobial peptide transporter subunit -!- periplasmic-binding component of ABC superfamily C Periplasmic heteromultimer; peptide uptake ABC transporter (b1290-b1291-b1293-b1292-b1294) 1-21 "COG4166;ABC-type oligopeptide transport system, periplasmic component" 53850; Periplasmic binding protein-like II PF00496;Bacterial extracellular solute-binding prot;7.9e-72;codon 78-459 GO:0042597 periplasmic space GO:0009063 amino acid catabolism CDS ECK1290 ymjA ymjA b1295 1355447 1355692 - (no change) JW1288 1359137 1359382 - o predicted protein C Cytoplasmic CDS ECK1291 puuP puuP ycjJ b1296 1355826 1357211 - start codon change JW1289 1359516 1360901 - t putrescine importer putrescine utilization pathway E 15590624 Integral Membrane Protein 12 12 in PF00324;Amino acid permease;2.3e-23;codon 44-471 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1292 puuA puuA ycjK b1297 1357514 1358932 - start codon change JW5201 1361204 1362622 - e gamma-Glu-putrescine synthase "putrescine utilization pathway, cold shock protein" E 15590624 Cytoplasmic "54368; Glutamine synthetase, N-terminal domain -!- 55931; Glutamine synthase/guanidino kinase catalytic domain" "PF00120;Glutamine synthetase, catalytic domain;2.4e-104;codon 159-420" GO:0006542 glutamine biosynthesis -!- GO:0006807 nitrogen metabolism CDS ECK1293 puuD puuD ycjL b1298 1359144 1359908 + start codon change JW1291 1362834 1363598 + e gamma-Glu-GABA hydrolase putrescine utilization pathway E 15590624 Cytoplasmic C26 family; unassigned peptidases 52317; Class I glutamine amidotransferase-like PF07722;Peptidase C26;6.6e-112;codon 12-228 -!- PF00117;Glutamine amidotransferase class-I;0.00041;codon 30-247 GO:0009310 amine catabolism CDS ECK1294 puuR puuR ycjC b1299 1359935 1360492 + (no change) JW1292 1363625 1364182 + r DNA-binding transcriptional repressor repressor for the puu divergon; putrescine utilization pathway E 15590624 Cytoplasmic Unclass COG1396;Predicted transcriptional regulators 47413; lambda repressor-like DNA-binding domains -!- 51182; RmlC-like PF01381;Helix-turn-helix;2e-15;codon 12-66 -!- PF07883;Cupin domain;8.1e-22;codon 110-180 CDS ECK1295 puuC puuC aldH b1300 1360767 1362254 + (no change) JW1293 1364457 1365944 + e "gamma-Glu-gamma-aminobutyraldehyde dehydrogenase, NAD(P)H-dependent" putrescine utilization pathway E 91216440 -!- 15590624 Cytoplasmic 1.2.1.3 COG1012;NAD-dependent aldehyde dehydrogenases 53720; ALDH-like PF00171;Aldehyde dehydrogenase family;5.7e-258;codon 28-493 GO:0005737 cytoplasm GO:0006113 fermentation CDS ECK1296 puuB puuB ycjA -!- ordL b1301 1362256 1363536 + (no change) JW1294 1365946 1367226 + e "gamma-Glu-putrescine oxidase, FAD/NAD(P)-binding" putrescine utilization pathway E 9150200 -!- 15590624 Cytoplasmic COG0665;Glycine/D-amino acid oxidases (deaminating) 51905; FAD/NAD(P)-binding domain PF01266;FAD dependent oxidoreductase;2.9e-105;codon 29-381 CDS ECK1297 puuE puuE goaG b1302 1363574 1364839 + (no change) JW1295 1367264 1368529 + e "GABA aminotransferase, PLP-dependent" putrescine utilization pathway E 9150200 -!- 15590624 Periplasmic 2.6.1.19 COG0160;4-aminobutyrate aminotransferase and related aminotransferases 53383; PLP-dependent transferases PF00202;Aminotransferase class-III;7.5e-163;codon 13-421 TIGR00700;GABAtrnsam: 4-aminobutyrate aminotransfera;0;codon 8-421 GO:0005737 cytoplasm GO:0009310 amine catabolism -!- GO:0008615 pyridoxine biosynthesis CDS ECK1298 pspF pspF ycjB b1303 1364959 1365936 - start codon change JW1296 1368649 1369626 - r DNA-binding transcriptional activator stress response E 14659000 -!- 15111053 -!- 97405926 -!- 9878422 -!- 1712397 -!- 7920643 -!- 7984428 -!- 8606168 Cytoplasmic monomeric multimer; PspF homo-oligomer (b1303) EBP pspABCDE -!- pspG 48283; FIS-like -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00158;Sigma-54 interaction domain;2.3e-125;codon 13-235 "TIGR01199;HTH_fis: Helix-turn-helix domain, fis-type;1e-10;codon 288-330" GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1299 pspA pspA cog b1304 1366103 1366771 + (no change) JW1297 1369793 1370461 + r regulatory protein for phage-shock-protein operon binds PspB and PspC E 91295203 -!- 95005446 -!- 8598199 -!- 9493373 Cytoplasmic "COG1842;Phage shock protein A (IM30), suppresses sigma54-dependent transcription" PF04012;PspA/IM30 family;3.2e-54;codon 2-218 GO:0005737 cytoplasm GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1300 pspB pspB b1305 1366825 1367049 + (no change) JW1298 1370515 1370739 + r DNA-binding transcriptional regulator of psp operon activates expression of phage-shock-protein operon with PspC -!- binds PspA; expressed in response to stress E 91295203 Membrane Anchored PF06667;Phage shock protein B;1.5e-50;codon 1-74 GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1301 pspC pspC b1306 1367049 1367408 + (no change) JW1299 1370739 1371098 + r DNA-binding transcriptional activator facilitates binding of phage shock proteins PspA and PspB E 91295203 -!- 12562786 -!- 1717346 Membrane Anchored monomeric multimer; PspC dimer (b1306) COG1983;Putative stress-responsive transcriptional regulator PF04024;PspC domain;2.2e-30;codon 7-69 GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1302 pspD pspD b1307 1367417 1367638 + (no change) JW1300 1371107 1371328 + ph peripheral inner membrane phage-shock protein expressed in response to stress as part of psp operon E 91295203 -!- 97303082 Cytoplasmic CDS ECK1303 pspE pspE b1308 1367713 1368027 + (no change) JW1301 1371403 1371717 + e thiosulfate:cyanide sulfurtransferase (rhodanese) "phage shock protein -!- expressed in response to stress as part of psp operon, but also transcribed independently" E 11997041 -!- 91295203 -!- 9868784 Periplasmic 2.8.1.1 1-19 104 COG0607;Rhodanese-related sulfurtransferase 52821; Rhodanese/Cell cycle control phosphatase PF00581;Rhodanese-like domain;5.3e-15;codon 9-100 CDS ECK1304 ycjM ycjM sucP b1309 1368240 1369919 + start codon change JW1302 1371930 1373609 + pe predicted glucosyltransferase similarity with sucrose phosphorylase C Cytoplasmic regulated by attenuation (ycjM-ycjN-ycjO-ycjP-ycjQ-ycjR-ycjS-ycjT-ycjU-ycjV) 51445; (Trans)glycosidases "PF00128;Alpha amylase, catalytic domain;4.6e-06;codon 61-489" GO:0000272 polysaccharide catabolism CDS ECK1305 ycjN ycjN b1310 1369933 1371225 + (no change) JW1303 1373623 1374915 + pt predicted sugar transporter subunit: periplasmic-binding component of ABC superfamily C Outer membrane Lipoprotein heteromultimer; YcjN/YcjO/YcjP ABC transporter (b1312-b1311-b1310) "COG1653;ABC-type sugar transport system, periplasmic component" 53850; Periplasmic binding protein-like II PF01547;Bacterial extracellular solute-binding prot;6.4e-40;codon 5-329 GO:0042597 periplasmic space CDS ECK1306 ycjO ycjO b1311 1371246 1372127 + (no change) JW1304 1374936 1375817 + pt predicted sugar transporter subunit: membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YcjN/YcjO/YcjP ABC transporter (b1312-b1311-b1310) 6 6 in "COG1175;ABC-type sugar transport systems, permease components" PF00528;Binding-protein-dependent transport syst;1e-19;codon 69-291 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1307 ycjP ycjP b1312 1372114 1372956 + (no change) JW1305 1375804 1376646 + pt predicted sugar transporter subunit: membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YcjN/YcjO/YcjP ABC transporter (b1312-b1311-b1310) 7 7 in "COG0395;ABC-type sugar transport system, permease component" PF00528;Binding-protein-dependent transport syst;3e-15;codon 70-274 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1308 ycjQ ycjQ b1313 1372987 1374039 + (no change) JW1306 1376677 1377729 + pe "predicted oxidoreductase, Zn-dependent and NAD(P)-binding" C Cytoplasmic COG1063;Threonine dehydrogenase and related Zn-dependent dehydrogenases 50129; GroES-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF00107;Zinc-binding dehydrogenase;1.5e-40;codon 17-350 CDS ECK1309 ycjR ycjR b1314 1374058 1374846 + start codon change JW5202 1377748 1378536 + pe predicted enzyme C Cytoplasmic COG1082;Sugar phosphate isomerases/epimerases 51658; Xylose isomerase-like PF01261;Xylose isomerase-like TIM barrel;2.8e-39;codon 22-222 CDS ECK1310 ycjS ycjS b1315 1374856 1375911 + (no change) JW1308 1378546 1379601 + pe "predicted oxidoreductase, NADH-binding" C Cytoplasmic COG0673;Predicted dehydrogenases and related proteins "51735; NAD(P)-binding Rossmann-fold domains -!- 55347; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain" "PF01408;Oxidoreductase family, NAD-binding Ros;7.3e-54;codon 10-130 -!- PF02894;Oxidoreductase family, C-terminal alph;3e-20;codon 142-253" CDS ECK1311 ycjT ycjT b1316 1375908 1378175 + (no change) JW1309 1379598 1381865 + pe predicted hydrolase C Cytoplasmic COG1554;Trehalose and maltose hydrolases (possible phosphorylases) 48208; Six-hairpin glycosyltransferases "PF03636;Glycosyl hydrolase family 65, N-termi;1.1e-102;codon 6-241 -!- PF03632;Glycosyl hydrolase family;1.2e-212;codon 298-677 -!- PF03633;Glycosyl hydrolase family 65, C-termi;1.7e-17;codon 681-731" CDS ECK1312 ycjU ycjU pgmB b1317 1378172 1378831 + (no change) JW1310 1381862 1382521 + pe predicted beta-phosphoglucomutase C Cytoplasmic COG0637;Predicted phosphatase/phosphohexomutase 56784; HAD-like PF00702;haloacid dehalogenase-like hydrolase;3.2e-36;codon 3-193 "TIGR02009;PGMB-YQAB-SF: beta-phosphoglucomutase fa;9.1e-110;codon 3-190 -!- TIGR01990;bPGM: beta-phosphoglucomutase;3.3e-137;codon 3-191 -!- TIGR01509;HAD-SF-IA-v3: HAD-superfamily hydrolase,;6e-20;codon 5-190" CDS ECK1313 ycjV ycjV b1318 1378845 1379813 + (no change) JW1311 1382535 1383503 + pt predicted sugar transporter subunit: ATP-binding component of ABC superfamily C Cytoplasmic "COG3839;ABC-type sugar transport systems, ATPase components" 50331; MOP-like -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;2.2e-60;codon 30-211 GO:0005737 cytoplasm CDS ECK1314 ymjB ymjB b4524 1379813 1379926 + new JW5203 1383503 1383616 + possibly split by frameshift (upper ORF) o predicted protein part of ycjV pseudogene C 50331; MOP-like CDS ECK1315 ompG ompG b1319 1379971 1380876 + (no change) JW1312 1383661 1384566 + t outer membrane porin induced by AI-2 signal protein E 20464934 -!- 89327119 -!- 9721282 Periplasmic 1.B.21; The OmpG Porin (OmpG) Family 1-20 301 56935; Porins GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK1316 ycjW ycjW b1320 1380987 1381985 - (no change) JW1313 1384677 1385675 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic GalR/LacI COG1609;Transcriptional regulators 47413; lambda repressor-like DNA-binding domains -!- 53822; Periplasmic binding protein-like I "PF00356;Bacterial regulatory proteins, lacI fami;1.4e-11;codon 3-28 -!- PF00532;Periplasmic binding proteins and sugar b;2.3e-09;codon 65-331" GO:0042597 periplasmic space GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1317 ycjX ycjX b1321 1382141 1383538 + (no change) JW1314 1385831 1387228 + d conserved protein with nucleoside triphosphate hydrolase domain C Cytoplasmic COG3106;Predicted ATPase 52540; P-loop containing nucleotide triphosphate hydrolases "PF04317;YcjX-like family, DUF463;0;codon 1-464" CDS ECK1318 ycjF ycjF b1322 1383535 1384596 + (no change) JW1315 1387225 1388286 + pm conserved inner membrane protein C Integral Membrane Protein 4 3 in COG3768;Predicted membrane protein PF05128;Family of unknown function (DUF697);2.1e-215;codon 54-341 TIGR01620;hyp_HI0043: conserved hypothetical protein;4.1e-214;codon 54-341 CDS ECK1319 tyrR tyrR b1323 1384744 1386285 + (no change) JW1316 1388434 1389975 + r "DNA-binding transcriptional dual regulator, tyrosine-binding" E 20115550 -!- 92048474 -!- 93106971 -!- 94148980 -!- 3001057 -!- 8176727 -!- 8444880 -!- 8449883 -!- 8947567 Cytoplasmic EBP aroF-tyrA -!- aroG -!- aroL-yaiA-aroM -!- aroP -!- mtr -!- tyrB -!- tyrP -!- tyrR COG3283;Transcriptional regulator of aromatic amino acids metabolism 52540; P-loop containing nucleotide triphosphate hydrolases -!- 55021; Regulatory domain in the aminoacid metabolism -!- 55785; PYP-like sensor domain PF01842;ACT domain;1.5e-06;codon 1-70 -!- PF00158;Sigma-54 interaction domain;4.1e-113;codon 206-420 "TIGR01199;HTH_fis: Helix-turn-helix domain, fis-type;3.1e-07;codon 465-506" GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK1320 tpx tpx yzzJ b1324 1386329 1386835 - (no change) JW1317 1390019 1390525 - e lipid hydroperoxide peroxidase E 12777775 -!- 14676195 -!- 96081923 -!- 97312505 -!- 10594830 -!- 9298646 Cytoplasmic 1.11.1.- 1QXH COG2077;Peroxiredoxin 52833; Thioredoxin-like PF00578;AhpC/TSA family;7.6e-47;codon 21-163 GO:0042597 periplasmic space GO:0006805 xenobiotic metabolism CDS ECK1321 ycjG ycjG ycjH b1325 1386954 1387919 + start codon change JW1318 1390644 1391609 + e L-Ala-D/L-Glu epimerase E 11747447 -!- 11747448 -!- 7499381 Cytoplasmic 51604; Enolase C-terminal domain-like -!- 54826; Enolase N-terminal domain-like PF02746;Mandelate racemase / muconate lactonizing en;4.6e-50;codon 11-126 -!- PF01188;Mandelate racemase / muconate lactonizing en;9e-84;codon 129-335 CDS ECK1322 mpaA mpaA ycjI b1326 1387894 1388682 - (no change) JW1319 1391584 1392372 - e murein peptide amidase A E 12511517 Cytoplasmic M14C family; hypothetical protein YcjI (Escherichia coli) COG2866;Predicted carboxypeptidase 53187; Zn-dependent exopeptidases PF00246;Zinc carboxypeptidase;9.7e-28;codon 23-252 CDS ECK1323 ymjC ymjC b4525 1388704 1388886 - new JW5960 1392394 1392576 - possibly split by frameshift (downstream ORF) pe predicted oxidoreductase pseudogene C 51735; NAD(P)-binding Rossmann-fold domains CDS ECK1324 ycjY ycjY b1327 1388957 1389889 - (no change) JW5804 1392647 1393579 - pe predicted hydrolase C S9B family; non-peptidase homologues COG1073;Hydrolases of the alpha/beta superfamily 53474; alpha/beta-Hydrolases CDS ECK1325 ycjZ ycjZ b1328 1390015 1390914 + (no change) JW1321 1393705 1394604 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;2.2e-21;codon 6-65 -!- PF03466;LysR substrate binding domain;2.4e-43;codon 89-298 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK1326 mppA mppA ynaH b1329 1391251 1392864 + start codon change JW1322 1394941 1396554 + t murein tripeptide (L-ala-gamma-D-glutamyl-meso-DAP) transporter subunit -!- periplasmic-binding component of ABC superfamily E 10438753 -!- 9495761 Periplasmic 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-30 537 "COG4166;ABC-type oligopeptide transport system, periplasmic component" 53850; Periplasmic binding protein-like II PF00496;Bacterial extracellular solute-binding prot;1e-83;codon 84-463 GO:0009274 cell wall (sensu Bacteria) -!- GO:0042597 periplasmic space GO:0000270 peptidoglycan metabolism CDS ECK1327 ynaI ynaI b1330 1392915 1393946 - (no change) JW1323 1396605 1397636 - pm conserved inner membrane protein C Integral Membrane Protein 4 4 in COG0668;Small-conductance mechanosensitive channel PF00924;Mechanosensitive ion channel;6.1e-79;codon 120-325 GO:0009274 cell wall (sensu Bacteria) CDS ECK1328 ynaJ ynaJ b1332 1395389 1395646 + (no change) JW1326 1399079 1399336 + pm predicted inner membrane protein C Integral Membrane Protein 2 2 CDS ECK1329 uspE uspE ydaA b1333 1395696 1396646 - (no change) JW1327 1399386 1400336 - cp stress-induced protein C 10493123 -!- 11849540 -!- 6292868 -!- 9600841 Cytoplasmic COG0589;Universal stress protein UspA and related nucleotide-binding proteins 52431; ETFP adenine nucleotide-binding domain-like PF00582;Universal stress protein family;1.5e-16;codon 3-146 -!- PF00582;Universal stress protein family;5.4e-11;codon 153-300 CDS ECK1330 fnr fnr frdB -!- nirA -!- nirR -!- ossA b1334 1396798 1397550 - (no change) JW1328 1400488 1401240 - r "DNA-binding transcriptional dual regulator, global regulator of anaerobic growth" E ############################################################################################################################################################################################################################################################### Cytoplasmic CRP acnA -!- adhE -!- ansB -!- arcA -!- aspA-dcuA -!- caiF -!- cydAB -!- cydDC -!- cyoABCDE -!- dcuB-fumB -!- dcuC -!- dmsABC -!- fdnGHI -!- fnr -!- focA-pflB -!- frdABCD -!- fumA -!- glpABC -!- glpTQ -!- hcp -!- hemA -!- hlyE -!- hmpA -!- hyfA COG0664;cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases 46785; Winged helix -!- 51206; cAMP-binding domain-like "PF00027;Cyclic nucleotide-binding domain;4.2e-20;codon 46-138 -!- PF00325;Bacterial regulatory proteins, crp famil;3.3e-15;codon 193-224" GO:0005737 cytoplasm GO:0009061 anaerobic respiration -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK1331 ogt ogt b1335 1397745 1398260 - (no change) JW1329 1401435 1401950 - e O-6-alkylguanine-DNA:cysteine-protein methyltransferase E 88067749 -!- 91161525 -!- 94252990 -!- 98125595 -!- 1520330 Cytoplasmic 2.1.1.63 COG0350;Methylated DNA-protein cysteine methyltransferase "46767; Methylated DNA-protein cysteine methyltransferase, C-terminal domain" PF02870;6-O-methylguanine DNA methyltransfera;3.2e-27;codon 3-84 -!- PF01035;6-O-methylguanine DNA methyltransfera;3.4e-59;codon 86-171 TIGR00589;ogt: methylated-DNA--protein-cysteine methyl;1.1e-59;codon 87-166 GO:0005737 cytoplasm GO:0006306 DNA methylation CDS ECK1332 abgT abgT ydaH b1336 1398271 1399797 - start codon change JW5822 1401961 1403487 - pt predicted cryptic aminobenzoyl-glutamate transporter cryptic C 9829935 -!- 2825131 -!- 7567469 Integral Membrane Protein 2.A.68; The p-Aminobenzoyl-glutamate Transporter (AbgT) Family 13 13 COG2978;Putative p-aminobenzoyl-glutamate transporter PF03806;AbgT putative transporter family;0;codon 16-509 TIGR00819;ydaH: AbgT transporter family;0;codon 1-510 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1333 abgB abgB ydaI b1337 1399834 1401279 - (no change) JW1331 1403524 1404969 - pe "predicted peptidase, aminobenzoyl-glutamate utilization protein" C 9829935 Cytoplasmic M20D family; non-peptidase homologues (aminobenzoyl-glutamate utilization protein B) COG1473;Metal-dependent amidase/aminoacylase/carboxypeptidase "53187; Zn-dependent exopeptidases -!- 55031; Carboxypeptidase G2, dimerisation domain" TIGR01891;amidohydrolases: amidohydrolase;1.3e-161;codon 19-433 GO:0016052 carbohydrate catabolism CDS ECK1334 abgA abgA ydaJ b1338 1401279 1402589 - start codon change JW5205 1404969 1406279 - pe "predicted peptidase, aminobenzoyl-glutamate utilization protein" C 9829935 Cytoplasmic 3.5.1.14 M20D family; unassigned peptidases (YdaJ protein) "53187; Zn-dependent exopeptidases -!- 55031; Carboxypeptidase G2, dimerisation domain" PF01546;Peptidase family M20/M25/M40;1.3e-36;codon 117-434 -!- PF07687;Peptidase dimerisation domain;0.0022;codon 222-332 TIGR01891;amidohydrolases: amidohydrolase;3.5e-141;codon 20-424 GO:0016052 carbohydrate catabolism CDS ECK1335 abgR abgR ydaK b1339 1402765 1403673 + (no change) JW1333 1406455 1407363 + pr predicted DNA-binding transcriptional regulator of p-aminobenzoyl-glutamate utilization C 9829935 Cytoplasmic LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;1.9e-19;codon 7-66 -!- PF03466;LysR substrate binding domain;8.5e-41;codon 90-298 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity misc_RNA ECK1336 isrA IS061 b4426 1403676 1403833 - (no change) JWR0233 1407366 1407523 - n small RNA E 12069726 CDS ECK1337 ydaL ydaL b1340 1404003 1404566 + (no change) JW1334 1407693 1408256 + o conserved protein C Cytoplasmic COG2840;Uncharacterized protein conserved in bacteria PF01713;Smr domain;2.3e-31;codon 88-169 CDS ECK1338 ydaM ydaM b1341 1404587 1405819 - start codon change JW5206 1408277 1409509 - pr "predicted diguanylate cyclase, GGDEF domain signalling protein" C Cytoplasmic COG2199;FOG: GGDEF domain 55785; PYP-like sensor domain PF00990;GGDEF domain;1.8e-68;codon 269-426 TIGR00229;sensory_box: PAS domain S-box;3.2e-12;codon 145-269 -!- TIGR00254;GGDEF: putative diguanylate cyclase (GGDE;7.7e-41;codon 269-430 CDS ECK1339 ydaN ydaN b1342 1406074 1407057 + (no change) JW1336 1409764 1410747 + pt predicted Zn(II) transporter C Integral Membrane Protein 2 2 in COG0598;Mg2+ and Co2+ transporters PF01544;CorA-like Mg2+ transporter protein;0.0003;codon 37-327 CDS ECK1340 dbpA dbpA rhlC b1343 1407535 1408908 + (no change) JW1337 1411225 1412598 + e "ATP-dependent RNA helicase, specific for 23S rRNA" member of DEAD box family E 15173385 -!- 91016823 -!- 94074560 -!- 9836593 -!- 11350034 -!- 9016593 Cytoplasmic COG0513;Superfamily II DNA and RNA helicases 52540; P-loop containing nucleotide triphosphate hydrolases PF00270;DEAD/DEAH box helicase;6.5e-67;codon 26-194 -!- PF00271;Helicase conserved C-terminal domain;5.8e-31;codon 260-336 -!- PF03880;DbpA RNA binding domain;2.6e-37;codon 372-457 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK1341 ydaO ydaO b1344 1409037 1409972 - (no change) JW1338 1412727 1413662 - pe predicted C32 tRNA thiolase C Cytoplasmic COG0037;Predicted ATPase of the PP-loop superfamily implicated in cell cycle control 52402; Adenine nucleotide alpha hydrolases CDS ECK1342 intR intR ydaP b1345 1410024 1411259 - (no change) JW1339 1413714 1414949 - h Rac prophage; integrase C Cytoplasmic cryptic prophage Rac COG0582;Integrase "47823; lambda integrase-like, N-terminal domain -!- 56349; DNA breaking-rejoining enzymes" PF00589;Phage integrase family;1.7e-14;codon 202-401 CDS ECK1343 ydaQ ydaQ xisR b1346 1411261 1411476 - start codon change JW5207 1414951 1415166 - h Rac prophage; conserved protein predicted Rac prophage excisionase C Cytoplasmic cryptic prophage Rac PF06806;Putative excisionase (DUF1233);0.00015;codon 9-79 CDS ECK1344 ydaC ydaC b1347 1411555 1411764 - (no change) JW1341 1415245 1415454 - h Rac prophage; predicted protein C Cytoplasmic cryptic prophage Rac PF06688;Protein of unknown function (DUF1187);2.1e-46;codon 2-62 CDS ECK1345 lar lar ydaB b1348 1411757 1411951 - (no change) JW5208 1415447 1415641 - h Rac prophage; restriction alleviation protein E 95386512 -!- 7476171 -!- 8244937 Cytoplasmic cryptic prophage Rac CDS ECK1346 recT recT b1349 1412008 1412817 - (no change) JW1343 1415698 1416507 - h Rac prophage; recombination and repair protein promotes DNA renaturation and strand exchange E 93106966 -!- 94064562 -!- 95058623 Cytoplasmic cryptic prophage Rac COG3723;Recombinational DNA repair protein (RecE pathway) PF03837;RecT family;4.9e-87;codon 52-267 "TIGR00616;rect: recombinase, phage RecT family;1.6e-186;codon 1-243" CDS ECK1347 recE recE rac -!- sbcA -!- rmuB b1350 1412810 1415410 - (no change) JW1344 1416500 1419100 - h "Rac prophage; exonuclease VIII, 5' -> 3' specific dsDNA exonuclease" E 21588244 -!- 89197781 -!- 92002343 -!- 95058623 -!- 2199308 -!- 8244937 Cytoplasmic cryptic prophage Rac 3.1.11.- PF06630;Enterobacterial exodeoxyribonuclease VIII;3.9e-135;codon 1-178 GO:0005737 cytoplasm GO:0006308 DNA catabolism -!- GO:0006281 DNA repair -!- GO:0006308 DNA catabolism CDS ECK1348 racC racC sbcA b1351 1415512 1415787 - (no change) JW1345 1419202 1419477 - h Rac prophage; predicted protein C 90236868 -!- 2649487 Cytoplasmic cryptic prophage Rac CDS ECK1349 ydaE ydaE b4526 1415862 1416032 - new JW1346 1419552 1419722 - pseudogene -!- prophage h Rac prophage; conserved protein C Cytoplasmic GO:0005737 cytoplasm CDS ECK1350 kil kil ydaD b1352 1416032 1416253 - start codon change JW1347 1419722 1419943 - h "Rac prophage; inhibitor of ftsZ, killing protein" responsible for the killing function of the Rac prophage -!- inhibitor of ftsZ E 11747448 -!- 96359361 -!- 7508908 Cytoplasmic cryptic prophage Rac CDS ECK1351 sieB sieB b1353 1416695 1417183 + start codon change JW5209 1420385 1420873 + h Rac prophage; phage superinfection exclusion protein C 7508908 Integral Membrane Protein cryptic prophage Rac 2 2 CDS ECK1352 ydaF ydaF b4527 1417180 1417335 - new JW1349 1420870 1421025 - h Rac prophage; predicted protein C Cytoplasmic GO:0005737 cytoplasm CDS ECK1353 ydaG ydaG b1355 1417346 1417480 - start codon change JW5210 1421036 1421170 - h Rac prophage; predicted protein C Cytoplasmic cryptic prophage Rac 46934; UBA-like CDS ECK1354 racR racR ydaR -!- rarC b1356 1417789 1418265 - (no change) JW1351 1421479 1421955 - h Rac prophage; predicted DNA-binding transcriptional regulator predicted repressor C Cytoplasmic cryptic prophage Rac CDS ECK1355 ydaS ydaS b1357 1418389 1418685 + (no change) JW1352 1422079 1422375 + h Rac prophage; predicted DNA-binding transcriptional regulator C Periplasmic cryptic prophage Rac "COG4197;Uncharacterized protein conserved in bacteria, prophage-related" CDS ECK1356 ydaT ydaT b1358 1418708 1419130 + (no change) JW1353 1422398 1422820 + h Rac prophage; predicted protein C Cytoplasmic cryptic prophage Rac PF06254;Protein of unknown function (DUF1019);2.8e-82;codon 1-140 CDS ECK1357 ydaU ydaU b1359 1419143 1420000 + (no change) JW1354 1422833 1423690 + h Rac prophage; conserved protein C Cytoplasmic cryptic prophage Rac COG3756;Uncharacterized protein conserved in bacteria PF07120;Protein of unknown function (DUF1376);5.1e-57;codon 22-106 CDS ECK1358 ydaV ydaV b1360 1420007 1420753 + (no change) JW1355 1423697 1424443 + h Rac prophage; predicted DNA replication protein C Cytoplasmic cryptic prophage Rac COG1484;DNA replication protein 52540; P-loop containing nucleotide triphosphate hydrolases PF01695;IstB-like ATP binding protein;2.4e-07;codon 52-229 CDS ECK1359 ydaW ydaW b1361 1420776 1421336 + start codon change JW5211 1424466 1425026 + h Rac prophage; predicted DNA-binding protein C Cytoplasmic cryptic prophage Rac 46785; Winged helix PF07789;Protein of unknown function (DUF1627);1e-14;codon 105-200 CDS ECK1360 rzpR rzpR ydaX b1362 1421369 1421668 + start codon change JW5212 1425059 1425358 + h Rac prophage; predicted defective peptidase similarity with murein endopeptidase C Cytoplasmic cryptic prophage Rac PF03245;Bacteriophage lysis protein;2.1e-48;codon 1-100 CDS ECK1361 rzoR rzoR b4528 1421424 1421609 + new JW5213 1425114 1425299 + h Rac prophage; predicted lipoprotein C Outer membrane Lipoprotein GO:0009279 outer membrane (sensu Gram-negative Bacteria) CDS ECK1362 trkG trkG b1363 1421806 1423263 + (no change) JW1358 1425496 1426953 + h Rac prophage; potassium transporter subunit E 91100357 Integral Membrane Protein cryptic prophage Rac 11 11 in "COG0168;Trk-type K+ transport systems, membrane components" PF02386;Cation transport protein;8.4e-115;codon 155-483 "TIGR00933;2a38: potassium uptake protein, TrkH family;7.3e-186;codon 86-468" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1363 ynaK ynaK b1365 1423401 1423664 + (no change) JW1359 1427091 1427354 + h Rac prophage; conserved protein C Cytoplasmic cryptic prophage Rac COG1475;Predicted transcriptional regulators PF02195;ParB-like nuclease domain;3.5e-21;codon 8-87 CDS ECK1364 ydaY ydaY b1366 1423645 1424004 + (no change) JW1360 1427335 1427694 + h Rac prophage; predicted protein C Cytoplasmic cryptic prophage Rac CDS ECK1365 ynaA ynaA b1368 1424478 1425506 + (no change) JW1361 1428168 1429196 + h Rac prophage; predicted tail protein C Cytoplasmic cryptic prophage Rac ECK1366 lomR lomR b4570 1425482 1425637 + "pseudogene; interrupted by IS5 and N-ter deletion -!- join(1425419..1425622,1426823..1427008)" JW5884+JW5904 1429172 1430698 + ancestral gene su Rac prophage; predicted protein (pseudogene) C Cytoplasmic cryptic prophage Rac COG3637;Opacity protein and related surface antigens 56925; Outer membrane protein CDS ECK1366 lomR lomR_2 b1371 1426838 1427008 + pseudogene fragment -!- start codon change JW5904 1430528 1430698 + "pseudogene -!- change 5' to 1426838, disrupted by IS (b1370 = IS5D), could be fused with b1369" su "Rac prophage; predicted protein, C-ter fragment (pseudogene)" C 2144037 -!- 6221115 cryptic prophage Rac COG3637;Opacity protein and related surface antigens 56925; OMPA-like PF06316;Enterobacterial Ail/Lom protein;5.4e-09;codon 1-153 CDS ECK1366 lomR lomR_1 b1369 1425482 1425637 + pseudogene fragment -!- (no change) JW5884 1429172 1429327 + "pseudogene -!- disrupted by IS (b1370 = IS5D), could be fused with b1371 -!- GeneMark can predict -!- similar to putative outer membrane protein of prophage of CFT073" su "Rac prophage; predicted protein, N-ter fragment (pseudogene)" C Cytoplasmic cryptic prophage Rac COG3637;Opacity protein and related surface antigens 56925; Outer membrane protein CDS ECK1367 stfR stfR ynaB b1372 1427073 1430435 + start codon change JW1366 1430763 1434125 + h Rac prophage; predicted tail fiber protein C Cytoplasmic cryptic prophage Rac "49464; Carboxypeptidase D, a regulatory domain" PF03406;Phage tail fibre repeat;4.3e-19;464-507 -!- PF07484;Phage Tail Collar Domain;1.1e-22;909-956 -!- 6 of PF03335;Phage tail fibre repeat: 1.1;972-985 -!- 0.019;1004-1017 -!- 1.1;1018-1031 -!- 0.042;1057-1070 -!- 0.67;1071-1084 -!- 0.61;1089-1102 CDS ECK1368 tfaR tfaR ynaC b1373 1430435 1431010 + (no change) JW1367 1434125 1434700 + h Rac prophage; predicted tail fiber assembly protein C 14727089 Cytoplasmic cryptic prophage Rac PF02413;Caudovirales tail fibre assembly protein;8.1e-65;codon 53-191 CDS ECK1369 pinR pinR ynaD b1374 1431108 1431698 - (no change) JW1368 1434798 1435388 - h Rac prophage; predicted site-specific recombinase C Cytoplasmic cryptic prophage Rac "COG1961;Site-specific recombinases, DNA invertase Pin homologs" 46689; Homeodomain-like -!- 53041; Resolvase-like "PF00239;Resolvase, N terminal domain;8.5e-60;codon 4-145 -!- PF02796;Helix-turn-helix domain of resolvase;7e-12;codon 147-191" CDS ECK1370 ynaE ynaE b1375 1432015 1432281 - (no change) JW1369 1435705 1435971 - h Rac prophage; predicted DNA-binding transcriptional regulator C Cytoplasmic cryptic prophage Rac CDS ECK1371 uspF uspF ynaF -!- yzzL -!- up03 b1376 1433209 1433643 - start codon change JW1370 1436899 1437333 - f "stress-induced protein, ATP-binding protein" E 12732303 -!- 12381839 -!- 11849540 -!- 9298646 Cytoplasmic monomeric multimer; UspF homodimer (b1376) 52431; ETFP adenine nucleotide-binding domain-like PF00582;Universal stress protein family;1.1e-19;codon 25-168 CDS ECK1372 ompN ompN yaaG -!- ynaG b1377 1433784 1434917 - (no change) JW1371 1437474 1438607 - t "outer membrane pore protein N, non-specific" E 9642192 Outer Membrane B-barrel protein 1-21 377 COG3203;Outer membrane protein (porin) 56935; Porins PF00267;Gram-negative porin;2.5e-215;codon 27-377 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) misc_RNA ECK1373 micC tke8 IS063 b4427 1435145 1435252 + (no change) JWR0234 1438835 1438942 + n regulatory sRNA E 15466019 -!- 12069726 ompC CDS ECK1374 ydbK ydbK nifJ b1378 1435284 1438808 - (no change) JW1372 1438974 1442498 - pc fused predicted pyruvate-flavodoxin oxidoreductase: conserved protein -!- conserved protein -!- FeS binding protein C 9025293 Cytoplasmic regulated by attenuation (ydbK) fused predicted pyruvate-flavodoxin oxidoreductase: unknown function (aa1-403) -!- unknown function (aa418-758) -!- FeS binding protein (aa817-1174) "COG0674;Pyruvate and related 2-oxoacid :ferredoxin oxidoreductases, alpha subunit -!- COG1014;Pyruvate and related 2-oxoacid :ferredoxin oxidoreductases, gamma subunit -!- COG1013;Pyruvate and related 2-oxoacid :ferredoxin oxidoreductases, beta subunit" "52518; Thiamin diphosphate-binding fold (THDP-binding) (2) -!- 52922; Transketolase C-terminal domain-like -!- 53323; Pyruvate-ferredoxin oxidoreductase, PFOR, domain III -!- 54862; 4Fe-4S ferredoxins" "PF01855;Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-binding domain;2.5e-122;codon 12-244 -!- PF01558;Pyruvate ferredoxin/flavodoxin oxidoreductase;2.7e-82;codon 426-610 -!- PF00037;4Fe-4S binding domain;5.7e-06;codon 682-705 -!- PF00037;4Fe-4S binding domain;7.3e-05;codon 738-761 -!- PF02775;Thiamine pyrophosphate enzyme, C-terminal TPP binding domain;1.5e-91;codon 817-1074" TIGR02176;pyruv_ox_red: pyruvate:ferredoxin (flavo;0;codon 1-1166 CDS ECK1375 ydbJ ydbJ b4529 1439082 1439348 + new JW5215 1442772 1443038 + o predicted protein C Outer membrane Lipoprotein GO:0009279 outer membrane (sensu Gram-negative Bacteria) CDS ECK1376 hslJ hslJ ydbI b1379 1439345 1439767 - (no change) JW1374 1443035 1443457 - f heat-inducible protein involved in novobiocin resistance -!- CysR regulated -!- overexpression causes abnormal biofilm architecture E 12892888 -!- 8349564 -!- 9025293 Outer membrane Lipoprotein COG3187;Heat shock protein PF03724;Domain of unknown function (306);1.4e-33;codon 29-126 GO:0009266 response to temperature CDS ECK1377 ldhA ldhA hslF -!- hslI -!- htpH b1380 1439878 1440867 - (no change) JW1375 1443568 1444557 - e "fermentative D-lactate dehydrogenase, NAD-dependent" E 4297266 -!- 89123040 -!- 90198524 -!- 8349564 -!- 9025293 Cytoplasmic 1.1.1.28 COG1052;Lactate dehydrogenase and related dehydrogenases 51735; NAD(P)-binding Rossmann-fold domains -!- 52283; Formate/glycerate dehydrogenase catalytic domain-like PF00389;D-isomer specific 2-hydroxyacid dehydrog;5.1e-23;codon 3-99 -!- PF02826;D-isomer specific 2-hydroxyacid dehydrog;2.2e-92;codon 105-295 GO:0006113 fermentation CDS ECK1378 ydbH ydbH b1381 1441075 1443714 + (no change) JW1376 1444765 1447404 + o predicted protein C Membrane Anchored CDS ECK1379 ynbE ynbE b1382 1443711 1443896 + (no change) JW1377 1447401 1447586 + lp predicted lipoprotein C Outer membrane Lipoprotein CDS ECK1380 ydbL ydbL b1383 1443904 1444230 + start codon change JW5216 1447594 1447920 + o conserved protein C 1-23 COG3784;Uncharacterized protein conserved in bacteria PF07027;Protein of unknown function (DUF1318);2.7e-63;codon 16-109 CDS ECK1381 feaR feaR maoB -!- maoR -!- maoX -!- ydbM b1384 1444402 1445307 - (no change) JW1379 1448092 1448997 - r DNA-binding transcriptional dual regulator activator of 2-phenylethylamine catabolism E 97195795 -!- 8631685 -!- 9109378 Cytoplasmic AraC/XylS tynA -!- fadB COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like -!- 51215; Regulatory protein AraC PF00165;Bacterial regulatory helix-turn-helix protei;0.5;codon 200-246 -!- PF00165;Bacterial regulatory helix-turn-helix protei;2e-11;codon 253-298 GO:0005737 cytoplasm GO:0009063 amino acid catabolism -!- GO:0009310 amine catabolism -!- GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1382 feaB feaB padA -!- ydbG b1385 1445543 1447042 + start codon change JW1380 1449233 1450732 + e phenylacetaldehyde dehydrogenase E 96213037 -!- 97263463 -!- 9043126 1.2.1.39 monomeric multimer; putative succinate-semialdehyde dehydrogenase / putative aminobutyraldehyde dehydrogenase / phenylacetaldehyde dehydrogenase (b1385) 53720; ALDH-like PF00171;Aldehyde dehydrogenase family;2.2e-184;codon 32-500 GO:0009310 amine catabolism -!- GO:0009435 nicotinamide adenine dinucleotide biosynthesis CDS ECK1383 tynA tynA feaA -!- maoA b1386 1447100 1449373 - (no change) JW1381 1450790 1453063 - e "tyramine oxidase, copper-requiring" E 94231582 -!- 95284034 -!- 95352083 -!- 96213037 -!- 10387067 -!- 10576737 -!- 8591028 -!- 9043126 -!- 9048544 -!- 9109378 -!- 9748275 -!- 8631685 Periplasmic 1.4.3.6 monomeric multimer; phenylethylamine oxidase / aminoacetone oxidase / amine oxidase (Cu containing) (b1386) 757 regulated by attenuation (tynA) 1DYU COG3733;Cu2+-containing amine oxidase "49998; Copper amine oxidase, domain 3 (catalytic) -!- 54416; Copper amine oxidase, domains 1 and 2 -!- 55383; Copper amine oxidase, domain N" "PF07833;Copper amine oxidase N-terminal domain;2.7e-35;32-119 -!- PF02727;Copper amine oxidase, N2 domain;3e-38;124-210 -!- PF02728;Copper amine oxidase, N3 domain;5.5e-41;215-317 -!- PF01179;Copper amine oxidase, enzyme domain;6.9e-262;331-757" GO:0042597 periplasmic space GO:0009063 amino acid catabolism -!- GO:0009310 amine catabolism CDS ECK1384 maoC maoC paaZ -!- ydbN b1387 1449621 1451666 - (no change) JW1382 1453311 1455356 - e fused aldehyde dehydrogenase -!- enoyl-CoA hydratase involved in aerobic catabolism of phenylacetic acid E 12846838 -!- 12949091 -!- 9748275 -!- 10766858 fused: aldehyde dehydrogenase (aa1-506) -!- enoyl CoA dehydtratase (aa519-681) COG1012;NAD-dependent aldehyde dehydrogenases -!- COG2030;Acyl dehydratase 53720; ALDH-like PF00171;Aldehyde dehydrogenase family;2.7e-16;codon 12-503 -!- PF01575;MaoC like domain;3.7e-43;codon 533-652 TIGR02278;PaaN-DH: phenylacetic acid degradation prote;0;codon 4-674 GO:0016052 carbohydrate catabolism CDS ECK1385 paaA paaA ydbO b1388 1451951 1452880 + (no change) JW1383 1455641 1456570 + pe predicted multicomponent oxygenase/reductase subunit for phenylacetic acid degradation C 12846838 -!- 9748275 -!- 10766858 Cytoplasmic heteromultimer; putative phenylacetate-CoA oxygenase (b1388-b1389-b1390-b1391-b1392) COG3396;Uncharacterized conserved protein 47240; Ferritin-like PF05138;Phenylacetic acid catabolic protein;1.3e-198;codon 1-291 "TIGR02156;PA_CoA_Oxy1: phenylacetate-CoA oxygenase,;2.4e-218;codon 7-295" GO:0016052 carbohydrate catabolism CDS ECK1386 paaB paaB ynbF b1389 1452892 1453179 + (no change) JW1384 1456582 1456869 + pe predicted multicomponent oxygenase/reductase subunit for phenylacetic acid degradation C 12846838 -!- 9748275 Cytoplasmic heteromultimer; putative phenylacetate-CoA oxygenase (b1388-b1389-b1390-b1391-b1392) COG3460;Uncharacterized enzyme of phenylacetate metabolism PF06243;Phenylacetic acid degradation B;2.8e-71;codon 6-95 "TIGR02157;PA_CoA_Oxy2: phenylacetate-CoA oxygenase,;2.5e-65;codon 6-95" GO:0016052 carbohydrate catabolism CDS ECK1387 paaC paaC ydbP b1390 1453188 1453934 + (no change) JW1385 1456878 1457624 + pe predicted multicomponent oxygenase/reductase subunit for phenylacetic acid degradation C 12846838 -!- 9748275 Cytoplasmic heteromultimer; putative phenylacetate-CoA oxygenase (b1388-b1389-b1390-b1391-b1392) 1OTK COG3396;Uncharacterized conserved protein PF05138;Phenylacetic acid catabolic protein;3.5e-140;codon 1-248 "TIGR02158;PA_CoA_Oxy3: phenylacetate-CoA oxygenase,;8.9e-171;codon 11-248" GO:0016052 carbohydrate catabolism CDS ECK1388 paaD paaD ydbQ b1391 1453949 1454446 + start codon change JW5217 1457639 1458136 + pe predicted multicomponent oxygenase/reductase subunit for phenylacetic acid degradation C 12846838 -!- 9748275 Cytoplasmic heteromultimer; putative phenylacetate-CoA oxygenase (b1388-b1389-b1390-b1391-b1392) COG2151;Predicted metal-sulfur cluster biosynthetic enzyme PF01883;Domain of unknown function DUF59;2.3e-31;codon 13-87 "TIGR02159;PA_CoA_Oxy4: phenylacetate-CoA oxygenase,;8.2e-114;codon 24-167" GO:0016052 carbohydrate catabolism CDS ECK1389 paaE paaE ydbR b1392 1454454 1455524 + (no change) JW1387 1458144 1459214 + pe predicted multicomponent oxygenase/reductase subunit for phenylacetic acid degradation "first step of pathway -!- cofactors NAD(P), FAD, and ferrodoxin" C 12846838 -!- 9748275 heteromultimer; putative phenylacetate-CoA oxygenase (b1388-b1389-b1390-b1391-b1392) COG1018;Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 "52343; Ferredoxin reductase-like, C-terminal NADP-linked domain -!- 54292; 2Fe-2S ferredoxin-like -!- 63380; Riboflavin synthase domain-like" PF00970;Oxidoreductase FAD-binding domain;5.9e-18;codon 6-105 -!- PF00175;Oxidoreductase NAD-binding domain;3.1e-11;codon 112-228 -!- PF00111;2Fe-2S iron-sulfur cluster binding doma;1.5e-23;codon 266-343 TIGR02160;PA_CoA_Oxy5: phenylacetate-CoA oxygenase/;1.1e-278;codon 4-351 GO:0016052 carbohydrate catabolism CDS ECK1390 paaF paaF ydbS -!- ydbR b1393 1455521 1456288 + (no change) JW1388 1459211 1459978 + e enoyl-CoA hydratase-isomerase E 12846838 -!- 9748275 -!- 10766858 Cytoplasmic 4.2.1.17 COG1024;Enoyl-CoA hydratase/carnithine racemase 52096; ClpP/crotonase PF00378;Enoyl-CoA hydratase/isomerase family;7.3e-67;codon 13-179 GO:0016052 carbohydrate catabolism CDS ECK1391 paaG paaG ydbT b1394 1456288 1457076 + (no change) JW1389 1459978 1460766 + e acyl-CoA hydratase E 12846838 -!- 9748275 -!- 10766858 4.2.1.17 COG1024;Enoyl-CoA hydratase/carnithine racemase 52096; ClpP/crotonase PF00378;Enoyl-CoA hydratase/isomerase family;2.9e-54;codon 14-186 TIGR02280;PaaB1: phenylacetate degradation probable en;4.1e-229;codon 5-262 GO:0016052 carbohydrate catabolism CDS ECK1392 paaH paaH ydbU -!- hbdH b1395 1457078 1458505 + (no change) JW1390 1460768 1462195 + e 3-hydroxybutyryl-CoA dehydrogenase E 12846838 -!- 9748275 -!- 10766858 Periplasmic 1.1.1.157 COG1250;3-hydroxyacyl-CoA dehydrogenase 48179; 6-phosphogluconate dehydrogenase C-terminal domain-like -!- 51735; NAD(P)-binding Rossmann-fold domains "PF02737;3-hydroxyacyl-CoA dehydrogenase, NAD binding;1.1e-72;codon 3-186 -!- PF00725;3-hydroxyacyl-CoA dehydrogenase, C-terminal;8.4e-45;codon 188-285 -!- PF00725;3-hydroxyacyl-CoA dehydrogenase, C-terminal;7.4e-11;codon 387-475" TIGR02279;PaaC-3OHAcCoADH: 3-hydroxyacyl-CoA de;0;codon 1-475 GO:0016052 carbohydrate catabolism CDS ECK1393 paaI paaI ydbV b1396 1458495 1458917 + (no change) JW1391 1462185 1462607 + pe predicted thioesterase not essential for phenylacetic acid metabolism C 12846838 -!- 9748275 Cytoplasmic 1PSU "COG2050;Uncharacterized protein, possibly involved in aromatic compounds catabolism" 54637; Thioesterase/thiol ester dehydrase-isomerase PF03061;Thioesterase superfamily;1.5e-21;codon 48-123 TIGR00369;unchar_dom_1: uncharacterized domain;7.9e-51;codon 17-131 -!- TIGR02286;PaaD: phenylacetic acid degradation prot;1.6e-82;codon 19-132 GO:0016052 carbohydrate catabolism CDS ECK1394 paaJ paaJ ydbW b1397 1458917 1460122 + (no change) JW1392 1462607 1463812 + pe predicted beta-ketoadipyl CoA thiolase phenylacetate degradation C 12846838 -!- 9748275 -!- 10766858 Cytoplasmic COG0183;Acetyl-CoA acetyltransferase 53901; Thiolase-like "PF00108;Thiolase, N-terminal domain;1.6e-97;codon 1-269 -!- PF02803;Thiolase, C-terminal domain;1.2e-64;codon 276-400" TIGR01930;AcCoA-C-Actrans: acetyl-CoA acyltrans;6e-181;codon 6-399 GO:0016052 carbohydrate catabolism CDS ECK1395 paaK paaK b1398 1460149 1461462 + (no change) JW5218 1463839 1465152 + e phenylacetyl-CoA ligase E 12846838 -!- 9748275 -!- 10766858 Cytoplasmic 6.2.1.30 COG1541;Coenzyme F390 synthetase 56801; Firefly luciferase-like TIGR02155;PA_CoA_ligase: phenylacetate-CoA ligase;0;codon 11-432 GO:0016052 carbohydrate catabolism CDS ECK1396 paaX paaX ydbY b1399 1461563 1462513 + (no change) JW1394 1465253 1466203 + r "DNA-binding transcriptional repressor of phenylacetic acid degradation, aryl-CoA responsive" E 12846838 -!- 20229831 -!- 9748275 Cytoplasmic paaABCDEFGHIJK -!- paaZ COG3327;Phenylacetic acid-responsive transcriptional repressor 46785; Winged helix PF07848;PaaX-like protein;3.9e-146;codon 18-282 TIGR02277;PaaX_trns_reg: phenylacetic acid degrad;1.8e-190;codon 21-303 GO:0016052 carbohydrate catabolism CDS ECK1397 paaY paaY ydbZ b1400 1462495 1463085 + (no change) JW1395 1466185 1466775 + pe predicted hexapeptide repeat acetyltransferase phenylacetic acid degradation protein C 12846838 -!- 9748275 Cytoplasmic "COG0663;Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily" 51161; Trimeric LpxA-like enzymes 4 of PF00132;Bacterial transferase hexapeptide (three repeats): 0.4;codon 28-45 -!- 35;codon 49-66 -!- 0.59;codon 88-105 -!- 1;codon 106-123 TIGR02287;PaaY: phenylacetic acid degradation protein;4.2e-177;codon 3-195 ECK1398 ydbA ybda b4492 1463416 1472037 + "pseudogene; interrupted by IS2 and IS30 -!- join(1463416..1465933,1467270..1467319,1468543..1472037)" JW5802+JW1402 1467106 1475727 + ancestral gene su predicted outer membrane protein (pseudogene) C Outer Membrane B-barrel protein PF05594;Haemagluttinin repeat;1.6;aa 218-285 -!- PF05594;Haemagluttinin repeat;1.5;aa 323-383 -!- PF05594;Haemagluttinin repeat;1.7;aa 421-481 -!- PF00665;Integrase core;2.8e-33;aa 1537-1687 -!- PF03797;Autotransporter beta-domain;1.1e-35;aa 2585-2852 CDS ECK1398 ydbA ydbA_2 b1405 1468714 1472037 + pseudogene fragment -!- (no change) JW1402 1472404 1475727 + pseudogene su "predicted outer membrane protein, C-ter fragment (pseudogene)" C CDS ECK1398 ydbA ydbA_1 b1401 1463416 1465974 + pseudogene fragment -!- (no change) JW5802 1467106 1469664 + pseudogene su "predicted outer membrane protein, N-ter fragment (pseudogene)" C CDS ECK1399 ydbC ydbC b1406 1472245 1473105 + (no change) JW1403 1475935 1476795 + pe "predicted oxidoreductase, NAD(P)-binding" C Cytoplasmic regulated by attenuation (ydbC-ydbD) COG0667;Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) 51430; NAD(P)-linked oxidoreductase PF00248;Aldo/keto reductase family;3.3e-70;codon 14-285 CDS ECK1400 ydbD ydbD b1407 1473168 1475474 + start codon change JW5221 1476858 1479164 + o predicted protein C Periplasmic CDS ECK1401 ynbA ynbA b1408 1475645 1476250 + start codon change JW1405 1479335 1479940 + pm predicted inner membrane protein C Integral Membrane Protein 6 5 in PF01066;CDP-alcohol phosphatidyltransferase;2.3e-22;codon 61-199 CDS ECK1402 ynbB ynbB b1409 1476250 1477146 + (no change) JW1406 1479940 1480836 + pe predicted CDP-diglyceride synthase C Integral Membrane Protein 8 9 out COG4589;Predicted CDP-diglyceride synthetase/phosphatidate cytidylyltransferase PF01148;Cytidylyltransferase family;5.6e-92;codon 36-296 "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK1403 ynbC ynbC b1410 1477162 1478919 + (no change) JW1407 1480852 1482609 + pe predicted hydrolase C Cytoplasmic S33 family; non-peptidase homologues (YnbC protein) COG2267;Lysophospholipase -!- COG0500;SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases -!- 53474; alpha/beta-Hydrolases CDS ECK1404 ynbD ynbD b1411 1478933 1480225 + (no change) JW1408 1482623 1483915 + pe "predicted phosphatase, inner membrane protein" C Integral Membrane Protein 9 8 COG0671;Membrane-associated phospholipid phosphatase -!- COG2453;Predicted protein-tyrosine phosphatase 52799; (Phosphotyrosine protein) phosphatases II "PF01569;PAP2 superfamily;3.4e-19;codon 69-201 -!- PF00782;Dual specificity phosphatase, catalytic doma;4e-42;codon 298-430" CDS ECK1405 azoR azoR azoR -!- acpD b1412 1480279 1480884 - (no change) JW1409 1483969 1484574 - e "NADH-azoreductase, FMN-dependent" E 21588205 -!- 90368607 -!- 7899078 3.1.4.14 regulated by attenuation (acpD) COG1182;Acyl carrier protein phosphodiesterase 52218; Flavoproteins PF02525;Flavodoxin-like fold;5.8e-62;codon 2-196 CDS ECK1406 hrpA hrpA moc b1413 1481142 1484987 + (no change) JW5905 1484832 1488677 + e ATP-dependent helicase member of DEAD box family E 95206938 Cytoplasmic 52540; P-loop containing nucleotide triphosphate hydrolases PF00270;DEAD/DEAH box helicase;3.2e-07;aa 71-218 -!- PF00271;Helicase conserved C-terminal domain;7e-12;aa 293-385 -!- PF04408;Helicase associated domain (HA2);2.1e-29;aa 445-540 -!- PF07717;Domain of unknown function (DUF1605);1.5e-24;aa 580-680 TIGR01967;DEAH_box_HrpA: ATP-dependent helicase H;0;codon 1-1278 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK1407 ydcF ydcF b1414 1485259 1486059 + (no change) JW1411 1488949 1489749 + o conserved protein C Cytoplasmic COG1434;Uncharacterized conserved protein PF02698;DUF218 domain;4e-29;codon 36-219 CDS ECK1408 aldA aldA ald b1415 1486256 1487695 + (no change) JW1412 1489946 1491385 + e "aldehyde dehydrogenase A, NAD-linked" E 92011371 -!- 9298646 1.2.1.22 monomeric multimer; putative succinate-semialdehyde dehydrogenase / aldehyde dehydrogenase (b1415) COG1012;NAD-dependent aldehyde dehydrogenases 53720; ALDH-like PF00171;Aldehyde dehydrogenase family;3.6e-248;codon 15-479 GO:0016052 carbohydrate catabolism -!- GO:0009438 methylglyoxal metabolism -!- GO:0006113 fermentation -!- GO:0009441 glycolate metabolism ECK1409 gapC gapC b4493 1487737 1488737 - pseudogene; interrupted by frameshift and in-frame stop JW5906+JW1413 1491427 1492427 - ancestral gene su glyceraldehyde-3-phosphate dehydrogenase C (pseudogene) C Cytoplasmic "PF02800;Glyceraldehyde 3-phosphate dehydrogenase, C-;7.6e-51;codon 35-183" CDS ECK1409 gapC gapC_1 b1417 1487985 1488737 - pseudogene fragment -!- start codon change JW5906 1491675 1492427 - "pseudogene, inner stop codon" su "glyceraldehyde-3-phosphate dehydrogenase C, C-ter fragment (pseudogene)" E 96233136 1.2.1.12 CDS ECK1409 gapC gapC_2 b1416 1487737 1487988 - pseudogene fragment -!- (no change) JW1413 1491427 1491678 - "pseudogene, frameshift" su "glyceraldehyde-3-phosphate dehydrogenase C, N-ter fragment (pseudogene)" E 96233136 1.2.1.12 CDS ECK1410 cybB cybB b1418 1488926 1489456 + start codon change JW5224 1492616 1493146 + c cytochrome b561 E 89313673 -!- 92104149 -!- 92112945 -!- 2836696 -!- 3510204 Integral Membrane Protein 4 4 in COG3038;Cytochrome B561 PF01292;Cytochrome b561 family;7.2e-77;codon 14-185 GO:0017004 cytochrome biogenesis GO:0009055 electron carrier activity CDS ECK1411 ydcA ydcA b1419 1489701 1489874 + (no change) JW1416 1493391 1493564 + o predicted protein C Periplasmic CDS ECK1412 hokB hokB ydcB b4428 1489946 1490095 - (no change) JW5225 1493636 1493785 - f "toxic polypeptide, small" E 11014799 -!- 99291074 Membrane Anchored PF01848;Hok/gef family;3.5e-27;codon 1-49 CDS ECK1413 mokB mokB b1420 1489986 1490153 - (no change) JW5882 1493676 1493843 - mokB gene r regulatory peptide translation enables hokB expression E 9689094 Cytoplasmic misc_RNA ECK1414 sokB sokB b4429 1490143 1490195 + (no change) JWR0235 1493833 1493885 + n "regulatory, antisense sRNA" blocks mokB and hence hokB translation E 11014799 CDS ECK1415 trg trg b1421 1490494 1492134 + (no change) JW1417 1494184 1495824 + r "methyl-accepting chemotaxis protein III, ribose and galactose sensor receptor" flagellar regulon E 90008892 -!- 92390356 -!- 93259131 -!- 6374654 Integral Membrane Protein heteromultimer; MCP-III (b1421-b1887-b1888) 2 2 in COG0840;Methyl-accepting chemotaxis protein "47170; Aspartate receptor, ligand-binding domain" PF02203;Tar ligand binding domain homologue;1.6e-53;codon 47-185 -!- PF00672;HAMP domain;2.7e-16;codon 204-273 -!- PF00015;Methyl-accepting chemotaxis protein (MCP) s;2.5e-121;codon 304-526 GO:0019866 inner membrane GO:0042330 taxis CDS ECK1416 ydcI ydcI b1422 1492172 1493095 - start codon change JW5226 1495862 1496785 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic LysR regulated by attenuation (ydcI) COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II "PF00126;HTH_1: transcriptional regulator, LysR famil;1.9e-20;codon 13-72 -!- PF03466;LysR_substrate: LysR substrate binding domai;7.1e-35;codon 96-306" GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK1417 ydcJ ydcJ b1423 1493312 1494655 + (no change) JW1419 1497002 1498345 + o conserved protein C Cytoplasmic COG5383;Uncharacterized protein conserved in bacteria PF07063;Protein of unknown function (DUF1338);1.5e-78;codon 333-444 CDS ECK1418 mdoD mdoD ydcG -!- opgD -!- yzzZ b1424 1494910 1496535 + start codon change JW1420 1498600 1500225 + e "glucan biosynthesis protein, periplasmic" "length determining, osmoregulated" E 15175282 -!- 9298646 Periplasmic 1-32 541 "PF04349;Periplasmic glucan biosynthesis protein, Mdo;2.2e-168;codon 45-539" TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.0016;codon 1-32 GO:0042597 periplasmic space GO:0006970 response to osmotic stress CDS ECK1419 ydcH ydcH b1426 1496675 1496899 + start codon change JW5823 1500365 1500589 + o predicted protein C Cytoplasmic PF04325;Protein of unknown function (DUF465);4.2e-17;codon 1-49 CDS ECK1420 rimL rimL b1427 1496962 1497501 + (no change) JW1423 1500652 1501191 + e ribosomal-protein-L7/L12-serine acetyltransferase E 89364711 Cytoplasmic 2.3.1.- regulated by attenuation (rimL) "COG1670;Acetyltransferases, including N-acetylases of ribosomal proteins" 55729; Acyl-CoA N-acyltransferases (Nat) PF00583;Acetyltransferase (GNAT) family;2.4e-14;codon 70-151 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006464 protein modification CDS ECK1421 ydcK ydcK b1428 1497493 1498473 - (no change) JW1424 1501183 1502163 - pe predicted enzyme C Cytoplasmic 51161; Trimeric LpxA-like enzymes 6 of PF00132;Bacterial transferase hexapeptide (three repeats);40;codon 71-88 -!- 13;codon 100-117 -!- 28;codon 179-196 -!- 7.8;codon 237-254 -!- 1.1e+02;codon 262-279 -!- 13;codon 280-297 CDS ECK1422 tehA tehA b1429 1498597 1499589 + (no change) JW1425 1502287 1503279 + t potassium-tellurite ethidium and proflavin transporter E 94222856 -!- 2060788 Integral Membrane Protein 2.A.16; The Telurite-resistance/Dicarboxylate Transporter (TDT) Family 10 8 in COG1275;Tellurite resistance protein and related permeases PF03595;C4-dicarboxylate transporter/malic aci;5.1e-88;codon 11-270 TIGR00816;tdt: C4-dicarboxylate transporter/malic acid;1.9e-172;codon 9-312 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK1423 tehB tehB b1430 1499586 1500179 + (no change) JW1426 1503276 1503869 + pe predicted S-adenosyl-L-methionine-dependent methyltransferase multidrug resistance C 20507823 -!- 94222856 -!- 2060788 Cytoplasmic COG0500;SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases PF03848;Tellurite resistance protein TehB;1.3e-161;codon 1-193 TIGR00477;tehB: tellurite resistance protein TehB;1.6e-156;codon 1-196 GO:0042493 response to drug CDS ECK1424 ydcL ydcL b1431 1500481 1501149 + (no change) JW1427 1504171 1504839 + lp predicted lipoprotein C Outer membrane Lipoprotein regulated by attenuation (ydcL) ECK1425 yncK yncK b4578 1501167 1501673 - pseudogene; interrupted by in-frame stop -!- join(1501167..1501673) JW5227+JW5961 1504857 1505363 - ancestral gene su predicted transposase (pseudogene) C PF01797; Transposase 17; 1.6e-12; codon82-149 CDS ECK1425 yncK yncK_2 b4531 1501386 1501673 - pseudogene fragment -!- new JW5961 1505076 1505363 - pseudogene su "predicted transposase, C-ter fragment (pseudogene)" C PF01797;Transposase_17: Transposase IS200 like;1.2e-11;codon 27-94 CDS ECK1425 yncK yncK_1 b4530 1501167 1501334 - pseudogene fragment -!- new JW5227 1504857 1505024 - pseudogene su "predicted transposase, N-ter fragment (pseudogene)" C CDS ECK1426 ydcM ydcM b1432 1501681 1502889 + (no change) JW5228 1505371 1506579 + ph predicted transposase C Cytoplasmic COG0675;Transposase and inactivated derivatives PF01385;Probable transposase;1.3e-144;codon 8-277 -!- PF07282;Putative transposase DNA-binding domai;1.6e-33;codon 304-373 "TIGR01766;tspaseT_teng_C: transposase, IS605 Orf;2.7e-10;codon 242-331" CDS ECK1427 ydcO ydcO b1433 1502929 1504104 - start codon change JW5229 1506619 1507794 - pt predicted benzoate transporter C Integral Membrane Protein 13 10 in PF00860;xan_ur_permease: Xanthine/uracil permeases;0.016;codon 21-366 TIGR00843;benE: benzoate transporter;2.8e-293;codon 1-382 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1428 ydcN ydcN b1434 1504196 1504732 + (no change) JW1430 1507886 1508422 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic Unclass COG1396;Predicted transcriptional regulators 47413; lambda repressor-like DNA-binding domains -!- 51182; RmlC-like PF01381;Helix-turn-helix;1.4e-17;codon 12-66 -!- PF07883;Cupin domain;1.7e-08;codon 102-173 CDS ECK1429 ydcP ydcP b1435 1504805 1506766 + start codon change JW1431 1508495 1510456 + include signal peptide pe predicted peptidase C Cytoplasmic U32 family; unassigned peptidases (YdcP protein) COG0826;Collagenase and related proteases PF01136;Peptidase family U32;4.2e-97;codon 92-304 CDS ECK1430 yncJ yncJ b1436 1506858 1507088 - (no change) JW1432 1510548 1510778 - o predicted protein C Periplasmic 1-22 CDS ECK1431 yncN yncN b4532 1507310 1507486 + new JW5230 1511000 1511176 + o predicted protein C CDS ECK1432 ydcQ ydcQ b1438 1507511 1507948 + (no change) JW1433 1511201 1511638 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic Unclass COG1598;Uncharacterized conserved protein 47413; lambda repressor-like DNA-binding domains PF03681;Uncharacterised protein family (UPF0150);3.8e-21;codon 8-70 -!- PF01381;Helix-turn-helix;3e-06;codon 89-143 CDS ECK1433 ydcR ydcR b1439 1508027 1509433 + (no change) JW1434 1511717 1513123 + pr fused predicted DNA-binding transcriptional regulator -!- predicted amino transferase "transcriptional regulator, member of GntR family and amino transferase" C Cytoplasmic fused: predited transcriptional regulator (aa1-117) -!- predicted amino transferase (aa118-468) COG1167;Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs 46785; Winged helix -!- 53383; PLP-dependent transferases "PF00392;Bacterial regulatory proteins, gntR fam;4.7e-15;codon 3-66 -!- PF00155;Aminotransferase class I and II;1.4e-11;codon 157-460" "GO:0006355 regulation of transcription, DNA-dependent" GO:0004009 ATP-binding cassette (ABC) transporter activity CDS ECK1434 ydcS ydcS b1440 1509678 1510823 + (no change) JW1435 1513368 1514513 + pt predicted spermidine/putrescine transporter subunit -!- periplasmic-binding component of ABC superfamily C Periplasmic heteromultimer; YdcS/YdcT/YdcV/YdcU ABC transporter (b1440-b1441-b1443-b1442) 1-22 COG0687;Spermidine/putrescine-binding periplasmic protein 53850; Periplasmic binding protein-like II PF01547;Bacterial extracellular solute-binding prot;1e-22;codon 6-313 GO:0042597 periplasmic space CDS ECK1435 ydcT ydcT b1441 1510841 1511854 + (no change) JW1436 1514531 1515544 + pt predicted spermidine/putrescine transporter subunit -!- ATP-binding component of ABC superfamily C Cytoplasmic heteromultimer; YdcS/YdcT/YdcV/YdcU ABC transporter (b1440-b1441-b1443-b1442) "COG3842;ABC-type spermidine/putrescine transport systems, ATPase components" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;8.9e-62;codon 30-211 GO:0005737 cytoplasm CDS ECK1436 ydcU ydcU b1442 1511855 1512796 + (no change) JW1437 1515545 1516486 + pt predicted spermidine/putrescine transporter subunit -!- membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YdcS/YdcT/YdcV/YdcU ABC transporter (b1440-b1441-b1443-b1442) 6 8 in "COG1176;ABC-type spermidine/putrescine transport system, permease component I" PF00528;Binding-protein-dependent transport syst;1.2e-06;codon 87-309 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1437 ydcV ydcV b1443 1512786 1513580 + (no change) JW1438 1516476 1517270 + pt predicted spermidine/putrescine transporter subunit -!- membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YdcS/YdcT/YdcV/YdcU ABC transporter (b1440-b1441-b1443-b1442) 6 6 in "COG1177;ABC-type spermidine/putrescine transport system, permease component II" PF00528;Binding-protein-dependent transport syst;8.3e-10;codon 61-262 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1438 ydcW ydcW b1444 1513602 1515026 + (no change) JW1439 1517292 1518716 + e medium chain aldehyde dehydrogenase E 15381418 Cytoplasmic COG1012;NAD-dependent aldehyde dehydrogenases 53720; ALDH-like PF00171;Aldehyde dehydrogenase family;1.4e-180;codon 11-474 CDS ECK1439 ydcX ydcX b1445 1515413 1515586 + start codon change JW5232 1519103 1519276 + pm predicted inner membrane protein C Integral Membrane Protein 2 2 CDS ECK1440 ydcY ydcY b1446 1515672 1515905 + (no change) JW1441 1519362 1519595 + o predicted protein C Cytoplasmic CDS ECK1441 ydcZ ydcZ b1447 1515906 1516355 - (no change) JW1442 1519596 1520045 - pm predicted inner membrane protein C Integral Membrane Protein 5 5 in COG3238;Uncharacterized protein conserved in bacteria "PF04657;Protein of unknown function, DUF606;9.9e-58;codon 4-143" CDS ECK1442 yncA yncA b1448 1516352 1516870 - (no change) JW5233 1520042 1520560 - pe predicted acyltransferase with acyl-CoA N-acyltransferase domain C Cytoplasmic COG1247;Sortase and related acyltransferases 55729; Acyl-CoA N-acyltransferases (Nat) PF00583;Acetyltransferase (GNAT) family;6.4e-24;codon 54-137 GO:0042493 response to drug CDS ECK1443 yncB yncB b1449 1517051 1518088 + start codon change JW5907 1520741 1521778 + pe "predicted oxidoreductase, Zn-dependent and NAD(P)-binding" C Cytoplasmic 50129; GroES-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF00107;Zinc-binding dehydrogenase;5.9e-33;codon 52-372 CDS ECK1444 yncC yncC b1450 1518286 1518951 + start codon change JW1445 1521976 1522641 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic COG1802;Transcriptional regulators 46785; Winged helix "PF00392;Bacterial regulatory proteins, gntR family;1.9e-10;codon 31-93 -!- PF07729;FCD domain;1.9e-09;codon 103-229" "GO:0006350 transcription -!- GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1445 yncD yncD b1451 1518987 1521089 - (no change) JW1446 1522677 1524779 - pt predicted iron outer membrane transporter C Periplasmic 1-23 "COG1629;Outer membrane receptor proteins, mostly Fe transport" 56935; Porins PF07715;TonB-dependent Receptor Plug Domain;1.6e-24;codon 39-151 -!- PF00593;TonB dependent receptor;2.1e-33;codon 448-697 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK1446 yncE yncE b1452 1521331 1522392 + (no change) JW1447 1525021 1526082 + d conserved protein predicted beta-barrel structure C Periplasmic 1-30 COG3391;Uncharacterized conserved protein 50969; Quinoprotein amine dehydrogenase catalytic subunit CDS ECK1447 ansP ansP yncF b1453 1522505 1524004 - start codon change JW5234 1526195 1527694 - t L-asparagine transporter E 76005443 Integral Membrane Protein 12 12 in PF00324;Amino acid permease;5.2e-171;codon 51-494 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006529 asparagine biosynthesis CDS ECK1448 yncG yncG b1454 1524271 1524888 + (no change) JW1449 1527961 1528578 + pe predicted enzyme C Cytoplasmic COG0625;Glutathione S-transferase "47616; Glutathione S-transferases, C-terminal domain -!- 52833; Thioredoxin-like" CDS ECK1449 yncH yncH b1455 1524964 1525176 + (no change) JW5235 1528654 1528866 + o predicted protein C CDS ECK1450 rhsE rhsE b1456 1525914 1527962 + (no change) JW1451 1529604 1531652 + h rhsE element core protein RshE E 92115567 -!- 7934896 Cytoplasmic COG3209;Rhs family protein PF05593;RHS Repeat;3.2;codon 23-60 -!- PF05593;RHS Repeat;0.0031;codon 145-176 -!- PF05593;RHS Repeat;1.5;codon 225-274 -!- PF03527;RHS protein;2.3e-32;codon 423-469 CDS ECK1451 ydcD ydcD b1457 1527946 1528428 + (no change) JW1452 1531636 1532118 + o predicted protein C Membrane Anchored CDS ECK1452 yncI yncI b1458 1528610 1529356 + (no change) JW1453 1532300 1533046 + o predicted protein C 7868617 -!- 8387990 Periplasmic PF01609;Transposase DDE domain;8.9e-13;codon 105-244 CDS ECK1453 yncM yncM b1459 1529400 1529600 + (no change) JW5237 1533090 1533290 + o predicted protein C 7868617 -!- 8387990 CDS ECK1454 ydcC ydcC b1460 1529840 1530976 + (no change) JW1455 1533530 1534666 + d conserved protein C Cytoplasmic PF01609;Transposase DDE domain;1.7e-51;codon 105-343 CDS ECK1455 ydcE ydcE b1461 1531076 1531309 + (no change) JW1456 1534766 1534999 + e 4-oxalocrotonate tautomerase E 12356301 Cytoplasmic 5.3.2.- monomeric multimer; probable 4-oxalocrotonate tautomerase (4-OT) (b1461) 1GYY "COG1942;Uncharacterized protein, 4-oxalocrotonate tautomerase homolog" 55331; Tautomerase/MIF PF01361;Tautomerase enzyme;4.2e-15;codon 2-58 CDS ECK1456 yddH yddH b1462 1531306 1531875 - start codon change JW1457 1534996 1535565 - o conserved protein C Cytoplasmic "COG1853;Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family" 50475; FMN-binding split barrel PF01613;Flavin reductase like domain;7.1e-05;codon 31-181 CDS ECK1457 nhoA nhoA ydcE -!- yddI b1463 1532048 1532893 + (no change) JW1458 1535738 1536583 + e N-hydroxyarylamine O-acetyltransferase E 20267568 Cytoplasmic 2.3.1.118 monomeric multimer; N-hydroxyarylamine O-acetyltransferase (b1463) COG2162;Arylamine N-acetyltransferase 54001; Cysteine proteinases PF00797;N-acetyltransferase;1.6e-100;cod on 21-257 GO:0008152 metabolism CDS ECK1458 yddE yddE b1464 1532989 1533882 - (no change) JW1459 1536679 1537572 - o conserved protein C 14611652 -!- 15103639 -!- 2233673 Cytoplasmic 1QYA "COG0384;Predicted epimerase, PhzC/PhzF homolog" PF02567;Phenazine biosynthesis-like protein;1.3e-131;codon 2-291 TIGR00654;PhzF_family: phenazine biosynthesis prote;3.2e-201;codon 1-295 CDS ECK1459 narV narV chlZ b1465 1533961 1534641 - (no change) JW1460 1537651 1538331 - e "nitrate reductase 2 (NRZ), gamma subunit" E 91042410 Integral Membrane Protein 1.7.99.4 heteromultimer; nitrate reductase Z (b1468-b1467-b1465) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 5 5 in COG2181;Nitrate reductase gamma subunit PF02665;Nitrate reductase gamma subunit;4.7e-125;codon 4-226 "TIGR00351;narI: respiratory nitrate reductase, gamma s;5.5e-133;codon 2-226" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration GO:0009054 electron acceptor activity CDS ECK1460 narW narW chlZ b1466 1534638 1535333 - (no change) JW1461 1538328 1539023 - f "nitrate reductase 2 (NRZ), delta subunit (assembly subunit)" E 91042410 -!- 92186712 Cytoplasmic 1.7.99.4 COG2180;Nitrate reductase delta subunit PF02613;Nitrate reductase delta subunit;1e-94;codon 3-159 TIGR00684;narJ: nitrate reductase molybdenum cofactor;3.1e-33;codon 8-154 GO:0009061 anaerobic respiration -!- GO:0006457 protein folding CDS ECK1461 narY narY chlZ b1467 1535333 1536877 - (no change) JW1462 1539023 1540567 - c "nitrate reductase 2 (NRZ), beta subunit" E 91042410 Cytoplasmic 1.7.99.4 heteromultimer; nitrate reductase Z (b1468-b1467-b1465) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family COG1140;Nitrate reductase beta subunit 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;0.015;codon 176-201 -!- PF00037;4Fe-4S binding domain;0.015;codon 209-232 "TIGR01660;narH: nitrate reductase, beta subunit;0;codon 1-494" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration GO:0009054 electron acceptor activity CDS ECK1462 narZ narZ chlZ b1468 1536874 1540614 - (no change) JW1463 1540564 1544304 - e "nitrate reductase 2 (NRZ), alpha subunit" E 91042410 Cytoplasmic 1.7.99.4 heteromultimer; nitrate reductase Z (b1468-b1467-b1465) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family COG5013;Nitrate reductase alpha subunit "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3" PF00384;Molybdopterin oxidoreductase;1.1e-145;codon 108-832 -!- PF01568;Molydopterin dinucleotide binding dom;3.7e-44;codon 1086-1207 "TIGR01580;narG: nitrate reductase, alpha subunit;0;codon 2-1234" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration GO:0009054 electron acceptor activity CDS ECK1463 narU narU yddF b1469 1540696 1542084 - (no change) JW1464 1544386 1545774 - t nitrate/nitrite transporter E 95266795 -!- 2233673 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG2223;Nitrate/nitrite transporter PF07690;Major Facilitator Superfamily;5.3e-12;codon 42-427 TIGR00886;2A0108: nitrate transporter;1.1e-144;codon 34-415 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006807 nitrogen metabolism CDS ECK1464 yddJ yddJ b1470 1542408 1542743 - (no change) JW1466 1546098 1546433 - o predicted protein C Cytoplasmic CDS ECK1465 yddK yddK b1471 1542782 1543738 - (no change) JW1467 1546472 1547428 - o predicted protein C Cytoplasmic COG4886;Leucine-rich repeat (LRR) protein 52058; L domain-like 7 of PF00560;Leucine Rich Repeat: 11;codon 33-57 -!- 29;codon 109-132 -!- 23;codon 153-176 -!- 37;codon 195-214 -!- 0.2;codon 216-239 -!- 6;codon 260-283 -!- 17;codon 284-303 GO:0009101 glycoprotein biosynthesis CDS ECK1466 yddL yddL b1472 1543762 1544052 - (no change) JW1468 1547452 1547742 - lp predicted lipoprotein C 7926834 Periplasmic 1-21 COG3203;Outer membrane protein (porin) 56935; Porins GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK1467 yddG yddG b1473 1544312 1545136 - start codon change JW1469 1548002 1548826 - pt predicted methyl viologen efflux pump C 12410826 Integral Membrane Protein 10 10 in GO:0009274 cell wall (sensu Bacteria) CDS ECK1468 fdnG fdnG b1474 1545425 1548472 + "(no change) -!- (pos:1546010..1546012, aa:Sec)" JW1470 1549115 1552162 + Sec included e "formate dehydrogenase-N, alpha subunit, nitrate-inducible" E 90375017 -!- 92332427 -!- 94148228 -!- 11884747 -!- 1834669 -!- Jones RW;FEMS Microbiology Letters;1980;8:167-171 1.2.1.2 "heteromultimer; formate dehydrogenase-N (b1474-b1475-b1476) -!- heteromultimer; trimer complex of formate dehydrogenase-N alpha, beta and gamma subunits (b1474-b1475-b1476)" 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 1-22 regulated by attenuation (fdnG-fdnH-fdnI) 1KQG "COG0243;Anaerobic dehydrogenases, typically selenocysteine-containing" "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3" PF04879;Molybdopterin oxidoreductase Fe4S4 do;1.1e-22;codon 43-104 -!- PF00384;Molybdopterin oxidoreductase;6.3e-28;codon 107-658 -!- PF01568;Molydopterin dinucleotide binding dom;1.1e-43;codon 889-1008 TIGR01553;formate-DH-alph: formate dehydrogenas;0;codon 2-1013 -!- TIGR01409;TAT_signal_seq: Tat (twin-arginine tr;0.0078;codon 3-33 GO:0005737 cytoplasm GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK1469 fdnH fdnH b1475 1548485 1549369 + (no change) JW1471 1552175 1553059 + c "formate dehydrogenase-N, Fe-S (beta) subunit, nitrate-inducible" E 76005553 -!- 90375017 -!- 92332427 -!- 11884747 -!- 1834669 -!- Jones RW;FEMS Microbiology Letters;1980;8:167-171 "heteromultimer; formate dehydrogenase-N (b1474-b1475-b1476) -!- heteromultimer; trimer complex of formate dehydrogenase-N alpha, beta and gamma subunits (b1474-b1475-b1476)" 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 1KQG COG0437;Fe-S-cluster-containing hydrogenase components 1 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;3.2e-05;codon 126-149 "TIGR01582;FDH-beta: formate dehydrogenase, beta subuni;5.1e-205;codon 7-290" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK1470 fdnI fdnI b1476 1549362 1550015 + (no change) JW1472 1553052 1553705 + c "formate dehydrogenase-N, cytochrome B556 (gamma) subunit, nitrate-inducible" E 76005553 -!- 90375017 -!- 92332427 -!- Jones RW;FEMS Microbiology Letters;1980;8:167-171 Integral Membrane Protein "heteromultimer; formate dehydrogenase-N (b1474-b1475-b1476) -!- heteromultimer; trimer complex of formate dehydrogenase-N alpha, beta and gamma subunits (b1474-b1475-b1476)" 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 4 4 in COG2864;Cytochrome b subunit of formate dehydrogenase TIGR01583;formate-DH-gamm: formate dehydrogenas;8.2e-83;codon 6-207 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration -!- GO:0017004 cytochrome biogenesis GO:0009053 electron donor activity CDS ECK1471 yddM yddM b1477 1550422 1550784 - (no change) JW5908 1554112 1554474 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic ~OmpR 47413; lambda repressor-like DNA-binding domains PF01381;Helix-turn-helix;4.8e-08;codon 39-93 "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1472 adhP adhP yddN b1478 1550852 1551862 - start codon change JW1474 1554542 1555552 - c "alcohol dehydrogenase, 1-propanol preferring" E 99337666 1.1.1.1 Zn2+ 50129; GroES-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF00107;Zinc-binding dehydrogenase;1.4e-101;codon 17-344 GO:0009061 anaerobic respiration CDS ECK1473 sfcA sfcA mae -!- maeA b1479 1551996 1553693 - start codon change JW5238 1555686 1557383 - e "malate dehydrogenase, (decarboxylating, NAD-requiring) (malic enzyme)" E 6360216 -!- 90337272 Cytoplasmic 1.1.1.38 Mn2+ "monomeric multimer; malic enzyme, NAD-linked (b1479)" COG0281;Malic enzyme "51735; NAD(P)-binding Rossmann-fold domains -!- 53223; Aminoacid dehydrogenase-like, N-terminal domain" "PF00390;Malic enzyme, N-terminal domain;2.6e-124;codon 91-278 -!- PF03949;Malic enzyme, NAD binding domain;5.5e-139;codon 280-540" GO:0006094 gluconeogenesis CDS ECK1474 sra sra rpsV b1480 1553850 1553987 - (no change) JW5962 1557540 1557677 - s 30S ribosomal subunit protein S22 E 8332529 -!- 90337272 -!- 10094780 -!- 11292794 Cytoplasmic GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006412 protein biosynthesis GO:0003735 structural constituent of ribosome CDS ECK1475 bdm bdm yddX b1481 1554089 1554304 - start codon change JW5239 1557779 1557994 - f biofilm-dependent modulation protein E 10498711 -!- 13129944 Cytoplasmic CDS ECK1476 osmC osmC b1482 1554649 1555080 + (no change) JW1477 1558339 1558770 + m "osmotically inducible, stress-inducible membrane protein" involved in defense against oxidative compounds E 14512736 -!- 91350191 -!- 9298646 Cytoplasmic 1NYE "COG1764;Predicted redox protein, regulator of disulfide bond formation" PF02566;OsmC-like protein;3e-38;codon 11-142 GO:0006970 response to osmotic stress CDS ECK1477 ddpF ddpF yddO b1483 1555136 1556062 - (no change) JW1478 1558826 1559752 - t D-ala-D-ala transporter subunit -!- ATP-binding component of ABC superfamily E 99432174 Cytoplasmic heteromultimer; YddO/YddP/YddQ/YddR/YddS ABC transporter (b1486-b1485-b1487-b1484-b1483) "COG1124;ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.3e-59;codon 42-219 TIGR01727;oligo_HPY: oligopeptide/dipeptide ABC trans;6.8e-18;codon 220-306 GO:0005737 cytoplasm CDS ECK1478 ddpD ddpD yddP b1484 1556055 1557041 - (no change) JW1479 1559745 1560731 - t D-ala-D-ala transporter subunit -!- ATP-binding component of ABC superfamily E 99432174 Cytoplasmic heteromultimer; YddO/YddP/YddQ/YddR/YddS ABC transporter (b1486-b1485-b1487-b1484-b1483) "COG0444;ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;5.5e-57;codon 35-233 TIGR01727;oligo_HPY: oligopeptide/dipeptide ABC trans;4.2e-22;codon 234-320 GO:0005737 cytoplasm CDS ECK1479 ddpC ddpC yddQ b1485 1557038 1557934 - (no change) JW1480 1560728 1561624 - t D-ala-D-ala transporter subunit -!- membrane component of ABC superfamily E 99432174 Integral Membrane Protein heteromultimer; YddO/YddP/YddQ/YddR/YddS ABC transporter (b1486-b1485-b1487-b1484-b1483) 6 5 in "COG1173;ABC-type dipeptide/oligopeptide/nickel transport systems, permease components" PF00528;Binding-protein-dependent transport syst;4.5e-48;codon 93-295 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1480 ddpB ddpB yddR b1486 1557931 1558953 - (no change) JW1481 1561621 1562643 - t D-ala-D-ala transporter subunit -!- membrane component of ABC superfamily E 99432174 Integral Membrane Protein heteromultimer; YddO/YddP/YddQ/YddR/YddS ABC transporter (b1486-b1485-b1487-b1484-b1483) 7 7 in "COG0601;ABC-type dipeptide/oligopeptide/nickel transport systems, permease components" PF00528;Binding-protein-dependent transport syst;5.8e-55;codon 97-336 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1481 ddpA ddpA yddS b1487 1558955 1560505 - (no change) JW5240 1562645 1564195 - t D-ala-D-a la transporter subunit -!- periplasmic-binding component of ABC superfamily E 99432174 Periplasmic heteromultimer; YddO/YddP/YddQ/YddR/YddS ABC transporter (b1486-b1485-b1487-b1484-b1483) "COG0747;ABC-type dipeptide transport system, periplasmic component" 53850; Periplasmic binding protein-like II PF00496;Bacterial extracellular solute-binding prot;1.5e-85;codon 77-435 GO:0042597 periplasmic space CDS ECK1482 ddpX ddpX vanX -!- yddT b1488 1560519 1561100 - (no change) JW1483 1564209 1564790 - e "D-ala-D-ala dipeptidase, Zn-dependent" E 99432174 -!- 9751644 Cytoplasmic 3.4.13.- M15D family; unassigned peptidases (VanX protein) COG2173;D-alanyl-D-alanine dipeptidase PF01427;D-ala-D-ala dipeptidase;1.1e-117;codon 3-187 GO:0042597 periplasmic space GO:0006970 response to osmotic stress CDS ECK1483 dos dos yddU b1489 1561358 1563757 - start codon change JW1484 1565048 1567447 - e "cAMP phosphodiesterase, heme-regulated" E 10704219 -!- 11970957 -!- 12271121 -!- 14982921 -!- 15005609 Cytoplasmic Mg2+ monomeric multimer; heme-regulated phosphodiesterase (b1489) COG2202;FOG: PAS/PAC domain -!- COG2199;FOG: GGDEF domain -!- COG2200;FOG: EAL domain 55785; PYP-like sensor domain PF00989;PAS domain;2.3e-09;codon 21-82 -!- PF00785;PAC motif;0.36;codon 96-136 -!- PF00785;PAC motif;4e-07;codon 217-259 -!- PF00990;GGDEF domain;2.9e-18;codon 380-534 -!- PF00563;EAL domain;9e-124;codon 548-789 TIGR00229;sensory_box: PAS domain S-box;5.9e-17;codon 17-139 -!- TIGR00229;sensory_box: PAS domain S-box;2.9e-14;codon 140-266 -!- TIGR00254;GGDEF: putative diguanylate cyclase (GGDE;9.6e-14;codon 380-539 CDS ECK1484 yddV yddV b1490 1563782 1564825 - start codon change JW5241 1567472 1568515 - pr predicted diguanylate cyclase C Cytoplasmic COG2199;FOG: GGDEF domain PF00990;GGDEF domain;1.7e-71;codon 178-339 TIGR00254;GGDEF: putative diguanylate cyclase (GGDEF);1.3e-49;codon 178-344 CDS ECK1485 yddW yddW b1491 1565528 1566847 - (no change) JW1486 1569218 1570537 - lp predicted liprotein C Outer membrane Lipoprotein regulated by attenuation (yddW) COG1649;Uncharacterized protein conserved in bacteria 51445; (Trans)glycosidases "PF02638;Uncharacterized BCR, COG1649;0;codon 3-431" CDS ECK1486 gadC gadC xas -!- xasA -!- acsA b1492 1566978 1568513 - (no change) JW1487 1570668 1572203 - pt predicted glutamate:gamma-aminobutyric acid antiporter C 8885264 Integral Membrane Protein 12 12 in COG0531;Amino acid transporters PF00324;Amino acid permease;1.5e-05;codon 12-477 TIGR00910;2A0307: Glutamate:g-aminobutyrate antiporter;0;codon 1-511 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1487 gadB gadB b1493 1568669 1570069 - (no change) JW1488 1572359 1573759 - e "glutamate decarboxylase B, PLP-dependent" E 12912902 -!- 92155241 -!- 92394884 -!- 99406302 -!- 8455549 Cytoplasmic 4.1.1.15 monomeric multimer; glutamate decarboxylase B (b1493) 1PMO COG0076;Glutamate decarboxylase and related PLP-dependent proteins 53383; PLP-dependent transferases PF00282;Pyridoxal-dependent decarboxylase conse;2.2e-176;codon 33-383 TIGR01788;Glu-decarb-GAD: glutamate decarboxylas;0;codon 16-449 GO:0005737 cytoplasm GO:0009063 amino acid catabolism -!- GO:0006520 amino acid metabolism CDS ECK1488 pqqL pqqL pqqE -!- pqqM -!- yddC b1494 1570431 1573226 - (no change) JW1489 1574121 1576916 - pe predicted peptidase C 1659611 -!- 11514505 M16B family; unassigned peptidases (PqqL protein) COG0612;Predicted Zn-dependent peptidases 63411; LuxS/MPP-like metallohydrolase PF00675;Insulinase (Peptidase family M16);3.6e-60;codon 46-204 -!- PF05193;Peptidase M16 inactive domain;4.6e-31;codon 206-388 -!- PF05193;Peptidase M16 inactive domain;2.7e-21;codon 683-863 GO:0005737 cytoplasm CDS ECK1489 yddB yddB b1495 1573271 1575643 - (no change) JW1490 1576961 1579333 - pt predicted porin protein C Periplasmic 56935; Porins PF07715;TonB-dependent Receptor Plug Domain;1.1e-14;codon 37-167 -!- PF00593;TonB dependent receptor;1.6e-10;codon 484-790 CDS ECK1490 yddA yddA b1496 1575681 1577366 - (no change) JW5242 1579371 1581056 - pt fused predicted multidrug transporter subunits of ABC superfamily: membrane component -!- ATP-binding component C Integral Membrane Protein monomeric multimer; abc-39-cplx (b1496) 5 5 in "fused predicted transport protein, ABC superfamily: membrane component (aa1-355) -!- atp_binding component (aa356-561)" "COG4178;ABC-type uncharacterized transport system, permease and ATPase components" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;4.8e-44;codon 393-560 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1491 ydeM ydeM b1497 1577657 1578814 - start codon change JW1492 1581347 1582504 - pr conserved protein radical SAM superfamily C Cytoplasmic PF04055;Radical SAM superfamily;9.1e-23;codon 11-180 CDS ECK1492 ydeN ydeN b1498 1578866 1580548 - start codon change JW5243 1582556 1584238 - d conserved protein C Periplasmic COG3119;Arylsulfatase A and related enzymes 53649; Alkaline phosphatase-like PF00884;Sulfatase;1e-95;codon 67-527 GO:0006790 sulfur metabolism CDS ECK1493 ydeO ydeO b1499 1580950 1581711 - (no change) JW1494 1584640 1585401 - pr predicted DNA-binding transcriptional acfivator C 12399493 Cytoplasmic AraC/XylS gadE COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like PF00165;Bacterial regulatory helix-turn-helix protei;0.00027;codon 138-183 -!- PF00165;Bacterial regulatory helix-turn-helix protei;1.2e-06;codon 189-232 GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1494 ydeP ydeP b1501 1582231 1584510 - (no change) JW1495 1585921 1588200 - pe predicted oxidoreductase required for acid resistance conferred by EvgA overexpression C 12399493 -!- 9781871 Cytoplasmic "COG0243;Anaerobic dehydrogenases, typically selenocysteine-containing" "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3" PF00384;Molybdopterin oxidoreductase;1.6e-10;codon 108-561 TIGR01701;Fdhalpha-like: oxidoreductase alpha (mo;0;codon 11-758 CDS ECK1495 ydeQ ydeQ b1502 1584844 1585758 - (no change) JW1496 1588534 1589448 - ps predicted fimbrial-like adhesin protein C 49401; Bacterial adhesins PF00419;Fimbrial protein;0.00044;codon 177-304 CDS ECK1496 ydeR ydeR b1503 1585817 1586320 - (no change) JW1497 1589507 1590010 - ps predicted fimbrial-like adhesin protein C Periplasmic 1-23 "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;1.6e-06;codon 26-167 GO:0009289 fimbria CDS ECK1497 ydeS ydeS b1504 1586333 1586863 - (no change) JW1498 1590023 1590553 - ps predicted fimbrial-like adhesin protein C "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;1.7e-35;codon 25-176 GO:0009289 fimbria CDS ECK1498 ydeT ydeT b1505 1586877 1588025 - (no change) JW1499 1590567 1591715 - o predicted protein C Cytoplasmic "COG3188;P pilus assembly protein, porin PapC" PF00577;Fimbrial Usher protein;3.3e-09;codon 1-366 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK1499 yneL yneL b1506 1588381 1588560 - (no change) JW5244 1592071 1592250 - pr predicted transcriptional regulator C Cytoplasmic COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like CDS ECK1500 hipA hipA b1507 1588878 1590200 - (no change) JW1500 1592568 1593890 - r regulator with hipB E 91358364 -!- 94292428 -!- 15576765 Cytoplasmic COG3550;Uncharacterized protein related to capsule biosynthesis enzymes PF07805;HipA-like N-terminal domain;9.9e-23;codon 150-238 -!- PF07804;HipA-like C-terminal domain;2.6e-39;codon 249-332 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009252 peptidoglycan biosynthesis -!- GO:0006259 DNA metabolism CDS ECK1501 hipB hipB b1508 1590200 1590466 - (no change) JW1501 1593890 1594156 - r DNA-binding transcriptional regulator E 91358364 -!- 94292428 -!- 15576765 -!- 8021189 Cytoplasmic Unclass COG1396;Predicted transcriptional regulators 47413; lambda repressor-like DNA-binding domains PF01381;Helix-turn-helix;1.4e-13;codon 17-71 GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009252 peptidoglycan biosynthesis -!- GO:0006259 DNA metabolism CDS ECK1502 ydeU ydeU b1509 1590689 1592089 - (no change) JW1502 1594379 1595779 - su "conserved protein, predicted pseudogene" predicted pseudogene -!- member of the AIDA-I family of autotransporter proteins. Passenger and autotransport C Cytoplasmic "COG3468;Type V secretory pathway, adhesin AidA" 51126; Pectin lyase-like PF03212;Pertactin;0.00015;codon 1-113 -!- PF03797;Autotransporter beta-domain;1.3e-41;codon 179-457 TIGR01414;autotrans_barl: outer membrane autotra;7.1e-118;codon 5-466 CDS ECK1503 ydeK ydeK orfT b1510 1592133 1596110 - (no change) JW1503 1595823 1599800 - lp predicted lipoprotein C 8274505 Outer membrane Lipoprotein regulated by attenuation (ydeK) PF05594;no description;5.7;codon 529-627 CDS ECK1504 ydeV ydeV b1511 1596641 1598233 - (no change) JW1504 1600331 1601923 - pe predicted sugar kinase upregulated in biofilms C Cytoplasmic 53067; Actin-like ATPase domain "PF00370;FGGY family of carbohydrate kinases, N-termi;1.4e-46;codon 13-260 -!- PF02782;FGGY family of carbohydrate kinases, C-termi;5e-11;codon 263-499" CDS ECK1505 ydeW ydeW b1512 1598312 1599265 - (no change) JW1505 1602002 1602955 - pr predicted DNA-binding transcriptional regulator of lsr operon C Cytoplasmic ~YjhU "COG2390;Transcriptional regulator, contains sigma factor-related N-terminal domain" 46785; Winged helix PF04198;Putative sugar-binding domain;5.3e-98;codon 66-316 GO:0016564 transcriptional repressor activity CDS ECK1506 ego ego lsrA -!- ydeX b1513 1599514 1601049 + (no change) JW1506 1603204 1604739 + t fused AI2 transporter subunits of ABC superfamily: ATP-binding components E 12657059 -!- 11722742 Cytoplasmic heteromultimer; YdeX/YdeY/YdeZ/YneA ABC transporter (b1516-b1515-b1514-b1513) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "fused predicted sugar transport protein, ABC superfamily: atp_binding component (aa1-264) -!- atp_binding component (aa265-511)" "COG1129;ABC-type sugar transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;4.3e-49;codon 37-216 -!- PF00005;ABC transporter;1.3e-27;codon 289-479 GO:0005737 cytoplasm CDS ECK1507 lsrC lsrC ydeY b1514 1601043 1602071 + (no change) JW1507 1604733 1605761 + t AI2 transporter -!- membrane component of ABC superfamily E 11722742 Integral Membrane Protein heteromultimer; YdeX/YdeY/YdeZ/YneA ABC transporter (b1516-b1515-b1514-b1513) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 8 9 in "COG1172;Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components" PF02653;Branched-chain amino acid transport syst;6.7e-52;codon 36-301 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1508 lsrD lsrD ydeZ b1515 1602071 1603063 + (no change) JW1508 1605761 1606753 + t AI2 transporter -!- membrane component of ABC superfamily E 11722742 Integral Membrane Protein heteromultimer; YdeX/YdeY/YdeZ/YneA ABC transporter (b1516-b1515-b1514-b1513) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 10 9 in "COG1172;Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components" PF02653;Branched-chain amino acid transport syst;4.7e-66;codon 34-305 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1509 lsrB lsrB yneA b1516 1603075 1604097 + (no change) JW1509 1606765 1607787 + t AI2 transporter -!- periplasmic-binding component of ABC superfamily E 11722742 Periplasmic heteromultimer; YdeX/YdeY/YdeZ/YneA ABC transporter (b1516-b1515-b1514-b1513) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-26 "COG1879;ABC-type sugar transport system, periplasmic component" 53822; Periplasmic binding protein-like I GO:0042597 periplasmic space CDS ECK1510 lsrF lsrF yneB b1517 1604124 1604999 + (no change) JW1510 1607814 1608689 + pe predicted aldolase regulated by LsrR and LuxS through autoinducer 2 -!- part of operon for autoinducer-2 uptake in Salmonella -!- ribulose-phosphate binding barrel C Cytoplasmic "COG1830;DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes" 51366; Ribulose-phoshate binding barrel PF01791;Deoxyribose-phosphate aldolase;3e-14;codon 51-271 CDS ECK1511 lsrG lsrG yneC b1518 1605023 1605313 + (no change) JW1511 1608713 1609003 + o conserved protein C Cytoplasmic COG1359;Uncharacterized conserved protein PF03992;Antibiotic biosynthesis monooxygenase;7.6e-19;codon 10-73 CDS ECK1512 tam tam yneD b1519 1605370 1606128 + (no change) JW1512 1609060 1609818 + e trans-aconitate methyltransferase E 10224113 Cytoplasmic 2.1.1.144 COG4106;Trans-aconitate methyltransferase 53335; S-adenosyl-L-methionine-dependent methyltransferases GO:0005737 cytoplasm CDS ECK1513 yneE yneE b1520 1606132 1607046 - start codon change JW5245 1609822 1610736 - pm conserved inner membrane protein C Integral Membrane Protein 3 3 COG3781;Predicted membrane protein PF05249;Uncharacterised protein family (UPF0187);3.1e-202;codon 18-318 GO:0009274 cell wall (sensu Bacteria) CDS ECK1514 uxaB uxaB b1521 1607253 1608704 - (no change) JW1514 1610943 1612394 - e "altronate oxidoreductase, NAD-dependent" E 72233233 -!- 86280350 Cytoplasmic 1.1.1.58 PF01232;Mannitol dehydrogenase;4.7e-186;codon 16-459 GO:0016052 carbohydrate catabolism CDS ECK1515 yneF yneF b1522 1608931 1609878 - (no change) JW5825 1612621 1613568 - pr predicted diguanylate cyclase C Integral Membrane Protein 4 4 in COG2199;FOG: GGDEF domain PF00990;GGDEF domain;7.4e-56;codon 142-304 TIGR00254;GGDEF: putative diguanylate cyclase (GGDEF);3.6e-33;codon 142-309 CDS ECK1516 yneG yneG b1523 1609990 1610349 - (no change) JW1516 1613680 1614039 - o conserved protein C Cytoplasmic CDS ECK1517 yneH yneH b1524 1610349 1611275 - (no change) JW1517 1614039 1614965 - pe predicted glutaminase simlarity with Rhizobium etli glutaminase A C Cytoplasmic COG2066;Glutaminase 56601; beta-Lactamase/D-ala carboxypeptidase PF04960;Glutaminase;5.4e-192;codon 24-308 GO:0009063 amino acid catabolism CDS ECK1518 yneI yneI b1525 1611339 1612727 - start codon change JW5247 1615029 1616417 - pe predicted aldehyde dehydrogenase C Cytoplasmic COG1012;NAD-dependent aldehyde dehydrogenases 53720; ALDH-like PF00171;Aldehyde dehydrogenase family;2e-134;codon 11-469 CDS ECK1519 yneJ yneJ b1526 1612828 1613709 + (no change) JW1519 1616518 1617399 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;8.9e-18;codon 3-62 -!- PF03466;LysR substrate binding domain;9.1e-50;codon 84-286 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK1520 yneK yneK b1527 1613787 1614902 + (no change) JW1520 1617477 1618592 + o predicted protein C Cytoplasmic CDS ECK1521 ydeA ydeA sotB b1528 1615052 1616242 + (no change) JW1521 1618742 1619932 + pt predicted arabinose transporter C 10094697 -!- 99369894 -!- 8383113 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG2814;Arabinose efflux permease PF07690;Major Facilitator Superfamily;2.2e-41;codon 18-358 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism GO:0015524 L-arabinose/beta-D-thiogalactopyranoside:hydrogen antiporter activity CDS ECK1522 marC marC ydeB -!- ydeC b1529 1616267 1616932 - (no change) JW1522 1619957 1620622 - pt predicted transporter C 8383113 Integral Membrane Protein 9.B.10; The 6 TMS Putative MarC Transporter (MarC) Family 6 5 out COG2095;Multiple antibiotic transporter PF01914;MarC family integral membrane protein;1e-105;codon 5-217 TIGR00427;TIGR00427: conserved hypothetical protein T;1e-21;codon 2-213 GO:0009274 cell wall (sensu Bacteria) CDS ECK1523 marR marR cfxB -!- soxQ -!- inaR b1530 1617144 1617578 + start codon change JW5248 1620834 1621268 + r DNA-binding transcriptional repressor of multiple antibiotic resistance E 93186717 -!- 94110219 -!- 99255562 -!- 99350435 -!- 10760140 -!- 7768850 Cytoplasmic marRAB 1JGS 46785; Winged helix PF01047;MarR family;2.3e-34;codon 19-123 GO:0005737 cytoplasm GO:0006350 transcription -!- GO:0042493 response to drug GO:0016564 transcriptional repressor activity CDS ECK1524 marA marA cfxB -!- norB -!- soxQ -!- inaR -!- nfxC b1531 1617598 1617981 + start codon change JW5249 1621288 1621671 + r DNA-binding transcriptional dual activator of multiple antibiotic resistance E 14701822 -!- 91358332 -!- 94110219 -!- 99429996 -!- 8383113 -!- 8491710 -!- 9724717 Cytoplasmic AraC/XylS acrAB -!- fpr -!- fumC -!- inaA -!- marRAB -!- micF -!- nfnB -!- nfo -!- poxB -!- pqiAB -!- putA -!- slp -!- sodA -!- zwf 1BL0 COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like PF00165;Bacterial regulatory helix-turn-helix protei;3.7e-13;codon 15-61 -!- PF00165;Bacterial regulatory helix-turn-helix protei;3.3e-10;codon 67-111 GO:0005737 cytoplasm GO:0006350 transcription -!- GO:0042493 response to drug -!- GO:0006805 xenobiotic metabolism GO:0016563 transcriptional activator activity CDS ECK1525 marB marB b1532 1618013 1618231 + (no change) JW1525 1621703 1621921 + o predicted protein encoded within multiple antibiotic resistance operon marRAB C 93186717 -!- 93259932 -!- 94110219 -!- 99429996 Periplasmic 1-11 GO:0042493 response to drug -!- GO:0006805 xenobiotic metabolism CDS ECK1526 eamA eamA ydeD b1533 1618262 1619161 - start codon change JW5250 1621952 1622851 - t cysteine and O-acetyl-L-serine efflux system E 20305052 Integral Membrane Protein 2.A.7; The Drug/Metabolite Transporter (DMT) Superfamily 10 10 in PF00892;Integral membrane protein DUF6;2.7e-20;codon 120-254 CDS ECK1527 ydeE ydeE ydeF b1534 1619356 1620543 + (no change) JW1527 1623046 1624233 + pt predicted transporter C Integral Membrane Protein 12 12 COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;4.2e-36;codon 12-358 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1528 ydeH ydeH ydeG b1535 1620984 1621874 - (no change) JW1528 1624674 1625564 - o conserved protein C Cytoplasmic COG2199;FOG: GGDEF domain PF00990;GGDEF domain;1.5e-67;codon 125-283 TIGR00254;GGDEF: putative diguanylate cyclase (GGDEF);2e-36;codon 125-288 CDS ECK1529 ydeI ydeI b1536 1622129 1622521 - (no change) JW1529 1625819 1626211 - o conserved protein C Periplasmic COG3111;Uncharacterized conserved protein PF04076;Domain unknown function (DUF388);4.5e-75;codon 1-130 TIGR00156;TIGR00156: conserved hypothetical protein T;1e-61;codon 1-130 CDS ECK1530 ydeJ ydeJ b1537 1622797 1623315 + (no change) JW1530 1626487 1627005 + o conserved protein C Cytoplasmic COG1546;Uncharacterized protein (competence- and mitomycin-induced) PF02464;Competence-damaged protein;2.4e-86;codon 17-171 TIGR00199;cinA_cterm: competence/damage-inducible pr;2.9e-90;codon 24-168 CDS ECK1531 dcp dcp b1538 1623359 1625404 - (no change) JW1531 1627049 1629094 - e dipeptidyl carboxypeptidase II E 216006 -!- 8226676 Cytoplasmic 3.4.15.5 M3A family; peptidyl-dipeptidase Dcp COG0339;Zn-dependent oligopeptidases "55486; Metalloproteases (zincins), catalytic domain" PF01432;Peptidase family M3;8.2e-208;codon 229-679 CDS ECK1532 ydfG ydfG b1539 1625541 1626287 + (no change) JW1532 1629231 1629977 + e "L-allo-threonine dehydrogenase, NAD(P)-binding" "other substrates include L-serine, D-serine, D-threonine and 3-hydroxyisobutyrate" E 22422630 Cytoplasmic monomeric multimer; 3-hydroxy acid dehydrogenase (b1539) COG4221;Short-chain alcohol dehydrogenase of unknown specificity 51735; NAD(P)-binding Rossmann-fold domains PF00106;short chain dehydrogenase;8.7e-66;codon 3-244 CDS ECK1533 ydfH ydfH b1540 1626376 1627062 + (no change) JW1533 1630066 1630752 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic GntR COG1802;Transcriptional regulators 46785; Winged helix "PF00392;Bacterial regulatory proteins, gntR family;4.2e-19;codon 13-75 -!- PF07729;FCD domain;1.1e-15;codon 85-209" GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1534 ydfZ ydfZ b1541 1627239 1627442 + (no change) JW1534 1630929 1631132 + o conserved protein C Cytoplasmic regulated by attenuation (ydfZ) CDS ECK1535 ydfI ydfI b1542 1627477 1628937 - (no change) JW1535 1631167 1632627 - pe predicted mannonate dehydrogenase C Cytoplasmic regulated by attenuation (ydfI) COG0246;Mannitol-1-phosphate/altronate dehydrogenases PF01232;Mannitol dehydrogenase;5.2e-261;codon 22-460 CDS ECK1536 ydfJ ydfJ b1543 1629026 1630309 - (no change) JW1536 1632716 1633999 - pt predicted transporter C Integral Membrane Protein 11 9 in COG0477;Permeases of the major facilitator superfamily PF00083;Sugar (and other) transporter;8.8e-08;codon 1-411 -!- PF07690;Major Facilitator Superfamily;1.6e-18;codon 10-370 TIGR00883;2A0106: metabolite:proton symporter family p;5.3e-201;codon 1-390 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1537 ydfK ydfK b1544 1631063 1631329 + (no change) JW1537 1634753 1635019 + h Qin prophage; predicted DNA-binding transcriptional regulator C Cytoplasmic cryptic prophage Qin CDS ECK1538 pinQ pinQ ydfL b1545 1631646 1632236 + (no change) JW1538 1635336 1635926 + h Qin prophage; predicted site-specific recombinase C Cytoplasmic cryptic prophage Qin "COG1961;Site-specific recombinases, DNA invertase Pin homologs" 46689; Homeodomain-like -!- 53041; Resolvase-like "PF00239;Resolvase, N terminal domain;8.5e-60;codon 4-145 -!- PF02796;Helix-turn-helix domain of resolvase;3.6e-12;codon 147-191" CDS ECK1539 tfaQ tfaQ ydfM b1546 1632334 1632909 - (no change) JW1539 1636024 1636599 - h Qin prophage; predicted tail fibre assembly protein C Cytoplasmic cryptic prophage Qin PF02413;Caudovirales tail fibre assembly protein;4.1e-65;codon 53-191 CDS ECK1540 stfQ stfQ b1547 1632909 1633871 - (no change) JW1540 1636599 1637561 - h Qin prophage; predicted side tail fibre assembly protein C Cytoplasmic cryptic prophage Qin PF07484;Phage Tail Collar Domain;6.8e-23;codon 94-141 -!- 6 of PF03335;Phage tail fibre repeat: 1.1;codon 157-170 -!- 0.025;codon 189-202 -!- 1;codon 203-216 -!- 0.12;codon 255-268 -!- 0.67;codon 269-282 -!- 0.61;codon 287-300 CDS ECK1541 nohA nohA b1548 1633822 1634391 - (no change) JW1541 1637512 1638081 - h Qin prophage; predicted packaging protein NU-1 homologue -!- Fur regulon C 92334985 Cytoplasmic cryptic prophage Qin "COG4220;Phage DNA packaging protein, Nu1 subunit of terminase" 46955; Putative DNA-binding domain PF07471;Phage DNA packaging protein Nu1;1.7e-122;codon 1-164 CDS ECK1542 ynfO ynfO b4533 1634780 1635013 + new JW5251 1638470 1638703 + h Qin prophage; predicted protein C CDS ECK1543 ydfO ydfO b1549 1635071 1635481 + start codon change JW5252 1638761 1639171 + h Qin prophage; predicted protein C Cytoplasmic cryptic prophage Qin PF07166;Protein of unknown function (DUF1398);6e-95;codon 8-132 CDS ECK1544 gnsB gnsB ydfY b1550 1635633 1635806 - start codon change JW5253 1639323 1639496 - h Qin prophage; predicted protein Multicopy suppressor of cold/temperature sensitive mutants -!- overexpression increases unsaturated fatty acid content of phospholipids -!- paralog of GnsA C 21429224 Cytoplasmic cryptic prophage Qin CDS ECK1545 ynfN ynfN b1551 1635978 1636133 - start codon change JW5254 1639668 1639823 - h Qin prophage; predicted protein C Cytoplasmic cryptic prophage Qin regulated by attenuation (ynfN) "55347; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain" CDS ECK1546 cspI cspI cspJ b1552 1636479 1636691 - (no change) JW1544 1640169 1640381 - h Qin prophage; cold shock protein cold shock inducible E 9484881 Cytoplasmic cryptic prophage Qin COG1278;Cold shock proteins 50249; Nucleic acid-binding proteins PF00313;'Cold-shock' DNA-binding domain;4.4e-42;codon 4-70 CDS ECK1547 ydfP ydfP b1553 1637054 1637551 - (no change) JW1545 1640744 1641241 - h Qin prophage; conserved protein C Membrane Anchored cryptic prophage Qin CDS ECK1548 ydfQ ydfQ b1554 1637548 1638081 - (no change) JW1546 1641238 1641771 - h Qin prophage; predicted lysozyme C cryptic prophage Qin 1-24 COG3772;Phage-related lysozyme (muraminidase) 53955; Lysozyme-like PF00959;Phage lysozyme;9.6e-37;codon 48-166 CDS ECK1549 ydfR ydfR b1555 1638078 1638389 - (no change) JW1547 1641768 1642079 - h Qin prophage; predicted protein C Cytoplasmic cryptic prophage Qin PF07041;Protein of unknown function (DUF1327);6.3e-35;codon 1-93 CDS ECK1550 essQ essQ ydfS b1556 1638394 1638609 - start codon change JW5255 1642084 1642299 - h Qin prophage; predicted S lysis protein C Integral Membrane Protein cryptic prophage Qin 1.E.1; The P21 Holin S (P21 Holin) Family 2 2 PF04971;Lysis protein S;5.8e-52;codon 29-96 CDS ECK1551 cspB cspB b1557 1639363 1639578 - (no change) JW1549 1643053 1643268 - h Qin prophage; cold shock protein cold-shock inducible E 94293754 -!- 94293756 -!- 9439003 Cytoplasmic cryptic prophage Qin COG1278;Cold shock proteins 50249; Nucleic acid-binding proteins PF00313;'Cold-shock' DNA-binding domain;2.8e-42;codon 4-70 CDS ECK1552 cspF cspF b1558 1639879 1640091 + (no change) JW1550 1643569 1643781 + h Qin prophage; cold shock protein E 9484881 -!- 8022261 -!- 9439003 Cytoplasmic cryptic prophage Qin COG1278;Cold shock proteins 50249; Nucleic acid-binding proteins PF00313;'Cold-shock' DNA-binding domain;8.9e-25;codon 4-70 CDS ECK1553 ydfT ydfT b1559 1640513 1641265 - start codon change JW1551 1644203 1644955 - h Qin prophage; predicted antitermination protein Q C Cytoplasmic cryptic prophage Qin 57938; Cysteine-rich domain of the chaperone protein DnaJ. PF03589;Antitermination protein;6.6e-54;codon 24-117 -!- PF03589;Antitermination protein;4.2e-55;codon 166-257 CDS ECK1554 ydfU ydfU b1560 1641279 1642328 - start codon change JW5909 1644969 1646018 - h Qin prophage; predicted protein C Cytoplasmic cryptic prophage Qin PF06914;Protein of unknown function (DUF1277);5.6e-232;codon 63-362 CDS ECK1555 rem rem b1561 1642675 1642926 - (no change) JW1553 1646365 1646616 - h Qin prophage; predicted protein C 2990907 Cytoplasmic cryptic prophage Qin regulated by attenuation (rem) CDS ECK1556 hokD hokD relF b1562 1643143 1643298 - (no change) JW1554 1646833 1646988 - h Qin prophage; small toxic polypeptide upstream regulatory elements absent suggesting inactivating rearrangement E 90094252 -!- 90136075 -!- 91329297 -!- 99291074 -!- 2990907 cryptic prophage Qin PF01848;Hok/gef family;3.7e-27;codon 2-51 CDS ECK1557 relE relE b1563 1643370 1643657 - (no change) JW1555 1647060 1647347 - h Qin prophage; toxin of the RelE-RelB toxin-antitoxin system E 21592958 -!- 99141390 -!- 2990907 Cytoplasmic cryptic prophage Qin COG2026;Cytotoxic translational repressor of toxin-antitoxin stability system PF05016;Plasmid stabilisation system protein;1.8e-16;codon 5-85 GO:0005737 cytoplasm GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1558 relB relB RC b1564 1643657 1643896 - (no change) JW1556 1647347 1647586 - h Qin prophage; bifunctional antitoxin of the RelE-RelB toxin-antitoxin system and transcriptional repressor E 21592958 -!- 342488 -!- 99141390 -!- 2990907 Cytoplasmic cryptic prophage Qin COG3077;DNA-damage-inducible protein J PF04221;RelB antitoxin;1.8e-38;codon 1-79 GO:0005737 cytoplasm GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1559 ydfV ydfV b1565 1643921 1644226 + (no change) JW1557 1647611 1647916 + h Qin prophage; predicted protein C cryptic prophage Qin CDS ECK1560 flxA flxA b1566 1644429 1644761 + (no change) JW1558 1648119 1648451 + h Qin prophage; predicted protein C 9358034 Cytoplasmic cryptic prophage Qin CDS ECK1561 ydfW ydfW b1567 1645198 1645347 - (no change) JW1559 1648888 1649037 - h Qin prophage; predicted protein C Cytoplasmic cryptic prophage Qin CDS ECK1562 ydfX ydfX b1568 1645370 1645660 - (no change) JW1560 1649060 1649350 - h Qin prophage; predicted protein C Cytoplasmic cryptic prophage Qin PF06254;Protein of unknown function (DUF1019);4.7e-24;codon 1-96 CDS ECK1563 dicC dicC ftsT b1569 1645644 1645874 - (no change) JW1561 1649334 1649564 - h Qin prophage; DNA-binding transcriptional regulator for DicB E 88232418 -!- 3532030 Cytoplasmic cryptic prophage Qin CDS ECK1564 dicA dicA ftsT b1570 1645958 1646365 + (no change) JW1562 1649648 1650055 + h Qin prophage; predicted regulator for DicB C 88232418 -!- 3532030 Cytoplasmic cryptic prophage Qin COG1396;Predicted transcriptional regulators 47413; lambda repressor-like DNA-binding domains PF01381;Helix-turn-helix;1.2e-15;codon 12-66 CDS ECK1565 ydfA ydfA b1571 1646532 1646687 + (no change) JW1563 1650222 1650377 + h Qin prophage; predicted protein C Cytoplasmic cryptic prophage Qin PF07151;Protein of unknown function (DUF1391);1.2e-38;codon 1-50 CDS ECK1566 ydfB ydfB b1572 1646689 1646817 + start codon change JW1564 1650379 1650507 + h Qin prophage; predicted protein C Cytoplasmic cryptic prophage Qin CDS ECK1567 ydfC ydfC b1573 1646847 1647065 + (no change) JW1565 1650537 1650755 + h Qin prophage; predicted protein C Cytoplasmic cryptic prophage Qin misc_RNA ECK1568 dicF dicF b1574 1647406 1647458 + (no change) JWR0030 1651096 1651148 + h Qin prophage; DicF antisense RNA regulator of ftsZ translation -!- blocks cell division E 90219018 -!- 92204016 cryptic prophage Qin CDS ECK1569 dicB dicB ftsT b1575 1647633 1647821 + (no change) JW1566 1651323 1651511 + h Qin prophage; cell division inhibition protein complexes with MinC and causes FtsZ depolymerisation E 88232418 -!- 88289404 -!- 92104987 Cytoplasmic cryptic prophage Qin regulated by attenuation (dicB-ydfD) PF05358;DicB protein;1.2e-51;codon 1-62 CDS ECK1570 ydfD ydfD b1576 1647818 1648009 + (no change) JW1567 1651508 1651699 + h Qin prophage; predicted protein C Periplasmic cryptic prophage Qin PF07358;Protein of unknown function (DUF1482);1.1e-40;codon 5-62 CDS ECK1571 ydfE ydfE b1577 1648102 1649022 + (no change) JW1568 1651792 1652712 + h Qin prophage; predicted protein C 2477663 Cytoplasmic cryptic prophage Qin CDS ECK1572 insD insD b1578 1648905 1649561 + (no change) JW1570 1652595 1653251 + h Qin prophage; predicted transposase C 2830172 cryptic prophage Qin -!- IS2 COG2801;Transposase and inactivated derivatives 53098; Ribonuclease H-like PF00665;Integrase core domain;5.5e-34;codon 38-203 CDS ECK1573 intQ intQ b1579 1649536 1650732 + (no change) JW1571 1653226 1654422 + h Qin prophage; predicted defective integrase C Cytoplasmic cryptic prophage Qin COG0582;Integrase "47823; lambda integrase-like, N-terminal domain -!- 56349; DNA breaking-rejoining enzymes" PF00589;Phage integrase family;3.2e-09;codon 172-374 CDS ECK1574 ynfP ynfP b4534 1650752 1650862 - pseudogene -!- new JW5257 1654442 1654552 - pseudogene su predicted protein (pseudogene) N-terminus of split pseudogene ydfJ C CDS ECK1575 rspB rspB b1580 1650920 1651939 - (no change) JW1572 1654610 1655629 - pe "predicted oxidoreductase, Zn-dependent and NAD(P)-binding" starvation induced -!- co-transcribed with rspA C 7545940 Cytoplasmic COG1063;Threonine dehydrogenase and related Zn-dependent dehydrogenases 50129; GroES-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF00107;Zinc-binding dehydrogenase;2.7e-89;codon 7-337 GO:0042594 response to starvation CDS ECK1576 rspA rspA b1581 1651951 1653165 - (no change) JW1573 1655641 1656855 - pe predicted dehydratase starvation induced C 93341455 -!- 94310441 Cytoplasmic COG4948;L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily 51604; Enolase C-terminal domain-like -!- 54826; Enolase N-terminal domain-like PF02746;Mandelate racemase / muconate lactonizing en;2e-60;codon 1-110 -!- PF01188;Mandelate racemase / muconate lactonizing en;5.9e-162;codon 113-385 GO:0042594 response to starvation CDS ECK1577 ynfA ynfA b1582 1653371 1653697 - (no change) JW1574 1657061 1657387 - pm conserved inner membrane protein C Integral Membrane Protein 9.B.45; The YnfA (YnfA) Family 4 4 out COG1742;Uncharacterized conserved protein "PF02694;Uncharacterized BCR, YnfA/UPF0060 family;4.3e-77;codon 1-108" GO:0009274 cell wall (sensu Bacteria) CDS ECK1578 ynfB ynfB b1583 1653832 1654173 + (no change) JW1575 1657522 1657863 + o predicted protein C Periplasmic 1-27 PF06932;Protein of unknown function (DUF1283);8.2e-89;codon 5-113 CDS ECK1579 speG speG b1584 1654208 1654768 + (no change) JW1576 1657898 1658458 + e spermidine N1-acetyltransferase E 94357898 Cytoplasmic 2.3.1.57 monomeric multimer; spermidine acetyltransferase (b1584) "COG1670;Acetyltransferases, including N-acetylases of ribosomal proteins" 55729; Acyl-CoA N-acyltransferases (Nat) PF00583;Acetyltransferase (GNAT) family;1.3e-20;codon 60-141 GO:0006596 polyamine biosynthesis CDS ECK1580 ynfC ynfC b1585 1654771 1655481 - start codon change JW5258 1658461 1659171 - o predicted protein C Inner membrane Lipoprotein PF06788;Uncharacterised protein family (UPF0257);1.4e-196;codon 13-248 CDS ECK1581 ynfD ynfD b1586 1655589 1655894 + start codon change JW5259 1659279 1659584 + o predicted protein C 9868784 Periplasmic 1-35 101 PF06649;Protein of unknown function (DUF1161);2e-45;codon 14-94 CDS ECK1582 ynfE ynfE b1587 1656093 1658519 + (no change) JW1579 1659783 1662209 + e oxidoreductase subunit "paralog of DMSO reductase, subunit A" E 14522592 Periplasmic heteromultimer; dimethyl sulfoxide reductase paralogue (b1587-b1588-b1589-b1590) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 1-27 "COG0243;Anaerobic dehydrogenases, typically selenocysteine-containing" "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3" PF04879;Molybdopterin oxidoreductase Fe4S4 do;3.9e-15;codon 49-108 -!- PF00384;Molybdopterin oxidoreductase;2.2e-142;codon 111-566 -!- PF01568;Molydopterin dinucleotide binding dom;1.5e-47;codon 687-802 TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.06;codon 10-43 -!- TIGR02166;dmsA_ynfE: anaerobic dimethyl sulfoxid;0;codon 10-808 CDS ECK1583 ynfF ynfF b1588 1658580 1661003 + start codon change JW5260 1662270 1664693 + e oxidoreductase subunit "paralog of DMSO reductase, subunit A" E 14522592 Periplasmic heteromultimer; dimethyl sulfoxide reductase paralogue (b1587-b1588-b1589-b1590) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 1-32 "COG0243;Anaerobic dehydrogenases, typically selenocysteine-containing" "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3" PF04879;Molybdopterin oxidoreductase Fe4S4 do;8.7e-13;codon 53-112 -!- PF00384;Molybdopterin oxidoreductase;1e-134;codon 115-566 -!- PF01568;Molydopterin dinucleotide binding dom;1.1e-43;codon 687-802 TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.0024;codon 15-46 -!- TIGR02166;dmsA_ynfE: anaerobic dimethyl sulfoxid;0;codon 15-808 CDS ECK1584 ynfG ynfG b1589 1661014 1661631 + (no change) JW1581 1664704 1665321 + c "oxidoreductase, Fe-S subunit" E 14522592 Cytoplasmic heteromultimer; dimethyl sulfoxide reductase paralogue (b1587-b1588-b1589-b1590) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family COG0437;Fe-S-cluster-containing hydrogenase components 1 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;0.015;codon 7-29 -!- PF00037;4Fe-4S binding domain;1.4e-07;codon 92-115 CDS ECK1585 ynfH ynfH b1590 1661633 1662487 + (no change) JW5261 1665323 1666177 + m "oxidoreductase, membrane subunit" E 14522592 Integral Membrane Protein heteromultimer; dimethyl sulfoxide reductase paralogue (b1587-b1588-b1589-b1590) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family 8 8 out COG3302;DMSO reductase anchor subunit PF04976;DMSO reductase anchor subunit (DmsC);7.6e-177;codon 1-274 GO:0009274 cell wall (sensu Bacteria) CDS ECK1586 dmsD dmsD ynfI b1591 1662530 1663144 + start codon change JW5262 1666220 1666834 + f twin-argninine leader-binding protein for DmsA and TorA E 14766221 -!- 21206221 Cytoplasmic COG3381;Uncharacterized component of anaerobic dehydrogenases PF06192;Cytoplasmic chaperone TorD;4.7e-58;codon 36-169 CDS ECK1587 clcB clcB mriT -!- ynfJ -!- yntJ b1592 1663339 1664595 + start codon change JW5263 1667029 1668285 + pt predicted voltage-gated chloride channel C Integral Membrane Protein 11 10 in COG0038;Chloride channel protein EriC 56869; Membrane all-alpha PF00654;Voltage gated chloride channel;9.9e-17;codon 76-425 CDS ECK1588 ynfK ynfK b1593 1664548 1665243 - start codon change JW5264 1668238 1668933 - pe predicted dethiobiotin synthetase C Cytoplasmic 52540; P-loop containing nucleotide triphosphate hydrolases PF01656;CobQ/CobB/MinD/ParA nucleotide binding domai;1.1e-29;codon 9-223 TIGR00347;bioD: dethiobiotin synthase;6.7e-51;codon 10-176 GO:0009102 biotin biosynthesis CDS ECK1589 dgsA dgsA mlc b1594 1665368 1666588 - (no change) JW1586 1669058 1670278 - r DNA-binding transcriptional repressor E 10318813 -!- 20490366 -!- 6989798 -!- 99340206 -!- 99395104 -!- 99398866 -!- 7766024 Cytoplasmic NagC/XylR malT -!- manXYZ -!- mlc -!- ptsG -!- ptsHI-crr COG1940;Transcriptional regulator/sugar kinase 46785; Winged helix PF00480;ROK family;3.7e-33;codon 89-274 GO:0005737 cytoplasm GO:0000271 polysaccharide biosynthesis -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1590 ynfL ynfL b1595 1666723 1667616 - (no change) JW1587 1670413 1671306 - pr predicted DNA-binding transcriptional regulator C LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;2.1e-19;codon 5-64 -!- PF03466;LysR substrate binding domain;4e-53;codon 88-297 "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1591 ynfM ynfM yzyC b1596 1667723 1668976 + (no change) JW1588 1671413 1672666 + pt predicted transporter C Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG0477;Permeases of the major facilitator superfamily PF00083;Sugar (and other) transporter;0.00012;codon 36-416 -!- PF07690;Major Facilitator Superfamily;5.5e-45;codon 41-386 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1592 asr asr b1597 1669400 1669708 + start codon change JW5826 1673090 1673398 + f acid shock-inducible periplasmic protein required for acid tolerance -!- expression controlled by phoBR E 10094685 -!- 12670971 Periplasmic 1-30 PF06392;Acid shock protein repeat;0.0049;codon 53-71 -!- PF06392;Acid shock protein repeat;0.011;codon 72-92 GO:0009268 response to pH CDS ECK1593 ydgD ydgD b1598 1669984 1670805 + (no change) JW1590 1673674 1674495 + pe predicted peptidase C Periplasmic S1A family; B1598 endopeptidase 1-21 COG3591;V8-like Glu-specific endopeptidase 50494; Trypsin-like serine proteases PF00089;Trypsin;0.00025;codon 41-267 CDS ECK1594 mdtI mdtI mtdI -!- ydgE b1599 1670844 1671173 - (no change) JW1591 1674534 1674863 - t multidrug efflux system transporter E 21450803 Integral Membrane Protein heteromultimer; YdgEF-CPLX (b1599-b1600) 4 4 out COG2076;Membrane transporters of cations and cationic drugs PF00893;Small Multidrug Resistance protein;8e-47;codon 4-99 CDS ECK1595 mdtJ mdtJ ydgF b1600 1671160 1671525 - (no change) JW1592 1674850 1675215 - t multidrug efflux system transporter E 21450803 Integral Membrane Protein heteromultimer; YdgEF-CPLX (b1599-b1600) 4 4 in COG2076;Membrane transporters of cations and cationic drugs PF00893;Small Multidrug Resistance protein;8.1e-39;codon 3-95 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1596 ydgG ydgG b1601 1671937 1672971 + (no change) JW1593 1675627 1676661 + pm predicted inner membrane protein C 14727089 Integral Membrane Protein 8 8 in COG0628;Predicted permease PF01594;Domain of unknown function DUF20;1.3e-92;codon 13-329 CDS ECK1597 pntB pntB b1602 1672996 1674384 - (no change) JW1594 1676686 1678074 - e "pyridine nucleotide transhydrogenase, beta subunit" E 92031646 -!- 92202262 -!- 92339464 -!- 3525165 Integral Membrane Protein 1.6.1.2 heteromultimer; pyridine nucleotide transhydrogenase (b1602-b1603) 3.D.2; The Proton-translocating Transhydrogenase (PTH) Family 10 9 in COG1282;NAD/NADP transhydrogenase beta subunit 52467; DHS-like NAD/FAD-binding domain PF02233;NAD(P) transhydrogenase beta subunit;0;codon 4-462 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1598 pntA pntA b1603 1674395 1675927 - (no change) JW1595 1678085 1679617 - e "pyridine nucleotide transhydrogenase, alpha subunit" E 92031646 -!- 92202262 -!- 94124004 -!- 1633824 -!- 3525165 Integral Membrane Protein 1.6.1.2 heteromultimer; pyridine nucleotide transhydrogenase (b1602-b1603) 3.D.2; The Proton-translocating Transhydrogenase (PTH) Family 5 5 in COG3288;NAD/NADP transhydrogenase alpha subunit 52283; Formate/glycerate dehydrogenase catalytic domain-like "PF05222;Alanine dehydrogenase/PNT, N-terminal dom;8.7e-76;codon 4-137 -!- PF01262;Alanine dehydrogenase/PNT, C-terminal dom;3.2e-114;codon 144-350" "TIGR00561;pntA: NAD(P) transhydrogenase, alpha subunit;0;codon 2-510" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1599 ydgH ydgH b1604 1676451 1677395 + (no change) JW1596 1680141 1681085 + o predicted protein C Periplasmic 1-22 regulated by attenuation (ydgH) PF07338;Protein of unknown function (DUF1471);8.1e-11;codon 1-90 -!- PF07338;Protein of unknown function (DUF1471);0.00066;codon 237-314 CDS ECK1600 ydgI ydgI arcD b1605 1677581 1678963 + (no change) JW1597 1681271 1682653 + pt predicted arginine/ornithine antiporter transporter C Integral Membrane Protein 13 13 out COG0531;Amino acid transporters PF00324;Amino acid permease;6.7e-05;codon 12-436 TIGR00905;2A0302: arginine/ornithine antiporter;3.8e-288;codon 1-460 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1601 folM folM ydgB b1606 1679000 1679722 + (no change) JW1598 1682690 1683412 + e dihydrofolate reductase isozyme E 14617668 Cytoplasmic 1.5.1.3 COG1028;Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) 51735; NAD(P)-binding Rossmann-fold domains PF00106;short chain dehydrogenase;3e-07;codon 9-237 CDS ECK1602 ydgC ydgC b1607 1679719 1680054 - (no change) JW1599 1683409 1683744 - pm conserved inner membrane protein associated with alginate biosynthesis C Integral Membrane Protein 4 4 out COG3136;Uncharacterized membrane protein required for alginate biosynthesis PF06942;GlpM protein;4.2e-83;codon 5-111 GO:0009274 cell wall (sensu Bacteria) CDS ECK1603 rstA rstA urpT b1608 1680174 1680902 + (no change) JW1600 1683864 1684592 + r DNA-binding response regulator in two-component regulatory system with RstB drug resistance phenotype E 12399493 -!- 15522865 -!- 12951338 -!- 12897016 -!- 12813061 -!- 12618449 -!- 1495392 Cytoplasmic Two COG0745;Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;5.4e-23;codon 5-123 -!- PF00486;Transcriptional regulatory protein, C te;1.9e-19;codon 160-236" GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1604 rstB rstB uspT b1609 1680906 1682207 + (no change) JW1601 1684596 1685897 + r sensory histidine kinase in two-component regulatory system with RstA drug resistance phenotype E 93086426 -!- 1495392 -!- 1925016 -!- 2646639 Integral Membrane Protein 3 2 in COG0642;Signal transduction histidine kinase 47384; Homodimeric domain of signal transducing histidine kinase -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF00672;HAMP domain;1e-07;codon 138-207 -!- PF00512;His Kinase A (phosphoacceptor) domain;4.2e-10;codon 211-271 -!- PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;1.3e-37;codon 315-424" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006464 protein modification CDS ECK1605 tus tus tau b1610 1682283 1683212 + (no change) JW1602 1685973 1686902 + f "inhibitor of replication at Ter, DNA-binding protein" "binds and arrests the DnaB helicase at Ter sites, blocking replication fork" E 92177415 -!- 92218396 -!- 92283849 -!- 99303844 -!- 2646639 -!- 2687269 -!- 3541901 -!- 8547250 -!- 8857533 Cytoplasmic 1ECR 56596; Replication terminator protein (Tus) PF05472;DNA replication terminus site-binding protei;9.2e-228;codon 8-309 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK1606 fumC fumC b1611 1683209 1684612 - (no change) JW1603 1686899 1688302 - e "fumarate hydratase (fumarase C),aerobic Class II" E 87099873 -!- 92335203 -!- 93267645 -!- 1917897 -!- 3282546 -!- 6328431 -!- 8909293 -!- 9098893 Cytoplasmic 4.2.1.2 monomeric multimer; fumarase C (b1611) regulated by attenuation (fumC) COG0114;Fumarase 48557; L-aspartase-like PF00206;Lyase;3.1e-196;codon 12-342 "TIGR00979;fumC_II: fumarate hydratase, class II;0;codon 4-461" GO:0006099 tricarboxylic acid cycle -!- GO:0006113 fermentation -!- GO:0009061 anaerobic respiration CDS ECK1607 fumA fumA b1612 1684755 1686401 - (no change) JW1604 1688445 1690091 - e "fumarate hydratase (fumarase A), aerobic Class I" E 88193096 -!- 88268900 -!- 92011457 -!- 3005475 -!- 6328431 -!- 9298646 Cytoplasmic 4.2.1.2 monomeric multimer; fumarase A (b1612) "COG1951;Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain -!- COG1838;Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain" PF05681;Fumarate hydratase (Fumerase);2.4e-144;codon 47-328 -!- PF05683;Fumarase C-terminus;6.5e-120;codon 332-541 "TIGR00722;ttdA_fumA_fumB: hydro-lyases, Fe-S typ;9.8e-26;codon 47-328 -!- TIGR00723;ttdB_fumA_fumB: hydro-lyases, Fe-S typ;1.8e-68;codon 372-537" GO:0006099 tricarboxylic acid cycle CDS ECK1608 manA manA pmi b1613 1686600 1687775 + (no change) JW1605 1690290 1691465 + e mannose-6-phosphate isomerase E 82100097 -!- 6397402 Cytoplasmic 5.3.1.8 51182; RmlC-like PF01238;Phosphomannose isomerase type I;3.9e-211;codon 1-357 "TIGR00218;manA: mannose-6-phosphate isomerase, class I;1.3e-160;codon 2-387" GO:0030113 capsule (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0009226 nucleotide-sugar biosynthesis -!- GO:0009242 colanic acid biosynthesis -!- GO:0009269 response to dessication CDS ECK1609 ydgA ydgA b1614 1687876 1689384 + (no change) JW1606 1691566 1693074 + o conserved protein C COG5339;Uncharacterized protein conserved in bacteria PF06097;Bacterial protein of unknown function (DUF94;0;codon 1-482 CDS ECK1610 uidC uidC gusC b1615 1689610 1690875 - start codon change JW1607 1693300 1694565 - pt predicted outer membrane porin protein C 15774881 Periplasmic 417 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1611 uidB uidB gusB -!- uidP b1616 1690914 1692287 - (no change) JW1608 1694604 1695977 - t glucuronide transporter E 3534890 Integral Membrane Protein 2.A.2; The Glycoside-Pentoside-Hexuronide (GPH):Cation Symporter Family 11 12 in COG2211;Na+/melibiose symporter and related transporters PF07690;Major Facilitator Superfamily;1.9e-10;codon 13-387 TIGR00792;gph: sugar (Glycoside-Pentoside-Hexuronide);9.4e-223;codon 10-444 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK1612 uidA uidA gurA -!- gusA -!- bglR -!- vidA b1617 1692284 1694095 - (no change) JW1609 1695974 1697785 - e beta-D-glucuronidase E 87041472 -!- 88038341 -!- 2103475 -!- 8125312 Cytoplasmic 3.2.1.31 COG3250;Beta-galactosidase/beta-glucuronidase 49303; beta-Galactosidase/glucuronidase domain -!- 49785; Galactose-binding domain-like -!- 51445; (Trans)glycosidases "PF02837;Glycosyl hydrolases family 2, sugar b;1.3e-68;codon 9-180 -!- PF00703;Glycosyl hydrolases family 2, immunog;5.6e-36;codon 182-272 -!- PF02836;Glycosyl hydrolases family 2, TIM bar;4.3e-181;codon 274-593" GO:0016052 carbohydrate catabolism CDS ECK1613 uidR uidR gusR b1618 1694486 1695076 - (no change) JW1610 1698176 1698766 - r DNA-binding transcriptional repressor E 88038341 -!- 2823062 -!- 3934044 -!- 11115104 Cytoplasmic Unclass uidA -!- uidR COG1309;Transcriptional regulator 46689; Homeodomain-like "PF00440;Bacterial regulatory proteins, tetR family;2.3e-19;codon 16-62" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1614 hdhA hdhA hsdH -!- hsd b1619 1695297 1696064 - (no change) JW1611 1698987 1699754 - e "7-alpha-hydroxysteroid dehydrogenase, NAD-dependent" E 91177803 -!- 8672472 Cytoplasmic 1.1.1.159 monomeric multimer; 7-alpha-hydroxysteroid dehydrogenase (b1619) regulated by attenuation (hdhA) COG1028;Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) 51735; NAD(P)-binding Rossmann-fold domains PF00106;short chain dehydrogenase;4.5e-100;codon 14-250 GO:0005737 cytoplasm CDS ECK1615 malI malI b1620 1696176 1697204 - (no change) JW1612 1699866 1700894 - r DNA-binding transcriptional repressor E 89359124 -!- 91310596 GalR/LacI 1-21 malI -!- malXY COG1609;Transcriptional regulators 47413; lambda repressor-like DNA-binding domains -!- 53822; Periplasmic binding protein-like I "PF00356;Bacterial regulatory proteins, lacI fami;1.3e-10;codon 7-32 -!- PF00532;Periplasmic binding proteins and sugar b;4.3e-113;codon 64-342" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1616 malX malX b1621 1697379 1698971 + (no change) JW1613 1701069 1702661 + t fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component E 91310596 -!- 2670898 Integral Membrane Protein 2.7.1.69 heteromultimer; EIIBCMalX (b2417-b2416-b2415-b1621) 4.A.1; The PTS Glucose-Glucoside (Glc) Family 8 8 in "fused PTS family enzyme, maltose/glucose-specific: enzyme IIC (aa1-383) -!- enzyme IIB (aa409-530)" "COG1263;Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific -!- COG1264;Phosphotransferase system IIB components" 55604; Glucose permease domain IIB "PF02378;Phosphotransferase system, EIIC;1.1e-112;codon 19-361 -!- PF00367;phosphotransferase system, EIIB;4.3e-19;codon 452-486" "TIGR02004;PTS-IIBC-malX: PTS system, maltose and;0;codon 8-525 -!- TIGR00852;pts-Glc: PTS system, maltose and glucos;8e-149;codon 70-372 -!- TIGR00826;EIIB_glc: PTS system, glucose-like IIB;3e-41;codon 420-511" GO:0016052 carbohydrate catabolism CDS ECK1617 malY malY b1622 1698981 1700153 + (no change) JW1614 1702671 1703843 + e "bifunctional beta-cystathionase, PLP-dependent and regulator of maltose regulon" E 20164451 -!- 7665481 -!- 91310596 Cytoplasmic 4.4.1.8 1D2F COG1168;Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities 53383; PLP-dependent transferases PF00155;Aminotransferase class I and II;7.8e-58;codon 74-383 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK1618 add add b1623 1700257 1701258 + (no change) JW1615 1703947 1704948 + e adenosine deaminase E 76125643 -!- 79010020 -!- 91152042 Cytoplasmic 3.5.4.4 regulated by attenuation (add) COG1816;Adenosine deaminase 51556; Metallo-dependent hydrolases PF00962;Adenosine/AMP deaminase;3e-144;codon 5-329 TIGR01430;aden_deam: adenosine deaminase;1.8e-146;codon 6-330 "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK1619 ydgJ ydgJ b1624 1701292 1702332 - start codon change JW5265 1704982 1706022 - pe predicted oxidoreductase C Cytoplasmic "51735; NAD(P)-binding Rossmann-fold domains -!- 55347; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain" "PF01408;Oxidoreductase family, NAD-binding Ros;5e-44;codon 18-135 -!- PF02894;Oxidoreductase family, C-terminal alph;1e-26;codon 147-254" CDS ECK1620 blr blr b4409 1702575 1702700 + (no change) JW5963 1706265 1706390 + m beta-lactam resistance membrane protein E 20392465 -!- 10931331 Membrane Anchored CDS ECK1621 ydgT ydgT b1625 1702973 1703188 + (no change) JW1617 1706663 1706878 + pr predicted regulator C Cytoplasmic 68989; Hemolysin expression modulating protein HHA PF05321;Haemolysin expression modulating protein;9.4e-34;codon 8-68 CDS ECK1622 ydgK ydgK b1626 1703274 1703714 + start codon change JW1618 1706964 1707404 + pm conserved inner membrane protein C Integral Membrane Protein 4 4 in regulated by attenuation (ydgK) CDS ECK1623 rsxA rsxA ydgL -!- rnfA b1627 1703791 1704372 + (no change) JW1619 1707481 1708062 + pm predicted inner membrane subunit required for the reduction of SoxR C 10411911 -!- 10637328 -!- 12773378 Integral Membrane Protein 6 6 out regulated by attenuation (rnfA-rnfB-rnfC-rnfD-rnfG-rnfE-nth) "COG4657;Predicted NADH:ubiquinone oxidoreductase, subunit RnfA" "PF02508;Rnf-Nqr subunit, membrane protein;3.3e-116;codon 1-192" "TIGR01943;rnfA: electron transport complex, RnfABCDGE;4e-149;codon 2-191" GO:0009274 cell wall (sensu Bacteria) CDS ECK1624 rsxB rsxB ydgM -!- rnfB b1628 1704372 1704950 + (no change) JW1620 1708062 1708640 + pc predicted iron-sulfur protein required for the reduction of SoxR C 10637328 -!- 12773378 "COG2878;Predicted NADH:ubiquinone oxidoreductase, subunit RnfB" 54862; 4Fe-4S ferredoxins PF04060;Putative Fe-S cluster;1.7e-15;codon 43-77 -!- PF00037;4Fe-4S binding domain;1.3e-07;codon 110-133 -!- PF00037;4Fe-4S binding domain;9.2e-06;codon 140-163 "TIGR01944;rnfB: electron transport complex, RnfABCDGE;2.8e-144;codon 1-192" GO:0009055 electron carrier activity CDS ECK1625 rsxC rsxC ydgN -!- rnfC b1629 1704943 1707165 + (no change) JW1621 1708633 1710855 + pc fused predicted 4Fe-4S ferredoxin-type protein -!- conserved protein required for the reduction of SoxR C Cytoplasmic fused electron transport protein: Fe-S binding protein (aa1-448) -!- unknown function protein (aa450-740) "COG4656;Predicted NADH:ubiquinone oxidoreductase, subunit RnfC" 46548; alpha-helical ferredoxin -!- 51246; Rudiment single hybrid motif PF01512;Respiratory-chain NADH dehydrogenase;5.5e-107;codon 117-340 -!- PF00037;4Fe-4S binding domain;0.0011;codon 370-393 -!- PF00037;4Fe-4S binding domain;7.1e-05;codon 409-432 "TIGR01945;rnfC: electron transport complex, RnfABCDGE;2.5e-256;codon 13-447" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1626 rsxD rsxD ydgO -!- rnfD b1630 1707166 1708224 + (no change) JW1622 1710856 1711914 + pe predicted inner membrane oxidoreductase required for the reduction of SoxR C 10637328 -!- 12773378 Integral Membrane Protein 10 10 "COG4658;Predicted NADH:ubiquinone oxidoreductase, subunit RnfD" "PF03116;NQR2, RnfD, RnfE family;3.3e-208;codon 2-350" "TIGR01946;rnfD: electron transport complex, RnfABCDGE;2.1e-248;codon 8-349" GO:0009274 cell wall (sensu Bacteria) CDS ECK1627 rsxG rsxG ydgP -!- rnfG b1631 1708228 1708848 + (no change) JW1623 1711918 1712538 + pe predicted oxidoreductase required for the reduction of SoxR C 10637328 -!- 12773378 Periplasmic "COG4659;Predicted NADH:ubiquinone oxidoreductase, subunit RnfG" PF04205;FMN-binding domain;5.1e-25;codon 99-191 "TIGR01947;rnfG: electron transport complex, RnfABCDGE;9.7e-108;codon 9-193" CDS ECK1628 rsxE rsxE ydgQ -!- rnfE b1632 1708852 1709547 + (no change) JW1624 1712542 1713237 + pc predicted inner membrane NADH-quinone reductase required for the reduction of SoxR C 10411911 -!- 10637328 -!- 12773378 Integral Membrane Protein 5 5 in "COG4660;Predicted NADH:ubiquinone oxidoreductase, subunit RnfE" "PF02508;Rnf-Nqr subunit, membrane protein;1.3e-120;codon 1-201" "TIGR01948;rnfE: electron transport complex, RnfABCDGE;8.4e-123;codon 5-209" GO:0009274 cell wall (sensu Bacteria) CDS ECK1629 nth nth b1633 1709547 1710182 + (no change) JW1625 1713237 1713872 + e DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III) acts on 5-formyluracil and 5-hydroxymethyluracil E 20519646 -!- 89352503 -!- 97315256 -!- 99427442 -!- 1411536 -!- 7664751 -!- 8092678 Cytoplasmic 4.2.99.18 COG0177;Predicted EndoIII-related endonuclease 48150; DNA-glycosylase PF00730;HhH-GPD superfamily base excision DNA repair;6.7e-22;codon 34-169 -!- PF00633;Helix-hairpin-helix motif;3e-05;codon 99-128 TIGR01083;nth: endonuclease III;1.4e-141;codon 3-194 GO:0005737 cytoplasm GO:0006308 DNA catabolism -!- GO:0006308 DNA catabolism -!- GO:0009314 response to radiation CDS ECK1630 ydgR ydgR tppB b1634 1710793 1712295 + (no change) JW1626 1714483 1715985 + pt predicted transporter C 15175316 Integral Membrane Protein 14 14 in COG3104;Dipeptide/tripeptide permease PF07690;Major Facilitator Superfamily;1.7e-14;codon 26-443 -!- PF00854;POT family;8.1e-113;codon 88-431 TIGR00924;yjdL_sub1_fam: amino acid/peptide trans;4.6e-162;codon 17-486 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1631 gst gst b1635 1712401 1713006 + (no change) JW1627 1716091 1716696 + e glutathionine S-transferase E 95096109 -!- 2185038 -!- 9680481 Cytoplasmic 2.5.1.18 monomeric multimer; glutathione transferase (b1635) regulated by attenuation (gst) COG0625;Glutathione S-transferase "47616; Glutathione S-transferases, C-terminal domain -!- 52833; Thioredoxin-like" "PF02798;Glutathione S-transferase, N-terminal domain;4.3e-21;codon 1-75 -!- PF00043;Glutathione S-transferase, C-terminal domain;2.1e-24;codon 87-189" CDS ECK1632 pdxY pdxY f287 -!- ydgS b1636 1713050 1713913 - (no change) JW1628 1716740 1717603 - e pyridoxal kinase 2/pyridoxine kinase E 9537380 Cytoplasmic 2.7.1.35 COG2240;Pyridoxal/pyridoxine/pyridoxamine kinase 53613; Ribokinase-like TIGR00687;pyridox_kin: pyridoxal kinase;7.2e-148;codon 1-287 GO:0009443 pyridoxal 5'-phosphate salvage CDS ECK1633 tyrS tyrS b1637 1713972 1715246 - (no change) JW1629 1717662 1718936 - e tyrosyl-tRNA synthetase E 90299820 -!- 91129301 -!- 94079900 -!- 1356963 -!- 6761148 Cytoplasmic 6.1.1.1 monomeric multimer; tyrosyl-tRNA synthetase (b1637) COG0162;Tyrosyl-tRNA synthetase 52374; Nucleotidylyl transferase PF00579;tRNA synthetases class I (W and Y);6.6e-133;codon 29-329 -!- PF01479;S4 domain;1.5e-06;codon 359-404 TIGR00234;tyrS: tyrosyl-tRNA synthetase;1.5e-160;codon 1-424 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK1634 pdxH pdxH b1638 1715375 1716031 - (no change) JW1630 1719065 1719721 - e pyridoxine 5'-phosphate oxidase E 93015640 -!- 98359888 -!- 10903950 -!- 11453690 -!- 7860596 Cytoplasmic 1.4.3.5 monomeric multimer; pyridoxine 5'-phosphate oxidase / pyridoxamine 5'-phosphate oxidase (b1638) 1G76 COG0259;Pyridoxamine-phosphate oxidase 50475; FMN-binding split barrel PF01243;Pyridoxamine 5'-phosphate oxidase;9.2e-32;codon 39-125 TIGR00558;pdxH: pyridoxamine 5'-phosphate oxidase;1.7e-163;codon 2-218 GO:0008615 pyridoxine biosynthesis -!- GO:0009443 pyridoxal 5'-phosphate salvage CDS ECK1635 ydhA ydhA b1639 1716090 1716419 - start codon change JW1631 1719780 1720109 - lp predicted lipoprotein C Cytoplasmic CDS ECK1636 ydhH ydhH b1640 1716517 1717626 - (no change) JW1632 1720207 1721316 - d conserved protein C Cytoplasmic COG2377;Predicted molecular chaperone distantly related to HSP70-fold metalloproteases 53067; Actin-like ATPase domain PF03702;Uncharacterised protein family (UPF0075);1.4e-265;codon 4-367 CDS ECK1637 slyB slyB b1641 1717900 1718367 + (no change) JW1633 1721590 1722057 + lp outer membrane lipoprotein C 8544813 Outer membrane Lipoprotein PF05433;Rickettsia 17 kDa surface antigen;5.7e-10;codon 60-103 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1638 slyA slyA b1642 1718414 1718848 - start codon change JW5267 1722104 1722538 - r DNA-binding transcriptional activator activator of slyA regulon E 10027972 -!- 12088660 -!- 99028910 -!- 11053378 -!- 12057949 -!- 8544813 -!- 8861216 Cytoplasmic MarR hlyE COG1846;Transcriptional regulators 46785; Winged helix PF01047;MarR family;1.9e-34;codon 31-135 GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1639 ydhI ydhI b1643 1719049 1719285 + (no change) JW1635 1722739 1722975 + pm predicted inner membrane protein C Integral Membrane Protein 2 2 PF07869;Protein of unknown function (DUF1656);2.8e-25;codon 12-75 CDS ECK1640 ydhJ ydhJ b1644 1719288 1720145 + start codon change JW1636 1722978 1723835 + e undecaprenyl pyrophosphate phosphatase E 12900028 Membrane Anchored 51230; Single hybrid motif PF00529;HlyD family secretion protein;5.3e-54;codon 57-296 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1641 ydhK ydhK b1645 1720145 1722157 + (no change) JW1637 1723835 1725847 + pm conserved inner membrane protein C Integral Membrane Protein 12 10 COG1289;Predicted membrane protein 53383; PLP-dependent transferases PF04632;Fusaric acid resistance protein conserved re;9.3e-50;codon 349-468 CDS ECK1642 sodC sodC b1646 1722158 1722679 - (no change) JW1638 1725848 1726369 - e "superoxide dismutase, Cu, Zn" E 98157961 -!- 7589534 -!- 7786035 -!- 7929223 -!- 8626323 -!- 9003353 -!- 9405149 Periplasmic 1.15.1.1 Cu2+ 1-19 173 1ESO COG2032;Cu/Zn superoxide dismutase "49329; Cu,Zn superoxide dismutase-like" PF00080;Copper/zinc superoxide dismutase (SODC);1.1e-39;codon 24-173 GO:0042597 periplasmic space GO:0006805 xenobiotic metabolism CDS ECK1643 ydhF ydhF b1647 1722760 1723656 - (no change) JW1639 1726450 1727346 - pe predicted oxidoreductase C Cytoplasmic 51430; NAD(P)-linked oxidoreductase PF00248;Aldo/keto reductase family;1.9e-74;codon 8-293 CDS ECK1644 ydhL ydhL b1648 1723705 1723944 - start codon change JW5827 1727395 1727634 - o conserved protein C Cytoplasmic COG3313;Predicted Fe-S protein PF06945;Protein of unknown function (DUF1289);7.1e-27;codon 57-111 CDS ECK1645 ydhM ydhM b1649 1724131 1724646 + start codon change JW5874 1727821 1728336 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic COG1309;Transcriptional regulator 46689; Homeodomain-like "PF00440;Bacterial regulatory proteins, tetR family;7.3e-13;codon 13-59" "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1646 nemA nemA ydhN b1650 1724683 1725780 + (no change) JW1642 1728373 1729470 + e "N-ethylmaleimide reductase, FMN-linked" E 97165929 Cytoplasmic 1.-.-.- "COG1902;NADH:flavin oxidoreductases, Old Yellow Enzyme family" 51395; FMN-linked oxidoreductases PF00724;NADH:flavin oxidoreductase / NADH oxidas;7.1e-101;codon 5-344 GO:0006805 xenobiotic metabolism CDS ECK1647 gloA gloA b1651 1725861 1726268 + (no change) JW1643 1729551 1729958 + e "glyoxalase I, Ni-dependent" E 14556652 -!- 98149312 -!- 98292407 -!- 10913283 -!- 9047352 Cytoplasmic 4.4.1.5 Ni2+ monomeric multimer; glyoxalase I (b1651) 1FA8 COG0346;Lactoylglutathione lyase and related lyases 54593; Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase PF00903;Glyoxalase/Bleomycin resistance protein/Di;4.6e-43;codon 2-123 TIGR00068;glyox_I: lactoylglutathione lyase;4.5e-98;codon 2-135 GO:0009438 methylglyoxal metabolism CDS ECK1648 rnt rnt b1652 1726371 1727018 + (no change) JW1644 1730061 1730708 + e ribonuclease T (RNase T) catalyzes tRNA end-turnover E 10049912 -!- 91139578 -!- 93015723 -!- 93094287 -!- 99428662 -!- 12050169 Cytoplasmic 3.1.13.- "COG0847;DNA polymerase III, epsilon subunit and related 3'-5' exonucleases" 53098; Ribonuclease H-like PF00929;Exonuclease;1.5e-40;codon 19-194 TIGR01298;RNaseT: ribonuclease T;1.8e-161;codon 10-209 GO:0006401 RNA catabolism -!- GO:0006308 DNA catabolism -!- GO:0006401 RNA catabolism -!- GO:0006308 DNA catabolism CDS ECK1649 lhr lhr rhlF b1653 1727111 1731727 + (no change) JW1645 1730801 1735417 + pe predicted ATP-dependent helicase member of DEAD box family C 7559321 -!- 93094287 Cytoplasmic COG1201;Lhr-like helicases 46785; Winged helix -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00270;DEAD/DEAH box helicase;3.4e-40;codon 30-223 -!- PF00271;Helicase conserved C-terminal domain;1.1e-13;codon 344-420 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK1650 ydhD ydhD b1654 1731778 1732125 - (no change) JW1646 1735468 1735815 - d conserved protein C Cytoplasmic COG0278;Glutaredoxin-related protein 52833; Thioredoxin-like TIGR00365;TIGR00365: glutaredoxin-related protein;2.7e-76;codon 5-103 CDS ECK1651 ydhO ydhO b1655 1732459 1733274 + (no change) JW5270 1736149 1736964 + lp predicted lipoprotein possible peptidase C Periplasmic C40 family; unassigned peptidases (YdhO protein) COG0791;Cell wall-associated hydrolases (invasion-associated proteins) PF00877;NlpC/P60 family;1.1e-58;codon 153-263 CDS ECK1652 sodB sodB b1656 1733402 1733983 + (no change) JW1648 1737092 1737673 + e "superoxide dismutase, Fe" E 11766965 -!- 89352497 -!- 92140024 -!- 92250511 Cytoplasmic 1.15.1.1 Fe3+ monomeric multimer; superoxide dismutase (Fe) (b1656) regulated by attenuation (sodB) COG0605;Superoxide dismutase "46609; Fe,Mn superoxide dismutase (SOD), N-terminal domain -!- 54719; Fe,Mn superoxide dismutase (SOD), C-terminal domain" "PF00081;Iron/manganese superoxide dismutases, alpha-;6.3e-53;codon 2-82 -!- PF02777;Iron/manganese superoxide dismutases, C-term;6.3e-72;codon 86-191" GO:0005737 cytoplasm GO:0006805 xenobiotic metabolism CDS ECK1653 ydhP ydhP b1657 1734145 1735314 - (no change) JW1649 1737835 1739004 - pt predicted transporter C Integral Membrane Protein 12 12 in COG2814;Arabinose efflux permease PF07690;Major Facilitator Superfamily;5.7e-39;codon 10-350 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1654 purR purR b1658 1735868 1736893 + (no change) JW1650 1739558 1740583 + r "DNA-binding transcriptional repressor, hypoxanthine-binding" E 90299801 -!- 93286053 -!- 94179115 -!- 96303520 -!- 10438625 -!- 2404765 -!- 3058704 -!- 7553867 -!- 7973627 -!- 8591032 -!- 9278422 -!- 9454587 -!- 9628480 Cytoplasmic monomeric multimer; PurR transcriptional repressor (b1658) GalR/LacI codBA -!- cvpA-purF-ubiX -!- gcvTHP -!- glnB -!- glyA -!- guaBA -!- hflD-purB -!- prsA -!- purC -!- purEK -!- purHD -!- purL -!- purMN -!- purR -!- pyrC -!- pyrD -!- speAB 1QPZ COG1609;Transcriptional regulators 47413; lambda repressor-like DNA-binding domains -!- 53822; Periplasmic binding protein-like I "PF00356;Bacterial regulatory proteins, lacI fami;2.1e-11;codon 2-27 -!- PF00532;Periplasmic binding proteins and sugar b;2.5e-32;codon 59-329" GO:0005737 cytoplasm GO:0006164 -!- GO:0006596 polyamine biosyn -!- GO:0000105 histidine biosyn -!- GO:0009063 aa catab -!- GO:0006545 glycine biosyn -!- GO:0006807 N-metab -!- GO:0009257 10-formylTHF biosyn -!- GO:0006221 -!- GO:0015949 -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1655 ydhB ydhB b1659 1736890 1737822 - (no change) JW1651 1740580 1741512 - pr predicted DNA-binding transcriptional regulator C 2404765 Cytoplasmic LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;2.8e-18;codon 4-63 -!- PF03466;LysR substrate binding domain;1.7e-26;codon 87-293 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK1656 ydhC ydhC b1660 1737935 1739146 + (no change) JW1652 1741625 1742836 + pt predicted transporter C Integral Membrane Protein 12 12 in PF07690;Major Facilitator Superfamily;8.4e-58;codon 11-356 TIGR00710;efflux_Bcr_CflA: drug resistance tran;7e-218;codon 2-382 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1657 cfa cfa cdfA b1661 1739437 1740585 + (no change) JW1653 1743127 1744275 + e cyclopropane fatty acyl phospholipid synthase (unsaturated-phospholipid methyltransferase) E 20353464 -!- 93075691 Cytoplasmic 2.1.1.79 monomeric multimer; cyclopropane fatty acid synthase (b1661) COG2230;Cyclopropane fatty acid synthase and related methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases PF02353;Cyclopropane-fatty-acyl-phosphol ipid synthas;3.1e-96;codon 215-372 CDS ECK1658 ribC ribC ribE -!- ybaF b1662 1740625 1741266 - (no change) JW1654 1744315 1744956 - e "riboflavin synthase, alpha subunit" E 12927541 -!- 21381952 -!- 9022701 -!- 9023191 Cytoplasmic 2.5.1.9 1I8D COG0307;Riboflavin synthase alpha chain 63380; Riboflavin synthase domain-like PF00677;Lumazine binding domain;8.7e-45;codon 3-87 -!- PF00677;Lumazine binding domain;2.9e-45;codon 100-185 "TIGR00187;ribE: riboflavin synthase, alpha subunit;2.2e-135;codon 1-204" CDS ECK1659 mdtK mdtK ydhE -!- norM b1663 1741481 1742854 + (no change) JW1655 1745171 1746544 + t multidrug efflux system transporter E 21450803 -!- 9023191 -!- 9661020 -!- 9987140 Integral Membrane Protein 2.A.66; The Multidrug/Oligosaccharidyl-lipid/Polysaccharide (MOP) Flippase Superfamily 12 12 in regulated by attenuation (norM) PF01554;MatE;6e-49;codon 17-177 -!- PF01554;MatE;2.3e-49;codon 244-405 TIGR00797;matE: MATE efflux family protein;2.3e-185;codon 17-422 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK1660 ydhQ ydhQ b1664 1742895 1744151 - (no change) JW1656 1746585 1747841 - d conserved protein similarity to functional domains of autotransporters e.g. Ag43 C Cytoplasmic "COG3468;Type V secretory pathway, adhesin AidA" 51126; Pectin lyase-like tRNA ECK1661 valV valV b1665 1744459 1744535 + (no change) JWR0031 1748149 1748225 + n tRNA-Val(GAC) (Valine tRNA2B) E 91264822 tRNA ECK1662 valW valW b1666 1744540 1744616 + (no change) JWR0032 1748230 1748306 + n tRNA-Val(GAC) (Valine tRNA2A) E 91264822 CDS ECK1663 ydhR ydhR b1667 1744724 1745029 + (no change) JW1657 1748414 1748719 + o predicted protein C Cytoplasmic regulated by attenuation (ydhR) CDS ECK1664 ydhS ydhS b1668 1745155 1746759 + (no change) JW1658 1748845 1750449 + d conserved protein with FAD/NAD(P)-binding domain C Periplasmic COG4529;Uncharacterized protein conserved in bacteria 51905; FAD/NAD(P)-binding domain CDS ECK1665 ydhT ydhT b1669 1746771 1747583 - (no change) JW1659 1750461 1751273 - d conserved protein C Cytoplasmic 47986; DEATH domain CDS ECK1666 ydhU ydhU phsC b1670 1747587 1748372 - (no change) JW1660 1751277 1752062 - pc predicted cytochrome C Integral Membrane Protein 5 5 COG4117;Thiosulfate reductase cytochrome B subunit (membrane anchoring protein) PF01292;Cytochrome b561 family;0.00011;codon 66-257 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1667 ydhX ydhX b1671 1748369 1749037 - start codon change JW5271 1752059 1752727 - pc predicted 4Fe-4S ferridoxin-type protein C COG0437;Fe-S-cluster-containing hydrogenase components 1 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;0.0056;codon 56-79 -!- PF00037;4Fe-4S binding domain;4.5e-05;codon 134-157 CDS ECK1668 ydhW ydhW b1672 1749101 1749748 - (no change) JW1662 1752791 1753438 - o predicted protein C Cytoplasmic CDS ECK1669 ydhV ydhV b1673 1749752 1751854 - (no change) JW5272 1753442 1755544 - pe predicted oxidoreductase C Cytoplasmic COG2414;Aldehyde:ferredoxin oxidoreductase "48310; Aldehyde ferredoxin oxidoreductase, C-terminal domains -!- 56228; Aldehyde ferredoxin oxidoreductase, N-terminal domain" "PF02730;Aldehyde ferredoxin oxidoreductase, N-termin;8e-126;codon 5-206 -!- PF01314;Aldehyde ferredoxin oxidoreductase, domains;1.4e-259;codon 225-685" CDS ECK1670 ydhY ydhY b1674 1751875 1752501 - (no change) JW1664 1755565 1756191 - pc predicted 4Fe-4S ferridoxin-type protein C Cytoplasmic COG0437;Fe-S-cluster-containing hydrogenase components 1 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;0.0041;codon 116-141 -!- PF00037;4Fe-4S binding domain;4.2e-05;codon 149-172 -!- PF00037;4Fe-4S binding domain;9.4e-07;codon 176-199 CDS ECK1671 ydhZ ydhZ b1675 1752956 1753165 - (no change) JW1665 1756646 1756855 - o predicted protein C Cytoplasmic CDS ECK1672 pykF pykF b1676 1753722 1755134 + (no change) JW1666 1757412 1758824 + e pyruvate kinase I formerly pyruvate kinase F E 89228557 -!- 89386643 -!- 10751408 -!- 1859631 -!- 8591049 -!- 9023191 -!- 9298646 Cytoplasmic 2.7.1.40 K+ -!- Mg2+ monomeric multimer; pyruvate kinase I (b1676) 1PKY COG0469;Pyruvate kinase "50800; PK beta-barrel domain-like -!- 51621; Phosphoenolpyruvate/pyruvate domain -!- 52935; Pyruvate kinase, C-terminal domain" "PF00224;Pyruvate kinase, barrel domain;2.2e-209;codon 1-345 -!- PF02887;Pyruvate kinase, alpha/beta domain;3.8e-31;codon 355-469" TIGR01064;pyruv_kin: pyruvate kinase;2.6e-295;codon 2-470 GO:0006096 glycolysis -!- GO:0006113 fermentation -!- GO:0009061 anaerobic respiration CDS ECK1673 lpp lpp mlpA -!- mulI b1677 1755445 1755681 + (no change) JW1667 1759135 1759371 + lp murein lipoprotein E 334727 -!- 338599 -!- 322142 -!- 353292 -!- 391404 -!- 4261992 -!- 4575979 -!- 6765942 Outer membrane Lipoprotein 1-25 78 COG4238;Murein lipoprotein PF04728;Repeated sequence found in lipoprotein LPP;0.011;codon 24-34 -!- PF04728;Repeated sequence found in lipoprotein LPP;0.012;codon 38-48 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009252 peptidoglycan biosynthesis CDS ECK1674 ynhG ynhG b1678 1755745 1756749 - (no change) JW1668 1759435 1760439 - d conserved protein predicted ATP synthase subunit C Periplasmic 1-21 COG1376;Uncharacterized protein conserved in bacteria 54106; LysM domain PF01476;LysM domain;7.7e-10;codon 42-85 -!- PF03734;ErfK/YbiS/YcfS/YnhG;3.1e-64;codo n 93-232 CDS ECK1675 sufE sufE ynhA b1679 1756898 1757314 - (no change) JW1669 1760588 1761004 - c sulfur acceptor protein E 12089140 -!- 12876288 -!- 12941942 -!- 14644425 -!- 15522304 Cytoplasmic monomeric multimer; SufE homodimer (b1679) COG2166;SufE protein probably involved in Fe-S center assembly PF02657;Fe-S metabolism associated domain;1.6e-74;codon 10-135 CDS ECK1676 sufS sufS csdB -!- f406 -!- ynhB b1680 1757327 1758547 - (no change) JW1670 1761017 1762237 - e "selenocysteine lyase, PLP-dependent" E 10322040 -!- 10329673 -!- 12089140 -!- 14644425 -!- 10684605 -!- 10739946 -!- 10829016 Cytoplasmic 4.4.1.16 pyridoxal 5'-phosphate monomeric multimer; selenocysteine lyase (b1680) 1I29 COG0520;Selenocysteine lyase 53383; PLP-dependent transferases PF00266;Aminotransferase class-V;1.7e-11;codon 35-394 "TIGR01979;sufS: cysteine desulfurases, SufS subfamily;2.4e-304;codon 6-406" CDS ECK1677 sufD sufD ynhC b1681 1758544 1759815 - (no change) JW1671 1762234 1763505 - f component of SufBCD complex enhances SufS cysteine desulfurase activity -!- required for stability of iron-sulfur component of FhuF E 10322040 -!- 12089140 Cytoplasmic heteromultimer; SufB-SufC-SufD cysteine desulfurase (SufS) activator complex (b1681-b1682-b1683) 1VH4 "COG0719;ABC-type transport system involved in Fe-S cluster assembly, permease component" PF01458;Uncharacterized protein family (UPF0051);1e-112;codon 163-393 TIGR01981;sufD: FeS assembly protein SufD;1.2e-172;codon 41-410 CDS ECK1678 sufC sufC ynhD b1682 1759790 1760536 - (no change) JW1672 1763480 1764226 - t "component of SufBCD complex, ATP-binding component of ABC superfamily" modulates SufS activity E 12089140 -!- 10322040 Cytoplasmic heteromultimer; SufB-SufC-SufD cysteine desulfurase (SufS) activator complex (b1681-b1682-b1683) "COG0396;ABC-type transport system involved in Fe-S cluster assembly, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;2.5e-33;codon 27-222 TIGR01978;sufC: FeS assembly ATPase SufC;1.2e-187;codon 2-244 GO:0005737 cytoplasm CDS ECK1679 sufB sufB ynhE b1683 1760546 1762033 - start codon change JW5273 1764236 1765723 - pt component of SufBCD complex modulates SufS activity C 12089140 -!- 10322040 Cytoplasmic heteromultimer; SufB-SufC-SufD cysteine desulfurase (SufS) activator complex (b1681-b1682-b1683) "COG0719;ABC-type transport system involved in Fe-S cluster assembly, permease component" PF01458;Uncharacterized protein family (UPF0051);7.4e-149;codon 240-479 TIGR01980;sufB: FeS assembly protein SufB;3.7e-286;codon 32-499 GO:0006457 protein folding CDS ECK1680 sufA sufA ydiC b1684 1762042 1762410 - (no change) JW1674 1765732 1766100 - f Fe-S cluster assembly protein E 12089140 -!- 12876288 -!- 15754061 -!- 10322040 Cytoplasmic COG0316;Uncharacterized conserved protein PF01521;HesB-like domain;1.6e-53;codon 17-121 TIGR01997;sufA_proteo: FeS assembly scaffold SufA;3.8e-78;codon 16-122 -!- TIGR00049;TIGR00049: Iron-sulfur cluster assembly a;2.8e-54;codon 18-122 misc_RNA ECK1681 rydB rydB IS082 -!- tpe7 b4430 1762737 1762804 - (no change) JWR0236 1766427 1766494 - n regulatory sRNA E 11445539 rpoS CDS ECK1682 ydiH ydiH b1685 1762958 1763227 - (no change) JW1675 1766648 1766917 - o predicted protein C Cytoplasmic CDS ECK1683 ydiI ydiI b1686 1763246 1763656 - (no change) JW1676 1766936 1767346 - o conserved protein C Cytoplasmic 1VI8 "COG2050;Uncharacterized protein, possibly involved in aromatic compounds catabolism" PF03061;Thioesterase superfamily;1.1e-17;codon 50-127 TIGR00369;unchar_dom_1: uncharacterized domain;9.7e-57;codon 19-135 CDS ECK1684 ydiJ ydiJ b1687 1763653 1766709 - (no change) JW1677 1767343 1770399 - pe predicted FAD-linked oxidoreductase C Cytoplasmic COG0277;FAD/FMN-containing dehydrogenases -!- COG0247;Fe-S oxidoreductase "55103; FAD-linked oxidases, C-terminal domain -!- 56176; FAD-binding domain" "PF01565;FAD binding domain;9.8e-63;codon 52-267 -!- PF02913;FAD linked oxidases, C-terminal domain;9e-75;codon 281-539" CDS ECK1685 ydiK ydiK b1688 1767098 1768210 + (no change) JW1678 1770788 1771900 + pm predicted inner membrane protein C Integral Membrane Protein 10 9 in COG0628;Predicted permease PF01594;Domain of unknown function DUF20;2.1e-78;codon 14-345 misc_RNA ECK1686 rprA rprA IS083 -!- psrA5 b4431 1768396 1768500 + (no change) JWR0203 1772086 1772190 + n regulatory sRNA E 12410838 -!- 12753181 -!- 21150481 -!- 21341747 rpoS CDS ECK1687 ydiL ydiL b1689 1768639 1768995 + start codon change JW1679 1772329 1772685 + o conserved protein C Cytoplasmic regulated by attenuation (ydiL) CDS ECK1688 ydiM ydiM b1690 1769095 1770309 + (no change) JW1680 1772785 1773999 + pt predicted transporter C Integral Membrane Protein 12 12 in COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;1.7e-29;codon 12-359 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1689 ydiN ydiN b1691 1770536 1771801 + start codon change JW5274 1774226 1775491 + pt predicted transporter C Integral Membrane Protein 12 12 in PF07690;Major Facilitator Superfamily;6e-32;codon 20-366 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1690 ydiB ydiB b1692 1771813 1772679 + (no change) JW1682 1775503 1776369 + e "quinate/shikimate 5-dehydrogenase, NAD(P)-binding" E 12624088 -!- 12637497 -!- 3541912 Cytoplasmic 1.1.1.25 1VI2 COG0169;Shikimate 5-dehydrogenase 51735; NAD(P)-binding Rossmann-fold domains PF01488;Shikimate / quinate 5-dehydrogenase;4.7e-116;codon 25-273 CDS ECK1691 aroD aroD b1693 1772710 1773468 + (no change) JW1683 1776400 1777158 + e 3-dehydroquinate dehydratase E 90293024 -!- 91207275 -!- 92207154 -!- 1429576 -!- 3541912 Cytoplasmic 4.2.1.10 monomeric multimer; 3-dehydroquinate dehydratase (b1693) COG0710;3-dehydroquinate dehydratase 51569; Aldolase PF01487;Type I 3-dehydroquinase;3e-118;codon 18-245 "TIGR01093;aroD: 3-dehydroquinate dehydratase, type I;4.4e-130;codon 17-246" GO:0009423 chorismate biosynthesis CDS ECK1692 ydiF ydiF b1694 1773611 1775206 + (no change) JW1684 1777301 1778896 + pe fused predicted acetyl-CoA:acetoacetyl-CoA transferase: alpha subunit -!- beta subunit C Cytoplasmic fused predicted acetyl-CoA:acetoacetyl-CoA transferase: alpha subunit (aa1-258) -!- beta subunit (aa281-531) COG4670;Acyl CoA:acetate/3-ketoacid CoA transferase 53316; Glutaconate-CoA transferase subunits -!- 53316; Glutaconate-CoA transferase subunits PF01144;Coenzyme A transferase;3.7e-71;codon 15-253 GO:0019395 fatty acid oxidation CDS ECK1693 ydiO ydiO b1695 1775220 1776371 + start codon change JW5275 1778910 1780061 + pe predicted acyl-CoA dehydrogenase predicted flavoprotein C Cytoplasmic "47203; Acyl-CoA dehydrogenase (flavoprotein), C-terminal domain -!- 56645; Acyl-CoA dehydrogenase (flavoprotein), N-terminal and middle domains" "PF02771;Acyl-CoA dehydrogenase, N-terminal doma;1e-15;codon 24-131 -!- PF02770;Acyl-CoA dehydrogenase, middle domain;2.8e-29;codon 141-242 -!- PF00441;Acyl-CoA dehydrogenase, C-terminal doma;4e-65;codon 246-395" CDS ECK1694 ydiP ydiP b1696 1776414 1777325 - (no change) JW1686 1780104 1781015 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic regulated by attenuation (ydiP) COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like -!- 51182; RmlC-like "PF02311;AraC-like ligand binding domain;0.00047;21-164 -!- PF07883;Cupin domain;6.4e-09;25-94 -!- PF00165;Bacterial regulatory helix-turn-helix prot, AraC fam;0.0059;184-230 -!- PF00165;Bacterial regulatory helix-turn-helix prot, AraC fam;0.0005;236-280" "GO:0006350 transcription -!- GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1695 ydiQ ydiQ b1697 1777641 1778405 + (no change) JW5276 1781331 1782095 + d conserved protein C Cytoplasmic "COG2086;Electron transfer flavoprotein, beta subunit" 52431; ETFP adenine nucleotide-binding domain-like PF01012;Electron transfer flavoprotein beta subunit;2.8e-110;codon 1-253 CDS ECK1696 ydiR ydiR b1698 1778425 1779363 + (no change) JW1688 1782115 1783053 + pc "predicted electron transfer flavoprotein, FAD-binding" C Cytoplasmic "COG2025;Electron transfer flavoprotein, alpha subunit" 52431; ETFP adenine nucleotide-binding domain-like -!- 52467; DHS-like NAD/FAD-binding domain PF00766;Electron transfer flavoprotein alpha subuni;3.4e-127;codon 6-274 GO:0009055 electron carrier activity CDS ECK1697 ydiS ydiS b1699 1779419 1780708 + (no change) JW1689 1783109 1784398 + pc predicted oxidoreductase with FAD/NAD(P)-binding domain C COG0644;Dehydrogenases (flavoproteins) 51905; FAD/NAD(P)-binding domain GO:0009055 electron carrier activity CDS ECK1698 ydiT ydiT b1700 1780705 1780998 + (no change) JW1690 1784395 1784688 + pc predicted 4Fe-4S ferredoxin-type protein C Cytoplasmic COG2440;Ferredoxin-like protein 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;0.012;codon 58-81 GO:0009055 electron carrier activity CDS ECK1699 ydiD ydiD fadK b1701 1781001 1782701 + (no change) JW5910 1784691 1786391 + e "short chain acyl-CoA synthetase, anaerobic" E 12535077 -!- 15213221 -!- 7984428 Cytoplasmic monomeric multimer; short chain acyl-CoA synthetase (b1701) 56801; Firefly luciferase-like PF00501;AMP-binding enzyme;1e-123;codon 70-482 CDS ECK1700 pps pps ppsA b1702 1782758 1785136 - (no change) JW1692 1786448 1788826 - e phosphoenolpyruvate synthase E "93077431 -!- 94042858 -!- 1310524 -!- 16880 -!- Cooper RA, Kornberg HL;Academic Press, New York;1969;13:309-314" Cytoplasmic 2.7.9.2 Mg2+ monomeric multimer; phosphoenolpyruvate synthase (b1702) COG0574;Phosphoenolpyruvate synthase/pyruvate phosphate dikinase 51621; Phosphoenolpyruvate/pyruvate domain -!- 52009; Phosphohistidine domain -!- 56059; Glutathione synthetase ATP-binding domain-like "PF01326;Pyruvate phosphate dikinase, PEP/pyru;6.4e-175;codon 8-366 -!- PF00391;PEP-utilising enzyme, mobile domain;5.6e-45;codon 369-460 -!- PF02896;PEP-utilising enzyme, TIM barrel doma;4.2e-58;codon 465-792" TIGR01418;PEP_synth: phosphoenolpyruvate synthase;0;codon 9-792 GO:0006094 gluconeogenesis CDS ECK1701 ydiA ydiA b1703 1785469 1786302 + (no change) JW1693 1789159 1789992 + d conserved protein C Cytoplasmic COG1806;Uncharacterized protein conserved in bacteria 53850; Periplasmic binding protein-like II PF03618;Domain of unknown function (DUF299);2.9e-167;codon 4-272 CDS ECK1702 aroH aroH b1704 1786459 1787505 + (no change) JW1694 1790149 1791195 + e "3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, tryptophan repressible" E 89053867 -!- 91161502 -!- 91323737 -!- 98062296 -!- 6167722 Cytoplasmic 2.5.1.54 monomeric multimer; 2-dehydro-3-deoxyphosphoheptonate aldolase (b1704) regulated by attenuation (aroH) COG0722;3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase 51569; Aldolase PF00793;DAHP synthetase I family;4.3e-178;codon 24-338 TIGR00034;aroFGH: phospho-2-dehydro-3-deoxyheptonate a;1.3e-273;codon 5-348 GO:0000162 tryptophan biosynthesis CDS ECK1703 ydiE ydiE b1705 1787637 1787828 + (no change) JW1695 1791327 1791518 + o conserved protein C Cytoplasmic COG4256;Hemin uptake protein CDS ECK1704 ydiU ydiU b1706 1787832 1789268 - (no change) JW1696 1791522 1792958 - o conserved protein C Cytoplasmic COG0397;Uncharacterized conserved protein "PF02696;Uncharacterized ACR, YdiU/UPF0061 family;0;codon 1-454" CDS ECK1705 ydiV ydiV b1707 1789331 1790044 - (no change) JW1697 1793021 1793734 - o conserved protein C Cytoplasmic COG2200;FOG: EAL domain CDS ECK1706 nlpC nlpC b1708 1790291 1790755 - (no change) JW1698 1793981 1794445 - lp predicted lipoprotein possible peptidase C Outer membrane Lipoprotein C40 family; unassigned peptidases (NlpC protein) COG0791;Cell wall-associated hydrolases (invasion-associated proteins) PF00877;NlpC/P60 family;2.9e-51;codon 47-153 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1707 btuD btuD b1709 1790833 1791582 - (no change) JW1699 1794523 1795272 - t vitamin B12 transporter subunit : ATP-binding component of ABC superfamily E 89364713 -!- 12004122 -!- 3528129 Cytoplasmic 3.6.3.33 heteromultimer; vitamin B12 ABC transporter (b1710-b1709-b1711-b0158) -!- heteromultimer; vitamin B12 transport system (b0158-b1252-b1709-b1710-b1711-b3005-b3006-b3966) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1L7V "COG4138;ABC-type cobalamin transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.9e-35;codon 26-209 GO:0005737 cytoplasm GO:0009236 vitamin B12 biosynthesis CDS ECK1708 btuE btuE b1710 1791582 1792133 - (no change) JW1700 1795272 1795823 - pe predicted glutathione peroxidase C 89364713 -!- 3528129 Cytoplasmic heteromultimer; vitamin B12 ABC transporter (b1710-b1709-b1711-b0158) -!- heteromultimer; vitamin B12 transport system (b0158-b1252-b1709-b1710-b1711-b3005-b3006-b3966) COG0386;Glutathione peroxidase 52833; Thioredoxin-like PF00255;Glutathione peroxidase;6.3e-75;codon 4-112 GO:0042597 periplasmic space GO:0009236 vitamin B12 biosynthesis CDS ECK1709 btuC btuC b1711 1792196 1793176 - (no change) JW1701 1795886 1796866 - t vitamin B12 transporter subunit: membrane component of ABC superfamily E 89364713 -!- 11790740 -!- 12004122 -!- 3528129 Integral Membrane Protein heteromultimer; vitamin B12 ABC transporter (b1710-b1709-b1711-b0158) -!- heteromultimer; vitamin B12 transport system (b0158-b1252-b1709-b1710-b1711-b3005-b3006-b3966) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 9 9 in regulated by attenuation (btuC) "COG4139;ABC-type cobalamin transport system, permease component" PF01032;FecCD transport family;2.9e-129;codon 34-323 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009236 vitamin B12 biosynthesis CDS ECK1710 ihfA ihfA hid -!- himA b1712 1793277 1793576 - (no change) JW1702 1796967 1797266 - r "integration host factor (IHF), DNA-binding protein, alpha subunit" "sequence-specific DNA-binding and bending transcriptional activator -!- site-specific recombination -!- host infection, mutant phage lambda" E 91348524 -!- 92021785 -!- 92155171 -!- 2991205 -!- 3528129 -!- 6397321 -!- 8980235 Cytoplasmic heteromultimer; IHF transcriptional dual regulator (b0912-b1712) aceBAK -!- acs-yjcHG -!- adiA -!- amiA-hemF -!- caiTABCDE -!- carAB -!- dmsABC -!- dppABCDF -!- dps -!- dusB-fis -!- ecpD-htrE -!- fimAICDFGH -!- focA-pflB -!- gcd -!- glcDEFGBA -!- glnHPQ -!- gltA -!- hemA -!- himA -!- himD -!- hpt -!- hyc 1OWG COG0776;Bacterial nucleoid DNA-binding protein 47729; IHF-like DNA-binding proteins PF00216;Bacterial DNA-binding protein;6.3e-47;codon 3-92 "TIGR00987;himA: integration host factor, alpha subunit;6.8e-76;codon 2-97" GO:0005737 cytoplasm GO:0006310 DNA recombination CDS ECK1711 pheT pheT b1713 1793581 1795968 - (no change) JW1703 1797271 1799658 - e "phenylalanine tRNA synthetase, beta subunit" E 91210297 -!- 92046090 -!- 93041726 -!- 2991205 Cytoplasmic 6.1.1.20 heteromultimer; phenylalanyl-tRNA synthetase (b1714-b1713) COG0073;EMAP domain -!- COG0072;Phenylalanyl-tRNA synthetase beta subunit "46955; Putative DNA-binding domain -!- 50249; Nucleic acid-binding proteins -!- 54991; Anticodon-binding domain of PheRS -!- 55681; Class II aaRS and biotin synthetases -!- 56037; B3/B4 domain of PheRS, PheT" PF01588;Putative tRNA binding domain;2e-42;codon 45-146 -!- PF03483;B3/4 domain;5.8e-114;codon 212-385 -!- PF03484;tRNA synthetase B5 domain;3.5e-32;codon 403-471 -!- PF03147;Ferredoxin-fold anticodon binding domain;1.2e-47;codon 701-794 "TIGR00472;pheT_bact: phenylalanyl-tRNA synthetase, be;0;codon 1-795" GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK1712 pheS pheS phe-act b1714 1795983 1796966 - (no change) JW5277 1799673 1800656 - e "phenylalanine tRNA synthetase, alpha subunit" E 91210297 -!- 92046090 -!- 93041726 -!- 1537809 -!- 1959653 -!- 2991205 -!- 6317865 Cytoplasmic 6.1.1.20 heteromultimer; phenylalanyl-tRNA synthetase (b1714-b1713) regulated by attenuation (pheS-pheT-himA) COG0016;Phenylalanyl-tRNA synthetase alpha subunit 46589; A class II aminoacyl-tRNA synthetase N-domain -!- 55681; Class II aaRS and biotin synthetases "PF02912;Aminoacyl tRNA synthetase class II, N;1.7e-39;codon 16-88 -!- PF01409;tRNA synthetases class II core domain;1.3e-140;codon 108-313" "TIGR00468;pheS: phenylalanyl-tRNA synthetase, alpha su;1.6e-141;codon 37-327" GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK1713 pheM pheM phtL b1715 1797250 1797294 - (no change) JW1705 1800940 1800984 - l phenylalanyl-tRNA synthetase operon leader peptide E 6317865 -!- 3158742 -!- 3126825 Cytoplasmic regulated by attenuation (pheM) GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK1714 rplT rplT pdzA b1716 1797417 1797773 - (no change) JW1706 1801107 1801463 - s 50S ribosomal subunit protein L20 autoregulator E 91176995 -!- 93085722 -!- 8628231 -!- 10094780 -!- 12809609 -!- 3158742 -!- 381019 -!- 6317865 Cytoplasmic COG0292;Ribosomal protein L20 PF00453;Ribosomal protein L20;2.7e-69;codon 2-109 TIGR01032;rplT_bact: ribosomal protein L20;2.1e-80;codon 1-114 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006412 protein biosynthesis GO:0003735 structural constituent of ribosome CDS ECK1715 rpmI rpmI b1717 1797826 1798023 - (no change) JW1707 1801516 1801713 - s 50S ribosomal subunit protein L35 ribosomal protein A E 93085722 -!- 10094780 -!- 3298224 -!- 3542048 -!- 6325158 Cytoplasmic regulated by attenuation (rpmI-rplT) PF01632;Ribosomal protein L35;1.1e-32;codon 4-62 TIGR00001;rpmI_bact: ribosomal protein L35;3.9e-35;codon 2-64 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006412 protein biosynthesis GO:0003735 structural constituent of ribosome CDS ECK1716 infC infC fit -!- srjA b1718 1798120 1798662 - (no change) -!- AUU start JW5829 1801810 1802352 - f protein chain initiation factor IF-3 E 90060786 -!- 1457399 -!- 1742345 -!- 2954162 -!- 330233 -!- 6325158 -!- 7705354 -!- 9054966 -!- 9614948 Cytoplasmic COG0290;Translation initiation factor 3 (IF-3) "54364; Translation initiation factor IF3, N-terminal domain -!- 55200; Translation initiation factor IF3, C-terminal domain" "PF05198;Translation initiation factor IF-3, N-termin;3.2e-49;codon 10-85 -!- PF00707;Translation initiation factor IF-3, C-termin;2.6e-55;codon 90-178" TIGR00168;infC: translation initiation factor IF-3;6.5e-79;codon 15-179 GO:0005737 cytoplasm GO:0006412 protein biosynthesis CDS ECK1717 thrS thrS b1719 1798666 1800594 - (no change) JW1709 1802356 1804284 - e threonyl-tRNA synthetase E 91073394 -!- 93021106 -!- 93087171 -!- 10319817 -!- 10881191 -!- 3086882 -!- 6353409 Cytoplasmic 6.1.1.3 monomeric multimer; threonyl-tRNA synthetase (b1719) 1QF6 COG0441;Threonyl-tRNA synthetase "52954; Anticodon-binding domain of Class II aaRS -!- 55174; Alpha-L RNA-binding motif -!- 55186; Threonyl-tRNA synthetase (ThrRS), second 'additional' domain -!- 55681; Class II aaRS and biotin synthetases" PF02824;TGS domain;8.6e-15;codon 1-61 -!- PF00587;tRNA synthetase class II core domain (;1.1e-56;codon 262-415 -!- PF03129;Anticodon binding domain;4.7e-34;codon 541-631 TIGR00418;thrS: threonyl-tRNA synthetase;0;codon 72-632 GO:0005737 cytoplasm GO:0006418 amino acid activation ECK1718 arpB arpB b4494 1801118 1803017 + pseudogene; interrupted by frameshift JW5278+JW1710 1804808 1806707 + ancestral gene su predicted protein (pseudogene) C Cytoplasmic CDS ECK1718 arpB arpB_2 b1721 1801602 1803017 + pseudogene fragment -!- (no change) JW1710 1805292 1806707 + "pseudogene, split by frameshift (arpB)" su "predicted protein, C-ter fragment (pseudogene)" C CDS ECK1718 arpB arpB_1 ydiW -!- ydiX b1720 1801118 1801591 + pseudogene fragment -!- (no change) JW5278 1804808 1805281 + "pseudogene, split by frameshift (arpB)" su "predicted protein, N-ter fragment (pseudogene)" C CDS ECK1719 yniD yniD b4535 1803174 1803296 + new JW5911 1806864 1806986 + o predicted protein C CDS ECK1720 ydiY ydiY b1722 1803349 1804107 - (no change) JW1711 1807039 1807797 - o conserved protein C Periplasmic 1-24 regulated by attenuation (ydiY) COG3137;Putative salt-induced outer membrane protein "PF04338;Protein of unknown function, DUF481;1.9e-130;codon 24-252" CDS ECK1721 pfkB pfkB b1723 1804394 1805323 + (no change) JW5280 1808084 1809013 + e 6-phosphofructokinase II E 78194149 -!- 88292964 -!- 6235149 -!- 6310120 Cytoplasmic 2.7.1.11 monomeric multimer; tagatose-6-phosphate kinase / 6-phosphofructokinase-2 (b1723) 53613; Ribokinase-like PF00294;pfkB family carbohydrate kinase;5.6e-68;codon 9-299 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK1722 ydiZ ydiZ b1724 1805424 1805714 + (no change) JW1713 1809114 1809404 + o predicted protein C Cytoplasmic CDS ECK1723 yniA yniA b1725 1805820 1806680 + (no change) JW1714 1809510 1810370 + pe predicted phosphotransferase/kinase C Cytoplasmic COG3001;Fructosamine-3-kinase 56112; Protein kinase-like (PK-like) PF03881;Fructosamine kinase;5.4e-227;codon 1-286 -!- PF01636;Phosphotransferase enzyme family;7.2e-35;codon 20-255 CDS ECK1724 yniB yniB b1726 1806721 1807257 - (no change) JW1715 1810411 1810947 - pm predicted inner membrane protein C Integral Membrane Protein 3 3 CDS ECK1725 yniC yniC b1727 1807404 1808072 + (no change) JW1716 1811094 1811762 + pe predicted hydrolase C Cytoplasmic 1TE2 COG0637;Predicted phosphatase/phosphohexomutase 56784; HAD-like PF00702;haloacid dehalogenase-like hydrolase;1.1e-31;codon 7-194 "TIGR01509;HAD-SF-IA-v3: HAD-superfamily hydrolase,;2.1e-07;codon 9-191" CDS ECK1726 ydjM ydjM b1728 1808235 1808825 + start codon change JW5281 1811925 1812515 + pm predicted inner membrane protein regulated by LexA C 10760155 Integral Membrane Protein 4 2 out regulated by attenuation (ydjM) PF04307;Predicted membrane-bound metal-dependent hyd;2.3e-41;codon 44-137 GO:0009432 SOS response CDS ECK1727 ydjN ydjN b1729 1808958 1810349 + (no change) JW1718 1812648 1814039 + pt predicted transporter C Integral Membrane Protein 10 9 in COG1823;Predicted Na+/dicarboxylate symporter PF00375;Sodium:dicarboxylate symporter family;8.3e-113;codon 29-443 CDS ECK1728 ydjO ydjO b1730 1810353 1811168 - (no change) JW1719 1814043 1814858 - o predicted protein C Cytoplasmic CDS ECK1729 cedA cedA ydjP b1731 1811445 1811708 - (no change) JW1720 1815135 1815398 - cp cell division modulator affects inhibition after overreplication of chromosome in dnaAcos mutants E 9427399 Cytoplasmic CDS ECK1730 katE katE b1732 1811891 1814152 + (no change) JW1721 1815581 1817842 + e hydroperoxidase HPII(III) (catalase) E 10091651 -!- 90292022 -!- 92111721 -!- 94156832 -!- 11455600 -!- 1987146 -!- 7663946 -!- 9144772 Cytoplasmic 1.11.1.6 monomeric multimer; hydroperoxidase II (b1732) regulated by attenuation (katE) 52317; Class I glutamine amidotransferase-like -!- 56634; Heme-linked catalases PF00199;Catalase;2.6e-284;codon 81-469 -!- PF06628;Catalase-related;9.5e-31;codon 514-567 GO:0005737 cytoplasm GO:0006805 xenobiotic metabolism CDS ECK1731 chbG chbG ydjC -!- celG b1733 1814410 1815159 - (no change) JW1722 1818100 1818849 - o conserved protein C 20042356 -!- 1987146 -!- 2179047 -!- 8121401 -!- 9405618 Cytoplasmic COG3394;Uncharacterized protein conserved in bacteria PF04794;YdjC-like protein;1.9e-140;codon 3-239 CDS ECK1732 chbF chbF celF -!- ydjD b1734 1815172 1816524 - (no change) JW1723 1818862 1820214 - e "cryptic phospho-beta-glucosidase, NAD(P)-binding" E 20042356 -!- 90185127 -!- 9405618 Cytoplasmic 3.2.1.86 "COG1486;Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases" 51735; NAD(P)-binding Rossmann-fold domains PF02056;Family 4 glycosyl hydrolase;2.4e-238;codon 6-415 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0009435 nicotinamide adenine dinucleotide biosynthesis CDS ECK1733 chbR chbR celD b1735 1816629 1817471 - (no change) JW1724 1820319 1821161 - r DNA-binding transcriptional dual regulator E 15066032 -!- 90185127 -!- 9405618 Cytoplasmic AraC/XylS celABCDF-ydjC COG2207;AraC-type DNA-binding domain-containing proteins 46689; Homeodomain-like PF07883;Cupin domain;1.4e-05;codon 26-95 -!- PF00165;Bacterial regulatory helix-turn-helix protei;0.053;codon 176-223 -!- PF00165;Bacterial regulatory helix-turn-helix protei;1.3e-13;codon 229-273 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1734 chbA chbA celC b1736 1817479 1817829 - (no change) JW1725 1821169 1821519 - t "N,N'-diacetylchitobiose-specific enzyme IIA component of PTS" E 91227627 -!- 92334137 -!- 9405618 -!- 10913117 -!- 10913118 -!- 10913122 -!- 2179047 Cytoplasmic 2.7.1.69 heteromultimer; EIIChb (b1736-b1737-b1738-b2415-b2416) "4.A.3; The PTS Lactose-N,N'-Diacetylchitobiose-?-glucoside (Lac) Family" COG1447;Phosphotransferase system cellobiose-specific component IIA "46973; Enzyme IIa from lactose specific PTS, IIa-lac" "PF02255;PTS system, Lactose/Cellobiose specific IIA;1.3e-53;codon 18-113" "TIGR00823;EIIA-LAC: PTS system, lactose-specific IIa c;1.3e-60;codon 15-113" GO:0016052 carbohydrate catabolism CDS ECK1735 chbC chbC celB -!- hic b1737 1817880 1819238 - (no change) JW1726 1821570 1822928 - t "N,N'-diacetylchitobiose-specific enzyme IIC component of PTS" E 90185127 -!- 91227627 -!- 9405618 -!- 10913117 Integral Membrane Protein 2.7.1.69 heteromultimer; EIIChb (b1736-b1737-b1738-b2415-b2416) "4.A.3; The PTS Lactose-N,N'-Diacetylchitobiose-?-glucoside (Lac) Family" 10 10 in COG1455;Phosphotransferase system cellobiose-specific component IIC "PF02378;Phosphotransferase system, EIIC;1e-90;codon 29-365" "TIGR00359;cello_pts_IIC: PTS system, cellobiose-s;3.1e-293;codon 12-440 -!- TIGR00410;lacE: PTS system, lactose/cellobiose fa;3.1e-293;codon 12-440" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK1736 chbB chbB celA b1738 1819323 1819643 - (no change) JW1727 1823013 1823333 - t "N,N'-diacetylchitobiose-specific enzyme IIB component of PTS" E 90185127 -!- 91227627 -!- 9405618 -!- 10913117 -!- 10913119 -!- 10913122 -!- 8003964 -!- 9032081 -!- 9041631 Periplasmic 2.7.1.69 heteromultimer; EIIChb (b1736-b1737-b1738-b2415-b2416) "4.A.3; The PTS Lactose-N,N'-Diacetylchitobiose-?-glucoside (Lac) Family" COG1440;Phosphotransferase system cellobiose-specific component IIB 52794; Enzyme IIB-cellobiose "PF02302;PTS system, Lactose/Cellobiose specific IIB;2.7e-31;codon 5-98" "TIGR00853;pts-lac: PTS system, lactose/cellobiose fami;6.8e-37;codon 1-95" GO:0016052 carbohydrate catabolism CDS ECK1737 osmE osmE anr b1739 1819942 1820280 - (no change) JW1728 1823632 1823970 - r DNA-binding transcriptional activator E 91072202 -!- 96037798 Outer membrane Lipoprotein Unclass 1-13 ntrL PF04355;SmpA / OmlA family;2.9e-22;codon 21-97 GO:0005737 cytoplasm GO:0006350 transcription -!- GO:0006970 response to osmotic stress GO:0016563 transcriptional activator activity CDS ECK1738 nadE nadE efg -!- ntrL b1740 1820482 1821309 + (no change) JW1729 1824172 1824999 + e "NAD synthetase, NH3/glutamine-dependent" E 67134293 -!- 94253014 -!- 1512214 -!- 3025172 -!- 9298646 Cytoplasmic 6.3.5.1 Mg2+ "monomeric multimer; NAD+ synthase, glutamine dependent / NAD+ synthase, NH3-dependent (b1740)" COG0171;NAD synthase 52402; Adenine nucleotide alpha hydrolases PF02540;NAD synthase;5.4e-82;codon 83-269 TIGR00552;nadE: NAD+ synthetase;1.3e-119;codon 15-275 GO:0009435 nicotinamide adenine dinucleotide biosynthesis CDS ECK1739 ydjQ ydjQ cho -!- sosD b1741 1821539 1822426 + (no change) JW1730 1825229 1826116 + e endonuclease of nucleotide excision repair E 11818552 Cytoplasmic 3.1.25.- COG0322;Nuclease subunit of the excinuclease complex PF01541;GIY-YIG catalytic domain;1.2e-16;codon 34-113 CDS ECK1740 ydjR ydjR ves b1742 1822386 1822961 - start codon change JW1731 1826076 1826651 - o conserved protein C 21862596 Cytoplasmic COG3758;Uncharacterized protein conserved in bacteria PF05962;Bacterial protein of unknown function (DUF88;5.4e-97;codon 22-212 CDS ECK1741 spy spy b1743 1823164 1823649 - (no change) JW1732 1826854 1827339 - cp envelope stress induced periplasmic protein part of cpxR and baeSR regulons E 97221612 -!- 9694902 -!- 9068658 -!- 10648109 Periplasmic 1-23 161 "COG3678;P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein" PF07813;LTXXQ motif;1.4e-05;codon 47-69 -!- PF07813;LTXXQ motif;0.0015;codon 120-142 GO:0042597 periplasmic space CDS ECK1742 astE astE ydjS b1744 1823979 1824947 - (no change) JW1733 1827669 1828637 - e succinylglutamate desuccinylase E 98361920 Cytoplasmic 3.5.1.- COG2988;Succinylglutamate desuccinylase 53187; Zn-dependent exopeptidases PF04952;Succinylglutamate desuccinylase / Aspartoac;5.7e-98;codon 42-322 GO:0009063 amino acid catabolism CDS ECK1743 astB astB ydjT b1745 1824940 1826283 - (no change) JW1734 1828630 1829973 - e succinylarginine dihydrolase E 14675764 -!- 98361920 Cytoplasmic 3.5.3.- COG3724;Succinylarginine dihydrolase PF04996;Succinylarginine dihydrolase;0;codon 1-447 GO:0009063 amino acid catabolism CDS ECK1744 astD astD ydjU b1746 1826280 1827758 - (no change) JW5282 1829970 1831448 - e succinylglutamic semialdehyde dehydrogenase E 98361920 Cytoplasmic 1.2.1.- COG1012;NAD-dependent aldehyde dehydrogenases 53720; ALDH-like PF00171;Aldehyde dehydrogenase family;1.4e-73;codon 9-471 GO:0009063 amino acid catabolism CDS ECK1745 astA astA ydjV b1747 1827755 1828789 - (no change) JW1736 1831445 1832479 - e arginine succinyltransferase E 14675764 -!- 98361920 Cytoplasmic 2.3.1.109 COG3138;Arginine/ornithine N-succinyltransferase beta subunit 55729; Acyl-CoA N-acyltransferases (Nat) PF04958;Arginine N-succinyltransferase beta subunit;3.3e-256;codon 1-337 GO:0009063 amino acid catabolism CDS ECK1746 astC astC argM -!- cstC -!- ydjW b1748 1828786 1830006 - (no change) JW1737 1832476 1833696 - e "succinylornithine transaminase, PLP-dependent" E 98361920 -!- 98361921 Cytoplasmic 2.6.1.17 -!- 2.6.1.11 "monomeric multimer; acetylornithine transaminase, catabolic / succinylornithine transaminase (b1748)" COG4992;Ornithine/acetylornithine aminotransferase 53383; PLP-dependent transferases PF00202;Aminotransferase class-III;1.5e-166;codon 12-401 TIGR00707;argD: acetylornithine and succinylornithine;1.8e-273;codon 13-398 GO:0009063 amino acid catabolism CDS ECK1747 xthA xthA xth b1749 1830452 1831258 + (no change) JW1738 1834142 1834948 + e exonuclease III E 20013871 -!- 20042356 -!- 89213938 -!- 89240715 -!- 94342390 -!- 99427442 -!- 3049539 -!- 7885481 -!- 8948651 Cytoplasmic 3.1.11.2 regulated by attenuation (xthA) 1AKO COG0708;Exonuclease III 56219; DNase I-like PF03372;Endonuclease/Exonuclease/phospha tase fa;1.8e-51;codon 1-266 -!- TIGR00195;exoDNase_III: exodeoxyribonuclease III;1.5e-189;codon 1-266 -!- TIGR00633;xth: exodeoxyribonuclease III (xth);3.5e-167;codon 1-267 GO:0006308 DNA catabolism -!- GO:0006308 DNA catabolism -!- GO:0009314 response to radiation CDS ECK1748 ydjX ydjX b1750 1831425 1832135 + start codon change JW1739 1835115 1835825 + pm predicted inner membrane protein C Integral Membrane Protein 9.B.27; The YdjX-Z (YdjX-Z) Family 6 5 in PF00597;DedA family;7.6e-08;codon 54-216 CDS ECK1749 ydjY ydjY b1751 1832140 1832817 + start codon change JW5283 1835830 1836507 + o predicted protein C Inner membrane Lipoprotein CDS ECK1750 ydjZ ydjZ b1752 1832832 1833539 + (no change) JW1741 1836522 1837229 + pm conserved inner membrane protein C Integral Membrane Protein 9.B.27; The YdjX-Z (YdjX-Z) Family 5 5 in COG0398;Uncharacterized conserved protein PF00597;DedA family;7.5e-06;codon 65-214 CDS ECK1751 ynjA ynjA b1753 1833539 1834087 + (no change) JW1742 1837229 1837777 + d conserved protein C COG2128;Uncharacterized conserved protein 69118; Antioxidant defence protein AhpD PF02627;Carboxymuconolactone decarboxylase family;0.00029;codon 38-122 CDS ECK1752 ynjB ynjB b1754 1834097 1835263 + start codon change JW5284 1837787 1838953 + d conserved protein C Periplasmic 1-21 "COG4134;ABC-type uncharacterized transport system, periplasmic component" 53850; Periplasmic binding protein-like II CDS ECK1753 ynjC ynjC b1755 1835281 1836771 + (no change) JW5285 1838971 1840461 + pt fused transporter subunits of ABC superfamily: membrane components C Integral Membrane Protein heteromultimer; YnjC/YnjD ABC transporter (b1755-b1756) 12 12 in "fused predicted transport protein, ABC superfamily: membrane component (aa1-251) -!- membrane component (aa293-496)" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1754 ynjD ynjD b1756 1836771 1837424 + (no change) JW5286 1840461 1841114 + pt predicted transporter subunit: ATP-binding component of ABC superfamily C Cytoplasmic heteromultimer; YnjC/YnjD ABC transporter (b1755-b1756) "COG4136;ABC-type uncharacterized transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;8.1e-36;codon 27-209 GO:0005737 cytoplasm CDS ECK1755 ynjE ynjE b1757 1837491 1838798 + start codon change JW5287 1841181 1842488 + pe predicted thiosulfate sulfur transferase C Periplasmic 1-28 52821; Rhodanese/Cell cycle control phosphatase GO:0006790 sulfur metabolism CDS ECK1756 ynjF ynjF b1758 1838807 1839427 - start codon change JW1747 1842497 1843117 - m "predicted phosphatidyl transferase, inner membrane protein" C Integral Membrane Protein 4 5 in COG0558;Phosphatidylglycerophosphate synthase PF01066;CDP-alcohol phosphatidyltransferase;1.8e-22;codon 57-201 CDS ECK1757 nudG nudG ynjG -!- orf135 b1759 1839514 1839921 + (no change) JW1748 1843204 1843611 + e pyrimidine (deoxy)nucleoside triphosphate pyrophosphohydrolase E 21101911 Cytoplasmic 3.6.1.- Mg2+ COG0494;NTP pyrophosphohydrolases including oxidative damage repair enzymes 55811; Nudix PF00293;NUDIX domain;6.7e-30;codon 2-128 CDS ECK1758 ynjH ynjH b1760 1839887 1840159 - (no change) JW1749 1843577 1843849 - o predicted protein C Periplasmic PF07383;Protein of unknown function (DUF1496);7.6e-62;codon 1-90 CDS ECK1759 gdhA gdhA b1761 1840395 1841738 + (no change) JW1750 1844085 1845428 + e "glutamate dehydrogenase, NADP-specific" E 75128035 -!- 76046227 -!- 94321339 -!- 6308576 -!- 6373501 -!- 9298646 Cytoplasmic 1.4.1.4 monomeric multimer; glutamate dehydrogenase (NADP+) (b1761) COG0334;Glutamate dehydrogenase/leucine dehydrogenase "51735; NAD(P)-binding Rossmann-fold domains -!- 53223; Aminoacid dehydrogenase-like, N-terminal domain" "PF02812;Glu/Leu/Phe/Val dehydrogenase, dimeri;1.3e-85;codon 57-187 -!- PF00208;Glutamate/Leucine/Phenylalanine/ Valin;5e-134;codon 202-445" GO:0005737 cytoplasm GO:0006537 glutamate biosynthesis CDS ECK1760 ynjI ynjI b1762 1841855 1842895 - start codon change JW5288 1845545 1846585 - pm predicted inner membrane protein C Integral Membrane Protein 3 2 in CDS ECK1761 topB topB mutR b1763 1843023 1844984 - (no change) JW1752 1846713 1848674 - e DNA topoisomerase III type 1 E 90036864 -!- 94124564 -!- 99288449 -!- 10574789 Cytoplasmic 5.99.1.2 COG0550;Topoisomerase IA 56712; Prokaryotic type I DNA topoisomerase PF01751;Toprim domain;2.7e-37;codon 1-135 -!- PF01131;DNA topoisomerase;8e-193;codon 151-564 TIGR01056;topB: DNA topoisomerase III;0;codon 1-653 GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication -!- GO:0006350 transcription CDS ECK1762 selD selD fdhB b1764 1844989 1846032 - (no change) JW1753 1848679 1849722 - e selenophosphate synthase E 90138866 -!- 91317715 -!- 92406923 -!- 2553698 -!- 8262938 -!- 8144648 2.7.9.3 Mg2+ COG0709;Selenophosphate synthase 55326; Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain "PF00586;AIR synthase related protein, N-terminal dom;1.4e-27;codon 13-158 -!- PF02769;AIR synthase related protein, C-terminal dom;3.6e-25;codon 169-345" "TIGR00476;selD: selenide, water dikinase;4.4e-227;codon 1-335" GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK1763 ydjA ydjA b1765 1846149 1846700 - (no change) JW1754 1849839 1850390 - pe predicted oxidoreductase C Cytoplasmic COG0778;Nitroreductase 55469; NADH oxidase/flavin reductase PF00881;Nitroreductase family;2.2e-51;codon 7-162 CDS ECK1764 sppA sppA b1766 1846861 1848717 + (no change) JW1755 1850551 1852407 + e protease IV (signal peptide peptidase) E 86250892 -!- 87222172 -!- 7973728 Membrane Anchored 3.4.-.- "monomeric multimer; protease IV, a signal peptide peptidase (b1766)" S49 family; peptidase IV COG0616;Periplasmic serine proteases (ClpP class) 52096; ClpP/crotonase PF01343;Peptidase family S49;3.5e-67;codon 140-296 -!- PF01343;Peptidase family S49;5.7e-80;codon 391-543 "TIGR00705;SppA_67K: signal peptide peptidase SppA, 67K;0;codon 16-609 -!- TIGR00706;SppA_dom: signal peptide peptidase SppA, 36K;2e-59;codon 327-541" CDS ECK1765 ansA ansA b1767 1848884 1849900 + (no change) JW1756 1852574 1853590 + e cytoplasmic L-asparaginase I E 6102982 -!- 86168005 -!- 89357501 Cytoplasmic 3.5.1.1 monomeric multimer; asparaginase I (b1767) regulated by attenuation (ansA-pncA) COG0252;L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D 53774; Glutaminase/Asparaginase PF00710;Asparaginase;1.7e-149;codon 10-325 "TIGR00519;asnASE_I: L-asparaginases, type I;7.2e-239;codon 3-336" GO:0005737 cytoplasm GO:0009063 amino acid catabolism CDS ECK1766 pncA pncA nam -!- ydjB b1768 1849911 1850552 + start codon change JW1757 1853601 1854242 + e nicotinamidase/pyrazinamidase E 72060410 -!- 2670682 -!- 8726014 Cytoplasmic 3.5.1.19 -!- 3.5.1.- 52499; Cysteine hydrolase PF00857;Isochorismatase family;5.2e-101;codon 7-215 GO:0005737 cytoplasm GO:0009435 nicotinamide adenine dinucleotide biosynthesis CDS ECK1767 ydjE ydjE b1769 1850645 1852003 - (no change) JW1758 1854335 1855693 - pt predicted transporter C Integral Membrane Protein 12 12 in COG0477;Permeases of the major facilitator superfamily PF00083;Sugar (and other) transporter;1.9e-22;codon 23-452 -!- PF07690;Major Facilitator Superfamily;1.9e-31;codon 27-411 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1768 ydjF ydjF b1770 1852120 1852878 - (no change) JW1759 1855810 1856568 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic COG1349;Transcriptional regulators of sugar metabolism 46785; Winged helix "PF00455;Bacterial regulatory proteins, deoR family;2.7e-69;codon 6-232" "GO:0006350 transcription -!- GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1769 ydjG ydjG b1771 1853015 1853995 - (no change) JW1760 1856705 1857685 - pe predicted oxidoreductase C Periplasmic COG0667;Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) 51430; NAD(P)-linked oxidoreductase PF00248;Aldo/keto reductase family;1.5e-40;codon 6-322 CDS ECK1770 ydjH ydjH b1772 1854005 1854952 - start codon change JW5289 1857695 1858642 - pe predicted kinase C Cytoplasmic 53613; Ribokinase-like PF00294;pfkB family carbohydrate kinase;8e-81;codon 12-310 CDS ECK1771 ydjI ydjI b1773 1854957 1855793 - (no change) JW1762 1858647 1859483 - pe predicted aldolase C Cytoplasmic COG0191;Fructose/tagatose bisphosphate aldolase 51569; Aldolase PF01116;Fructose-bisphosphate aldolase class-II;1.3e-65;codon 2-277 TIGR00167;cbbA: ketose-bisphosphate aldolases;2.5e-104;codon 1-277 CDS ECK1772 ydjJ ydjJ b1774 1855814 1856857 - (no change) JW1763 1859504 1860547 - pe "predicted oxidoreductase, Zn-dependent and NAD(P)-binding" C Cytoplasmic COG1063;Threonine dehydrogenase and related Zn-dependent dehydrogenases 50129; GroES-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF00107;Zinc-binding dehydrogenase;2.7e-98;codon 9-345 CDS ECK1773 ydjK ydjK b1775 1856874 1858253 - (no change) JW5290 1860564 1861943 - pt predicted transporter C Integral Membrane Protein 12 12 in COG0477;Permeases of the major facilitator superfamily PF00083;Sugar (and other) transporter;5.8e-19;codon 23-455 -!- PF07690;Major Facilitator Superfamily;5e-26;codon 27-414 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1774 ydjL ydjL b1776 1858280 1859356 - (no change) JW1765 1861970 1863046 - pe "predicted oxidoreductase, Zn-dependent and NAD(P)-binding" C Cytoplasmic COG1063;Threonine dehydrogenase and related Zn-dependent dehydrogenases 50129; GroES-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF00107;Zinc-binding dehydrogenase;2.9e-87;codon 9-354 CDS ECK1775 yeaC yeaC b1777 1859726 1859998 - start codon change JW1766 1863416 1863688 - o conserved protein C Cytoplasmic PF07023;Protein of unknown function (DUF1315);1.3e-64;codon 16-105 CDS ECK1776 yeaA yeaA msrB b1778 1860040 1860453 - (no change) JW1767 1863730 1864143 - e methionine sulfoxide reductase B E 11677230 -!- 12504094 -!- 12604343 -!- 2990926 -!- 7984428 Cytoplasmic 1.8.4.6 COG0229;Conserved domain frequently associated with peptide methionine sulfoxide reductase PF01641;SelR domain;3.7e-91;codon 7-129 TIGR00357;TIGR00357: methionine-R-sulfoxide reductase;4.3e-106;codon 4-137 CDS ECK1777 gapA gapA gad b1779 1860795 1861790 + (no change) JW1768 1864485 1865480 + e glyceraldehyde-3-phosphate dehydrogenase A E "775311 -!- 94131963 -!- 98361923 -!- 1862091 -!- 2124629 -!- 2990926 -!- 7896119 -!- 8636984 -!- 9298646 -!- Oxidation-Reduction, Part C.;The Enzymes, Vol.XIII;Academic Press, New York;1976;3rd Edition" Cytoplasmic 1.2.1.12 monomeric multimer; glyceraldehyde 3-phosphate dehydrogenase-A complex (b1779) 1S7C COG0057;Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase "51735; NAD(P)-binding Rossmann-fold domains -!- 55347; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain" "PF00044;Glyceraldehyde 3-phosphate dehydrogenase, NA;3.9e-97;codon 3-150 -!- PF02800;Glyceraldehyde 3-phosphate dehydrogenase, C-;2.9e-126;codon 151-312" TIGR01534;GAPDH-I: glyceraldehyde-3-phosphate dehydrog;2.5e-202;codon 4-324 GO:0005737 cytoplasm GO:0006096 glycolysis -!- GO:0008615 pyridoxine biosynthesis -!- GO:0006094 gluconeogenesis CDS ECK1778 yeaD yeaD up08 -!- yzzQ b1780 1861874 1862758 + start codon change JW1769 1865564 1866448 + d conserved protein C Cytoplasmic regulated by attenuation (yeaD) PF01263;Aldose 1-epimerase;2.9e-54;codon 35-295 CDS ECK1779 yeaE yeaE b1781 1862806 1863660 - (no change) JW1770 1866496 1867350 - pe predicted oxidoreductase NAD(P)-linked C Cytoplasmic regulated by attenuation (yeaE) "COG0656;Aldo/keto reductases, related to diketogulonate reductase" 51430; NAD(P)-linked oxidoreductase PF00248;Aldo/keto reductase family;2e-65;codon 8-273 CDS ECK1780 mipA mipA yeaF b1782 1863750 1864496 - (no change) JW1771 1867440 1868186 - f scaffolding protein for murein synthesizing machinery binds the bifunctional murein transglycosylase/transpeptidase MrcB and the membrane-bound lytic transglyc E 10037771 -!- 20267815 Outer Membrane B-barrel protein 1-22 248 COG3713;Outer membrane protein V PF06629;MltA-interacting protein MipA;3.3e-106;codon 25-248 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) GO:0009252 peptidoglycan biosynthesis CDS ECK1781 yeaG yeaG b1783 1864932 1866866 + (no change) JW1772 1868622 1870556 + d conserved protein with nucleoside triphosphate hydrolase domain C Cytoplasmic COG2766;Putative Ser protein kinase 52540; P-loop containing nucleotide triphosphate hydrolases PF06798;PrkA serine protein kinase;0;codon 19-636 CDS ECK1782 yeaH yeaH b1784 1866979 1868262 + (no change) JW1773 1870669 1871952 + o conserved protein C Cytoplasmic COG2718;Uncharacterized conserved protein PF04285;Protein of unknown function (DUF444);9.7e-292;codon 1-423 CDS ECK1783 yeaI yeaI b1785 1868409 1869884 + (no change) JW1774 1872099 1873574 + pr predicted diguanylate cyclase C Integral Membrane Protein 8 8 in regulated by attenuation (yeaI-yeaJ) COG2199;FOG: GGDEF domain PF00990;GGDEF domain;2e-58;codon 324-485 TIGR00254;GGDEF: putative diguanylate cyclase (GGDEF);8.9e-32;codon 324-490 CDS ECK1784 yeaJ yeaJ b1786 1870065 1871555 + start codon change JW5291 1873755 1875245 + pr predicted diguanylate cyclase C Integral Membrane Protein 2 2 in COG2199;FOG: GGDEF domain PF00990;GGDEF: GGDEF domain;4.2e-51;codon 340-495 TIGR00254;GGDEF: GGDEF domain;9.3e-27;codon 340-496 CDS ECK1785 yeaK yeaK b1787 1871598 1872101 + (no change) JW1776 1875288 1875791 + d conserved protein C Cytoplasmic COG2606;Uncharacterized conserved protein 55826; Hypothetical protein HI1434 (YbaK homologue) PF04073;YbaK / prolyl-tRNA synthetases associated do;2.9e-51;codon 20-163 CDS ECK1786 yoaI yoaI b1788 1872102 1872206 - start codon change JW5885 1875792 1875896 - "GeneMark can predict, but GeneMark predicted the position of complement(1872102..1872206)=MNDQM... on MG genome -!- similar to hypothetical protein of O157, CFT073, and Shigella" o predicted protein C CDS ECK1787 yeaL yeaL b1789 1872376 1872822 + (no change) JW1778 1876066 1876512 + pm conserved inner membrane protein C Integral Membrane Protein 4 4 COG2707;Predicted membrane protein PF04284;Protein of unknown function (DUF441);1.3e-85;codon 1-148 GO:0009274 cell wall (sensu Bacteria) CDS ECK1788 yeaM yeaM b1790 1872779 1873600 - (no change) JW1779 1876469 1877290 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic COG2207;AraC-type DNA-binding domain-containing proteins 51182; RmlC-like PF00165;Bacterial regulatory helix-turn-helix protei;0.00055;codon 214-257 "GO:0006350 transcription -!- GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1789 yeaN yeaN b1791 1873697 1874878 + (no change) JW1780 1877387 1878568 + pt predicted transporter C Integral Membrane Protein 12 12 in COG2807;Cyanate permease PF07690;Major Facilitator Superfamily;8.4e-24;codon 19-360 TIGR00896;CynX: cyanate transporter;3.6e-228;codon 15-368 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042886 amide transport CDS ECK1790 yeaO yeaO b1792 1874933 1875280 + start codon change JW1781 1878623 1878970 + o conserved protein C Cytoplasmic COG3189;Uncharacterized conserved protein "PF04343;Protein of unknown function, DUF488;5.8e-41;codon 9-120" CDS ECK1791 yoaF yoaF b1793 1875302 1875556 - (no change) JW1782 1878992 1879246 - pm conserved outer membrane protein C Outer membrane Lipoprotein COG3042;Putative hemolysin PF03891;Domain of unknown function (DUF333);2.5e-45;codon 2-79 CDS ECK1792 yeaP yeaP b1794 1875739 1876764 + start codon change JW5292 1879429 1880454 + pr predicted diguanylate cyclase C Cytoplasmic COG2203;FOG: GAF domain -!- COG2199;FOG: GGDEF domain 55781; GAF domain PF01590;GAF domain;3.9e-11;codon 61-197 -!- PF00990;GGDEF domain;9.1e-55;codon 213-374 TIGR00254;GGDEF: putative diguanylate cyclase (GGDEF);2.1e-35;codon 213-379 CDS ECK1793 yeaQ yeaQ b1795 1877031 1877279 - (no change) JW1784 1880721 1880969 - pm conserved inner membrane protein C Integral Membrane Protein 3 3 COG2261;Predicted membrane protein PF04226;Transglycosylase associated protein;4.6e-21;codon 33-82 CDS ECK1794 yoaG yoaG b1796 1877427 1877609 - (no change) JW1785 1881117 1881299 - o predicted protein C Cytoplasmic CDS ECK1795 yeaR yeaR b1797 1877613 1877972 - (no change) JW1786 1881303 1881662 - o conserved protein C Cytoplasmic "COG3615;Uncharacterized protein/domain, possibly involved in tellurite resistance" GO:0006805 xenobiotic metabolism CDS ECK1796 yeaS yeaS b1798 1878145 1878783 - (no change) JW1787 1881835 1882473 - pt neutral amino-acid efflux system C Integral Membrane Protein 6 6 in regulated by attenuation (yeaS) COG1280;Putative threonine efflux protein PF01810;LysE type translocator;2.3e-72;codon 18-211 CDS ECK1797 yeaT yeaT b1799 1878910 1879833 - start codon change JW1788 1882600 1883523 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic LysR 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;2.4e-16;codon 14-73 -!- PF03466;LysR substrate binding domain;1.1e-39;codon 97-303 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK1798 yeaU yeaU ttuC b1800 1879936 1881021 + (no change) JW1789 1883626 1884711 + pe predicted dehydrogenase C Cytoplasmic COG0473;Isocitrate/isopropylmalate dehydrogenase 53659; Isocitrate & isopropylmalate dehydrogenases PF00180;Isocitrate/isopropylmalate dehydrogenase;1.1e-96;codon 6-355 TIGR02089;TTC: tartrate dehydrogenase;1.1e-243;codon 2-359 GO:0006113 fermentation CDS ECK1799 yeaV yeaV b1801 1881212 1882657 + (no change) JW5293 1884902 1886347 + pt predicted transporter C Integral Membrane Protein 10 10 regulated by attenuation (yeaV-yeaW-yeaX) COG1292;Choline-glycine betaine transporter PF02028;BCCT family transporter;5e-52;codon 1-444 TIGR00842;bcct: choline/carnitine/betaine transport;1.1e-254;codon 1-444 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1800 yeaW yeaW b1802 1882689 1883813 + (no change) JW5294 1886379 1887503 + pc predicted 2Fe-2S cluster-containing protein C Cytoplasmic "COG4638;Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit" 50022; ISP domain -!- 55961; Bet v1-like PF00355;Rieske [2Fe-2S] domain;1.6e-27;codon 46-150 CDS ECK1801 yeaX yeaX b1803 1883869 1884834 + (no change) JW1792 1887559 1888524 + pe predicted oxidoreductase C Cytoplasmic COG1018;Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 "52343; Ferredoxin reductase-like, C-terminal NADP-linked domain -!- 54292; 2Fe-2S ferredoxin-like -!- 63380; Riboflavin synthase domain-like" PF00970;Oxidoreductase FAD-binding domain;1.1e-07;codon 8-108 -!- PF00175;Oxidoreductase NAD-binding domain;1.2e-05;codon 112-209 -!- PF00111;2Fe-2S iron-sulfur cluster binding doma;2.6e-16;codon 237-314 CDS ECK1802 rnd rnd b1804 1884888 1886015 - (no change) JW1793 1888578 1889705 - e ribonuclease D processes tRNA precursor E 88289400 -!- 89053950 -!- 93015723 -!- 8107670 Cytoplasmic 3.1.26.3 Mg2+ regulated by attenuation (rnd) COG0349;Ribonuclease D 53098; Ribonuclease H-like PF01612;3'-5' exonuclease;1.1e-72;codon 3-171 -!- PF00570;HRDC domain;2.1e-27;codon 210-289 TIGR01388;rnd: ribonuclease D;1.6e-251;codon 5-372 GO:0005737 cytoplasm GO:0006401 RNA catabolism -!- GO:0009451 RNA modification CDS ECK1803 fadD fadD oldD b1805 1886085 1887770 - (no change) JW1794 1889775 1891460 - e acyl-CoA synthetase (long-chain-fatty-acid--CoA ligase) E 93094273 -!- 12034706 -!- 8107670 6.2.1.3 Mg2+ monomeric multimer; fatty acyl-CoA synthetase (b1805) 9.B.17; The Putative Fatty Acid Transporter (FAT) Family COG0318;Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II 56801; Firefly luciferase-like PF00501;AMP-binding enzyme;1.4e-137;codon 50-485 GO:0009274 cell wall (sensu Bacteria) GO:0019395 fatty acid oxidation -!- GO:0008654 phospholipid biosynthesis CDS ECK1804 yeaY yeaY b1806 1887975 1888556 - (no change) JW1795 1891665 1892246 - lp predicted lipoprotein Slp paralog C Outer membrane Lipoprotein COG3065;Starvation-inducible outer membrane lipoprotein PF03843;Outer membrane lipoprotein Slp family;1.1e-101;codon 20-178 "TIGR00752;slp: outer membrane lipoprotein, Slp family;1.4e-135;codon 6-189" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1805 yeaZ yeaZ b1807 1888596 1889291 - (no change) JW1796 1892286 1892981 - pe predicted peptidase C M22 family; yeaZ protein "COG1214;Inactive homolog of metal-dependent proteases, putative molecular chaperone" 53067; Actin-like ATPase domain PF00814;Glycoprotease family;3.6e-19;codon 23-108 CDS ECK1806 yoaA yoaA b1808 1889349 1891259 - (no change) JW1797 1893039 1894949 - d conserved protein with nucleoside triphosphate hydrolase domain C Cytoplasmic COG1199;Rad3-related DNA helicases 52540; P-loop containing nucleotide triphosphate hydrolases GO:0005737 cytoplasm CDS ECK1807 yoaB yoaB b1809 1891391 1891735 + start codon change JW5295 1895081 1895425 + upstream Met could also be used d conserved protein C Cytoplasmic regulated by attenuation (yoaB) 55298; YjgF-like PF01042;Endoribonuclease L-PSP;3.4e-41;codon 18-130 CDS ECK1808 yoaC yoaC b1810 1892097 1892456 + (no change) JW5296 1895787 1896146 + o predicted protein C Cytoplasmic CDS ECK1809 yoaH yoaH b1811 1892576 1892755 - (no change) JW1800 1896266 1896445 - o conserved protein C Cytoplasmic COG3140;Uncharacterized protein conserved in bacteria PF03701;Uncharacterised protein family (UPF0181);4.4e-36;codon 1-52 CDS ECK1810 pabB pabB b1812 1892829 1894190 + (no change) JW1801 1896519 1897880 + e "aminodeoxychorismate synthase, subunit I" component of p-aminobenzoate synthase multienzyme complex E 88025006 -!- 91067712 -!- 91302313 -!- 96011382 -!- 6330050 -!- 7896119 Cytoplasmic 6.3.5.8 Mg2+ heteromultimer; aminodeoxychorismate synthase (b1812-b3360) -!- heteromultimer; para-aminobenzoate synthase multi-enzyme complex / para-aminobenzoate synthase (b1812-b3360-b1096) 1K0G COG0147;Anthranilate/para-aminobenzoate synthases component I 56322; ADC synthase "PF04715;Anthranilate synthase component I, N;3.9e-48;codon 12-154 -!- PF00425;chorismate binding enzyme;3.4e-151;codon 189-451" "TIGR00553;pabB: para-aminobenzoate synthase, component;1.6e-227;codon 106-447" GO:0046656 folic acid biosynthesis CDS ECK1811 yeaB yeaB b1813 1894194 1894772 + (no change) JW1802 1897884 1898462 + pe predicted NUDIX hydrolase C Cytoplasmic COG0494;NTP pyrophosphohydrolases including oxidative damage repair enzymes 55811; Nudix PF00293;NUDIX domain;7.6e-18;codon 30-161 CDS ECK1812 sdaA sdaA b1814 1894956 1896320 + (no change) JW1803 1898646 1900010 + e L-serine deaminase I E 15155761 -!- 89359152 -!- 91056090 -!- 93170282 Cytoplasmic 4.3.1.17 Fe4S4 iron-sulfur center COG1760;L-serine deaminase PF03315;Serine dehydratase beta chain;6.2e-109;codon 3-159 -!- PF03313;Serine dehydratase alpha chain;1.2e-208;codon 172-450 TIGR00720;sda_mono: L-serine ammonia-lyase;0;codon 1-454 GO:0009063 amino acid catabolism CDS ECK1813 yoaD yoaD b1815 1896451 1898049 + start codon change JW1804 1900141 1901739 + pe predicted phosphodiesterase C PF00563;EAL domain;5.5e-106;codon 275-511 CDS ECK1814 yoaE yoaE borG b1816 1898053 1899609 - (no change) JW1805 1901743 1903299 - pm fused predicted membrane protein -!- conserved protein C Integral Membrane Protein 7 7 in fused: predicted membrane protein (aa1-233) -!- unknown function protein (aa234-496) "COG0861;Membrane protein TerC, possibly involved in tellurium resistance -!- COG1253;Hemolysins and related proteins containing CBS domains" 54631; CBS-domain PF03741;Integral membrane protein TerC family;6.9e-78;codon 12-225 -!- PF00571;CBS domain;1.6e-06;codon 304-358 -!- PF00571;CBS domain;0.00037;codon 366-419 -!- PF03471;Transporter associated domain;3.2e-21;codon 431-511 GO:0009274 cell wall (sensu Bacteria) CDS ECK1815 manX manX gptB -!- mpt -!- ptsL -!- ptsM -!- ptsX b1817 1900072 1901043 + (no change) JW1806 1903762 1904733 + t fused mannose-specific PTS enzymes: IIA component -!- IIB component E 87165962 -!- 90036983 -!- 8131846 -!- 8676384 -!- 9074635 -!- 9298646 Cytoplasmic 2.7.1.69 heteromultimer; EIIMan (b2416-b2415-b1817-b1818-b1819) 4.A.6; The PTS Mannose-Fructose-Sorbose (Man) Family "fused PTS family enzyme, mannose-specific: enzyme IIA (aa1-132) -!- enzyme IIB (aa162-323)" "COG2893;Phosphotransferase system, mannose/fructose-specific component IIA -!- COG3444;Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB" "53062; IIA domain of mannose transporter, IIA-Man -!- 52728; Fructose permease, subunit IIb" PF03610;PTS system fructose IIA component;2.2e-52;codon 3-119 -!- PF03830;PTS system sorbose subfamily IIB componen;1.3e-99;codon 163-313 "TIGR00824;EIIA-man: PTS system, mannose/fructose/so;2.2e-81;codon 2-118 -!- TIGR00854;pts-sorbose: PTS system, mannose/fructose;3.7e-72;codon 163-313" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK1816 manY manY pel -!- ptsM -!- ptsP -!- ptsX b1818 1901106 1901906 + (no change) JW1807 1904796 1905596 + t mannose-specific enzyme IIC component of PTS E 10473571 -!- 87165962 -!- 90036983 -!- 94086520 -!- 97128775 -!- 7811395 -!- 8774730 Integral Membrane Protein heteromultimer; EIIMan (b2416-b2415-b1817-b1818-b1819) 4.A.6; The PTS Mannose-Fructose-Sorbose (Man) Family 7 7 in "COG3715;Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIC" PF03609;PTS system sorbose-specific iic component;6.5e-149;codon 3-238 "TIGR00822;EII-Sor: PTS system, mannose/fructose/sorbos;6.4e-199;codon 1-266" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK1817 manZ manZ gptB -!- mpt -!- ptsM -!- ptsX b1819 1901910 1902770 + (no change) JW1808 1905600 1906460 + t mannose-specific enzyme IID component of PTS E 87165962 -!- 90036983 -!- 7811395 -!- 8774730 Integral Membrane Protein heteromultimer; EIIMan (b2416-b2415-b1817-b1818-b1819) 4.A.6; The PTS Mannose-Fructose-Sorbose (Man) Family 4 2 out PF03613;PTS system mannose/fructose/sorbose family I;6.9e-190;codon 14-284 "TIGR00828;EIID-AGA: PTS system, mannose/fructose/sorbo;4.7e-220;codon 14-284" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK1818 yobD yobD b1820 1902825 1903283 + (no change) JW1809 1906515 1906973 + pm conserved inner membrane protein C Integral Membrane Protein 3 2 in COG4811;Predicted membrane protein PF06173;Protein of unknown function (DUF986);9.2e-111;codon 4-152 CDS ECK1819 yebN yebN b1821 1903712 1904278 + start codon change JW5830 1907402 1907968 + pm conserved inner membrane protein C Integral Membrane Protein 9.B.29; The YebN (YebN) Family 6 5 out COG1971;Predicted membrane protein PF02659;Domain of unknown function DUF;4.6e-42;codon 24-100 -!- PF02659;Domain of unknown function DUF;5.8e-35;codon 126-197 CDS ECK1820 rrmA rrmA yebH -!- RlmAI b1822 1904275 1905084 - (no change) JW1811 1907965 1908774 - e 23S rRNA m1G745 methyltransferase E 98101475 -!- 7984109 Cytoplasmic 2.1.1.51 Zn2+ regulated by attenuation (rrmA) 1P91 COG0500;SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK1821 cspC cspC msmB b1823 1905250 1905459 - (no change) JW1812 1908940 1909149 - f "stress protein, member of the CspA-family" related by sequence to the major cold shock protein A -!- constitutively expressed at 37C -!- affects rpoS and uspA expression E 20345064 -!- 21101802 -!- 94293754 -!- 12071744 -!- 7984109 -!- 8022261 -!- 9298646 -!- 9868784 -!- 9921691 Cytoplasmic COG1278;Cold shock proteins 50249; Nucleic acid-binding proteins PF00313;'Cold-shock' DNA-binding domain;2.9e-43;codon 3-69 GO:0006350 transcription -!- GO:0009266 response to temperature GO:0016563 transcriptional activator activity CDS ECK1822 yobF yobF b1824 1905472 1905615 - (no change) JW1813 1909162 1909305 - o predicted protein C Cytoplasmic CDS ECK1823 yebO yebO b1825 1906285 1906572 - (no change) JW1814 1909975 1910262 - o predicted protein C Membrane Anchored CDS ECK1824 yobG yobG b1826 1906647 1906790 - (no change) JW1815 1910337 1910480 - o predicted protein C CDS ECK1825 yobH yobH b4536 1906949 1907188 + new JW5298 1910639 1910878 + o predicted protein C CDS ECK1826 kdgR kdgR yebP b1827 1907332 1908123 - (no change) JW1816 1911022 1911813 - pr predicted DNA-binding transcriptional regulator C 4359651 Cytoplasmic IclR COG1414;Transcriptional regulator 46785; Winged helix PF01614;Bacterial transcriptional regulator;5e-99;codon 70-255 GO:0005737 cytoplasm GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK1827 yebQ yebQ b1828 1908300 1909673 + start codon change JW5299 1911990 1913363 + pt predicted transporter C Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 14 12 PF00083;sugar_tr: major facilitator superfamily pro;0.0057;codon 16-455 -!- PF01587;MCT: Monocarboxylate transporter;0.5;codon 21-443 "TIGR00711;efflux_EmrB: drug resistance transporter, E;9e-18;codon 17-454 -!- TIGR00880;2_A_01_02: Multidrug resistance protein;1.3e-15;codon 58-194 -!- TIGR00900;2A0121: H+ Antiporter protein;0.003;codon 18-424" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1828 htpX htpX b1829 1909719 1910600 - (no change) JW1818 1913409 1914290 - pe predicted endopeptidase part of the heat shock regulon -!- membrane-bound with cytosolic active site -!- RpoH regulon -!- synthetic lethal with hflB(ftsH) in sfhC(fabZ) background C 91210186 -!- 8524875 Integral Membrane Protein M48B family; HtpX endopeptidase 4 4 in regulated by attenuation (htpX) COG0501;Zn-dependent protease with chaperone function PF06509;HtpX N-terminus;1.5e-54;codon 1-77 -!- PF01435;Peptidase family M48;3.9e-44;codon 78-291 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009266 response to temperature CDS ECK1829 prc prc tsp b1830 1910792 1912840 - (no change) JW1819 1914482 1916530 - e carboxy-terminal protease for penicillin-binding protein 3 E 91310589 -!- 10049386 -!- 1447154 -!- 1729701 -!- 7499412 -!- 8576225 Periplasmic 3.4.21.102 S41A family; C-terminal processing peptidase-1 1-17 682 COG0793;Periplasmic protease 50156; PDZ domain-like -!- 52096; ClpP/crotonase PF00595;PDZ domain (Also known as DHR or GLGF);8.5e-17;codon 236-320 -!- PF03572;Peptidase family S41;5.2e-68;codon 356-530 TIGR00225;prc: carboxyl-terminal protease;1.4e-147;codon 194-551 GO:0009274 cell wall (sensu Bacteria) GO:0009252 peptidoglycan biosynthesis -!- GO:0006457 protein folding -!- GO:0042493 response to drug CDS ECK1830 proQ proQ yebJ -!- yobC -!- yobE b1831 1912860 1913558 - (no change) JW5300 1916550 1917248 - pt predicted structural transport element influences osmoregulation of ProP transporter C 10049386 -!- 89123175 -!- 1856173 -!- 7567469 Cytoplasmic PF04352;ProQ activator of osmoprotectant transporter;3.5e-111;codon 1-173 GO:0006970 response to osmotic stress CDS ECK1831 yebR yebR b1832 1913655 1914206 - (no change) JW1821 1917345 1917896 - d conserved protein C Cytoplasmic 1VHM 55781; GAF domain PF01590;GAF domain;2.4e-09;codon 41-169 CDS ECK1832 yebS yebS b1833 1914282 1915565 + (no change) JW1822 1917972 1919255 + pm conserved inner membrane protein C Integral Membrane Protein 8 8 in COG2995;Uncharacterized paraquat-inducible protein A 48695; Multiheme cytochromes PF04403;Paraquat-inducible protein A;1.6e-105;codon 20-221 -!- PF04403;Paraquat-inducible protein A;1.2e-106;codon 222-422 "TIGR00155;pqiA_fam: integral membrane protein, PqiA fa;1.7e-218;codon 16-417" GO:0009274 cell wall (sensu Bacteria) CDS ECK1833 yebT yebT b1834 1915534 1918167 + start codon change JW1823 1919224 1921857 + o conserved protein C Membrane Anchored COG3008;Paraquat-inducible protein B PF02470;mce related protein;0.0017;codon 22-175 GO:0009274 cell wall (sensu Bacteria) CDS ECK1834 yebU yebU b1835 1918247 1919686 + start codon change JW5301 1921937 1923376 + pe predicted methyltransferase C Cytoplasmic COG0144;tRNA and rRNA cytosine-C5-methylases -!- COG3270;Uncharacterized conserved protein 53335; S-adenosyl-L-methionine-dependent methyltransferases PF01189;NOL1/NOP2/sun family;3.1e-119;codon 193-481 TIGR00446;nop2p: NOL1/NOP2/sun family putative RNA met;1.5e-199;codon 43-312 GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK1835 yebV yebV b1836 1919804 1920040 + start codon change JW5302 1923494 1923730 + o predicted protein C Cytoplasmic PF07351;Protein of unknown function (DUF1480);1.2e-69;codon 6-83 CDS ECK1836 yebW yebW b1837 1920145 1920336 + start codon change JW5303 1923835 1924026 + o predicted protein C Cytoplasmic PF07358;Protein of unknown function (DUF1482);2.9e-42;codon 30-90 CDS ECK1837 pphA pphA prpA -!- yebX b1838 1920337 1920993 - start codon change JW1827 1924027 1924683 - e serine/threonine-specific protein phosphatase 1 E 9130712 Cytoplasmic 3.1.3.16 regulated by attenuation (pphA) 56300; Metallo-dependent phosphatases PF00149;Calcineurin-like phosphoesterase;4.7e-16;codon 18-192 GO:0005737 cytoplasm GO:0006464 protein modification -!- GO:0009266 response to temperature misc_RNA ECK1838 ryeA ryeA IS091 -!- sraC -!- tpke79 -!- psrA8 b4432 1921090 1921338 + (no change) JWR0237 1924780 1925028 + n small RNA interacts with Hfq E 14602901 -!- 11445539 -!- 21341747 misc_RNA ECK1839 ryeB ryeB tpke79 b4433 1921188 1921308 - (no change) JWR0238 1924878 1924998 - n small RNA interacts with Hfq E 14602901 -!- 11445539 regulated by attenuation (ryeB) CDS ECK1840 yebY yebY b1839 1921389 1921730 - (no change) JW1828 1925079 1925420 - o predicted protein C 1-20 CDS ECK1841 yebZ yebZ b1840 1921743 1922615 - (no change) JW1829 1925433 1926305 - pm predicted inner membrane protein C Integral Membrane Protein 8 8 out COG1276;Putative copper export protein PF05425;Copper resistance protein D;2.5e-139;codon 4-289 GO:0042493 response to drug CDS ECK1842 yobA yobA b1841 1922619 1922993 - (no change) JW1830 1926309 1926683 - o conserved protein C Periplasmic 1-26 "COG2372;Uncharacterized protein, homolog of Cu resistance protein CopC" PF04234;Copper resistance protein CopC;4.7e-71;codon 1-124 CDS ECK1843 holE holE b1842 1923132 1923362 + (no change) JW1831 1926822 1927052 + e "DNA polymerase III, theta subunit" E 15090519 -!- 92147649 -!- 92156151 -!- 94131961 -!- 1575709 -!- 8341603 -!- 8505306 Cytoplasmic 2.7.7.7 "heteromultimer; DNA polymerase III, core enzyme (b0184-b0215-b1842)" 1DU2 46575; Theta subunit of DNA polymerase III "PF06440;DNA polymerase III, theta subunit;7.3e-57;codon 1-76" GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication CDS ECK1844 yobB yobB b1843 1923464 1924120 + (no change) JW1832 1927154 1927810 + d conserved protein C Cytoplasmic COG0388;Predicted amidohydrolase 56317; Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase PF00795;Carbon-nitrogen hydrolase;2.6e-23;codon 5-160 CDS ECK1845 exoX exoX yobC b1844 1924144 1924806 + (no change) JW1833 1927834 1928496 + e DNA exonuclease X degrades ss and ds DNA with 3'-5' polarity E 21287280 -!- 99359338 -!- 99445570 Cytoplasmic 3.1.11.- "COG0847;DNA polymerase III, epsilon subunit and related 3'-5' exonucleases" 53098; Ribonuclease H-like PF00929;Exonuclease;1.9e-36;codon 2-147 GO:0005737 cytoplasm GO:0006308 DNA catabolism -!- GO:0006281 DNA repair -!- GO:0006308 DNA catabolism CDS ECK1846 ptrB ptrB tlp b1845 1924803 1926863 - (no change) JW1834 1928493 1930553 - e protease II E 92121142 Cytoplasmic 3.4.21.83 S9A family; oligopeptidase B COG1770;Protease II "50993; Prolyl oligopeptidase, N-terminal domain -!- 53474; alpha/beta-Hydrolases" "PF02897;Prolyl oligopeptidase, N-terminal beta;5.3e-170;codon 3-404 -!- PF00326;Prolyl oligopeptidase family;4.9e-106;codon 461-679" CDS ECK1847 yebE yebE b1846 1927072 1927731 - (no change) JW1835 1930762 1931421 - o conserved protein C Membrane Anchored in COG2979;Uncharacterized protein conserved in bacteria PF04391;Protein of unknown function (DUF533);1e-110;codon 22-212 CDS ECK1848 yebF yebF b1847 1928058 1928426 - (no change) JW1836 1931748 1932116 - o predicted protein C Periplasmic 1-25 CDS ECK1849 yebG yebG b1848 1928481 1928771 - (no change) JW1837 1932171 1932461 - cp conserved protein regulated by LexA E 9368369 -!- 99403401 Cytoplasmic regulated by attenuation (yebG-yebF) COG3141;Uncharacterized protein conserved in bacteria PF07130;YebG protein;2e-53;codon 1-75 GO:0005737 cytoplasm GO:0006281 DNA repair -!- GO:0009432 SOS response CDS ECK1850 purT purT b1849 1928905 1930083 + (no change) JW1838 1932595 1933773 + e phosphoribosylglycinamide formyltransferase 2 "synonyms GART, glycinamide ribonucleotide formyltransferase" E 94162268 -!- 97327484 -!- 10913290 Cytoplasmic 2.7.2.1 Mg2+ 1EZ1 COG0027;Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) 51246; Rudiment single hybrid motif -!- 52440; Biotin carboxylase N-terminal domain-like -!- 56059; Glutathione synthetase ATP-binding domain-like PF02222;ATP-grasp domain;2.1e-28;codon 41-209 TIGR01142;purT: phosphoribosylglycinamide formyltransf;8.3e-204;codon 14-391 GO:0005737 cytoplasm GO:0006164 purine nucleotide biosynthesis CDS ECK1851 eda eda hga -!- kdgA -!- kga b1850 1930139 1930780 - (no change) JW1839 1933829 1934470 - e multifunctional 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase and oxaloacetate decarboxylase E 88298837 -!- 92104948 -!- 92325055 -!- 11274385 -!- 11342129 -!- 1978721 -!- 8344525 -!- 14458448 -!- 4560498 -!- 7007372 -!- 7016177 Cytoplasmic 4.1.2.16 -!- 4.1.1.3 -!- 4.1.2.14 monomeric multimer; oxaloacetate decarboxylase / 2-keto-3-deoxy-6-phosphogluconate aldolase / 2-keto-4-hydroxyglutarate aldolase (b1850) 1FQ0 COG0800;2-keto-3-deoxy-6-phosphogluconate aldolase 51569; Aldolase PF01081;KDPG and KHG aldolase;1.2e-142;codon 8-203 TIGR01182;eda: 2-dehydro-3-deoxyphosphogluconate aldol;2.9e-133;codon 8-211 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0009255 Entner-Doudoroff pathway -!- GO:0009436 glyoxylate catabolism CDS ECK1852 edd edd b1851 1930817 1932628 - (no change) JW1840 1934507 1936318 - e 6-phosphogluconate dehydratase E 67161878 -!- 92325055 -!- 8344525 4.2.1.12 regulated by attenuation (edd) COG0129;Dihydroxyacid dehydratase/phosphogluconate dehydratase PF00920;Dehydratase family;2.2e-285;codon 65-601 TIGR01196;edd: 6-phosphogluconate dehydratase;0;codon 2-602 GO:0009255 Entner-Doudoroff pathway CDS ECK1853 zwf zwf b1852 1932863 1934338 - (no change) JW1841 1936553 1938028 - e glucose-6-phosphate dehydrogenase E 91123224 -!- 91310572 -!- 7973728 -!- 8344525 Cytoplasmic 1.1.1.49 COG0364;Glucose-6-phosphate 1-dehydrogenase "51735; NAD(P)-binding Rossmann-fold domains -!- 55347; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain" "PF00479;Glucose-6-phosphate dehydrogenase, NAD bindi;2.9e-107;codon 5-186 -!- PF02781;Glucose-6-phosphate dehydrogenase, C-termina;6.2e-207;codon 188-490" TIGR00871;zwf: glucose-6-phosphate 1-dehydrogenase;0;codon 8-490 GO:0005737 cytoplasm "GO:0016052 carbohydrate catabolism -!- GO:0009051 pentose-phosphate shunt, oxidative branch" CDS ECK1854 yebK yebK hexR b1853 1934676 1935545 + (no change) JW1842 1938366 1939235 + pr predicted DNA-binding transcriptional regulator C Cytoplasmic Unclass COG1737;Transcriptional regulators 53697; SIS domain "PF01418;Helix-turn-helix domain, rpiR family;1.6e-59;codon 1-106 -!- PF01380;SIS domain;2e-37;codon 122-256" "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK1855 pykA pykA b1854 1935673 1937115 + (no change) JW1843 1939363 1940805 + e pyruvate kinase II E 91072271 -!- 91315755 -!- 1732206 -!- 8439398 Cytoplasmic 2.7.1.40 K+ -!- Mg2+ monomeric multimer; pyruvate kinase II (b1854) COG0469;Pyruvate kinase "50800; PK beta-barrel domain-like -!- 51621; Phosphoenolpyruvate/pyruvate domain -!- 52935; Pyruvate kinase, C-terminal domain" "PF00224;Pyruvate kinase, barrel domain;9.4e-226;codon 5-351 -!- PF02887;Pyruvate kinase, alpha/beta domain;2.2e-63;codon 362-478" TIGR01064;pyruv_kin: pyruvate kinase;5.2e-270;codon 6-479 GO:0006096 glycolysis -!- GO:0006113 fermentation -!- GO:0009061 anaerobic respiration CDS ECK1856 lpxM lpxM mlt -!- msbB -!- waaN b1855 1937246 1938217 - (no change) JW1844 1940936 1941907 - e myristoyl-acyl carrier protein (ACP)-dependent acyltransferase lipid A synthesis E 11830595 -!- 92121107 -!- 1356966 -!- 9099672 Membrane Anchored 2.3.1.- regulated by attenuation (msbB) COG1560;Lauroyl/myristoyl acyltransferase PF03279;Bacterial lipid A biosynthesis acyltr;4.5e-160;codon 11-305 TIGR02208;lipid_A_msbB: lipid A biosynthesis (KDO);7.4e-238;codon 10-314 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009245 lipid A biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK1857 yebA yebA b1856 1938337 1939659 - start codon change JW5304 1942027 1943349 - pe predicted peptidase C 1732206 M23B family; unassigned peptidases (YebA protein) COG0739;Membrane proteins related to metalloendopeptidases 54106; LysM domain PF01476;LysM domain;1.8e-06;codon 77-121 -!- PF01551;Peptidase family M23;5.9e-52;codon 291-386 CDS ECK1858 znuA znuA yebL -!- yzzP b1857 1939675 1940607 - start codon change JW5831 1943365 1944297 - t zinc transporter subunit: periplasmic-binding component of ABC superfamily E 98343803 -!- 9298646 -!- 9600841 -!- 9740056 Periplasmic heteromultimer; ZnuA/ZnuB/ZnuC ABC transporter (b1858-b1859-b1857) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-41 310 53807; Helical backbone PF01297;Periplasmic solute binding protein family;2.9e-29;codon 25-325 GO:0042597 periplasmic space CDS ECK1859 znuC znuC yebM b1858 1940686 1941441 + (no change) JW1847 1944376 1945131 + t zinc transporter subunit: ATP-binding component of ABC superfamily E 98343803 Cytoplasmic heteromultimer; ZnuA/ZnuB/ZnuC ABC transporter (b1858-b1859-b1857) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG1121;ABC-type Mn/Zn transport systems, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.6e-49;codon 30-197 GO:0005737 cytoplasm CDS ECK1860 znuB znuB yebI b1859 1941438 1942223 + (no change) JW1848 1945128 1945913 + t zinc transporter subunit: membrane component of ABC superfamily E 98343803 Integral Membrane Protein heteromultimer; ZnuA/ZnuB/ZnuC ABC transporter (b1858-b1859-b1857) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 7 7 in "COG1108;ABC-type Mn2+/Zn2+ transport systems, permease components" PF00950;ABC 3 transport family;7.7e-128;codon 1-258 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1861 ruvB ruvB b1860 1942370 1943380 - (no change) JW1849 1946060 1947070 - e "ATP-dependent DNA helicase, component of RuvABC resolvasome" part of RuvABC Holliday junction branch migration and resolution complex E 93165688 -!- 93247553 -!- 93352499 -!- 9973614 -!- 10844644 -!- 10851230 -!- 2842314 -!- 3279394 -!- 9442895 Cytoplasmic 3.1.22.4 heteromultimer; ruvabc-cplx (b1860-b1861-b1863) "COG2255;Holliday junction resolvasome, helicase subunit" 46785; Winged helix -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF05496;Holliday junction DNA helicase ruvB N-termin;1.7e-28;codon 5-56 -!- PF00004;ATPase family associated with various cellul;5.5e-31;codon 57-236 -!- PF05491;Holliday junction DNA helicase ruvB C-termin;6.8e-56;codon 253-331 TIGR00635;ruvB: Holliday junction DNA helicase RuvB;6.9e-228;codon 26-330 GO:0005737 cytoplasm GO:0006281 DNA repair -!- GO:0006310 DNA recombination -!- GO:0009432 SOS response CDS ECK1862 ruvA ruvA b1861 1943389 1944000 - (no change) JW1850 1947079 1947690 - cp "component of RuvABC resolvasome, regulatory subunit" E 93051339 -!- 93165688 -!- 93343908 -!- 9973614 -!- 10772859 -!- 10851230 -!- 1885548 -!- 2842314 -!- 3279394 -!- 8832889 -!- 9442895 -!- 9493263 -!- 9628481 Cytoplasmic 3.1.22.4 heteromultimer; ruvabc-cplx (b1860-b1861-b1863) "COG0632;Holliday junction resolvasome, DNA-binding subunit" "46929; DNA helicase RuvA subunit, C-terminal domain -!- 47781; RuvA domain 2-like -!- 50249; Nucleic acid-binding proteins" "PF01330;RuvA N terminal domain;1.8e-30;codon 2-62 -!- PF00633;Helix-hairpin-helix motif;0.75;codon 63-92 -!- PF00633;Helix-hairpin-helix motif;0.14;codon 98-127 -!- PF07499;RuvA, C-terminal domain;1.6e-19;codon 158-203" TIGR00084;ruvA: Holliday junction DNA helicase RuvA;3.2e-116;codon 1-203 GO:0005737 cytoplasm GO:0006281 DNA repair -!- GO:0006310 DNA recombination -!- GO:0009432 SOS response CDS ECK1863 yebB yebB b1862 1944275 1944877 + start codon change JW5306 1947965 1948567 + o predicted protein C Cytoplasmic PF06520;Protein of unknown function (DUF1105);1.5e-136;codon 34-221 CDS ECK1864 ruvC ruvC b1863 1944879 1945400 - (no change) JW1852 1948569 1949090 - cp "component of RuvABC resolvasome, endonuclease" Holliday junction branch migration and resolution complex E 91358366 -!- 92097558 -!- 94006514 -!- 99400475 -!- 9973614 -!- 10851230 -!- 1657895 -!- 1758493 -!- 7923356 -!- 9442895 Cytoplasmic 3.1.22.4 heteromultimer; ruvabc-cplx (b1860-b1861-b1863) "COG0817;Holliday junction resolvasome, endonuclease subunit" 53098; Ribonuclease H-like PF02075;Crossover junction endodeoxyribonuclease Ruv;1.6e-99;codon 4-150 TIGR00228;ruvC: crossover junction endodeoxyribonuclea;2.7e-120;codon 4-159 GO:0005737 cytoplasm GO:0006281 DNA repair -!- GO:0006310 DNA recombination CDS ECK1865 yebC yebC b1864 1945435 1946175 - (no change) JW1853 1949125 1949865 - d conserved protein C Cytoplasmic 1KON COG0217;Uncharacterized conserved protein PF01709;Domain of unknown function DUF28;9.6e-151;codon 5-237 TIGR01033;TIGR01033: conserved hypothetical protein T;7.8e-116;codon 1-237 CDS ECK1866 nudB nudB ntpA -!- yebD b1865 1946204 1946656 - (no change) JW1854 1949894 1950346 - e dATP pyrophosphohydrolase E 96394625 -!- 1657895 -!- 1885548 -!- 8163538 Cytoplasmic 3.6.1.- Mg2+ COG0494;NTP pyrophosphohydrolases including oxidative damage repair enzymes 55811; Nudix PF00293;NUDIX domain;1e-27;codon 8-148 "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK1867 aspS aspS tls b1866 1946774 1948546 - (no change) JW1855 1950464 1952236 - e aspartyl-tRNA synthetase E 91088291 -!- 92112640 -!- 93352541 -!- 10562565 -!- 10873442 -!- 1885548 -!- 1944398 Cytoplasmic 6.1.1.12 monomeric multimer; aspartyl-tRNA synthetase (b1866) 1IL2 COG0173;Aspartyl-tRNA synthetase "50249; Nucleic acid-binding proteins -!- 55261; Prokaryotic AspRS, insert domain -!- 55681; Class II aaRS and biotin synthetases" "PF01336;OB-fold nucleic acid binding domain;3.5e-28;codon 18-102 -!- PF00152;tRNA synthetases class II (D, K and N);1.9e-19;codon 117-559 -!- PF02938;GAD domain;6.8e-51;codon 307-406" TIGR00459;aspS_bact: aspartyl-tRNA synthetase;0;codon 1-587 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK1868 yecD yecD b1867 1948856 1949422 + start codon change JW5307 1952546 1953112 + pe predicted hydrolase C Cytoplasmic 1J2R COG1335;Amidases related to nicotinamidase 52499; Cysteine hydrolase PF00857;Isochorismatase family;1.9e-83;codon 15-197 CDS ECK1869 yecE yecE b1868 1949419 1950237 + (no change) JW1857 1953109 1953927 + o conserved protein C 2129559 -!- 7984428 Cytoplasmic COG1801;Uncharacterized conserved protein PF01904;Protein of unknown function DUF72;7.4e-90;codon 10-249 CDS ECK1870 yecN yecN b1869 1950290 1950685 + start codon change JW5308 1953980 1954375 + pm predicted inner membrane protein C Integral Membrane Protein 4 3 out CDS ECK1871 yecO yecO b1870 1950726 1951469 + (no change) JW1859 1954416 1955159 + pe predicted methyltransferase C Cytoplasmic COG0500;SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases "TIGR00740;TIGR00740: methyltransferase, putative;3.1e-191;codon 4-242" CDS ECK1872 yecP yecP b1871 1951466 1952437 + (no change) JW1860 1955156 1956127 + pe predicted S-adenosyl-L-methionine-dependent methyltransferase C Cytoplasmic COG0500;SAM-dependent methyltransferases 53335; S-adenosyl-L-methionine-dependent methyltransferases "TIGR00452;TIGR00452: methyltransferase, putative;2.5e-263;codon 1-315" CDS ECK1873 torZ torZ bisZ b1872 1952602 1955031 - start codon change JW1861 1956292 1958721 - e "trimethylamine N-oxide reductase system III, catalytic subunit" E 97077292 -!- 11004177 Periplasmic 1.6.6.9 heteromultimer; trimethylamine N-oxide reductase III (b1872-b1873) 1-30 "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3" PF00384;Molybdopterin oxidoreductase;1.5e-161;codon 90-557 -!- PF01568;Molydopterin dinucleotide binding dom;1.5e-46;codon 676-792 TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;4.5e-08;codon 9-37 -!- TIGR00509;bisC_fam: molybdopterin guanine dinucl;0;codon 47-815 GO:0005737 cytoplasm GO:0009054 electron acceptor activity CDS ECK1874 torY torY yecK b1873 1955056 1956156 - (no change) JW1862 1958746 1959846 - c "TMAO reductase III (TorYZ), cytochrome c-type subunit" pentahaem E 20461225 -!- 8919859 heteromultimer; trimethylamine N-oxide reductase III (b1872-b1873) 5.A.3; The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family "COG3005;Nitrate/TMAO reductases, membrane-bound tetraheme cytochrome c subunit" 48695; Multiheme cytochromes "PF03264;NapC/NirT cytochrome c family, N-termin;1.5e-110;codon 2-175" GO:0009055 electron carrier activity CDS ECK1875 cutC cutC b1874 1956544 1957290 - start codon change JW1863 1960234 1960980 - t copper homeostasis protein mutations in both cutC and cut F appear to be required for a copper-sensitive phenotype E 95362641 -!- 7635807 Cytoplasmic 51391; Thiamin phosphate synthase PF03932;CutC family;2e-136;codon 2-201 GO:0005737 cytoplasm GO:0006805 xenobiotic metabolism CDS ECK1876 yecM yecM yecL b1875 1957304 1957870 - start codon change JW5309 1960994 1961560 - pe predicted metal-binding enzyme C 12660999 Cytoplasmic 1K4N PF06185;Protein of unknown function (DUF991);9e-128;codon 7-187 CDS ECK1877 argS argS lov b1876 1958086 1959819 + (no change) JW1865 1961776 1963509 + e arginyl-tRNA synthetase E 89118223 -!- 90221872 -!- 93037486 -!- 2668891 Cytoplasmic 6.1.1.19 Mg2+ regulated by attenuation (argS) COG0018;Arginyl-tRNA synthetase "47323; Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases -!- 52374; Nucleotidylyl transferase -!- 55190; Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain" PF03485;Arginyl tRNA synthetase N terminal do;2.3e-31;codon 5-87 -!- PF00750;tRNA synthetases class I (R);5.1e-219;codon 95-446 -!- PF05746;DALR anticodon binding domain;7.7e-54;codon 460-577 TIGR00456;argS: arginyl-tRNA synthetase;0;codon 3-577 GO:0005737 cytoplasm GO:0006418 amino acid activation CDS ECK1878 yecT yecT b1877 1959996 1960484 + start codon change JW5310 1963686 1964174 + o predicted protein C Periplasmic regulated by attenuation (yecT) PF07007;Protein of unknown function (DUF1311);4.1e-49;codon 41-154 CDS ECK1879 flhE flhE b1878 1960604 1960996 - (no change) JW1867 1964294 1964686 - o conserved protein "Previously annotated as flagellar protein, but shown not to be essential for flagellar function/formation." C 8002587 -!- 1482109 -!- 89181349 Periplasmic PF06366;Flagellar protein FlhE;1.2e-91;codon 1-130 CDS ECK1880 flhA flhA flaH b1879 1960996 1963074 - (no change) JW1868 1964686 1966764 - pt predicted flagellar export pore protein C 1482109 -!- 89181349 -!- 90130310 Integral Membrane Protein 8 7 "COG1298;Flagellar biosynthesis pathway, component FlhA" PF00771;FHIPEP family;0;codon 30-683 TIGR01398;FlhA: flagellar biosynthesis protein FlhA;0;codon 19-689 GO:0019861 flagellum -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1881 flhB flhB flaG -!- yecQ b1880 1963067 1964215 - (no change) JW1869 1966757 1967905 - pt predicted flagellar export pore protein C 1482109 -!- 89181349 Integral Membrane Protein 4 4 in "COG1377;Flagellar biosynthesis pathway, component FlhB" PF01312;FlhB HrpN YscU SpaS Family;3.3e-192;codon 4-347 TIGR00328;flhB: flagellar biosynthetic protein FlhB;1e-222;codon 6-353 GO:0019861 flagellum -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1882 cheZ cheZ b1881 1964417 1965061 - (no change) JW1870 1968107 1968751 - r "chemotaxis regulator, protein phosphatase for CheY" protein phosphatase for CheY E 87250383 -!- 94002264 -!- 94137719 -!- 9687492 -!- 3510184 -!- 6090423 Cytoplasmic monomeric multimer; CheZ (b1881) COG3143;Chemotaxis protein "PF04344;Chemotaxis phosphatase, CheZ;2.1e-162;codon 3-214" GO:0006464 protein modification -!- GO:0042330 taxis CDS ECK1883 cheY cheY b1882 1965072 1965461 - (no change) JW1871 1968762 1969151 - r chemotaxis regulator transmitting signal to flagellar motor component E 93293819 -!- 94072591 -!- 94261610 -!- 9687492 -!- 10731410 -!- 10748173 -!- 11023787 -!- 11359578 -!- 1390767 -!- 1869568 -!- 2689446 -!- 3280143 -!- 3510184 -!- 6090423 -!- 8176739 -!- 8354264 -!- 9437425 -!- 9560203 -!- 9636149 -!- 9761838 -!- 9761905 Cytoplasmic COG0784;FOG: CheY-like receiver 52172; CheY-like PF00072;Response regulator receiver domain;5.4e-44;codon 6-128 GO:0005737 cytoplasm GO:0042330 taxis CDS ECK1884 cheB cheB b1883 1965476 1966525 - (no change) JW1872 1969166 1970215 - r fused chemotaxis regulator -!- protein-glutamate methylesterase in two-component regulatory system with CheA protein-glutamate methylesterase E 89053899 -!- 90008896 -!- 93209955 -!- 9687492 -!- 99395068 -!- 3280143 -!- 3510184 Cytoplasmic 3.1.1.61 fused chemotaxis regulator: response regulator (aa1-108) -!- methylesterase (aa157-349) COG2201;Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain "52172; CheY-like -!- 52738; Methylesterase CheB, C-terminal domain" PF00072;Response regulator receiver domain;7.7e-35;codon 4-127 -!- PF01339;CheB methylesterase;1.5e-135;codon 158-340 GO:0005737 cytoplasm GO:0006464 protein modification -!- GO:0042330 taxis CDS ECK1885 cheR cheR cheX b1884 1966528 1967388 - (no change) JW1873 1970218 1971078 - r "chemotaxis regulator, protein-glutamate methyltransferase" protein-glutamate methyltransferase E 12101179 -!- 89291701 -!- 99395068 -!- 3510184 Cytoplasmic 2.1.1.80 COG1352;Methylase of chemotaxis methyl-accepting proteins "47757; Chemotaxis receptor methyltransferase CheR, N-terminal domain -!- 53335; S-adenosyl-L-methionine-dependent methyltransferases" "PF03705;CheR methyltransferase, all-alpha domain;1.3e-16;codon 23-79 -!- PF01739;CheR methyltransferase, SAM binding domain;4.9e-99;codon 92-283" GO:0005737 cytoplasm GO:0006464 protein modification -!- GO:0042330 taxis CDS ECK1886 tap tap b1885 1967407 1969008 - (no change) JW1874 1971097 1972698 - r methyl-accepting protein IV peptide sensor receptor E 86230850 -!- 6305515 Integral Membrane Protein heteromultimer; MCP-IV (b1885-b1887-b1888) 4 2 in COG0840;Methyl-accepting chemotaxis protein "47170; Aspartate receptor, ligand-binding domain" PF02203;Tar ligand binding domain homologue;1.2e-57;codon 44-177 -!- PF00672;HAMP domain;3.1e-11;codon 192-261 -!- PF00015;Methyl-accepting chemotaxis protein (MCP) s;2.8e-103;codon 292-514 GO:0019866 inner membrane GO:0042330 taxis CDS ECK1887 tar tar cheM b1886 1969054 1970715 - (no change) JW1875 1972744 1974405 - r methyl-accepting chemotaxis protein II aspartate sensor receptor E 90094243 -!- 92165727 -!- 6305515 -!- 9315712 Integral Membrane Protein heteromultimer; MCP-II (b1886-b1887-b1888) 2 2 in COG0840;Methyl-accepting chemotaxis protein "47170; Aspartate receptor, ligand-binding domain" PF02203;Tar ligand binding domain homologue;1.5e-43;codon 44-179 -!- PF00672;HAMP domain;6.3e-17;codon 194-263 -!- PF00015;Methyl-accepting chemotaxis protein (MCP) s;6.5e-120;codon 294-516 GO:0019866 inner membrane GO:0042330 taxis CDS ECK1888 cheW cheW b1887 1970860 1971363 - (no change) JW1876 1974550 1975053 - r purine-binding chemotaxis protein regulator of CheA activity E 91126073 -!- 91296802 -!- 91317710 -!- 2002011 -!- 3510184 Cytoplasmic heteromultimer; MCP-I (b4355-b1887-b1888) -!- heteromultimer; MCP-II (b1886-b1887-b1888) -!- heteromultimer; MCP-III (b1421-b1887-b1888) -!- heteromultimer; MCP-IV (b1885-b1887-b1888) COG0835;Chemotaxis signal transduction protein 50341; CheW-like PF01584;CheW-like domain;1.4e-33;codon 18-155 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042330 taxis CDS ECK1889 cheA cheA b1888 1971384 1973348 - (no change) JW1877 1975074 1977038 - r fused chemotactic sensory histidine kinase in two-component regulatory system with CheB and CheY: sensory histidine kinase -!- signal sensing protein phosphorylates CheY and CheB -!- senses chemotactic signal E 91126073 -!- 93349836 -!- 94261610 -!- 2002011 -!- 2068106 -!- 2832069 -!- 3510184 -!- 8555213 -!- 8639521 -!- 9020767 -!- 9437425 -!- 9636149 Cytoplasmic heteromultimer; MCP-I (b4355-b1887-b1888) -!- heteromultimer; MCP-II (b1886-b1887-b1888) -!- heteromultimer; MCP-III (b1421-b1887-b1888) -!- heteromultimer; MCP-IV (b1885-b1887-b1888) -!- monomeric multimer; CheA(L) (b1888) fused sensory histidine kinase: sensory histidine kinase (aa1-501) -!- signal sensing protein (aa502-654) COG0643;Chemotaxis protein histidine kinase and related kinases 47226; HPT domain -!- 47384; Homodimeric domain of signal transducing histidine kinase -!- 55052; CheY-binding domain of CheA -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase -!- 50341; CheW-like "PF01627;Hpt domain;9e-16;codon 7-108 -!- PF02895;Signal transducing histidine kinase, hom;6.9e-30;codon 261-324 -!- PF02518;Histidine kinase-, DNA gyrase B-, and HS;1.4e-29;codon 369-508 -!- PF01584;CheW-like domain;8.6e-29;codon 513-641" GO:0006464 protein modification -!- GO:0042330 taxis CDS ECK1890 motB motB flaJ b1889 1973353 1974279 - (no change) JW1878 1977043 1977969 - cp protein that enables flagellar motor rotation links torque machinery to cell wall E 14705928 -!- 90150271 -!- 91286189 -!- 92041594 -!- 2002011 -!- 2447650 -!- 3007435 Membrane Anchored heteromultimer; Flagellar Motor Complex (b1073-b1074-b1077-b1078-b1080-b1889-b1890-b1938-b 1945) 1.A.30; The H+- or Na+-translocating Bacterial Flagellar Motor 1ExbBD Outer Membrane Transport Energizer (Mot/Exb) Superfamily COG1360;Flagellar motor protein PF00691;OmpA family;1.9e-38;codon 160-258 GO:0019861 flagellum -!- GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042330 taxis CDS ECK1891 motA motA flaJ b1890 1974276 1975163 - (no change) JW1879 1977966 1978853 - cp proton conductor component of flagella motor E 14705928 -!- 90150271 -!- 92041594 -!- 92046074 -!- 3007435 -!- 6090403 -!- 7643400 Integral Membrane Protein heteromultimer; Flagellar Motor Complex (b1073-b1074-b1077-b1078-b1080-b1889-b1890-b1938-b 1945) 1.A.30; The H+- or Na+-translocating Bacterial Flagellar Motor 1ExbBD Outer Membrane Transport Energizer (Mot/Exb) Superfamily 4 4 in regulated by attenuation (motA-motB-cheA-cheW) COG1291;Flagellar motor component GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042330 taxis CDS ECK1892 flhC flhC flaI b1891 1975290 1975868 - (no change) JW1880 1978980 1979558 - r DNA-binding transcriptional dual regulator with FlhD activator of flagellar class II operons -! regulator of genes of aerobic metabolism E 12511500 -!- 1482109 -!- 89181349 -!- 2832369 -!- 12144778 Cytoplasmic PF05280;Flagellar transcriptional activator (FlhC);1e-158;codon 1-186 GO:0019861 flagellum -!- GO:0005737 cytoplasm GO:0009296 flagella biogenesis -!- GO:0006350 transcription -!- GO:0042330 taxis GO:0016563 transcriptional activator activity CDS ECK1893 flhD flhD flbB b1892 1975871 1976230 - (no change) JW1881 1979561 1979920 - r DNA-binding transcriptional dual regulator with FlhC activator of flagellar class II operons -!- dural regulator of genes of aerobic metabolism E 12511500 -!- 1482109 -!- 89181349 -!- 10601207 -!- 11169099 -!- 2832369 Cytoplasmic fliAZY -!- fliLMNOPQR -!- glpABC -!- hydN-hypF -!- mdh -!- mglBAC -!- nrfABCDEFG -!- ycgR -!- yhjH 1G8E 63592; Flagellar transcriptional activator FlhD PF05247;Flagellar transcriptional activator (FlhD);3.7e-74;codon 4-107 GO:0019861 flagellum -!- GO:0005737 cytoplasm GO:0009296 flagella biogenesis -!- GO:0006350 transcription -!- GO:0042330 taxis GO:0016563 transcriptional activator activity CDS ECK1894 yecG yecG uspC b1895 1977777 1978205 + (no change) JW1884 1981890 1982318 + f universal stress protein role in resistance to UV irradiation E 11849540 -!- 12732303 Periplasmic COG0589;Universal stress protein UspA and related nucleotide-binding proteins 52431; ETFP adenine nucleotide-binding domain-like PF00582;Universal stress protein family;4.7e-11;codon 2-138 CDS ECK1895 otsA otsA pexA b1896 1978212 1979636 - (no change) JW5312 1982325 1983749 - e trehalose-6-phosphate synthase E 92078100 -!- 92121128 -!- 93302496 -!- 8045430 Cytoplasmic 2.4.1.15 COG0380;Trehalose-6-phosphate synthase PF00982;Glycosyltransferase family;1.5e-222;codon 2-453 GO:0006006 glucose metabolism -!- GO:0006970 response to osmotic stress CDS ECK1896 otsB otsB otsP b1897 1979611 1980411 - (no change) JW1886 1983724 1984524 - e "trehalose-6-phosphate phosphatase, biosynthetic" E 92078100 -!- 92121128 -!- 93302496 -!- 8045430 Cytoplasmic 3.1.3.12 COG1877;Trehalose-6-phosphatase PF02358;Trehalose-phosphatase;4.4e-82;co don 18-234 "TIGR00685;T6PP: trehalose-phosphatase;9.3e-145;codon 12-245 -!- TIGR01484;HAD-SF-IIB: HAD-superfamily hydrolase, sub;7.4e-23;codon 16-215" GO:0005737 cytoplasm GO:0006006 glucose metabolism -!- GO:0006970 response to osmotic stress CDS ECK1897 araH araH b4460 1980578 1981567 - (no change) JW1887 1984691 1985680 - t fused L-arabinose transporter subunits of ABC superfamily: membrane components E 89255061 -!- 2445996 -!- 8045430 Integral Membrane Protein heteromultimer; arabinose ABC transporter (b1900-b4460-b1901) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 10 10 in PF02653;Branched-chain amino acid transport syst;3e-60;codon 51-316 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK1898 araG araG b1900 1981579 1983093 - (no change) JW1888 1985692 1987206 - t fused L-arabinose transporter subunits of ABC superfamily: ATP-binding components E 89255061 -!- 2445996 Cytoplasmic heteromultimer; arabinose ABC transporter (b1900-b4460-b1901) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "fused high-affinity L-arabinose transport protein, ABC superfamily: atp_binding component (aa1-267) -!- atp_binding component (aa268-504)" "COG1129;ABC-type sugar transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;3.6e-64;codon 33-219 -!- PF00005;ABC transporter;4.9e-22;codon 282-475 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK1899 araF araF b1901 1983163 1984152 - (no change) JW1889 1987276 1988265 - t L-arabinose transporter subunit -!- periplasmic-binding component of ABC superfamily E 89255061 -!- 90375534 -!- 2445996 -!- 326784 -!- 326785 -!- 6885805 -!- 7031057 -!- 9298646 Periplasmic heteromultimer; arabinose ABC transporter (b1900-b4460-b1901) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-23 329 5ABP "COG1879;ABC-type sugar transport system, periplasmic component" 53822; Periplasmic binding protein-like I PF00532;Periplasmic binding proteins and sugar b;3.2e-116;codon 25-320 GO:0042597 periplasmic space GO:0016052 carbohydrate catabolism CDS ECK1900 yecI yecI ftnB b1902 1984949 1985452 + (no change) JW1890 1989062 1989565 + pc predicted ferritin-like protein C Cytoplasmic COG1528;Ferritin-like protein 47240; Ferritin-like PF00210;Ferritin-like domain;5.8e-28;codon 7-144 GO:0005737 cytoplasm GO:0006826 iron ion transport CDS ECK1901 yecJ yecJ b4537 1985531 1985782 - new JW1891 1989644 1989895 - o predicted protein C Cytoplasmic GO:0005737 cytoplasm misc_RNA ECK1902 isrB IS092 b4434 1985863 1986022 - (no change) JWR0239 1989976 1990135 - n small RNA E 12069726 CDS ECK1903 yecR yecR b1904 1986246 1986569 + (no change) JW1892 1990359 1990682 + o predicted protein C Outer membrane Lipoprotein CDS ECK1904 ftn ftn gen-165 -!- rsgA -!- ftnA b1905 1986740 1987237 + (no change) JW1893 1990853 1991350 + c ferritin iron storage protein (cytoplasmic) E 10049371 -!- 91203828 -!- 94109400 -!- 98385881 -!- 11254384 Cytoplasmic 1EUM COG1528;Ferritin-like protein 47240; Ferritin-like PF00210;Ferritin-like domain;4.1e-45;codon 7-144 GO:0005737 cytoplasm GO:0006826 iron ion transport CDS ECK1905 yecH yecH b1906 1987275 1987514 - (no change) JW1894 1991388 1991627 - o predicted protein C Cytoplasmic regulated by attenuation (yecH) CDS ECK1906 tyrP tyrP b1907 1987705 1988916 + (no change) JW1895 1991818 1993029 + t tyrosine transporter E 89008121 -!- 2022620 Integral Membrane Protein 2.A.42; The Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family 11 11 out COG0814;Amino acid permeases PF03222;Tryptophan/tyrosine permease family;5.8e-222;codon 4-391 TIGR00837;araaP: aromatic amino acid transport protein;9.1e-232;codon 7-384 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006571 tyrosine biosynthesis CDS ECK1907 yecA yecA b1908 1988978 1989643 - (no change) JW1896 1993091 1993756 - d conserved metal-binding protein C Cytoplasmic COG3318;Predicted metal-binding protein related to the C-terminal domain of SecA PF02810;SEC-C motif;1.1e-06;codon 203-221 TIGR02292;ygfB_yecA: yecA family protein;3.3e-47;codon 10-182 tRNA ECK1908 leuZ leuZ b1909 1989839 1989925 - (no change) JWR0033 1993952 1994038 - n tRNA-Leu(UAA) (Leucine tRNA4) E 90230300 -!- 93287097 tRNA ECK1909 cysT cysT b1910 1989938 1990011 - (no change) JWR0034 1994051 1994124 - n tRNA-Cys(GCA) (Cysteine tRNA) E 2184240 -!- 2419743 tRNA ECK1910 glyW glyW ins -!- mutC -!- suA58 -!- suA78 b1911 1990066 1990141 - (no change) JWR0035 1994179 1994254 - n tRNA-Gly(GCC) (Glycine tRNA3) E 91067677 -!- 91296778 CDS ECK1911 pgsA pgsA b1912 1990293 1990841 - (no change) JW1897 1994406 1994954 - e phosphatidylglycerophosphate synthetase E 381294 -!- 7007311 -!- 94253011 -!- 1323047 -!- 3003065 -!- 8917447 Integral Membrane Protein 2.7.8.5 Mg2+ 6 4 in COG0558;Phosphatidylglycerophosphate synthase PF01066;CDP-alcohol phosphatidyltransferase;1.3e-46;codon 36-174 TIGR00560;pgsA: CDP-diacylglycerol--glycerol-3-phospha;1.9e-101;codon 3-182 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0008654 phospholipid biosynthesis CDS ECK1912 uvrC uvrC b1913 1990898 1992730 - start codon change JW1898 1995011 1996843 - e "excinuclease UvrABC, endonuclease subunit" nucleotide excision repair E 20138260 -!- 2843804 -!- 90377275 -!- 91319776 -!- 93221456 -!- 1387639 -!- 3003065 -!- 3295776 -!- 3515318 -!- 6330676 Cytoplasmic heteromultimer; UvrABC Nucleotide Excision Repair Complex (b0779-b1913-b3813-b4058) "46600; C-terminal, UvrC-binding domain of UvrB -!- 47781; RuvA domain 2-like" PF01541;GIY-YIG catalytic domain;3.7e-23;codon 1-77 -!- PF02151;UvrB/uvrC motif;1.5e-12;codon 182-217 -!- PF00633;Helix-hairpin-helix motif;2.5e-05;codon 524-553 -!- PF00633;Helix-hairpin-helix motif;2.6e-05;codon 556-585 "TIGR00194;uvrC: excinuclease ABC, C subunit;4.5e-242;codon 1-567" GO:0005737 cytoplasm GO:0006308 DNA catabolism -!- GO:0006281 DNA repair -!- GO:0006308 DNA catabolism -!- GO:0009314 response to radiation CDS ECK1913 uvrY uvrY yecB b1914 1992727 1993383 - (no change) JW1899 1996840 1997496 - r DNA-binding response regulator in two-component regulatory system with BarA E 20576358 -!- 12193630 -!- 12533459 -!- 3295776 -!- 3515318 Cytoplasmic LuxR/UhpA COG2197;Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;4.1e-46;codon 2-123 -!- PF00196;Bacterial regulatory proteins, luxR fami;6e-27;codon 147-204" GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1914 yecF yecF b1915 1993842 1994066 + (no change) JW1900 1997955 1998179 + o predicted protein C 3515318 -!- 7567469 Cytoplasmic CDS ECK1915 sdiA sdiA uvrX b1916 1994134 1994856 - (no change) JW1901 1998247 1998969 - r DNA-binding transcriptional activator E 11555297 -!- 92007787 -!- 3515318 Cytoplasmic LuxR/UhpA ftsQAZ COG2771;DNA-binding HTH domain-containing proteins "46894; C-terminal, effector domain of the bipartite response regulators" "PF03472;Autoinducer binding domain;2.2e-49;codon 22-167 -!- PF00196;Bacterial regulatory proteins, luxR fami;4.6e-26;codon 177-234" GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1916 yecC yecC b1917 1995086 1995838 - (no change) JW1902 1999199 1999951 - pt predicted transporter subunit: ATP-binding component of ABC superfamily C Cytoplasmic 3.A.1; The ATP-binding Cassette (ABC) Superfamily "COG1126;ABC-type polar amino acid transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1e-73;codon 29-220 GO:0005737 cytoplasm CDS ECK1917 yecS yecS b1918 1995835 1996503 - (no change) JW1903 1999948 2000616 - pt predicted transporter subunit: membrane component of ABC superfamily C Integral Membrane Protein 3.A.1; The ATP-binding Cassette (ABC) Superfamily 5 3 in "COG0765;ABC-type amino acid transport system, permease component" PF00528;Binding-protein-dependent transport syst;2.9e-37;codon 15-216 TIGR01726;HEQRo_perm_3TM: amino acid ABC transpo;2.8e-47;codon 11-109 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK1918 yedO yedO dcyD b1919 1996518 1997504 - start codon change JW5313 2000631 2001617 - e "D-cysteine desulfhydrase, PLP-dependent" E 21538853 -!- 3908101 Cytoplasmic 4.4.1.15 monomeric multimer; D-cysteine desulfhydrase / 3-chloro-D-alanine dehydrochlorinase (b1919) 53686; Tryptophan synthase beta subunit-like PLP-dependent enzymes PF00291;Pyridoxal-phosphate dependent enzyme;2.4e-07;codon 44-349 TIGR01275;ACC_deam_rel: pyridoxal phosphate-depend;9.5e-230;codon 44-360 CDS ECK1919 fliY fliY yzzR b1920 1997609 1998409 - (no change) JW1905 2001722 2002522 - t cystine transporter subunit -!- periplasmic-binding component of ABC superfamily E 96125225 -!- 8450713 -!- 8774726 -!- 9298646 -!- 9740056 Periplasmic 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-18 266 "COG0834;ABC-type amino acid transport/signal transduction systems, periplasmic component/domain" 53850; Periplasmic binding protein-like II PF00497;Bacterial extracellular solute-binding prot;6.6e-105;codon 43-262 GO:0042597 periplasmic space GO:0019344 cysteine biosynthesis -!- GO:0042883 L-cysteine transport CDS ECK1920 fliZ fliZ yedH b1921 1998497 1999048 - start codon change JW1906 2002610 2003161 - pr predicted regulator of FliA activity C 96125225 Cytoplasmic "47823; lambda integrase-like, N-terminal domain" "PF02899;Phage integrase, N-terminal SAM-like d;8.9e-12;codon 101-178" CDS ECK1921 fliA fliA flaD -!- rpoF b1922 1999094 1999813 - (no change) JW1907 2003207 2003926 - f "RNA polymerase, sigma 28 (sigma F) factor" regulates the transcription of late flagellar genes (class 3a and 3b operons) E 1482109 -!- 89181349 -!- 92407478 -!- 96125225 -!- 7590326 Cytoplasmic heteromultimer; RNA polymerase sigma 28 (b3987-b3988-b3295-b1922) regulated by attenuation (fliA-fliZ) 48329; sigma70 subunit fragment from RNA polymerase "PF04542;Sigma-70 region;4.2e-19;codon 16-89 -!- PF04539;Sigma-70 region;9.6e-23;codon 90-172 -!- PF04545;Sigma-70, region;7.9e-19;codon 185-234" GO:0019861 flagellum -!- GO:0005737 cytoplasm GO:0006350 transcription -!- GO:0042330 taxis CDS ECK1922 fliC fliC flaF -!- hag -!- H b1923 2000134 2001630 - (no change) JW1908 2004247 2005743 - s flagellar filament structural protein (flagellin) E 1482109 -!- 89181349 -!- 90299842 -!- 2659972 -!- 3536885 -!- 6305924 -!- 9298646 -!- 9600841 Cytoplasmic COG1344;Flagellin and related hook-associated proteins 64518; F41 fragment of flagellin PF00669;Bacterial flagellin N-terminus;5.9e-79;codon 29-169 -!- PF00700;Bacterial flagellin C-terminus;1.6e-39;codon 404-475 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1923 fliD fliD flbC -!- rfs b1924 2001896 2003302 + (no change) JW1909 2006009 2007415 + s flagellar filament capping protein E 1482109 -!- 89181349 -!- 90299842 -!- 1527488 -!- 2659972 -!- 6305924 Cytoplasmic COG1345;Flagellar capping protein PF02465;Flagellar hook-associated protein;2.4e-31;codon 10-107 -!- PF07196;Flagellin hook IN motif;8.4e-12;codon 127-184 -!- PF07195;Flagellar hook-associated protein;3.3e-77;codon 222-452 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1924 fliS fliS b1925 2003327 2003737 + (no change) JW1910 2007440 2007850 + f flagellar protein potentiates polymerization chaperone in flagella synthesis E 12620624 -!- 1482109 -!- 89181349 -!- 92407478 Cytoplasmic COG1516;Flagellin-specific chaperone FliS PF02561;Flagellar protein FliS;4e-71;codon 2-129 TIGR00208;fliS: flagellar protein FliS;1.6e-59;codon 1-129 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1925 fliT fliT b1926 2003737 2004102 + (no change) JW1911 2007850 2008215 + pf predicted chaperone predicted susbtrate-specific chaperone involved in the export of FlgK/FlgL and FliD C 10320579 -!- 1482109 -!- 89181349 -!- 92407478 Cytoplasmic PF05400;Flagellar protein FliT;5e-85;codon 1-121 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0006457 protein folding -!- GO:0042330 taxis CDS ECK1926 amyA amyA yedC b1927 2004180 2005667 + (no change) JW1912 2008293 2009780 + e cytoplasmic alpha-amylase E 93015717 -!- 93381452 -!- 1527488 Cytoplasmic 3.2.1.1 COG0366;Glycosidases "51011; alpha-Amylases, C-terminal beta-sheet domain -!- 51445; (Trans)glycosidases" "PF00128;Alpha amylase, catalytic domain;6e-95;codon 4-402" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0000272 polysaccharide catabolism CDS ECK1927 yedD yedD b1928 2005701 2006114 - (no change) JW1913 2009814 2010227 - o predicted protein C Outer membrane Lipoprotein CDS ECK1928 yedE yedE b1929 2006301 2007506 + (no change) JW1914 2010414 2011619 + pm predicted inner membrane protein C Integral Membrane Protein 10 10 in COG2391;Predicted transporter component PF04143;YeeE/YedE family (DUF395);3e-19;codon 106-170 -!- PF04143;YeeE/YedE family (DUF395);3.4e-22;codon 282-345 CDS ECK1929 yedF yedF b1930 2007503 2007736 + (no change) JW1915 2011616 2011849 + d conserved protein C Cytoplasmic "COG0425;Predicted redox protein, regulator of disulfide bond formation" 64307; SirA-like PF01206;SirA-like protein;4.8e-43;codon 4-77 CDS ECK1930 yedK yedK yedG b1931 2007845 2008513 + (no change) JW1916 2011958 2012626 + o predicted protein C Cytoplasmic "PF02586;Uncharacterised ACR, COG2135;1.3e-71;codon 1-217" CDS ECK1931 yedL yedL b1932 2008624 2009103 + (no change) JW1917 2012737 2013216 + pe predicted acyltransferase C Cytoplasmic COG0454;Histone acetyltransferase HPA2 and related acetyltransferases 55729; Acyl-CoA N-acyltransferases (Nat) PF00583;Acetyltransferase (GNAT) family;6.2e-12;codon 50-131 ECK1932 yedN yedN b4495 2009372 2009893 - pseudogene -!- interrupted by in-frame stop JW5912+JW1918 2013485 2014006 - ancestral gene su predicted protein (pseudogene) C Cytoplasmic CDS ECK1932 yedN yedN_1 b1934 2009573 2009893 - pseudogene fragment -!- (no change) JW5912 2013686 2014006 - pseudogene su "predicted protein, C-ter fragment (pseudogene)" C CDS ECK1932 yedN yedN_2 b1933 2009372 2009563 - pseudogene fragment -!- (no change) JW1918 2013485 2013676 - pseudogene su "predicted protein, N-ter fragment (pseudogene)" C CDS ECK1933 yedM yedM b1935 2010025 2010375 - (no change) JW1920 2014138 2014488 - o conserved protein C Cytoplasmic regulated by attenuation (yedM) COG4886;Leucine-rich repeat (LRR) protein CDS ECK1934 intG intG b1936 2010526 2010804 + pseudogene -!- (no change) JW5913 2014639 2014917 + "pseudogene, prophage" su predicted defective phage integrase (pseudogene) C Cytoplasmic COG0582;Integrase CDS ECK1935 fliE fliE flaN -!- fla AI -!- flaAI b1937 2010724 2011038 - (no change) JW1921 2014837 2015151 - s flagellar basal-body component E 1482109 -!- 89181349 -!- 92202159 -!- 8371104 Cytoplasmic COG1677;Flagellar hook-basal body protein PF02049;Flagellar hook-basal body complex protein Fl;5.2e-45;codon 5-104 TIGR00205;fliE: flagellar hook-basal body complex prot;6.7e-58;codon 1-104 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1936 fliF fliF flaBI -!- flaAII 1 -!- flaAII.1 b1938 2011253 2012911 + (no change) JW1922 2015366 2017024 + s flagellar basal-body MS-ring and collar protein E 1482109 -!- 89181349 -!- 92407478 -!- 1551848 -!- 8224881 Integral Membrane Protein heteromultimer; Flagellar Motor Complex (b1073-b1074-b1077-b1078-b1080-b1889-b1890-b1938-b 1945) 1-33 3 2 COG1766;Flagellar biosynthesis/type III secretory pathway lipoprotein PF01514;Secretory protein of YscJ/FliF family;2.5e-96;codon 17-225 TIGR00206;fliF: flagellar M-ring protein FliF;1.2e-241;codon 1-552 GO:0019861 flagellum -!- GO:0019866 inner membrane GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1937 fliG fliG flaBII -!- flaAII 2 -!- flaAII.2 b1939 2012904 2013899 + (no change) JW1923 2017017 2018012 + cp flagellar motor switching and energizing component E 1482109 -!- 92335216 -!- 94040782 -!- 8631704 Cytoplasmic COG1536;Flagellar motor switch protein 48029; FliG C-terminal domain PF01706;FliG C-terminal domain;4.7e-63;codon 215-324 TIGR00207;fliG: flagellar motor switch protein FliG;6.1e-227;codon 1-331 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1938 fliH fliH flaBIII -!- flaAII 3 -!- flaAII.3 b1940 2013892 2014578 + start codon change JW1924 2018005 2018691 + s flagellar biosynthesis protein modulates fliI expression-!- possible export of flagellar proteins E 1482109 -!- 89181349 -!- 92407478 -!- 8224881 Cytoplasmic COG1317;Flagellar biosynthesis/type III secretory pathway protein PF02108;Flagellar assembly protein FliH;3e-157;codon 8-227 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1939 fliI fliI flaC -!- fla AIII b1941 2014578 2015951 + (no change) JW1925 2018691 2020064 + e flagellum-specific ATP synthase E 1482109 Cytoplasmic 3.6.1.34 COG1157;Flagellar biosynthesis/type III secretory pathway ATPase 52540; P-loop containing nucleotide triphosphate hydrolases "PF00006;ATP synthase alpha/beta family, nucleotid;3.6e-109;codon 161-373" TIGR01026;fliI_yscN: ATPase FliI/YscN family;0;codon 5-454 GO:0019861 flagellum GO:0015986 ATP synthesis coupled proton transport CDS ECK1940 fliJ fliJ flaO b1942 2015970 2016413 + (no change) JW1926 2020083 2020526 + s flagellar protein E 1482109 -!- 8631687 Cytoplasmic COG2882;Flagellar biosynthesis chaperone PF02050;Flagellar FliJ protein;5.5e-125;codon 1-147 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1941 fliK fliK flaE b1943 2016410 2017537 + (no change) JW1927 2020523 2021650 + s flagellar hook-length control protein E 1482109 -!- 8631687 Cytoplasmic COG3144;Flagellar hook-length control protein PF02120;Flagellar hook-length control protein;4.4e-52;codon 181-324 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1942 fliL fliL flaAI -!- cheC1 -!- cheC2 -!- fla AI -!- fla QI -!- flaAII -!- flaQII -!- flaQI b1944 2017642 2018106 + (no change) JW1928 2021755 2022219 + s flagellar biosynthesis protein E 1482109 -!- 89181349 -!- 89213963 -!- 3519573 Outer membrane Lipoprotein 1-31 COG1580;Flagellar basal body-associated protein PF03748;Flagellar basal body-associated protein FliL;4.9e-49;codon 12-154 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1943 fliM fliM cheC -!- flaA -!- QII -!- cheC2 -!- fla AII -!- fla QII -!- flaAII -!- flaQII b1945 2018111 2019115 + (no change) JW1929 2022224 2023228 + cp flagellar motor switching and energizing component E 1482109 -!- 92335216 -!- 93015666 -!- 2651416 -!- 3519573 Cytoplasmic heteromultimer; Flagellar Motor Complex (b1073-b1074-b1077-b1078-b1080-b1889-b1890-b1938-b 1945) COG1868;Flagellar motor switch protein PF02154;Flagellar motor switch protein FliM;9.4e-126;codon 38-231 TIGR01397;fliM_switch: flagellar motor switch prote;5.9e-123;codon 4-322 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1944 fliN fliN motD b1946 2019112 2019525 + (no change) JW1930 2023225 2023638 + cp flagellar motor switching and energizing component E 1482109 -!- 92335216 -!- 93015666 -!- 2651416 Cytoplasmic COG1886;Flagellar motor switch/type III secretory pathway protein PF01052;Surface presentation of antigens (SPOA) prot;2.2e-36;codon 53-129 GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1945 fliO fliO flbD -!- flpD b1947 2019528 2019893 + start codon change JW5316 2023641 2024006 + s flagellar biosynthesis protein E 1482109 -!- 92407478 -!- 94110225 Membrane Anchored "PF04347;Flagellar biosynthesis protein, FliO;1.5e-48;codon 16-101" GO:0019861 flagellum GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1946 fliP fliP flaR b1948 2019893 2020630 + (no change) JW1932 2024006 2024743 + s flagellar biosynthesis protein E 1482109 -!- 92407478 -!- 94110225 Integral Membrane Protein 5 5 "COG1338;Flagellar biosynthesis pathway, component FliP" PF00813;FliP family;5.7e-126;codon 47-240 TIGR01103;fliP: flagellar biosynthetic protein FliP;1.3e-148;codon 47-243 GO:0019861 flagellum -!- GO:0009274 cell wall (sensu Bacteria) GO:0009296 flagella biogenesis -!- GO:0042330 taxis CDS ECK1947 fliQ fliQ flaQ b1949 2020640 2020909 + (no change) JW1933 2024753 2025022 + s flagellar biosynthesis protein E 1482109 -!- 92407478 -!- 94110225 Integral Membrane Protein 2 2 "COG1987;Flagellar biosynthesis pathway, component FliQ" "PF01313;Bacterial export proteins, family;8.6e-44;codon 4-79" TIGR01402;fliQ: flagellar biosynthetic protein FliQ;9.2e-54;codon 1-88 GO:0019861 flagellum -!- GO:0009274 cell wall (sensu Bacteria) GO:0009101 glycoprotein biosynthesis -!- GO:0009296 flagella biogenesis CDS ECK1948 fliR fliR flaP b1950 2020917 2021702 + (no change) JW1934 2025030 2025815 + pt flagellar export pore protein E 1482109 -!- 92407478 -!- 94110225 Integral Membrane Protein 6 6 "COG1684;Flagellar biosynthesis pathway, component FliR" "PF01311;Bacterial export proteins, family;1e-101;codon 7-252" TIGR01400;fliR: flagellar biosynthetic protein FliR;2.7e-115;codon 13-255 GO:0019861 flagellum -!- GO:0009274 cell wall (sensu Bacteria) CDS ECK1949 rcsA rcsA cpsR b1951 2021992 2022615 + (no change) JW1935 2026105 2026728 + r "DNA-binding transcriptional activator, co-regulator with RcsB" E 14514676 -!- 14766922 -!- 20167175 -!- 90130299 -!- 91154130 -!- 92048476 -!- 9882673 -!- 7534408 Cytoplasmic heteromultimer; RcsB transcriptional activator (b1951-b2217) LuxR/UhpA flhDC -!- ftsAZ -!- osmC -!- rcsA -!- wza-wzb-b2060-wcaA-wcaB -!- cpsBG COG2771;DNA-binding HTH domain-containing proteins "46894; C-terminal, effector domain of the bipartite response regulators" "PF00196;Bacterial regulatory proteins, luxR family;9e-22;codon 135-192" GO:0005737 cytoplasm GO:0009242 colanic acid biosynthesis -!- GO:0009248 K antigen biosynthesis -!- GO:0006350 transcription "GO:0016563 transcriptional activator activity -!- GO:0042280 cell surface antigen activity, host-interacting" CDS ECK1950 dsrB dsrB b1952 2022659 2022847 - (no change) JW1936 2026772 2026960 - o predicted protein C 96324407 -!- 7534408 Cytoplasmic GO:0005737 cytoplasm CDS ECK1951 yodD yodD b1953 2023010 2023237 + start codon change JW5317 2027123 2027350 + o predicted protein C Cytoplasmic regulated by attenuation (yodD) misc_RNA ECK1952 dsrA dsrA IS095 b1954 2023251 2023337 - (no change) JWR0036 2027364 2027450 - n "regulatory, anti-sense RNA" anti-silencer of rcsA transcription -!- antagonist of H-NS mediated repression of rcsA E 20420308 -!- 96324407 CDS ECK1953 yedP yedP b1955 2023535 2024350 + (no change) JW1938 2027648 2028463 + d conserved protein C Cytoplasmic COG3769;Predicted hydrolase (HAD superfamily) 56784; HAD-like TIGR01486;HAD-SF-IIB-YedP: YedP;1.4e-159;codon 7-235 -!- TIGR01484;HAD-SF-IIB: HAD-superfamily hydrolase;7.5e-64;codon 9-231 CDS ECK1954 yedQ yedQ b1956 2024347 2026041 - start codon change JW5832 2028460 2030154 - pr predicted diguanylate cyclase C Integral Membrane Protein 2 2 in COG2199;FOG: GGDEF domain 53383; PLP-dependent transferases PF00990;GGDEF domain;2.1e-71;codon 399-562 TIGR00254;GGDEF: putative diguanylate cyclase (GGDEF);5.1e-74;codon 399-567 CDS ECK1955 yodC yodC b1957 2026212 2026394 - (no change) JW1940 2030325 2030507 - o predicted protein C Cytoplasmic CDS ECK1956 yedI yedI b1958 2026473 2027390 - (no change) JW1941 2030586 2031503 - pm conserved inner membrane protein C Integral Membrane Protein 6 5 in COG2354;Uncharacterized protein conserved in bacteria PF05661;Protein of unknown function (DUF808);2.5e-192;codon 3-297 GO:0009274 cell wall (sensu Bacteria) CDS ECK1957 yedA yedA b1959 2027563 2028483 + (no change) JW1942 2031676 2032596 + pm predicted inner membrane protein C Integral Membrane Protein 10 10 in COG0697;Permeases of the drug/metabolite transporter (DMT) superfamily PF00892;Integral membrane protein DUF6;3.4e-28;codon 18-141 -!- PF00892;Integral membrane protein DUF6;5.7e-20;codon 160-285 TIGR00950;2A78: Carboxylate/Amino Acid/Amine Transport;1.6e-101;codon 20-281 GO:0009274 cell wall (sensu Bacteria) CDS ECK1958 vsr vsr b1960 2028472 2028942 - (no change) JW1943 2032585 2033055 - e DNA mismatch endonuclease of very short patch repair E 90330522 -!- 92049708 -!- 94049122 -!- 10360178 -!- 10612397 -!- 10871403 -!- 2527357 Cytoplasmic 3.1.-.- 1CW0 COG3727;DNA G:T-mismatch repair endonuclease 52980; Restriction endonuclease-like PF03852;DNA mismatch endonuclease Vsr;4e-50;codon 2-76 TIGR00632;vsr: DNA mismatch endonuclease (vsr);3e-86;codon 1-118 GO:0006308 DNA catabolism -!- GO:0006281 DNA repair -!- GO:0006308 DNA catabolism CDS ECK1959 dcm dcm mec b1961 2028923 2030341 - (no change) JW1944 2033036 2034454 - e DNA cytosine methylase E 90280700 -!- 91285397 -!- 93367813 -!- 2198248 -!- 2527357 Cytoplasmic 2.1.1.73 COG0270;Site-specific DNA methylase 53335; S-adenosyl-L-methionine-dependent methyltransferases PF00145;C-5 cytosine-specific DNA methylase;2.7e-85;codon 87-452 TIGR00675;dcm: DNA-cytosine methyltransferase;3.5e-145;codon 89-450 GO:0005737 cytoplasm GO:0006306 DNA methylation CDS ECK1960 yedJ yedJ b1962 2030408 2031103 - (no change) JW1945 2034521 2035216 - pe predicted phosphohydrolase C COG1418;Predicted HD superfamily hydrolase PF01966;HD domain;7.9e-21;codon 26-132 CDS ECK1961 yedR yedR b1963 2031143 2031508 - start codon change JW1946 2035256 2035621 - pm predicted inner membrane protein C Integral Membrane Protein 3 2 in ECK1962 yedS yedS b4496 2032045 2033267 + pseudogene; interrupted by frameshift and in-frame stop JW5319+JW1948+JW1949 2036188 2037380 + ancestral gene su predicted protein (pseudogene) C Periplasmic PF00267;Gram-negative porin;1.4e-09;codon 37-171 CDS ECK1962 yedS yedS_3 b1966 2032863 2033267 + pseudogene fragment -!- (no change) JW1949 2036976 2037380 + "pseudogene, split by frameshift (yedS)" su "predicted protein, C-ter fragment (pseudogene)" C CDS ECK1962 yedS yedS_2 b1965 2032570 2032779 + pseudogene fragment -!- (no change) JW1948 2036683 2036892 + "pseudogene, split by terminal codon (yedS)" su "predicted protein, middle fragment (pseudogene)" C CDS ECK1962 yedS yedS_1 yedT b1964 2032075 2032560 + pseudogene fragment -!- start codon change JW5319 2036188 2036673 + pseudogene (N-ter) su "predicted protein, N-ter fragment (pseudogene)" C CDS ECK1963 hchA hchA yedU -!- yzzC b1967 2033859 2034710 + (no change) JW1950 2037972 2038823 + f Hsp31 molecular chaperone E 12565879 -!- 14500888 -!- 12235139 -!- 12077448 -!- 8455549 Cytoplasmic monomeric multimer; Hsp31 homodimer (b1967) C56 family; Hsp31 g.p. (Escherichia coli) 1PV2 COG0693;Putative intracellular protease/amidase 52317; Class I glutamine amidotransferase-like PF01965;DJ-1/PfpI family;0.00026;codon 104-279 CDS ECK1964 yedV yedV b1968 2034818 2036176 - (no change) JW1951 2038931 2040289 - pr predicted sensory kinase in two-component regulatory system with YedW C in COG0642;Signal transduction histidine kinase 47384; Homodimeric domain of signal transducing histidine kinase -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF00672;HAMP domain;8.8e-09;codon 162-231 -!- PF00512;His Kinase A (phosphoacceptor) domain;3.9e-13;codon 235-301 -!- PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;1.3e-21;codon 344-451" TIGR01386;cztS_silS_copS: heavy metal sensor kin;5.6e-80;codon 3-449 GO:0006464 protein modification CDS ECK1965 yedW yedW b1969 2036176 2036847 - start codon change JW5322 2040289 2040960 - pr predicted DNA-binding response regulator in two-component system with YedV C Cytoplasmic Two COG0745;Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;1.4e-36;codon 17-135 -!- PF00486;Transcriptional regulatory protein, C te;9.8e-22;codon 159-234" TIGR01387;cztR_silR_copR: heavy metal response r;2.9e-183;codon 19-234 GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK1966 yedX yedX b1970 2036980 2037393 + (no change) JW1953 2041093 2041506 + d conserved protein C Periplasmic 1-24 137 COG2351;Transthyretin-like protein 49472; Transthyretin (prealbumin) PF00576;Transthyretin precursor (formerly preal;3.1e-66;codon 27-136 CDS ECK1967 yedY yedY b1971 2037502 2038506 + (no change) JW1954 2041615 2042619 + pe predicted reductase C 15355966 Periplasmic 1-41 COG2041;Sulfite oxidase and related enzymes "56524; Sulfite oxidase, middle catalytic domain" PF00174;Oxidoreductase molybdopterin binding d;9.8e-05;codon 48-268 TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.057;codon 20-44 CDS ECK1968 yedZ yedZ b1972 2038507 2039142 + (no change) JW1955 2042620 2043255 + pm conserved inner membrane protein C 15355966 Integral Membrane Protein 6 6 in COG2717;Predicted membrane protein PF05252;Uncharacterised protein family (UPF0191);8.9e-118;codon 7-199 CDS ECK1969 yodA yodA b1973 2039399 2040049 + (no change) JW1956 2043512 2044162 + d conserved metal-binding protein C 12077457 -!- 12480884 -!- 12909634 -!- 9579078 Periplasmic 1-23 216 COG3443;Predicted periplasmic or secreted protein CDS ECK1970 yodB yodB b1974 2040392 2040922 + start codon change JW5323 2044505 2045035 + pc predicted cytochrome cytochrome b561 family C Integral Membrane Protein 4 4 in PF01292;Cytochrome b561 family;1.5e-71;codon 11-184 GO:0017004 cytochrome biogenesis tRNA ECK1971 serU serU Su-1 -!- SuI -!- ftsM -!- su_1 -!- supD -!- supH -!- su1 b1975 2041492 2041581 - (no change) JWR0037 2045605 2045694 - n tRNA-Ser(CGA) (Serine tRNA2) E 2649486 -!- 91088251 -!- 93285328 CDS ECK1972 yeeI yeeI b1976 2041675 2042472 + start codon change JW1958 2045788 2046585 + o conserved protein C Cytoplasmic COG3228;Uncharacterized protein conserved in bacteria PF06167;Protein of unknown function (DUF980);3.3e-164;codon 14-278 tRNA ECK1973 asnT asnT b1977 2042573 2042648 + (no change) JWR0038 2046686 2046761 + n tRNA-Asn(GUU) (Asparagine tRNA) E 90230300 -!- 93352662 CDS ECK1974 yeeJ yeeJ b1978 2042935 2050038 + start codon change JW5833 2047048 2054151 + the next Met could be used f adhesin E 15659678 Periplasmic Unclass 49373; Invasin/intimin cell-adhesion fragments PF02369;Bacterial Ig-like domain (group 1);4.4e-29;codon 764-859 -!- PF02369;Bacterial Ig-like domain (group 1);2.2e-34;codon 866-956 -!- PF02369;Bacterial Ig-like domain (group 1);4e-39;codon 957-1058 -!- PF02369;Bacterial Ig-like domain (group 1);8.1e-40;codon 1067-1162 -!- PF02369;Bacterial Ig-like domain (group 1);5.6e-28;codon 1172-1262 -!- PF02369;Bacterial Ig-like domain (group 1);2e-30;codon 1272-1375 -!- PF02369;Bacterial Ig-like domain (group 1);2.2e-29;codon 1376-1473 -!- PF02369;Bacterial Ig-like domain (group 1);1.1e-39;codon 1478-1578 -!- PF02369;Bacterial Ig-like domain (group 1);6e-41;codon 1579-1680 -!- PF02369;Bacterial Ig-like domain (group 1);1.8e-32;codon 1687-1779 -!- PF02369;Bacterial Ig-like domain (group 1);9.3e-30;codon 1789-1878 -!- PF02369;Bacterial Ig-like domain (group 1);2.1e-30;codon 1881-1975 -!- PF02369;Bacterial Ig-like domain (group 1);2.8e-32;codon 1978-2078 "GO:0006355 regulation of transcription, DNA-dependent" ECK1975 yeeL yeeL b4497 2050300 2051352 - pseudogene; interrupted by in-frame stop JW1961+JW5325 2054413 2055465 - ancestral gene su predicted protein (pseudogene) C Cytoplasmic CDS ECK1975 yeeL yeeL_1 b1980 2050648 2051352 - pseudogene fragment -!- (no change) JW1961 2054761 2055465 - pseudogene su "predicted protein, N-ter fragment (pseudogene)" C CDS ECK1975 yeeL yeeL_2 yeeK b1979 2050300 2050626 - pseudogene fragment -!- (no change) JW5325 2054413 2054739 - "pseudogene, split by nonsense mutation" su "predicted protein, C-ter fragment (pseudogene)" C CDS ECK1976 shiA shiA yeeM b1981 2051667 2052983 + (no change) JW1962 2055780 2057096 + t shikimate transporter E 5332864 -!- 9524262 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG0477;Permeases of the major facilitator superfamily PF00083;Sugar (and other) transporter;1.2e-19;codon 22-431 -!- PF07690;Major Facilitator Superfamily;1.1e-19;codon 40-405 TIGR00883;2A0106: metabolite:proton symporter family p;3.4e-227;codon 30-426 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009423 chorismate biosynthesis CDS ECK1977 amn amn b1982 2053085 2054539 + (no change) JW1963 2057198 2058652 + e AMP nucleosidase E 90105402 -!- 9524262 Cytoplasmic 3.2.2.4 monomeric multimer; AMP nucleosidase (b1982) 1T8Y COG0775;Nucleoside phosphorylase 53167; Purine and uridine phosphorylases PF01048;Phosphorylase family;3.8e-99;codon 225-460 TIGR01717;AMP-nucleosdse: AMP nucleosidase;0;codon 10-484 GO:0042597 periplasmic space "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK1978 yeeN yeeN b1983 2054882 2055598 + (no change) JW1964 2058995 2059711 + d conserved protein C Cytoplasmic COG0217;Uncharacterized conserved protein PF01709;Domain of unknown function DUF28;1.2e-127;codon 3-236 TIGR01033;TIGR01033: conserved hypothetical protein T;8.5e-62;codon 1-236 tRNA ECK1979 asnW asnW b1984 2056051 2056126 - (no change) JWR0039 2060164 2060239 - n tRNA-Asn(GUU) (Asparagine tRNA) E 90230300 -!- 97251358 CDS ECK1980 yeeO yeeO b1985 2056227 2057870 - (no change) JW1965 2060340 2061983 - pt predicted multidrug efflux system C Integral Membrane Protein 13 11 in COG0534;Na+-driven multidrug efflux pump PF01554;MatE;3e-48;codon 100-262 -!- PF01554;MatE;7.4e-44;codon 330-491 TIGR00797;matE: MATE efflux family protein;2.1e-64;codon 100-504 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane tRNA ECK1981 asnU asnU b1986 2057875 2057950 + (no change) JWR0040 2061988 2062063 + n tRNA-Asn(GUU) (Asparagine tRNA) E 90230300 -!- 93352662 CDS ECK1982 cbl cbl b1987 2057988 2058938 - (no change) JW1966 2062101 2063051 - r DNA-binding transcriptional activator of cysteine biosynthesis E 96105196 -!- 99436146 Cytoplasmic LysR tauABCD COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;5.7e-16;codon 3-64 -!- PF03466;LysR substrate binding domain;9e-46;codon 88-296 GO:0005737 cytoplasm GO:0019344 cysteine biosynthesis -!- GO:0006790 sulfur metabolism -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK1983 nac nac b1988 2059040 2059957 - (no change) JW1967 2063153 2064070 - r DNA-binding transcriptional dual regulator of nitrogen assimilation E 99001630 -!- 9495755 Cytoplasmic LysR asnC -!- codBA -!- gabDTP -!- gdhA -!- gltBDF -!- nac -!- nupC COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;1.2e-19;codon 3-62 -!- PF03466;LysR substrate binding domain;7.2e-36;codon 86-292 GO:0005737 cytoplasm GO:0006807 nitrogen metabolism -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity -!- GO:0016563 transcriptional activator activity tRNA ECK1984 asnV asnV b1989 2060284 2060359 + (no change) JWR0041 2064397 2064472 + n tRNA-Asn(GUU) (Asparagine tRNA) E 90230300 -!- 93352662 CDS ECK1985 erfK erfK yeeG -!- yzzT b1990 2060415 2061347 - (no change) JW1968 2064528 2065460 - d conserved protein with NAD(P)-binding Rossmann-fold domain C 9298646 Periplasmic 1-21 310 COG1376;Uncharacterized protein conserved in bacteria 51735; NAD(P)-binding Rossmann-fold domains PF03734;ErfK/YbiS/YcfS/YnhG;3.9e-66;codo n 93-230 CDS ECK1986 cobT cobT b1991 2061412 2062491 - (no change) JW1969 2065525 2066604 - e nicotinate-nucleotide dimethylbenzimidazole-P phophoribosyl transferase E 96062218 2.4.2.21 monomeric multimer; dimethylbenzimidazole phosphoribosyltransferase (b1991) COG2038;NaMN:DMB phosphoribosyltransferase "52733; Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (C" PF02277;Phosphoribosyltransferase;2.4e-1 79;codon 7-347 GO:0009236 vitamin B12 biosynthesis CDS ECK1987 cobS cobS b1992 2062503 2063246 - (no change) JW1970 2066616 2067359 - e cobalamin 5'-phosphate synthase E 96062218 Integral Membrane Protein 2.-.-.- 5 4 COG0368;Cobalamin-5-phosphate synthase PF02654;Cobalamin-5-phosphate synthase;9e-127;codon 5-246 TIGR00317;cobS: cobalamin 5'-phosphate synthase;4.2e-142;codon 1-246 GO:0009236 vitamin B12 biosynthesis CDS ECK1988 cobU cobU b1993 2063243 2063788 - (no change) JW1971 2067356 2067901 - e bifunctional cobinamide kinase and cobinamide phosphate guanylyltransferase E 96062218 Cytoplasmic monomeric multimer; cobinamide-P guanylyltransferase / cobinamide kinase (b1993) regulated by attenuation (cobU-cobS-cobT) COG2087;Adenosyl cobinamide kinase/adenosyl cobinamide phosphate guanylyltransferase 52540; P-loop containing nucleotide triphosphate hydrolases PF02283;Cobinamide kinase / cobinamide phosphate gua;3.9e-133;codon 3-180 GO:0009236 vitamin B12 biosynthesis CDS ECK1989 yoeA yoeA b1995 2066659 2067051 + pseudogene -!- start codon change JW5326 2070772 2071164 + "pseudogene, split by IS" h CP4-44 prophage; predicted disrupted hemin or colicin receptor (pseudogene) C 12904577 Periplasmic cryptic prophage CP4-44 "COG1629;Outer membrane receptor proteins, mostly Fe transport" 56935; Porins CDS ECK1990 yoeE yoeE b1998 2068268 2068528 + (no change) JW1980 2072381 2072641 + h CP4-44 prophage; predicted disrupted hemin or colicin receptor C cryptic prophage CP4-44 "COG1629;Outer membrane receptor proteins, mostly Fe transport" 56935; Porins CDS ECK1991 yeeP yeeP b1999 2068810 2069235 + pseudogene -!- start codon change JW5327 2072923 2073348 + "pseudogene, can be extended by similarity" h CP4-44 prophage; predicted GTP-binding protein (pseudogene) C Cytoplasmic cryptic prophage CP4-44 COG3596;Predicted GTPase 52540; P-loop containing nucleotide triphosphate hydrolases misc_RNA ECK1992 isrC IS102 b4435 2069339 2069542 + (no change) JWR0240 2073452 2073655 + n small RNA E 12069726 CDS ECK1993 flu flu agn43 -!- agn -!- yeeQ -!- yzzX b2000 2069563 2072682 + (no change) JW1982 2073676 2076795 + h CP4-44 prophage; antigen 43 (Ag43) phase-variable biofilm formation autotransporter E 20392470 -!- 97257509 -!- 99212225 -!- 2661530 -!- 9298646 cryptic prophage CP4-44 1.B.12; The Autotransporter (AT) Family regulated by attenuation (flu) 51126; Pectin lyase-like PF03212;Pertactin;1.5e-06;codon 571-702 -!- PF03797;Autotransporter beta-domain;5.5e-35;codon 738-1023 TIGR01414;autotrans_barl: outer membrane autotra;1.2e-27;codon 592-1039 CDS ECK1994 yeeR yeeR b2001 2072803 2074335 + start codon change JW1983 2076916 2078448 + h CP4-44 prophage; predicted membrane protein C Integral Membrane Protein cryptic prophage CP4-44 5 6 in CDS ECK1995 yeeS yeeS b2002 2074332 2074778 + (no change) JW1984 2078445 2078891 + h CP4-44 prophage; predicted DNA repair protein similarity with RadC C Cytoplasmic cryptic prophage CP4-44 COG2003;DNA repair proteins "PF04002;RadC, DNA repair protein;1.6e-81;codon 24-148" TIGR00608;radc: DNA repair protein RadC;5e-29;codon 2-148 CDS ECK1996 yeeT yeeT b2003 2074841 2075062 + (no change) JW1985 2078954 2079175 + h CP4-44 prophage; predicted protein C Cytoplasmic cryptic prophage CP4-44 PF06174;Protein of unknown function (DUF987);3.8e-56;codon 1-66 CDS ECK1997 yeeU yeeU b2004 2075136 2075504 + (no change) JW1986 2079249 2079617 + h CP4-44 prophage; antitoxin of the YeeV-YeeU toxin-antitoxin system E 14594833 Cytoplasmic cryptic prophage CP4-44 PF06154;YagB/YeeU/YfjZ family;1.9e-81;codon 15-119 CDS ECK1998 yeeV yeeV b2005 2075593 2075967 + (no change) JW1987 2079706 2080080 + h CP4-44 prophage; toxin of the YeeV-YeeU toxin-antitoxin system E 14594833 Cytoplasmic cryptic prophage CP4-44 PF06755;Protein of unknown function (DUF1219);1.9e-105;codon 1-124 CDS ECK1999 yeeW yeeW b2006 2075964 2076158 + (no change) JW1988 2080077 2080271 + h CP4-44 prophage; predicted protein C Cytoplasmic cryptic prophage CP4-44 CDS ECK2000 yoeF yoeF b4538 2076599 2076955 + new JW5328 2080712 2081068 + o conserved protein C 52540; P-loop containing nucleoside triphosphate hydrolases CDS ECK2001 yeeX yeeX b2007 2077056 2077451 - (no change) JW1989 2081169 2081564 - o conserved protein C Cytoplasmic PF04363;Protein of unknown function (DUF496);1.5e-69;codon 30-124 CDS ECK2002 yeeA yeeA b2008 2077557 2078615 - (no change) JW1990 2081670 2082728 - pm conserved inner membrane protein C Integral Membrane Protein 5 5 in COG1289;Predicted membrane protein GO:0009274 cell wall (sensu Bacteria) CDS ECK2003 sbmC sbmC gyrI -!- yeeB -!- dgi b2009 2078813 2079286 - (no change) JW1991 2082926 2083399 - r DNA gyrase inhibitor in high copy protects cells from effects of the replication inhibitor MccB17 E 11850398 -!- 9442027 -!- 8709849 Cytoplasmic 1JYH COG3449;DNA gyrase inhibitor "PF06445;Bacterial transcription activator, effect;8.2e-38;codon 1-153" GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication -!- GO:0006281 DNA repair -!- GO:0009432 SOS response CDS ECK2004 dacD dacD pbp -!- phsE -!- yeeC b2010 2079405 2080571 - start codon change JW5329 2083518 2084684 - e D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 6b) E 97113530 -!- 8955390 Periplasmic 3.4.16.4 S11 family; penicillin-binding protein 6 (penicillin-binding protein pbp-6B) 1-23 COG1686;D-alanyl-D-alanine carboxypeptidase "56601; beta-Lactamase/D-ala carboxypeptidase -!- 69189; Penicillin-binding protein 5, C-terminal domain" "PF00144;Beta-lactamase;0.002;codon 15-283 -!- PF00768;D-alanyl-D-alanine carboxypeptidase;5.7e-150;codon 27-265 -!- PF07943;Penicillin-binding protein 5, C-termin;1e-31;codon 284-375" GO:0009274 cell wall (sensu Bacteria) CDS ECK2005 sbcB sbcB xonA -!- cpeA b2011 2080780 2082207 + (no change) JW1993 2084893 2086320 + e exonuclease I 3' --> 5'-specific -!- deoxyribophosphodiesterase E 21287280 -!- 88197996 -!- 91231162 -!- 91308087 -!- 1329027 -!- 3539937 Cytoplasmic 3.1.11.1 1FXX COG2925;Exonuclease I 53098; Ribonuclease H-like PF00929;Exonuclease;2e-33;codon 11-190 GO:0006308 DNA catabolism -!- GO:0006308 DNA catabolism CDS ECK2006 yeeD yeeD b2012 2082250 2082477 - (no change) JW1994 2086363 2086590 - d conserved protein C Cytoplasmic "COG0425;Predicted redox protein, regulator of disulfide bond formation" 64307; SirA-like PF01206;SirA-like protein;7.1e-40;codon 3-74 CDS ECK2007 yeeE yeeE b2013 2082491 2083549 - (no change) JW1995 2086604 2087662 - pm predicted inner membrane protein C Integral Membrane Protein 9 9 in regulated by attenuation (yeeE-yeeD) COG2391;Predicted transporter component PF04143;YeeE/YedE family (DUF395);3.2e-12;codon 70-132 -!- PF04143;YeeE/YedE family (DUF395);4.5e-17;codon 276-340 CDS ECK2008 yeeF yeeF b2014 2083728 2085086 - start codon change JW5330 2087841 2089199 - pt predicted amino-acid transporter C Integral Membrane Protein 12 12 in COG0531;Amino acid transporters PF00324;Amino acid permease;2.8e-20;codon 24-452 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2009 yeeY yeeY b2015 2085353 2086282 - start codon change JW5834 2089466 2090395 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic LysR 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;1.3e-15;codon 12-71 -!- PF03466;LysR substrate binding domain;9.7e-26;codon 95-301 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK2010 yeeZ yeeZ b2016 2086328 2087152 - (no change) JW1998 2090441 2091265 - pe "predicted epimerase, with NAD(P)-binding Rossmann-fold domain" C Periplasmic COG0451;Nucleoside-diphosphate-sugar epimerases 51735; NAD(P)-binding Rossmann-fold domains GO:0016052 carbohydrate catabolism CDS ECK2011 yoeB yoeB b4539 2087235 2087489 - new JW5331 2091348 2091602 - f toxin of the YoeB-YefM toxin-antitoxin system E Cytoplasmic GO:0005737 cytoplasm CDS ECK2012 yefM yefM b2017 2087486 2087737 - start codon change JW5835 2091599 2091850 - f antitoxin of the YoeB-YefM toxin-antitoxin system E 14672926 -!- 6170941 -!- 7567469 Cytoplasmic COG2161;Antitoxin of toxin-antitoxin stability system PF02604;Phd_YefM;3.5e-31;codon 10-83 TIGR01552;phd_fam: prevent-host-death family protein;6e-11;codon 12-65 CDS ECK2013 hisL hisL b2018 2088020 2088070 + (no change) JW2000 2092133 2092183 + l his operon leader peptide E 90062227 Cytoplasmic GO:0000105 histidine biosynthesis CDS ECK2014 hisG hisG b2019 2088216 2089115 + (no change) JW2001 2092329 2093228 + e ATP phosphoribosyltransferase E 89094829 -!- Martin RG;J Biol Chem;1963;238:257-268 Cytoplasmic 2.4.2.17 Mg2+ monomeric multimer; ATP phosphoribosyltransferase (b2019) regulated by attenuation (hisG-hisD-hisC-hisB-hisH-hisA-hisF-hisI) COG0040;ATP phosphoribosyltransferase PF01634;ATP phosphoribosyltransferase;2.2e-87;codon 53-221 TIGR00070;hisG: ATP phosphoribosyltransferase;1.2e-189;codon 6-299 GO:0005737 cytoplasm GO:0000105 histidine biosynthesis CDS ECK2015 hisD hisD b2020 2089121 2090425 + (no change) JW2002 2093234 2094538 + e bifunctional histidinal dehydrogenase and histidinol dehydrogenase E 86310273 -!- 89094829 -!- 90301483 -!- 11842181 -!- 2194167 -!- 3018428 -!- 3062174 -!- 6246067 -!- 9298646 Cytoplasmic 1.1.1.23 monomeric multimer; histidinal dehydrogenase / histidinol dehydrogenase (b2020) 1K75 COG0141;Histidinol dehydrogenase 53720; ALDH-like PF00815;Histidinol dehydrogenase;5.9e-276;codon 17-428 TIGR00069;hisD: histidinol dehydrogenase;1.1e-300;codon 12-432 GO:0000105 histidine biosynthesis CDS ECK2016 hisC hisC b2021 2090422 2091492 + (no change) JW2003 2094535 2095605 + e histidinol-phosphate aminotransferase E 89094829 -!- 11518529 -!- 2999081 -!- 3062174 -!- 8201624 Cytoplasmic 2.6.1.9 monomeric multimer; histidine-phosphate aminotransferase (b2021) 1GEY COG0079;Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase 53383; PLP-dependent transferases PF00155;Aminotransferase class I and II;6.4e-73;codon 69-355 TIGR01141;hisC: histidinol-phosphate aminotransferase;3e-200;codon 11-354 GO:0000105 histidine biosynthesis CDS ECK2017 hisB hisB b2022 2091492 2092559 + start codon change JW2004 2095605 2096672 + e fused histidinol-phosphatase -!- imidazoleglycerol-phosphate dehydratase E 86174354 -!- 89094829 -!- 3007936 -!- 3062174 Cytoplasmic 3.1.3.15 -!- 4.2.1.19 Mg2+ monomeric multimer; imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (b2022) fused: histidinol-phosphatase (aa1-167) -!- imidazoleglycerol-phosphate dehydratase (aa168-356) COG0241;Histidinol phosphatase and related phosphatases -!- COG0131;Imidazoleglycerol-phosphate dehydratase 56784; HAD-like PF00475;Imidazoleglycerol-phosphate dehydratase;7.3e-109;codon 197-339 "TIGR01261;hisB_Nterm: histidinol-phosphatase;5.8e-135;codon 4-164 -!- TIGR01656;Histidinol-ppas: histidinol-phosphate;2.1e-55;codon 5-161 -!- TIGR01662;HAD-SF-IIIA: hydrolase, HAD-superfami;1.3e-23;codon 5-152" GO:0000105 histidine biosynthesis CDS ECK2018 hisH hisH b2023 2092559 2093149 + (no change) JW2005 2096672 2097262 + e "imidazole glycerol phosphate synthase, glutamine amidotransferase subunit with HisF" E 89094829 -!- 93264432 -!- 94237842 -!- 11551184 -!- 3062174 -!- 8494895 Cytoplasmic 2.4.2.- heteromultimer; imidazole glycerol phosphate synthase (b2023-b2025) C56 family; non-peptidase homologues (imidazole glycerol phosphate synthase subunit HisH) COG0118;Glutamine amidotransferase 52317; Class I glutamine amidotransferase-like PF00117;Glutamine amidotransferase class-I;1e-43;codon 4-196 TIGR01855;IMP_synth_hisH: imidazole glycerol pho;1.8e-124;codon 3-196 GO:0000105 histidine biosynthesis CDS ECK2019 hisA hisA b2024 2093149 2093886 + start codon change JW2006 2097262 2097999 + e N-(5'-phospho-L-ribosyl-formimino)-5-amino-1-(5'-phosphoribosyl)-4-imidazolecarboxamide isomerase E 89094829 Cytoplasmic 5.3.1.16 COG0106;Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase 51366; Ribulose-phoshate binding barrel PF00977;Histidine biosynthesis protein;1.4e-105;codon 2-235 TIGR00007;TIGR00007: phosphoribosylformimino-5-aminoi;6e-127;codon 3-239 GO:0005737 cytoplasm GO:0000105 histidine biosynthesis CDS ECK2020 hisF hisF b2025 2093868 2094644 + (no change) JW2007 2097981 2098757 + e "imidazole glycerol phosphate synthase, catalytic subunit with HisH" E 4934198 -!- 93264432 -!- 94237842 -!- 10222209 Cytoplasmic 2.4.2.- heteromultimer; imidazole glycerol phosphate synthase (b2023-b2025) COG0107;Imidazoleglycerol-phosphate synthase 51366; Ribulose-phoshate binding barrel PF00977;Histidine biosynthesis protein;1.6e-120;codon 5-240 "TIGR00735;hisF: imidazoleglycerol phosphate synthase,;2e-187;codon 1-256" GO:0005737 cytoplasm GO:0000105 histidine biosynthesis CDS ECK2021 hisI hisI hisE -!- hisIE b2026 2094638 2095249 + (no change) JW2008 2098751 2099362 + e fused phosphoribosyl-AMP cyclohydrolase -!- phosphoribosyl-ATP pyrophosphatase E 86310273 -!- 89094829 -!- 3018428 -!- 3062174 -!- 7536735 -!- 8201624 Cytoplasmic 3.5.4.19 -!- 3.6.1.31 Mg2+ fused: phosphoribosyl-AMP cyclohydrolase (aa1-112) -!- phosphoribosyl-ATP pyrophosphatase (aa113-203) COG0139;Phosphoribosyl-AMP cyclohydrolase -!- COG0140;Phosphoribosyl-ATP pyrophosphohydrolase PF01502;Phosphoribosyl-AMP cyclohydrolase;2.1e-47;codon 33-107 -!- PF01503;Phosphoribosyl-ATP pyrophosphohydrolase;3.7e-51;codon 115-203 GO:0005737 cytoplasm GO:0000105 histidine biosynthesis CDS ECK2022 cld cld rol -!- wzz -!- wzzB b2027 2095345 2096325 - start codon change JW5836 2099458 2100438 - r regulator of length of O-antigen component of lipopolysaccharide chains E 98241528 Integral Membrane Protein 2 2 in regulated by attenuation (wzzB) PF02706;Chain length determinant protein;4.9e-30;codon 28-167 GO:0009243 O antigen biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2023 ugd ugd UDG8 -!- yefA -!- udg b2028 2096471 2097637 - (no change) JW2010 2100584 2101750 - e UDP-glucose 6-dehydrogenase E 9150218 -!- 96326333 Cytoplasmic 1.1.1.22 regulated by attenuation (ugd) COG1004;Predicted UDP-glucose 6-dehydrogenase "48179; 6-phosphogluconate dehydrogenase C-terminal domain-like -!- 51735; NAD(P)-binding Rossmann-fold domains -!- 52413; UDP-glucose dehydrogenase (UDPGDH), C-terminal (UDP-binding) domain" PF03721;UDP-glucose/GDP-mannose dehydrogenase;3e-44;codon 1-179 -!- PF00984;UDP-glucose/GDP-mannose dehydrogenase;5.4e-36;codon 190-283 -!- PF03720;UDP-glucose/GDP-mannose dehydrogenase;3.2e-07;codon 300-387 GO:0030113 capsule (sensu Bacteria) GO:0009242 colanic acid biosynthesis -!- GO:0009269 response to dessication "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2024 gnd gnd b2029 2097886 2099292 - (no change) JW2011 2101999 2103405 - e "gluconate-6-phosphate dehydrogenase, decarboxylating" E 786365 -!- 89145199 -!- 91310572 -!- 1938920 -!- 2050640 -!- 2464736 -!- 3275621 -!- 6329905 -!- 7677991 -!- 4151756 Cytoplasmic 1.1.1.44 monomeric multimer; 6-phosphogluconate dehydrogenase (decarboxylating) (b2029) COG0362;6-phosphogluconate dehydrogenase 48179; 6-phosphogluconate dehydrogenase C-terminal domain-like -!- 51735; NAD(P)-binding Rossmann-fold domains "PF03446;NAD binding domain of 6-phosphogluconat;5.6e-130;codon 3-175 -!- PF00393;6-phosphogluconate dehydrogenase, C-ter;4.9e-240;codon 177-467" "TIGR00873;gnd: 6-phosphogluconate dehydrogenase, decar;0;codon 5-468" "GO:0016052 carbohydrate catabolism -!- GO:0009051 pentose-phosphate shunt, oxidative branch -!- GO:0009052 pentose-phosphate shunt, non-oxidative branch" ECK2025 wbbL wbbL b4571 2099420 2101413 - "pseudogene; interrupted by IS5 -!- complement(join(2099420..2099768,2100968..2101413))" JW2016+JW2012 2103533 2105526 - ancestral gene su lipopolysaccharide biosynthesis protein (pseudogene) C CDS ECK2025 wbbL wbbL_2 b4540 2099420 2099701 - pseudogene fragment -!- start codon change JW2012 2103533 2103814 - pseudogene -!- split by IS su "lipopolysaccharide biosynthesis protein, C-ter fragment (pseudogene)" C CDS ECK2025 wbbL wbbL_1 yefJ b2031 2100940 2101413 - pseudogene fragment -!- start codon change JW2016 2105053 2105526 - pseudogene su "lipopolysaccharide biosynthesis protein, N-ter fragment (pseudogene)" E 10074083 Cytoplasmic PF00535;Glycosyl transferase;4.3e-13;codon 3-156 CDS ECK2026 wbbK wbbK yefI b2032 2101415 2102533 - (no change) JW2017 2105528 2106646 - pe lipopolysaccharide biosynthesis protein predicted glycosyl transferase C Cytoplasmic COG0438;Glycosyltransferase 53756; UDP-Glycosyltransferase/glycogen phosphorylase PF00534;Glycosyl transferases group;5.3e-29;codon 186-357 CDS ECK2027 wbbJ wbbJ yefH b2033 2102518 2103108 - (no change) JW2018 2106631 2107221 - pe predicted acyl transferase colanic acid biosynthesis C Cytoplasmic COG0110;Acetyltransferase (isoleucine patch superfamily) 51161; Trimeric LpxA-like enzymes 4 of PF00132;Bacterial transferase hexapeptide (three repeats): 42;codon 67-84 -!- 3.6;codon 87-104 -!- 17;codon 132-149 -!- 0.26;codon 150-167 GO:0009103 lipopolysaccharide biosynthesis CDS ECK2028 wbbI wbbI yefG b2034 2103089 2104081 - (no change) JW2019 2107202 2108194 - o conserved protein C Cytoplasmic CDS ECK2029 wbbH wbbH rfc -!- yefF b2035 2104084 2105250 - (no change) JW2020 2108197 2109363 - e O-antigen polymerase E 92355494 -!- 93225815 -!- 94018634 -!- 7517390 -!- 7517391 Integral Membrane Protein 12 12 GO:0009243 O antigen biosynthesis -!- GO:0009243 O antigen biosynthesis -!- GO:0009103 lipopolysaccharide biosynthesis "GO:0042280 cell surface antigen activity, host-interacting -!- GO:0008755 O antigen polymerase activity" CDS ECK2030 glf glf yefE b2036 2105250 2106353 - (no change) JW2021 2109363 2110466 - e "UDP-galactopyranose mutase, FAD/NAD(P)-binding" E 96165258 -!- 7517390 -!- 7517391 -!- 8576037 Cytoplasmic 5.4.99.9 COG0562;UDP-galactopyranose mutase "51971; Nucleotide-binding domain -!- 54373; FAD-linked reductases, C-terminal domain" PF03275;UDP-galactopyranose mutase;3e-145;codon 146-346 TIGR00031;UDP-GALP_mutase: UDP-galactopyranose;1.2e-273;codon 1-365 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009274 cell wall (sensu Bacteria) GO:0009243 O antigen biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2031 rfbX rfbX wzxB -!- wzx b2037 2106361 2107608 - (no change) JW2022 2110474 2111721 - pt predicted polisoprenol-linked O-antigen transporter C 94018634 -!- 94292434 -!- 94292435 -!- 7517390 -!- 7517391 Integral Membrane Protein 2.A.66; The Multidrug/Oligosaccharidyl-lipid/Polysaccharide (MOP) Flippase Superfamily 12 10 in COG2244;Membrane protein involved in the export of O-antigen and teichoic acid PF01943;Polysaccharide biosynthesis protein;6e-92;codon 8-279 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009243 O antigen biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2032 rfbC rfbC rfbD -!- rmlC b2038 2107605 2108162 - (no change) JW2023 2111718 2112275 - e "dTDP-4-deoxyrhamnose-3,5-epimerase" E "94292434 -!- 94292435 -!- 99231852 -!- 7517390 -!- 7517391 -!- Glaser L;Epimerases.;Academic Press, New York;1972;Third:355-380" Cytoplasmic 5.1.3.13 heteromultimer; dTDP-L-rhamnose synthetase (b2038-b2040) "COG1898;dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes" 51182; RmlC-like "PF00908;dTDP-4-dehydrorhamnose 3,5-epimerase;8.1e-122;codon 3-178" "TIGR01221;rmlC: dTDP-4-dehydrorhamnose 3,5-epimerase;4.4e-147;codon 2-179" GO:0005737 cytoplasm -!- GO:0005737 cytoplasm GO:0009226 nucleotide-sugar biosynthesis -!- GO:0009243 O antigen biosynthesis -!- GO:0009243 O antigen biosynthesis -!- GO:0009103 lipopolysaccharide biosynthesis -!- GO:0019305 dTDP-rhamnose biosynthesis "GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity -!- GO:0042803 protein homodimerization activity" CDS ECK2033 rfbA rfbA som -!- rmlA b2039 2108162 2109043 - (no change) JW2024 2112275 2113156 - e glucose-1-phosphate thymidylyltransferase E 5833803 -!- 92120472 -!- 94292435 -!- 96032389 -!- 7517390 -!- 7517391 -!- 14253441 2.7.7.24 Mg2+ 1H5S COG1209;dTDP-glucose pyrophosphorylase 53448; Nucleotide-diphospho-sugar transferases PF00483;Nucleotidyl transferase;1.6e-118;codon 5-243 TIGR01207;rmlA: glucose-1-phosphate thymidylyltransfer;1.8e-195;codon 5-290 GO:0005737 cytoplasm GO:0009243 O antigen biosynthesis -!- GO:0019305 dTDP-rhamnose biosynthesis -!- GO:0009103 lipopolysaccharide biosynthesis "GO:0042280 cell surface antigen activity, host-interacting -!- GO:0000287 magnesium ion binding -!- GO:0008879 glucose-1-phosphate thymidylyltransferase activity" CDS ECK2034 rfbD rfbD rfbC -!- rmlD b2040 2109101 2110000 - (no change) JW2025 2113214 2114113 - e "dTDP-4-dehydrorhamnose reductase subunit, NAD(P)-binding, of dTDP-L-rhamnose synthase" E "92120472 -!- 94292419 -!- 94292435 -!- 7517391 -!- Glaser L;Epimerases.;Academic Press, New York;1972;Third:355-380" Cytoplasmic 1.1.1.133 heteromultimer; dTDP-L-rhamnose synthetase (b2038-b2040) COG1091;dTDP-4-dehydrorhamnose reductase 51735; NAD(P)-binding Rossmann-fold domains PF04321;RmlD substrate binding domain;2.8e-75;codon 143-286 TIGR01214;rmlD: dTDP-4-dehydrorhamnose reductase;6.8e-122;codon 2-293 GO:0005737 cytoplasm GO:0009243 O antigen biosynthesis -!- GO:0009226 nucleotide-sugar biosynthesis CDS ECK2035 rfbB rfbB som -!- rmlB b2041 2110000 2111085 - (no change) JW2026 2114113 2115198 - e "dTDP-glucose 4,6 dehydratase, NAD(P)-binding" E "92120472 -!- 94292434 -!- 94292435 -!- 7517391 -!- Thorson JS, Oh E, Liu H;J Am Chem Soc;1992;114:6941-6942 -!- Glaser L, Zarkowsky H, Ward L;Methods Enzymology;1972;XXVIII:446-454" Cytoplasmic 4.2.1.46 "monomeric multimer; dTDP-glucose 4,6-dehydratase (b2041)" "COG1088;dTDP-D-glucose 4,6-dehydratase" 51735; NAD(P)-binding Rossmann-fold domains PF01370;NAD dependent epimerase/dehydratase family;3.4e-214;codon 3-338 "TIGR01181;dTDP_gluc_dehyt: dTDP-glucose 4,6-deh;4.9e-232;codon 2-344" GO:0009274 cell wall (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009243 O antigen biosynthesis -!- GO:0009226 nucleotide-sugar biosynthesis -!- GO:0009435 nicotinamide adenine dinucleotide biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2036 galF galF wcaN b2042 2111458 2112351 - (no change) JW2027 2115571 2116464 - pe predicted subunit with GalU similar to UDPGal transferase C 97126811 -!- 8971705 Periplasmic COG1210;UDP-glucose pyrophosphorylase 53448; Nucleotide-diphospho-sugar transferases PF00483;Nucleotidyl transferase;2.2e-11;codon 5-279 TIGR01105;galF: regulatory protein GalF;3.5e-269;codon 1-297 GO:0005737 cytoplasm GO:0009226 nucleotide-sugar biosynthesis CDS ECK2037 wcaM wcaM yefK b2043 2112526 2113920 - (no change) JW2028 2116639 2118033 - pm predicted colanic acid biosynthesis protein C Periplasmic 1-19 51126; Pectin lyase-like GO:0009242 colanic acid biosynthesis CDS ECK2038 wcaL wcaL yefL b2044 2113931 2115151 - (no change) JW2029 2118044 2119264 - pe predicted glycosyl transferase colanic acid biosynthesis C 96326333 Cytoplasmic COG0438;Glycosyltransferase 53756; UDP-Glycosyltransferase/glycogen phosphorylase PF00534;Glycosyl transferases group;1.1e-42;codon 209-385 GO:0009242 colanic acid biosynthesis CDS ECK2039 wcaK wcaK b2045 2115148 2116428 - (no change) JW2030 2119261 2120541 - pe predicted pyruvyl transferase colanic acid biosynthesis C 96326333 -!- 8759852 Cytoplasmic COG2327;Uncharacterized conserved protein PF04230;Polysaccharide pyruvyl transferase;2e-160;codon 2-415 GO:0009242 colanic acid biosynthesis CDS ECK2040 wzxC wzxC wzx b2046 2116704 2118182 - (no change) JW2031 2120817 2122295 - pt colanic acid exporter E 96326333 -!- 8759852 Integral Membrane Protein 2.A.66; The Multidrug/Oligosaccharidyl-lipid/Polysaccharide (MOP) Flippase Superfamily 14 12 in COG2244;Membrane protein involved in the export of O-antigen and teichoic acid PF01943;Polysaccharide biosynthesis protein;3.5e-77;codon 9-276 CDS ECK2041 wcaJ wcaJ b2047 2118184 2119578 - (no change) JW2032 2122297 2123691 - pe predicted UDP-glucose lipid carrier transferase colanic acid biosynthesis C 96326333 -!- 8759852 Integral Membrane Protein 7 5 in COG2148;Sugar transferases involved in lipopolysaccharide synthesis PF02397;Bacterial sugar transferase;2.5e-43;codon 274-464 GO:0009242 colanic acid biosynthesis CDS ECK2042 cpsG cpsG manB -!- rfbK b2048 2119633 2121003 - (no change) JW2033 2123746 2125116 - e phosphomannomutase E 93106949 -!- 96326333 -!- 7815923 -!- 8759852 Cytoplasmic 5.4.2.8 COG1109;Phosphomannomutase "53738; Phosphoglucomutase, first 3 domains" "PF02878;Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I;2.1e-49;codon 4-137 -!- PF02879;Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II;5.9e-59;codon 153-260 -!- PF02880;Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III;5.9e-56;codon 262-373 -!- PF00408;Phosphoglucomutase/phosphomannomutase, C-term;1e-31;codon 378-456" GO:0030113 capsule (sensu Bacteria) GO:0009226 nucleotide-sugar biosynthesis -!- GO:0009242 colanic acid biosynthesis -!- GO:0009269 response to dessication "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2043 cpsB cpsB manC -!- mni -!- wcaB -!- rfbM b2049 2121108 2122544 - (no change) JW2034 2125221 2126657 - e mannose-1-phosphate guanyltransferase E 82100097 -!- 85006781 -!- 92048476 -!- 93122523 -!- 96326333 -!- 7815923 -!- 8759852 Cytoplasmic 2.7.7.22 COG0836;Mannose-1-phosphate guanylyltransferase -!- COG0662;Mannose-6-phosphate isomerase 51182; RmlC-like -!- 53448; Nucleotide-diphospho-sugar transferases PF00483;Nucleotidyl transferase;1.2e-148;codon 7-296 -!- PF01050;Mannose-6-phosphate isomerase;1.7e-133;codon 307-473 -!- PF07883;Cupin domain;2.6e-11;codon 388-458 TIGR01479;GMP_PMI: mannose-1-phosphate guanylyltransfe;8.9e-281;codon 6-477 GO:0030113 capsule (sensu Bacteria) GO:0009242 colanic acid biosynthesis -!- GO:0016052 carbohydrate catabolism -!- GO:0009226 nucleotide-sugar biosynthesis -!- GO:0009269 response to dessication "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2044 wcaI wcaI yefD b2050 2122547 2123770 - (no change) JW2035 2126660 2127883 - pe predicted glycosyl transferase colanic acid biosynthesis C 96326333 COG0438;Glycosyltransferase 53756; UDP-Glycosyltransferase/glycogen phosphorylase PF00534;Glycosyl transferases group;1.3e-21;codon 218-391 GO:0009242 colanic acid biosynthesis CDS ECK2045 nudD nudD gmm -!- wcaH -!- yefC b2051 2123767 2124246 - start codon change JW5335 2127880 2128359 - e GDP-mannose mannosyl hydrolase E 96326333 -!- 10913267 -!- 7592609 -!- 7815923 -!- 8759852 Cytoplasmic 1.1.1.271 Mg2+ 1RYA COG0494;NTP pyrophosphohydrolases including oxidative damage repair enzymes 55811; Nudix PF00293;NUDIX domain;5.4e-23;codon 17-156 GO:0009226 nucleotide-sugar biosynthesis -!- GO:0009242 colanic acid biosynthesis CDS ECK2046 fcl fcl yefB -!- wcaG b2052 2124249 2125214 - (no change) JW2037 2128362 2129327 - e bifunctional GDP-fucose synthetase: GDP-4-dehydro-6-deoxy-D-mannose epimerase and GDP-4-dehydro-6-L-deoxygalactose reductase E 96326333 -!- 98132401 -!- 9862812 -!- 7815923 -!- 8759852 -!- 9473059 Cytoplasmic 5.1.3.- -!- 1.- 1FXS COG0451;Nucleoside-diphosphate-sugar epimerases 51735; NAD(P)-binding Rossmann-fold domains GO:0030113 capsule (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009242 colanic acid biosynthesis -!- GO:0009269 response to dessication "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2047 gmd gmd yefA -!- yefN b2053 2125217 2126338 - (no change) JW2038 2129330 2130451 - e "GDP-D-mannose dehydratase, NAD(P)-binding" E 20139699 -!- 97400210 -!- 10673432 -!- 7815923 -!- 8759852 -!- 9257704 -!- 14299611 Cytoplasmic 4.2.1.47 "monomeric multimer; GDP-mannose 4,6-dehydratase (b2053)" 1DB3 COG1089;GDP-D-mannose dehydratase 51735; NAD(P)-binding Rossmann-fold domains PF01370;NAD dependent epimerase/dehydratase family;1.9e-13;codon 5-354 "TIGR01472;gmd: GDP-mannose 4,6-dehydratase;1e-253;codon 3-354" GO:0030113 capsule (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009242 colanic acid biosynthesis -!- GO:0009435 nicotinamide adenine dinucleotide biosynthesis -!- GO:0009269 response to dessication "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2048 wcaF wcaF b2054 2126364 2126912 - (no change) JW2039 2130477 2131025 - pe predicted acyl transferase colanic acid biosynthesis C 96326333 Cytoplasmic COG0110;Acetyltransferase (isoleucine patch superfamily) 51161; Trimeric LpxA-like enzymes PF00132;Bacterial transferase hexapeptide (three rep;0.14;codon 51-68 -!- PF00132;Bacterial transferase hexapeptide (three rep;77;codon 91-108 -!- PF00132;Bacterial transferase hexapeptide (three rep;0.11;codon 136-153 GO:0009242 colanic acid biosynthesis CDS ECK2049 wcaE wcaE b2055 2126928 2127674 - (no change) JW2040 2131041 2131787 - pe predicted glycosyl transferase colanic acid biosynthesis C 96326333 -!- 8759852 Cytoplasmic COG0463;Glycosyltransferases involved in cell wall biogenesis 53448; Nucleotide-diphospho-sugar transferases PF00535;Glycosyl transferase;7e-14;codon 4-185 GO:0009242 colanic acid biosynthesis CDS ECK2050 wcaD wcaD b2056 2127685 2128902 - (no change) JW2041 2131798 2133015 - pe predicted colanic acid polymerase predicted inner membrane protein C 96326333 -!- 8759852 Integral Membrane Protein 14 11 CDS ECK2051 wcaC wcaC b2057 2128877 2130094 - (no change) JW2042 2132990 2134207 - pe predicted glycosyl transferase colanic acid biosynthesis C 96326333 Cytoplasmic COG0438;Glycosyltransferase 53756; UDP-Glycosyltransferase/glycogen phosphorylase GO:0009242 colanic acid biosynthesis CDS ECK2052 wcaB wcaB b2058 2130091 2130579 - (no change) JW2043 2134204 2134692 - pe predicted acyl transferase colanic acid biosynthesis C 96326333 -!- 8759852 Cytoplasmic COG1045;Serine acetyltransferase 51161; Trimeric LpxA-like enzymes PF00132;Bacterial transferase hexapeptide (three rep;85;codon 83-100 -!- PF00132;Bacterial transferase hexapeptide (three rep;11;codon 108-125 -!- PF00132;Bacterial transferase hexapeptide (three rep;0.74;codon 126-143 GO:0009242 colanic acid biosynthesis CDS ECK2053 wcaA wcaA b2059 2130582 2131421 - (no change) JW2044 2134695 2135534 - pe predicted glycosyl transferase colanic acid biosynthesis C 96326333 Cytoplasmic COG0463;Glycosyltransferases involved in cell wall biogenesis 53448; Nucleotide-diphospho-sugar transferases PF00535;Glycosyl transferase;8.7e-32;codon 8-172 GO:0009242 colanic acid biosynthesis CDS ECK2054 wzc wzc b2060 2131514 2133676 - start codon change JW2045 2135627 2137789 - e protein-tyrosine kinase E 10348860 -!- 11751920 -!- 12851388 -!- 21264679 -!- 96326333 -!- 11090276 -!- 8759852 Integral Membrane Protein 2.7.1.112 8.A.3; The Cytoplasmic Membrane-Periplasmic Auxiliary-1 (MPA1) Protein with Cytoplasmic (C) Domain (MPA1-C or MPA1+C) Family 3 2 in COG3206;Uncharacterized protein involved in exopolysaccharide biosynthesis -!- COG0489;ATPases involved in chromosome partitioning 52540; P-loop containing nucleotide triphosphate hydrolases PF02706;Chain length determinant protein;1.9e-93;codon 28-264 GO:0009242 colanic acid biosynthesis -!- GO:0006464 protein modification CDS ECK2055 wzb wzb b2061 2133679 2134122 - (no change) JW2046 2137792 2138235 - e protein-tyrosine phosphatase E 10348860 -!- 96326333 -!- 11090276 -!- 8759852 Cytoplasmic 3.1.3.48 COG0394;Protein-tyrosine-phosphatase 52788; Phosphotyrosine protein phosphatases I PF01451;Low molecular weight phosphotyrosine protein;2.7e-66;codon 3-141 GO:0009242 colanic acid biosynthesis CDS ECK2056 wza wza b2062 2134128 2135267 - (no change) JW2047 2138241 2139380 - lp lipoprotein required for capsular polysaccharide translocation through the outer membrane C 15090537 -!- 96326333 -!- 8759852 -!- 8763957 Outer membrane Lipoprotein 1.B.18; The Outer Membrane Auxiliary (OMA) Protein Family COG1596;Periplasmic protein involved in polysaccharide export PF02563;Polysaccharide biosynthesis/export protei;4.8e-67;codon 74-205 GO:0009242 colanic acid biosynthesis CDS ECK2057 yegH yegH b2063 2135926 2137509 + start codon change JW5336 2140039 2141622 + pm fused predicted membrane protein -!- predicted membrane protein C Integral Membrane Protein 7 7 in fused: predicted membrane protein (aa1-259) -!- predicted membrane protein (aa268-259) 54631; CBS-domain PF03741;Integral membrane protein TerC family;1.6e-72;codon 34-247 -!- PF00571;CBS domain;9.6e-08;codon 328-383 -!- PF00571;CBS domain;4.4e-08;codon 391-444 -!- PF03471;Transporter associated domain;1.2e-22;codon 461-540 GO:0009274 cell wall (sensu Bacteria) CDS ECK2058 asmA asmA yegA b2064 2137783 2139636 - (no change) JW2049 2141896 2143749 - pf predicted assembly protein inhibiting the assembly of mutant ompF proteins C 8866482 -!- 1324907 -!- 7476172 Membrane Anchored COG2982;Uncharacterized protein involved in outer membrane biogenesis PF05170;AsmA family;4.8e-257;codon 1-602 GO:0009103 lipopolysaccharide biosynthesis "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2059 dcd dcd paxA -!- dus b2065 2139658 2140239 - (no change) JW2050 2143771 2144352 - e 2'-deoxycytidine 5'-triphosphate deaminase E 92380941 -!- 94209217 -!- 1324907 Cytoplasmic 3.5.4.13 monomeric multimer; dCTP deaminase (b2065) COG0717;Deoxycytidine deaminase 51283; Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) PF00692;dUTPase;2.4e-39;codon 50-189 TIGR02274;dCTP_deam: deoxycytidine triphosphate deami;4.8e-112;codon 2-190 "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK2060 udk udk b2066 2140331 2140972 - start codon change JW2051 2144444 2145085 - e uridine/cytidine kinase E 79009989 -!- 8366067 Cytoplasmic 2.7.1.48 Mg2+ COG0572;Uridine kinase 52540; P-loop containing nucleotide triphosphate hydrolases PF00485;Phosphoribulokinase / Uridine kinase family;2e-50;codon 28-218 TIGR00235;udk: uridine kinase;1.6e-155;codon 19-231 "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK2061 yegE yegE b2067 2141290 2144607 + (no change) JW2052 2145403 2148720 + pr "predicted diguanylate cyclase, GGDEF domain signalling protein" C 15716451 Integral Membrane Protein 11 11 in COG3447;Predicted integral membrane sensor domain -!- COG2202;FOG: PAS/PAC domain -!- COG2199;FOG: GGDEF domain -!- COG2200;FOG: EAL domain 55785; PYP-like sensor domain PF05231;MASE1;2e-35;aa 18-295 -!- PF00785;PAC motif;2.1e-09;aa 375-417 -!- PF00785;PAC motif;4.2e-07;aa 502-543 -!- PF00785;PAC motif;0.00024;aa 629-671 -!- PF00990;GGDEF domain;5.7e-68;aa 678-839 -!- PF00563;EAL domain;5e-06;aa 886-1090 TIGR00229;PAS domain S-box;3.3e-37;codon 298-424 -!- TIGR00229;PAS domain S-box;6.9e-06;codon 425-550 -!- TIGR00229;PAS domain S-box;1.7e-13;codon 551-678 -!- TIGR00254;diguanylate cyclase (GGDEF) domain;4.6e-35;codon 678-844 GO:0006464 protein modification CDS ECK2062 alkA alkA aidA b2068 2144716 2145564 - (no change) JW2053 2148829 2149677 - e 3-methyl-adenine DNA glycosylase II inducible E 85054799 -!- 87056946 -!- 88151899 -!- 99387003 -!- 3529081 -!- 6094528 -!- 6389535 -!- 8706135 -!- 8706136 Cytoplasmic 3.2.2.21 regulated by attenuation (alkA) COG0122;3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase 48150; DNA-glycosylase -!- 55945; TATA-box binding protein-like PF06029;AlkA N-terminal domain;8.5e-67;codon 1-112 -!- PF00730;HhH-GPD superfamily base excision DNA repair;5.1e-22;codon 118-262 GO:0005737 cytoplasm GO:0006281 DNA repair CDS ECK2063 yegD yegD b2069 2145698 2147050 + start codon change JW2054 2149811 2151163 + pf predicted chaperone DnaK/Hsp70 family C 6094528 -!- 7940673 -!- 7984428 Cytoplasmic 53067; Actin-like ATPase domain GO:0006457 protein folding CDS ECK2064 yegI yegI b2070 2147063 2149009 - (no change) JW2055 2151176 2153122 - d conserved protein C COG4248;Uncharacterized protein with protein kinase and helix-hairpin-helix DNA-binding domains 56112; Protein kinase-like (PK-like) CDS ECK2065 yegJ yegJ b2071 2149209 2149670 + (no change) JW2056 2153322 2153783 + o predicted protein C Periplasmic COG3779;Uncharacterized protein conserved in bacteria CDS ECK2066 yegK yegK b2072 2149735 2150496 - (no change) JW2057 2153848 2154609 - o predicted protein C Cytoplasmic CDS ECK2067 yegL yegL b2073 2150493 2151152 - (no change) JW2058 2154606 2155265 - d conserved protein C Cytoplasmic "COG4245;Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain" 53300; Integrin A (or I) domain misc_RNA ECK2068 ryeC ryeC tp11 -!- QUAD1a b4436 2151299 2151447 + (no change) JWR0241 2155412 2155560 + n small RNA E 11445539 misc_RNA ECK2069 ryeD ryeD tpe60 -!- QUAD1b b4437 2151634 2151776 + (no change) JWR0242 2155747 2155889 + n small RNA E 11445539 CDS ECK2070 mdtA mdtA yegM b2074 2152040 2153287 + start codon change JW5338 2156153 2157400 + t "multidrug efflux system, subunit A" E 12107134 -!- 21450803 Membrane Anchored heteromultimer; MdtABC RND-type Drug Exporter (b2074-b2075-b2076-b3035) COG0845;Membrane-fusion protein "56954; Integral outer membrane protein TolC, efflux pump component" PF00529;HlyD: HlyD family secretion protein;3.3e-15;codon 86-376 TIGR00999;8a0102: Membrane Fusion Protein cluster 2 p;4.1e-11;codon 106-383 -!- TIGR00998;8a0101: efflux pump membrane protein;1.2e-05;codon 52-317 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2071 mdtB mdtB yegN b2075 2153287 2156409 + (no change) JW2060 2157400 2160522 + t "multidrug efflux system, subunit B" E 12107134 -!- 21450803 Integral Membrane Protein heteromultimer; MdtABC RND-type Drug Exporter (b2074-b2075-b2076-b3035) 2.A.6; The Resistance-Nodulation-Cell Division (RND) Superfamily 12 11 in COG0841;Cation/multidrug efflux pump PF00873;AcrB/AcrD/AcrF family;0;codon 12-1023 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK2072 mdtC mdtC yegO b2076 2156410 2159487 + (no change) JW2061 2160523 2163600 + t "multidrug efflux system, subunit C" E 12107134 -!- 21450803 Integral Membrane Protein heteromultimer; MdtABC RND-type Drug Exporter (b2074-b2075-b2076-b3035) 2.A.6; The Resistance-Nodulation-Cell Division (RND) Superfamily 12 10 in COG0841;Cation/multidrug efflux pump PF00873;AcrB/AcrD/AcrF family;0;codon 3-1009 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK2073 mdtD mdtD yegB b2077 2159488 2160903 + (no change) JW2062 2163601 2165016 + t multidrug efflux system protein E 12107134 -!- 21450803 -!- 8282725 Integral Membrane Protein 14 13 in COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;7e-55;codon 15-414 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2074 baeS baeS b2078 2160900 2162303 + (no change) JW2063 2165013 2166416 + r sensory histidine kinase in two-component regulatory system with BaeR E 94110256 -!- 8282725 Integral Membrane Protein 2 2 in mdtABCK -!- acrD COG0642;Signal transduction histidine kinase 47384; Homodimeric domain of signal transducing histidine kinase -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF00672;HAMP domain;3.9e-20;codon 167-236 -!- PF00512;His Kinase A (phosphoacceptor) domain;2e-18;codon 240-304 -!- PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;1.4e-37;codon 349-460" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0006464 protein modification CDS ECK2075 baeR baeR b2079 2162300 2163022 + (no change) JW2064 2166413 2167135 + r DNA-binding response regulator in two-component regulatory system with BaeS E 94110256 -!- 8282725 Cytoplasmic Two ! "mdtABCK, acrD" COG0745;Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;4.4e-30;codon 11-129 -!- PF00486;Transcriptional regulatory protein, C te;2.7e-21;codon 156-232" GO:0005737 cytoplasm GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK2076 yegP yegP b2080 2163213 2163545 + start codon change JW5339 2167326 2167658 + o predicted protein C Cytoplasmic PF07411;Domain of unknown function (DUF1508);3.3e-28;codon 23-71 -!- PF07411;Domain of unknown function (DUF1508);2.5e-27;codon 74-122 CDS ECK2077 yegQ yegQ b2081 2163692 2165053 + (no change) JW2066 2167805 2169166 + pe predicted peptidase C Cytoplasmic U32 family; unassigned peptidases (YegQ protein) COG0826;Collagenase and related proteases PF01136;Peptidase family U32;1.3e-150;codon 75-345 misc_RNA ECK2078 ryeE ryeE b4438 2165136 2165221 + (no change) JWR0243 2169249 2169334 + n small RNA interacts with Hfq E 11445539 CDS ECK2079 ogrK ogrK b2082 2165326 2165544 - (no change) JW2067 2169439 2169657 - h DNA-binding transcriptional regulator -!-prophage P2 remnant "phage remnant, for bacteriophage P2 late gene expression (Ogr)" E 92283767 -!- 8002564 Cytoplasmic "PF04606;Phage transcriptional activator, Ogr/Delta;1.1e-53;codon 1-72" CDS ECK2080 yegZ yegZ b2083 2165626 2165844 - pseudogene fragment -!- start codon change JW5886 2169739 2169957 - "pseudogene, changed original location, but complement(2165838) is pickable as a start position by similarity -!- GeneMark cannot predict" su predicted protein fragment (pseudogene) C 12426340 -!- 3458177 Cytoplasmic COG3500;Phage protein D CDS ECK2081 yegR yegR b2085 2166013 2166330 - start codon change JW5837 2170126 2170443 - o predicted protein C Outer membrane Lipoprotein CDS ECK2082 yegS yegS b2086 2166736 2167635 + (no change) JW2070 2170849 2171748 + d conserved protein C Cytoplasmic COG1597;Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase 50156; PDZ domain-like PF00781;Diacylglycerol kinase catalytic domain (pres;2.8e-39;codon 6-132 TIGR00147;TIGR00147: conserved hypothetical protein T;2e-184;codon 1-293 CDS ECK2083 gatR gatR_2 b2090 2169419 2169757 - pseudogene fragment -!- (no change) JW2074 2173532 2173870 - "pseudogene, split by IS" su "DNA-binding transcriptional repressor of galactitol utilization, C-ter fragment (pseudogene)" E 97113438 heteromultimer; GatR transcriptional repressor (b2087-b2090) gatYZABCDR_2 CDS ECK2083 gatR gatR_1 b2087 2167717 2168163 - pseudogene fragment -!- (no change) JW5340 2171830 2172276 - "pseudogene, split by IS" su "DNA-binding transcriptional repressor of galactitol utilization, N-ter fragment (pseudogene)" E 97113438 heteromultimer; GatR transcriptional repressor (b2087-b2090) gatYZABCDR_2 ECK2083 gatR gatR b4498 2167717 2169757 - "pseudogene; interrupted by IS3 -!- complement(join(2167717..2168191,2169453..2169757))" JW5340+JW2074 2171830 2173870 - ancestral gene su DNA-binding transcriptional regulator (pseudogene) C Cytoplasmic "PF00455;Bacterial regulatory proteins, deoR family;2.3e-07;codon 8-191" CDS ECK2084 gatD gatD b2091 2169857 2170897 - (no change) JW2075 2173970 2175010 - e "galactitol-1-phosphate dehydrogenase, Zn-dependent and NAD(P)-binding" E 7042910 -!- 77192083 -!- 97113438 -!- 7772602 1.1.1.251 COG1063;Threonine dehydrogenase and related Zn-dependent dehydrogenases 50129; GroES-like -!- 51735; NAD(P)-binding Rossmann-fold domains PF00107;Zinc-binding dehydrogenase;4.4e-86;codon 7-346 GO:0016052 carbohydrate catabolism CDS ECK2085 gatC gatC b2092 2170945 2172300 - (no change) JW2076 2175058 2176413 - t galactitol-specific enzyme IIC component of PTS E "76024805 -!- 77192083 -!- 97113438 -!- 7772602 -!- Reizer, J., Charbit, A., Reizer, A., et al;Genome Sci Technol;1996;1: 53-75" Integral Membrane Protein heteromultimer; EIIGat (b2092-b2093-b2094-b2415-b2416) 4.A.5; The PTS Galactitol (Gat) Family 11 11 "COG3775;Phosphotransferase system, galactitol-specific IIC component" PF03611;PTS system Galactitol-specific IIC component;3.8e-197;codon 108-412 "TIGR00827;EIIC-GAT: PTS system, galactitol-specific II;0;codon 9-413" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK2086 gatB gatB b2093 2172304 2172588 - (no change) JW2077 2176417 2176701 - t galactitol-specific enzyme IIB component of PTS E "7042910 -!- 77192083 -!- 97113438 -!- 7772602 -!- 9868784 -!- Reizer, J., Charbit, A., Reizer, A., et al;Genome Sci Technol;1996;1: 53-75" Periplasmic 2.7.1.69 heteromultimer; EIIGat (b2092-b2093-b2094-b2415-b2416) 4.A.5; The PTS Galactitol (Gat) Family 1-19 "COG3414;Phosphotransferase system, galactitol-specific IIB component" 52794; Enzyme IIB-cellobiose "PF02302;PTS system, Lactose/Cellobiose specific IIB;4.1e-24;codon 4-93" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK2087 gatA gatA b2094 2172619 2173071 - (no change) JW2081 2178069 2178383 - pseudogene t galactitol-specific enzyme IIA component of PTS CDS ECK2087 gatA gatA b2094 2172619 2173071 - (no change) JW2078 2176732 2177052 - pseudogene t galactitol-specific enzyme IIA component of PTS CDS ECK2087 gatA gatA b2094 2172619 2173071 - (no change) JW2078+JW2081 2176732 2178383 - "ancestral gene -!- b2094 is disrupted by IS in strain W.. b2094 is split into JW2078 & JW2081in strain W -!- b2094 of strain MG is intact, IS is inserted in strain W3110 -!- Initiation of JW2078 overlaps with IS" t galactitol-specific enzyme IIA component of PTS E "1100608 -!- 76024805 -!- 77192083 -!- 97113438 -!- 7772602 -!- Reizer, J., Charbit, A., Reizer, A., et al;Genome Sci Technol;1996;1: 53-75" Cytoplasmic 2.7.1.69 heteromultimer; EIIGat (b2092-b2093-b2094-b2415-b2416) 4.A.5; The PTS Galactitol (Gat) Family COG1762;Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) 55804; Phoshotransferase/anion transport protein GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK2088 gatZ gatZ b2095 2173081 2174343 - (no change) JW2082 2178393 2179655 - e "D-tagatose 1,6-bisphosphate aldolase 2, subunit" E 11976750 -!- 97113438 -!- 7772602 -!- 8932697 Cytoplasmic 4.1.2.40 "heteromultimer; tagatose-1,6-bisphosphate aldolase 2 (b2095-b2096)" COG4573;Predicted tagatose 6-phosphate kinase GO:0016052 carbohydrate catabolism CDS ECK2089 gatY gatY yegF b2096 2174372 2175226 - start codon change JW5343 2179684 2180538 - e "D-tagatose 1,6-bisphosphate aldolase 2, catalytic subunit" E 11976750 -!- 95290497 -!- 97113438 -!- 7772602 -!- 8932697 Cytoplasmic 4.1.2.40 "heteromultimer; tagatose-1,6-bisphosphate aldolase 2 (b2095-b2096)" regulated by attenuation (gatY-gatZ-gatA-gatB-gatC) COG0191;Fructose/tagatose bisphosphate aldolase 51569; Aldolase PF01116;Fructose-bisphosphate aldolase class-II;1.8e-157;codon 5-286 "TIGR00167;cbbA: ketose-bisphosphate aldolases;1.4e-117;codon 3-286 -!- TIGR01858;tag_bisphos_ald: class II aldolase, t;3.4e-253;codon 5-286" GO:0016052 carbohydrate catabolism CDS ECK2090 fbaB fbaB dhnA b2097 2175534 2176586 - start codon change JW5344 2180846 2181898 - e fructose-bisphosphate aldolase class I E 97113438 -!- 98198380 -!- 9531482 Cytoplasmic 4.1.2.13 monomeric multimer; fructose bisphosphate aldolase class I (b2097) 51569; Aldolase PF01791;Deoxyribose-phosphate aldolase;3.2e-128;codon 92-364 GO:0006096 glycolysis CDS ECK2091 yegT yegT b2098 2176843 2178120 + (no change) JW2085 2182155 2183432 + pt predicted nucleoside transporter C Integral Membrane Protein 12 12 in COG0477;Permeases of the major facilitator superfamily PF03825;Nucleoside H+ symporter;6.1e-293;codon 1-405 -!- PF07690;Major Facilitator Superfamily;1.3e-16;codon 7-362 TIGR00889;2A0110: nucleoside transporter;0;codon 1-419 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2092 yegU yegU b2099 2178117 2179121 + (no change) JW2086 2183429 2184433 + pe predicted hydrolase C Cytoplasmic COG1397;ADP-ribosylglycohydrolase PF03747;ADP-ribosylglycohydrolase;1.9e-1 13;codon 6-323 CDS ECK2093 yegV yegV b2100 2179118 2180083 + (no change) JW2087 2184430 2185395 + pe predicted kinase C Cytoplasmic "COG0524;Sugar kinases, ribokinase family" 53613; Ribokinase-like PF00294;pfkB family carbohydrate kinase;1.4e-63;codon 18-311 CDS ECK2094 yegW yegW b2101 2180057 2180803 - (no change) JW2088 2185369 2186115 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic GntR COG2188;Transcriptional regulators 46785; Winged helix "PF00392;Bacterial regulatory proteins, gntR family;1.5e-15;codon 24-87 -!- PF07702;UbiC transcription regulator-associated;3.2e-45;codon 107-243" GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK2095 yegX yegX b2102 2180855 2181673 - start codon change JW5345 2186167 2186985 - pe predicted hydrolase C Membrane Anchored "COG3757;Lyzozyme M1 (1,4-beta-N-acetylmuramidase)" 51445; (Trans)glycosidases PF01183;Glycosyl hydrolases family;1.4e-81;codon 73-248 CDS ECK2096 thiD thiD thiA -!- thiJ -!- thiN b2103 2181738 2182538 - (no change) JW2090 2187050 2187850 - e bifunctional hydroxy-methylpyrimidine kinase and hydroxy-phosphomethylpyrimidine kinase E "82117435 -!- 8432721 -!- 99173753 -!- 10075431 -!- Reddick JJ, Kinsland C, Nicewonger R, et al;Tetrahedron;1998;54:15983-15991" Cytoplasmic 2.7.4.7 -!- 2.7.1.49 monomeric multimer; hydroxymethylpyrimidine kinase 2 / HMP-P kinase (b2103) COG0351;Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase 53613; Ribokinase-like TIGR00097;HMP-P_kinase: phosphomethylpyrimidine ki;8e-175;codon 6-262 GO:0009228 thiamin biosynthesis CDS ECK2097 thiM thiM b2104 2182535 2183323 - (no change) JW2091 2187847 2188635 - e hydoxyethylthiazole kinase E 89255088 -!- 10075431 Cytoplasmic 2.7.1.50 "COG2145;Hydroxyethylthiazole kinase, sugar kinase family" 53613; Ribokinase-like PF02110;Hydroxyethylthiazole kinase family;1.7e-161;codon 15-259 TIGR00694;thiM: hydroxyethylthiazole kinase;2.7e-162;codon 15-262 GO:0009228 thiamin biosynthesis CDS ECK2098 yohL yohL b2105 2183546 2183818 - (no change) JW2092 2188858 2189130 - o conserved protein C Cytoplasmic COG1937;Uncharacterized protein conserved in bacteria "PF02583;Uncharacterised BCR, COG1937;9.1e-30;codon 28-89" CDS ECK2099 yohM yohM b2106 2183939 2184763 + (no change) JW2093 2189251 2190075 + m membrane protein conferring nickel and cobalt resistance C 15805538 Integral Membrane Protein 6 6 out "COG2215;ABC-type uncharacterized transport system, permease component" PF03824;High-affinity nickel-transport protein;4.1e-78;codon 13-273 GO:0009274 cell wall (sensu Bacteria) CDS ECK2100 yohN yohN b2107 2184982 2185320 + start codon change JW5346 2190294 2190632 + o predicted protein C CDS ECK2101 yehA yehA b2108 2185402 2186436 - (no change) JW2095 2190714 2191748 - ps predicted fimbrial-like adhesin protein C Periplasmic 49401; Bacterial adhesins CDS ECK2102 yehB yehB b2109 2186452 2188932 - (no change) JW2096 2191764 2194244 - pm predicted outer membrane protein C Outer Membrane B-barrel protein "COG3188;P pilus assembly protein, porin PapC" PF00577;Fimbrial Usher protein;0;codon 25-816 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK2103 yehC yehC b2110 2188948 2189667 - (no change) JW2097 2194260 2194979 - pf predicted periplasmic pilin chaperone C 1-33 "COG3121;P pilus assembly protein, chaperone PapD" 49354; PapD-like -!- 49584; Periplasmic chaperone C-domain PF00345;Gram-negative pili assembly chaperone;2.8e-69;codon 34-157 -!- PF02753;Gram-negative pili assembly chaperone;1.7e-26;codon 161-239 GO:0006457 protein folding CDS ECK2104 yehD yehD b2111 2189702 2190244 - (no change) JW2098 2195014 2195556 - ps predicted fimbrial-like adhesin protein C 1-22 "COG3539;P pilus assembly protein, pilin FimA" 49401; Bacterial adhesins PF00419;Fimbrial protein;0.0018;codon 28-180 GO:0009289 fimbria CDS ECK2105 yehE yehE b2112 2190537 2190818 - (no change) JW2099 2195849 2196130 - o predicted protein C Periplasmic regulated by attenuation (yehE) CDS ECK2106 mrp mrp apbC b2113 2191081 2192190 - start codon change JW2100 2196393 2197502 - t antiporter inner membrane protein sodium/proton-dependent E 91080852 -!- 15601724 -!- 2259334 Cytoplasmic 52540; P-loop containing nucleotide triphosphate hydrolases CDS ECK2107 metG metG b2114 2192322 2194355 + (no change) JW2101 2197634 2199667 + e methionyl-tRNA synthetase E 12390027 -!- 91132655 -!- 92001989 -!- 93077467 -!- 10600385 -!- 11243794 -!- 1702021 -!- 1959615 -!- 2126467 -!- 2254937 -!- 2259334 -!- 6094501 -!- 6756915 -!- 7042987 -!- 8515465 -!- 8515466 Cytoplasmic 6.1.1.10 Zn2+ monomeric multimer; methionyl-tRNA synthetase (b2114) 1F4L COG0143;Methionyl-tRNA synthetase -!- COG0073;EMAP domain "47323; Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases -!- 50249; Nucleic acid-binding proteins -!- 52374; Nucleotidylyl transferase -!- 57770; Methionyl-tRNA synthetase (MetRS), Zn-domain" "PF00133;tRNA synthetases class I (I, L, M and V);1.7e-05;codon 1-369 -!- PF01588;Putative tRNA binding domain;2.5e-41;codon 581-675" "TIGR00398;metG: methionyl-tRNA synthetase;0;codon 8-536 -!- TIGR00399;metG_C_term: methionyl-tRNA synthetase, b;1.9e-84;codon 541-677" GO:0005737 cytoplasm GO:0006418 amino acid activation ECK2108 molR molR b4499 2194496 2198291 + pseudogene; interrupted by frameshift and in-frame stop JW2102+JW5915+JW5916 2199808 2203603 + ancestral gene su DNA-binding transcriptional regulator (pseudogene) C Cytoplasmic PF05406;WGR domain;1.1e-18;codon 1-72 CDS ECK2108 molR molR_3 b2117 2197344 2198291 + pseudogene fragment -!- start codon change JW5916 2202656 2203603 + "pseudogene, split by IS, no initiation codon" su "DNA-binding transcriptional regulator, C-ter fragment (pseudogene)" E 90202730 CDS ECK2108 molR molR_2 b2116 2195432 2197369 + pseudogene fragment -!- (no change) JW5915 2200744 2202681 + "pseudogene, split by IS" su "DNA-binding transcriptional regulator, middle fragment (pseudogene)" E 90202730 CDS ECK2108 molR molR_1 yehF -!- yehG b2115 2194496 2195320 + pseudogene fragment -!- (no change) JW2102 2199808 2200632 + "pseudogene, split by IS" su "DNA-binding transcriptional regulator, N-ter fragment (pseudogene)" E 90202730 CDS ECK2109 yehI yehI b2118 2198301 2201933 + (no change) JW2105 2203613 2207245 + o conserved protein C Cytoplasmic CDS ECK2110 yehK yehK b4541 2201994 2202311 + new JW2106 2207306 2207623 + o predicted protein C Cytoplasmic GO:0005737 cytoplasm CDS ECK2111 yehL yehL b2119 2202618 2203706 + start codon change JW5349 2207930 2209018 + pt predicted transporter subunit: ATP-binding component of ABC superfamily C Cytoplasmic regulated by attenuation (yehL-yehM-yehP-yehQ) COG0714;MoxR-like ATPases 52540; P-loop containing nucleotide triphosphate hydrolases PF07728;ATPase family associated with various cellul;4e-79;codon 100-349 GO:0004009 ATP-binding cassette (ABC) transporter activity CDS ECK2112 yehM yehM yehN -!- yehO b2120 2203717 2205996 + (no change) JW2108 2209029 2211308 + o predicted protein C Cytoplasmic CDS ECK2113 yehP yehP b2121 2205989 2207125 + (no change) JW5350 2211301 2212437 + d conserved protein C Cytoplasmic 53300; Integrin A (or I) domain PF05762;VWA domain containing CoxE-like protein;6.1e-122;codon 97-378 CDS ECK2114 yehQ yehQ b2122 2207122 2208966 + start codon change JW2110 2212434 2214278 + d predicted protein C Cytoplasmic PF04434;SWIM zinc finger;0.0012;codon 63-97 CDS ECK2115 yehR yehR b2123 2209247 2209708 + start codon change JW5351 2214559 2215020 + lp conserved protein C Membrane Lipoprotein COG4808;Uncharacterized protein conserved in bacteria PF06998;Protein of unknown function (DUF1307);1.3e-72;codon 32-155 CDS ECK2116 yehS yehS b2124 2209748 2210218 - (no change) JW2112 2215060 2215530 - o conserved protein C Cytoplasmic COG4807;Uncharacterized protein conserved in bacteria PF07308;Protein of unknown function (DUF1456);1.2e-37;codon 3-70 -!- PF07308;Protein of unknown function (DUF1456);1.3e-37;codon 86-153 CDS ECK2117 yehT yehT b2125 2210265 2210984 - start codon change JW5352 2215577 2216296 - pr predicted response regulator in two-component system withYehU C 11111050 Cytoplasmic 52172; CheY-like PF00072;Response regulator receiver domain;3.2e-40;codon 7-125 -!- PF04397;LytTr DNA-binding domain;1.3e-27;codon 148-243 CDS ECK2118 yehU yehU b2126 2210981 2212666 - (no change) JW5353 2216293 2217978 - pr predicted sensory kinase in two-component system with YehT C Integral Membrane Protein 7 6 in COG3275;Putative regulator of cell autolysis 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF07694;5TMR of 5TMR-LYT;2.7e-41;codon 39-125 -!- PF01590;GAF domain;0.00065;codon 227-355 -!- PF06580;Histidine kinase;4.2e-43;codon 371-453 -!- PF02518;Histidine kinase-, DNA gyrase B-, and HS;6.7e-10;codon 459-558" GO:0006464 protein modification CDS ECK2119 mlrA mlrA yehV b2127 2212888 2213619 + (no change) JW2115 2218200 2218931 + r DNA-binding transcriptional regulator regulator of curli and extracellular matrix sythesis E 11489123 Cytoplasmic MerR COG0789;Predicted transcriptional regulators 46955; Putative DNA-binding domain PF00376;MerR family regulatory protein;2.3e-11;codon 5-42 GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK2120 yohO yohO b4542 2213679 2213786 + new JW5354 2218991 2219098 + o predicted protein C CDS ECK2121 yehW yehW b2128 2213767 2214498 - (no change) JW2116 2219079 2219810 - pt predicted transporter subunit: membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YehW/YehX/YehY/YehZ ABC transporter (b2131-b2129-b2128-b2130) 6 6 in "COG1174;ABC-type proline/glycine betaine transport systems, permease component" PF00528;Binding-protein-dependent transport syst;1.3e-32;codon 50-240 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2122 yehX yehX b2129 2214503 2215429 - (no change) JW2117 2219815 2220741 - pt predicted transporter subunit: ATP-binding component of ABC superfamily C Cytoplasmic heteromultimer; YehW/YehX/YehY/YehZ ABC transporter (b2131-b2129-b2128-b2130) "COG1125;ABC-type proline/glycine betaine transport systems, ATPase components" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 54631; CBS-domain PF00005;ABC transporter;3.5e-60;codon 27-211 GO:0005737 cytoplasm CDS ECK2123 yehY yehY b2130 2215422 2216579 - (no change) JW2118 2220734 2221891 - pt predicted transporter subunit: membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YehW/YehX/YehY/YehZ ABC transporter (b2131-b2129-b2128-b2130) 10 10 in "COG1174;ABC-type proline/glycine betaine transport systems, permease component" PF00528;Binding-protein-dependent transport syst;7.3e-31;codon 177-381 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2124 yehZ yehZ b2131 2216586 2217503 - (no change) JW2119 2221898 2222815 - pt predicted transporter subunit: periplasmic-binding component of ABC superfamily C Periplasmic heteromultimer; YehW/YehX/YehY/YehZ ABC transporter (b2131-b2129-b2128-b2130) 1-23 COG1732;Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) PF04069;Substrate binding domain of ABC-type glycine;6.5e-91;codon 26-305 GO:0042597 periplasmic space CDS ECK2125 bglX bglX glh -!- yohA b2132 2217714 2220011 - (no change) JW2120 2223026 2225323 - e "beta-D-glucoside glucohydrolase, periplasmic" E 96303506 Periplasmic 3.2.1.21 COG1472;Beta-glucosidase-related glycosidases "51445; (Trans)glycosidases -!- 52279; Beta-D-glucan exohydrolase, C-terminal domain" PF00933;Glycosyl hydrolase family 3 N termina;5.4e-108;codon 96-320 -!- PF01915;Glycosyl hydrolase family 3 C termina;2.3e-101;codon 395-650 GO:0042597 periplasmic space GO:0016052 carbohydrate catabolism CDS ECK2126 dld dld ldh b2133 2220207 2221922 + (no change) JW2121 2225519 2227234 + e "D-lactate dehydrogenase, FAD-binding, NADH independent" E 79052527 -!- 85130784 -!- 92031521 -!- 10944213 -!- 3882663 -!- 6386470 Cytoplasmic 1.1.1.28 1F0X COG0277;FAD/FMN-containing dehydrogenases "55103; FAD-linked oxidases, C-terminal domain -!- 56176; FAD-binding domain" PF01565;FAD binding domain;1.2e-19;codon 46-226 GO:0005737 cytoplasm GO:0009060 aerobic respiration GO:0009053 electron donor activity CDS ECK2127 pbpG pbpG yohB b2134 2221960 2222892 - start codon change JW5355 2227272 2228204 - e D-alanyl-D-alanine endopeptidase penicillin-binding proteins 7 and 8 E 95238279 -!- 6386470 -!- 7721700 -!- 7925376 Periplasmic 3.4.99.- S11 family; murein-DD-endopeptidase 1-19 310 COG1686;D-alanyl-D-alanine carboxypeptidase 56601; beta-Lactamase/D-ala carboxypeptidase PF00768;D-alanyl-D-alanine carboxypeptidase;1.8e-127;codon 32-265 GO:0009274 cell wall (sensu Bacteria) -!- GO:0042597 periplasmic space GO:0009252 peptidoglycan biosynthesis -!- GO:0042493 response to drug CDS ECK2128 yohC yohC b2135 2223066 2223653 - start codon change JW5356 2228378 2228965 - pm predicted inner membrane protein C Integral Membrane Protein 5 5 out PF06930;Protein of unknown function (DUF1282);2.1e-139;codon 15-203 CDS ECK2129 yohD yohD b2136 2223823 2224401 + start codon change JW2124 2229135 2229713 + pm conserved inner membrane protein C Integral Membrane Protein 4 4 in COG0586;Uncharacterized membrane-associated protein PF00597;DedA family;6.2e-55;codon 25-173 GO:0009274 cell wall (sensu Bacteria) CDS ECK2130 yohF yohF yohE b2137 2224531 2225292 - (no change) JW2125 2229843 2230604 - pe predicted oxidoreductase with NAD(P)-binding Rossmann-fold domain "RpoS regulon, acid sensitive, induced by ALS inhibition" C Cytoplasmic COG1028;Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) 51735; NAD(P)-binding Rossmann-fold domains PF00106;short chain dehydrogenase;5.9e-71;codon 5-243 CDS ECK2131 yohG yohG yohH b2138 2225345 2226433 - start codon change JW5838 2230657 2231745 - pm predicted outer membrane protein mutants are sensitive to acriflavin and puromycin -!- TolC paralog -!- putative outer membrane factor (OMF) protein of tripartite efflux pumps C Outer membrane Lipoprotein COG1538;Outer membrane protein "56954; Integral outer membrane protein TolC, efflux pump component" "PF02321;OEP: Outer membrane efflux protein;1.1e-46;codon 3-161,171-359" GO:0009274 cell wall (sensu Bacteria) CDS ECK2132 yohH yohH b2139 2226571 2226708 - start codon change JW5358 2231883 2232020 - o conserved protein C COG1538;Outer membrane protein CDS ECK2133 dusC dusC yohI b2140 2227460 2228407 - (no change) JW2128 2232772 2233719 - e tRNA-dihydrouridine synthase C E 22095566 Cytoplasmic COG0042;tRNA-dihydrouridine synthase 51395; FMN-linked oxidoreductases PF01207;Dihydrouridine synthase (Dus);3.6e-145;codon 4-308 CDS ECK2134 yohJ yohJ b2141 2228646 2229044 + (no change) JW2129 2233958 2234356 + pm conserved inner membrane protein C Integral Membrane Protein 4 4 out COG1380;Putative effector of murein hydrolase LrgA PF03788;LrgA family;7.3e-57;codon 11-120 CDS ECK2135 yohK yohK b2142 2229041 2229736 + (no change) JW2130 2234353 2235048 + pm predicted inner membrane protein C Integral Membrane Protein 5 6 out COG1346;Putative effector of murein hydrolase PF04172;LrgB-like family;4.1e-125;codon 12-226 TIGR00659;TIGR00659: conserved hypothetical protein T;9.8e-167;codon 2-227 CDS ECK2136 cdd cdd b2143 2229866 2230750 + (no change) JW2131 2235178 2236062 + e cytidine/deoxycytidine deaminase E 92232718 -!- 1567863 -!- 2575702 -!- 2692708 -!- 8289286 -!- 8506346 -!- 8550448 -!- 8634261 Cytoplasmic 3.5.4.5 Zn2+ monomeric multimer; cytidine deaminase (b2143) COG0295;Cytidine deaminase 53927; Cytidine deaminase PF00383;Cytidine and deoxycytidylate deaminase;2.7e-22;codon 48-149 TIGR01355;cyt_deam_dimer: cytidine deaminase;1e-101;codon 29-286 "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK2137 sanA sanA yeiF b2144 2230900 2231619 + (no change) JW2132 2236212 2236931 + d predicted protein over-expression abolishes a vancomycin-sensitive permeability defect C 96125233 -!- 1567863 -!- 8550448 Membrane Anchored regulated by attenuation (sanA-yeiS) COG2949;Uncharacterized membrane protein PF02698;DUF218 domain;4.5e-40;codon 44-186 GO:0042493 response to drug CDS ECK2138 yeiS yeiS b2145 2231622 2231861 + (no change) JW5359 2236934 2237173 + pm predicted inner membrane protein C Integral Membrane Protein 2 2 CDS ECK2139 yeiT yeiT b2146 2232055 2233293 + (no change) JW2133 2237367 2238605 + pe predicted oxidoreductase predicted malate:quinone oxidoreductase enhancer C 15601724 Cytoplasmic COG0493;NADPH-dependent glutamate synthase beta chain and related oxidoreductases 46548; alpha-helical ferredoxin PF00070;Pyridine nucleotide-disulphide oxidoreducta;1.4e-36;codon 126-385 CDS ECK2140 yeiA yeiA b2147 2233287 2234522 + start codon change JW2134 2238599 2239834 + pe predicted oxidoreductase C Cytoplasmic COG0167;Dihydroorotate dehydrogenase -!- COG1146;Ferredoxin 51395; FMN-linked oxidoreductases PF01180;Dihydroorotate dehydrogenase;5.1e-16;codon 7-306 -!- PF00037;4Fe-4S binding domain;0.00065;codon 339-362 -!- PF00037;4Fe-4S binding domain;3.2e-05;codon 373-396 TIGR01037;pyrD_sub1_fam: dihydroorotate dehydroge;9.8e-37;codon 8-322 CDS ECK2141 mglC mglC mglP b2148 2234765 2235775 - (no change) JW2135 2240077 2241087 - t methyl-galactoside transporter subunit -!- membrane component of ABC superfamily E 92049246 -!- 1719366 Integral Membrane Protein heteromultimer; galactose ABC transporter (b2149-b2148-b2150) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 8 9 in "COG4211;ABC-type glucose/galactose transport system, permease component" PF02653;Branched-chain amino acid transport syst;3.2e-64;codon 41-325 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK2142 mglA mglA mglP -!- PMG -!- mgl b2149 2235791 2237311 - (no change) JW2136 2241103 2242623 - t fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components E 92049246 -!- 1719366 -!- 3302609 Cytoplasmic heteromultimer; galactose ABC transporter (b2149-b2148-b2150) 3.A.1; The ATP-binding Cassette (ABC) Superfamily "fused methyl-galactoside transport protein, ABC superfamily: atp_binding component (aa1-258) -!- atp_binding component (aa259-506)" "COG1129;ABC-type sugar transport system, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases -!- 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;2.2e-48;codon 39-225 -!- PF00005;ABC transporter;5.5e-18;codon 289-482 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK2143 mglB mglB b2150 2237372 2238370 - (no change) JW2137 2242684 2243682 - t methyl-galactoside transporter subunit -!- periplasmic-binding component of ABC superfamily receptor for galactose taxis E 87286407 -!- 92049246 -!- 1719366 -!- 3057628 -!- 3302609 -!- 3600760 -!- 6340108 -!- 6885805 -!- 7012152 -!- 9298646 heteromultimer; galactose ABC transporter (b2149-b2148-b2150) 3.A.1; The ATP-binding Cassette (ABC) Superfamily 1-23 332 "COG1879;ABC-type sugar transport system, periplasmic component" 53822; Periplasmic binding protein-like I PF00532;Periplasmic binding proteins and sugar b;0.014;codon 25-324 GO:0042597 periplasmic space GO:0016052 carbohydrate catabolism -!- GO:0006457 protein folding CDS ECK2144 galS galS mglD b2151 2238650 2239690 - (no change) JW2138 2243962 2245002 - r DNA-binding transcriptional repressor E 1095564 -!- 87137462 -!- 91177824 -!- 93106962 -!- 1619663 -!- 8208287 -!- 8982002 Cytoplasmic GalR/LacI galS -!- mglBAC COG1609;Transcriptional regulators 47413; lambda repressor-like DNA-binding domains -!- 53822; Periplasmic binding protein-like I "PF00356;Bacterial regulatory proteins, lacI fami;1.1e-11;codon 2-27 -!- PF00532;Periplasmic binding proteins and sugar b;2.7e-06;codon 59-332" GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism -!- GO:0006350 transcription GO:0016564 transcriptional repressor activity CDS ECK2145 yeiB yeiB b2152 2239832 2240989 - (no change) JW2139 2245144 2246301 - pm conserved inner membrane protein C Integral Membrane Protein 9 10 COG2311;Predicted membrane protein PF04171;Protein of unknown function (DUF405);6.2e-67;codon 1-146 -!- PF04235;Protein of unknown function (DUF418);8.3e-73;codon 215-375 CDS ECK2146 folE folE b2153 2241006 2241674 - (no change) JW2140 2246318 2246986 - e GTP cyclohydrolase I E 92041545 -!- 93092993 -!- 94136208 -!- 1459137 -!- 1665332 -!- 7663943 -!- 8304099 -!- 9298646 Cytoplasmic 3.5.4.16 "monomeric multimer; GTP cyclohydrolase I (b2153) -!- monomeric multimer; subunit, GTP cyclohydrolase I (b2153)" COG0302;GTP cyclohydrolase I 55620; Tetrahydrobiopterin biosynthesis enzymes-like PF01227;GTP cyclohydrolase I;4.8e-55;codon 98-202 TIGR00063;folE: GTP cyclohydrolase I;4.4e-135;codon 40-220 GO:0046656 folic acid biosynthesis CDS ECK2147 yeiG yeiG b2154 2241932 2242768 + (no change) JW2141 2247244 2248080 + pe predicted esterase C Cytoplasmic 3.1.1.- COG0627;Predicted esterase 53474; alpha/beta-Hydrolases PF00756;Putative esterase;4.4e-118;codon 13-271 CDS ECK2148 cirA cirA feuA -!- cir b2155 2242800 2244791 - (no change) JW2142 2248112 2250103 - m ferric iron-catecholate outer membrane transporter receptor for colicin I E 90264362 -!- 90299805 -!- 1315732 -!- 2160948 -!- 2644220 -!- 3316180 Outer Membrane B-barrel protein 1.B.14; The Outer Membrane Receptor (OMR) Family 663 COG4771;Outer membrane receptor for ferrienterochelin and colicins 56935; Porins PF07715;TonB-dependent Receptor Plug Domain;9.3e-33;codon 43-152 -!- PF00593;TonB dependent receptor;5.7e-30;codon 395-663 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK2149 lysP lysP cadR b2156 2245085 2246554 - (no change) JW2143 2250397 2251866 - t lysine transporter E 92250419 -!- 94252996 -!- 1315732 -!- 7551055 Integral Membrane Protein 2.A.3; The Amino Acid-Polyamine-Organocation (APC) Family 12 12 in COG0833;Amino acid transporters PF00324;Amino acid permease;3.1e-205;codon 21-480 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009089 lysine biosynthesis via diaminopimelate CDS ECK2150 yeiE yeiE b2157 2246759 2247640 - (no change) JW2144 2252071 2252952 - pr predicted DNA-binding transcriptional regulator C 1315732 LysR COG0583;Transcriptional regulator 46785; Winged helix -!- 53850; Periplasmic binding protein-like II PF00126;Bacterial regulatory helix-turn-helix;2.2e-17;codon 5-64 -!- PF03466;LysR substrate binding domain;1.4e-59;codon 84-291 GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK2151 yeiH yeiH b2158 2247739 2248788 + (no change) JW2145 2253051 2254100 + pm conserved inner membrane protein C Integral Membrane Protein 9.B.63; The 9 TMS Putative Metabolite Efflux (9-PME) Family 1-45 10 8 out COG2855;Predicted membrane protein PF03601;Conserved hypothetical protein;1e-176;codon 18-326 TIGR00698;TIGR00698: conserved hypothetical protein;7e-172;codon 14-348 CDS ECK2152 nfo nfo b2159 2248862 2249719 + (no change) JW2146 2254174 2255031 + e endonuclease IV with intrinsic 3'-5' exonuclease activity E 12444080 -!- 88228024 -!- 94301781 -!- 94342390 -!- 99427442 -!- 10458614 -!- 1720775 -!- 2460435 Periplasmic 3.1.21.2 COG0648;Endonuclease IV 51658; Xylose isomerase-like PF01261;Xylose isomerase-like TIM barrel;7.7e-64;codon 18-239 TIGR00587;nfo: apurinic endonuclease (APN1);4.1e-187;codon 2-279 GO:0006308 DNA catabolism -!- GO:0006308 DNA catabolism -!- GO:0009314 response to radiation CDS ECK2153 yeiI yeiI b2160 2249722 2250810 + (no change) JW2147 2255034 2256122 + pe predicted kinase C Cytoplasmic "COG2771;DNA-binding HTH domain-containing proteins -!- COG0524;Sugar kinases, ribokinase family" 46785; Winged helix -!- 53613; Ribokinase-like PF00294;pfkB family carbohydrate kinase;2.6e-67;codon 59-353 CDS ECK2154 yeiJ yeiJ b2161 2250917 2252167 - (no change) JW2148 2256229 2257479 - pt predicted nucleoside transporter C Integral Membrane Protein 12 8 out COG1972;Nucleoside permease PF01773;Na+ dependent nucleoside transporter N;5e-34;codon 1-82 -!- PF07670;Nucleoside recognition;1.4e-11;codon 98-200 -!- PF07662;Na+ dependent nucleoside transporter C;1.6e-101;codon 202-413 "TIGR00804;nup: nucleoside transporter, NupC family;3.6e-226;codon 4-412" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2155 rihB rihB yeiK b2162 2252267 2253208 - (no change) JW2149 2257579 2258520 - e ribonucleoside hydrolase 2 E 21125610 Cytoplasmic 3.2.2.- 1Q8F COG1957;Inosine-uridine nucleoside N-ribohydrolase 53590; Nucleoside hydrolase PF01156;Inosine-uridine preferring nucleoside hy;2.7e-188;codon 3-310 CDS ECK2156 yeiL yeiL b2163 2253377 2254036 + (no change) JW2150 2258689 2259348 + r DNA-binding transcriptional activator of stationary phase nitrogen survival E 20553179 -!- 11101674 Cytoplasmic Unclass yeiL 51206; cAMP-binding domain-like PF00027;Cyclic nucleotide-binding domain;1.2e-09;codon 17-110 "GO:0006355 regulation of transcription, DNA-dependent" CDS ECK2157 yeiM yeiM b2164 2254107 2255357 - (no change) JW2151 2259419 2260669 - pt predicted nucleoside transporter C Integral Membrane Protein 12 8 out COG1972;Nucleoside permease PF01773;Na+ dependent nucleoside transporter N;3e-34;codon 1-82 -!- PF07670;Nucleoside recognition;1e-12;codon 98-200 -!- PF07662;Na+ dependent nucleoside transporter C;1.6e-98;codon 202-413 "TIGR00804;nup: nucleoside transporter, NupC family;4.4e-243;codon 4-412" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2158 yeiN yeiN b2165 2255451 2256389 - (no change) JW2152 2260763 2261701 - o conserved protein C COG2313;Uncharacterized enzyme involved in pigment biosynthesis PF04227;Indigoidine synthase A like protein;5e-226;codon 15-307 CDS ECK2159 yeiC yeiC b2166 2256377 2257318 - (no change) JW2153 2261689 2262630 - pe predicted kinase C Cytoplasmic "COG0524;Sugar kinases, ribokinase family" 53613; Ribokinase-like PF00294;pfkB family carbohydrate kinase;1.6e-68;codon 6-300 CDS ECK2160 fruA fruA ptsF b2167 2257741 2259432 - (no change) JW2154 2263053 2264744 - t fused fructose-specific PTS enzymes: IIBcomponent -!- IIC components IIB' is a duplicated IIB domain E 89341690 -!- 91164390 -!- 3076173 Integral Membrane Protein heteromultimer; EIIFru (b2416-b2415-b2167-b2169) 4.A.2; The PTS Fructose-Mannitol (Fru) Family 8 9 in "fused PTS family enzyme, fructose-specific: enzyme IIB'B (aa1-201) -!- enzyme IIC (aa228-563)" "COG1445;Phosphotransferase system fructose-specific component IIB -!- COG1299;Phosphotransferase system, fructose-specific IIC component" "PF02379;PTS system, Fructose specific IIB subuni;3.3e-63;codon 105-206 -!- PF02378;Phosphotransferase system, EIIC;1e-66;codon 231-496" "TIGR00829;FRU: PTS system, fructose-specific, II;2.1e-62;codon 107-190 -!- TIGR01427;PTS_IIC_fructo: PTS system, fructose s;2.4e-159;codon 212-552" GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK2161 fruK fruK fpk -!- fruF b2168 2259449 2260387 - (no change) JW2155 2264761 2265699 - e fructose-1-phosphate kinase E "91164390 -!- 1981619 -!- Buschmeier B, Hengstenberg W, Deutscher J;FEMS Microbiol Lett;1985;29-30:231-235" Cytoplasmic 2.7.1.56 Mg2+ monomeric multimer; 1-phosphofructokinase (b2168) COG1105;Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) 53613; Ribokinase-like PF00294;pfkB family carbohydrate kinase;8.1e-69;codon 10-298 GO:0006096 glycolysis CDS ECK2162 fruB fruB fruF -!- fpr b2169 2260387 2261517 - (no change) JW2156 2265699 2266829 - t fused fructose-specific PTS enzymes: IIA component -!- HPr component E 86310278 -!- 94047069 -!- 1981619 -!- 8013873 Cytoplasmic 2.7.1.69 heteromultimer; EIIFru (b2416-b2415-b2167-b2169) 4.A.2; The PTS Fructose-Mannitol (Fru) Family "fused PTS family enzyme, fructose-specific: enzyme IIA (aa1-149) -!- FPr (aa151-376)" "COG1925;Phosphotransferase system, HPr-related proteins" 55804; Phoshotransferase/anion transport protein -!- 55594; HPr-like PF00359;Phosphoenolpyruvate-dependent sugar phosph;3e-78;codon 2-142 -!- PF00381;PTS HPr component phosphorylation site;1.7e-50;codon 285-371 TIGR01003;PTS_HPr_family: phosphocarrier protein;2.9e-25;codon 286-369 GO:0005737 cytoplasm GO:0016052 carbohydrate catabolism CDS ECK2163 setB setB yeiO b2170 2261885 2263066 + (no change) JW2157 2267197 2268378 + t lactose/glucose efflux system E 10438463 -!- 10209755 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;2.8e-41;codon 20-365 TIGR00899;2A0120: sugar efflux transporter;1.6e-277;codon 19-392 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0016052 carbohydrate catabolism CDS ECK2164 yeiW yeiW b4502 2263063 2263317 - (no change) JW5361 2268375 2268629 - o conserved protein C Cytoplasmic GO:0005737 cytoplasm CDS ECK2165 yeiP yeiP b2171 2263472 2264044 + (no change) JW5362 2268784 2269356 + pf predicted elongtion factor low abundance C Cytoplasmic regulated by attenuation (yeiP) PF01132;Elongation factor P (EF-P);1.1e-116;codon 86-274 TIGR02178;yeiP: elongation factor P-like protein YeiP;2.7e-155;codon 88-274 GO:0006412 protein biosynthesis CDS ECK2166 yeiQ yeiQ b2172 2264267 2265733 + (no change) JW2160 2269579 2271045 + pe "predicted dehydrogenase, NAD-dependent" C Cytoplasmic regulated by attenuation (yeiQ) COG0246;Mannitol-1-phosphate/altronate dehydrogenases PF01232;Mannitol dehydrogenase;7.7e-259;codon 25-462 CDS ECK2167 yeiR yeiR b2173 2265851 2266837 + (no change) JW2161 2271163 2272149 + pe predicted enzyme C Cytoplasmic COG0523;Putative GTPases (G3E family) 52540; P-loop containing nucleotide triphosphate hydrolases "PF02492;CobW/HypB/UreG, nucleotide-binding domain;3.2e-44;codon 3-179 -!- PF07683;Cobalamin synthesis protein cobW C-terminal;2.2e-09;codon 240-323" CDS ECK2168 yeiU yeiU b2174 2266876 2267589 + start codon change JW2162 2272188 2272901 + e undecaprenyl pyrophosphate phosphatase E 15778224 Integral Membrane Protein 5 5 in 48317; Acid phosphatase/Vanadium-dependent haloperoxidase PF01569;PAP2 superfamily;1.4e-20;codon 85-230 CDS ECK2169 spr spr yeiV b2175 2268001 2268567 + (no change) JW2163 2273313 2273879 + pe "predicted peptidase, outer membrane lipoprotein" mutant suppresses thermosensitivity of prc mutants at low osmolality C 9158724 Outer membrane Lipoprotein C40 family; spr g.p. (Escherichia-type) (spr protein) 1-25 COG0791;Cell wall-associated hydrolases (invasion-associated proteins) PF00877;NlpC/P60 family;4.2e-56;codon 79-183 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2170 rtn rtn b2176 2268748 2270304 + (no change) JW2164 2274060 2275616 + o conserved protein C Membrane Anchored in regulated by attenuation (rtn) COG2200;FOG: EAL domain PF00563;EAL domain;2.3e-102;codon 260-500 CDS ECK2171 yejA yejA b2177 2270386 2272200 + start codon change JW2165 2275698 2277512 + pt predicted oligopeptide transporter subunit -!- periplasmic-binding component of ABC superfamily C heteromultimer; YejA/YejB/YejE/YejF ABC transporter (b2180-b2178-b2179-b2177) 1-21 53850; Periplasmic binding protein-like II PF00496;Bacterial extracellular solute-binding prot;9.4e-52;codon 99-510 GO:0042597 periplasmic space CDS ECK2172 yejB yejB b2178 2272201 2273295 + (no change) JW2166 2277513 2278607 + pt predicted oligopeptide transporter subunit -!- membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YejA/YejB/YejE/YejF ABC transporter (b2180-b2178-b2179-b2177) 6 6 in "COG4174;ABC-type uncharacterized transport system, permease component" PF00528;Binding-protein-dependent transport syst;1.5e-59;codon 133-361 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2173 yejE yejE b2179 2273295 2274320 + (no change) JW2167 2278607 2279632 + pt predicted oligopeptide transporter subunit -!- membrane component of ABC superfamily C Integral Membrane Protein heteromultimer; YejA/YejB/YejE/YejF ABC transporter (b2180-b2178-b2179-b2177) 6 6 in "COG4239;ABC-type uncharacterized transport system, permease component" PF00528;Binding-protein-dependent transport syst;7.5e-47;codon 140-341 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2174 yejF yejF b2180 2274322 2275911 + (no change) JW2168 2279634 2281223 + pt fused predicted oligopeptide transporter subunits of ABC superfamilly: ATP-binding components C Cytoplasmic heteromultimer; YejA/YejB/YejE/YejF ABC transporter (b2180-b2178-b2179-b2177) "fused predicted oligopeptide transport protein, ABC superfamily: atp_binding component (aa1-287) -!- atp_binding component (aa288-529)" "COG4172;ABC-type uncharacterized transport system, duplicated ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.7e-57;codon 35-233 -!- PF00005;ABC transporter;3.2e-58;codon 312-502 GO:0005737 cytoplasm CDS ECK2175 yejG yejG b2181 2275915 2276259 - (no change) JW2169 2281227 2281571 - o predicted protein C Cytoplasmic CDS ECK2176 bcr bcr bicA -!- bicR -!- sur -!- suxA b2182 2276592 2277782 - (no change) JW5363 2281904 2283094 - t bicyclomycin/multidrug efflux system E 21450803 -!- 93252267 -!- 2694948 -!- 8486276 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG0477;Permeases of the major facilitator superfamily PF07690;Major Facilitator Superfamily;7.1e-55;codon 15-366 -!- PF00083;Sugar (and other) transporter;0.00014;codon 15-395 TIGR00710;efflux_Bcr_CflA: drug resistance tran;2.5e-236;codon 6-391 -!- TIGR00880;2_A_01_02: Multidrug resistance prote;1e-61;codon 52-188 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0042493 response to drug CDS ECK2177 rsuA rsuA yejD b2183 2277810 2278505 - (no change) JW2171 2283122 2283817 - e 16S rRNA pseudouridylate 516 synthase E 10376875 -!- 11953756 -!- 7612632 Cytoplasmic 4.2.1.70 1KSV COG1187;16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases 55174; Alpha-L RNA-binding motif PF01479;S4 domain;1.5e-10;codon 1-47 -!- PF00849;RNA pseudouridylate synthase;2.3e-29;codon 61-192 TIGR00093;TIGR00093: conserved hypothetical protein;4.7e-98;codon 66-224 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009451 RNA modification CDS ECK2178 yejH yejH yejI -!- yejJ b2184 2278654 2280414 + (no change) JW2172 2283966 2285726 + pe predicted ATP-dependet helicase "Type III restriction enzyme," C Cytoplasmic COG1061;DNA or RNA helicases of superfamily II 52540; P-loop containing nucleotide triphosphate hydrolases "PF04851;Type III restriction enzyme, res subunit;3.2e-44;codon 3-155 -!- PF00270;DEAD/DEAH box helicase;1.1e-16;codon 5-160 -!- PF00271;Helicase conserved C-terminal domain;2.6e-12;codon 271-345" CDS ECK2179 rplY rplY b2185 2280539 2280823 + (no change) JW2173 2285851 2286135 + s 50S ribosomal subunit protein L25 E 88227168 -!- 10094780 -!- 10562563 -!- 10696113 -!- 10756104 -!- 1093874 -!- 1100506 -!- 12809609 -!- 2034228 -!- 9298646 -!- 9799245 -!- 9868784 Cytoplasmic 1P86 COG1825;Ribosomal protein L25 (general stress protein Ctc) 50715; Ribosomal protein L25-like PF01386;Ribosomal L25p family;4.6e-52;codon 4-91 GO:0009281 cytosolic ribosome (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0006412 protein biosynthesis GO:0003735 structural constituent of ribosome CDS ECK2180 yejK yejK b2186 2280962 2281969 - (no change) JW2174 2286274 2287281 - f nucleotide associated protein found in spermidine nucleoids E 99296598 -!- 10368163 Cytoplasmic COG3081;Nucleoid-associated protein PF04245;37-kD nucleoid-associated bacterial protein;6.4e-173;codon 3-330 GO:0005737 cytoplasm CDS ECK2181 yejL yejL b2187 2282151 2282378 + (no change) JW2175 2287463 2287690 + o conserved protein C Cytoplasmic COG3082;Uncharacterized protein conserved in bacteria PF07208;Protein of unknown function (DUF1414);2.4e-51;codon 1-69 CDS ECK2182 yejM yejM yejN b2188 2282398 2284158 + (no change) JW2176 2287710 2289470 + pe "predicted hydrolase, inner membrane" C Integral Membrane Protein 5 5 out COG3083;Predicted hydrolase of alkaline phosphatase superfamily 53649; Alkaline phosphatase-like PF00884;Sulfatase;2.4e-94;codon 258-569 tRNA ECK2183 proL proL proW b2189 2284233 2284309 + (no change) JWR0042 2289545 2289621 + n tRNA-Pro(GGG) (Proline tRNA2) E 89197758 -!- 90113884 -!- 90230300 -!- 92165733 CDS ECK2184 yejO yejO b2190 2284412 2286922 - (no change) JW5839 2289724 2292234 - pt predicted autotransporter outer membrane protein C 15659678 Periplasmic S8A family; unassigned peptidases "COG3468;Type V secretory pathway, adhesin AidA" 51126; Pectin lyase-like PF03212;Pertactin;2.5e-73;codon 403-529 -!- PF03797;Autotransporter beta-domain;4.4e-33;codon 569-822 TIGR01414;autotrans_barl: outer membrane autotra;2.5e-110;codon 428-836 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK2185 narP narP b2193 2288522 2289169 + (no change) JW2181 2293834 2294481 + r DNA-binding response regulator in two-component regulatory system with NarQ or NarX regulator of nitrate/nitrite response -!- senses nitrate/nitrite E 93273691 -!- 8501030 Cytoplasmic LuxR/UhpA hcp -!- hyaABCDEF -!- napFDAGHBC-ccmABCDEFGH -!- norVW COG2197;Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;6.8e-46;codon 7-128 -!- PF00196;Bacterial regulatory proteins, luxR fami;4e-30;codon 151-208" GO:0005737 cytoplasm GO:0009061 anaerobic respiration -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK2186 ccmH ccmH yejP b2194 2289380 2290432 - (no change) JW2182 2294692 2295744 - pe "heme lyase, CcmH subunit" c-type cytochrome biogenesis -!-required for transfer of heme to apocytochrome from heme-CcmE E 10339610 -!- 11756453 -!- 12196152 -!- 87260957 -!- 91194558 -!- 95362656 -!- 9914305 -!- 7635817 Integral Membrane Protein heteromultimer; CcmABCDEFGH cytochrome c biogenesis system (b2194-b2195-b2196-b2197-b2198-b2199-b2200-b2201) 1-18 3 3 out COG3088;Uncharacterized protein involved in biosynthesis of c-type cytochromes -!- COG4235;Cytochrome c biogenesis factor 48439; Protein prenylyltransferase PF03918;Cytochrome C biogenesis protein;4.6e-101;codon 3-153 -!- PF07719;Tetratricopeptide repeat;0.04;codon 222-255 -!- PF07719;Tetratricopeptide repeat;0.013;codon 293-326 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0017004 cytochrome biogenesis -!- GO:0006457 protein folding CDS ECK2187 ccmG ccmG dsbE -!- yejQ b2195 2290429 2290986 - (no change) JW2183 2295741 2296298 - e periplasmic thioredoxin of cytochrome c-type biogenesis E 10339610 -!- 12196152 -!- 9716493 -!- 9770295 -!- 11256948 -!- 11350062 -!- 11843181 -!- 7635817 -!- 9537397 heteromultimer; CcmABCDEFGH cytochrome c biogenesis system (b2194-b2195-b2196-b2197-b2198-b2199-b2200-b2201) COG0526;Thiol-disulfide isomerase and thioredoxins 52833; Thioredoxin-like TIGR00385;dsbE: periplasmic protein thiol:disulfide ox;2.9e-130;codon 6-178 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0017004 cytochrome biogenesis -!- GO:0006457 protein folding CDS ECK2188 ccmF ccmF yejR b2196 2290983 2292926 - (no change) JW2184 2296295 2298238 - e "heme lyase, CcmF subunit" c-type cytochrome biogenesis E 10339610 -!- 11756453 -!- 12196152 -!- 87260957 -!- 8842153 -!- 91194558 -!- 95362656 -!- 9716493 -!- 7635817 Integral Membrane Protein heteromultimer; CcmABCDEFGH cytochrome c biogenesis system (b2194-b2195-b2196-b2197-b2198-b2199-b2200-b2201) 15 15 in COG1138;Cytochrome c biogenesis factor PF01578;Cytochrome C assembly protein;2e-89;codon 89-299 TIGR00353;nrfE: cytochrome c-type biogenesis protein C;0;codon 53-634 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0017004 cytochrome biogenesis CDS ECK2189 ccmE ccmE yejS b2197 2292923 2293402 - (no change) JW2185 2298235 2298714 - f periplasmic heme chaperone in c-type cytochrome biogenesis E 10339610 -!- 12196152 -!- 12486054 -!- 21413853 -!- 87260957 -!- 8842153 -!- 91194558 -!- 95362656 -!- 9716493 -!- 9770295 -!- 7635817 Membrane Anchored heteromultimer; CcmABCDEFGH cytochrome c biogenesis system (b2194-b2195-b2196-b2197-b2198-b2199-b2200-b2201) 1SR3 COG2332;Cytochrome c-type biogenesis protein CcmE PF03100;CcmE;6.2e-94;codon 2-138 GO:0019866 inner membrane GO:0017004 cytochrome biogenesis -!- GO:0006457 protein folding CDS ECK2190 ccmD ccmD yojM b2198 2293399 2293608 - (no change) JW2186 2298711 2298920 - f cytochrome c biogenesis protein stabilizes CcmE in the membrane E 10339610 -!- 12196152 -!- 95362656 -!- 9716493 -!- 7635817 Membrane Anchored heteromultimer; CcmABCDEFGH cytochrome c biogenesis system (b2194-b2195-b2196-b2197-b2198-b2199-b2200-b2201) COG3114;Heme exporter protein D PF04995;Heme exporter protein D (CcmD);8.8e-20;codon 15-60 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0017004 cytochrome biogenesis -!- GO:0006457 protein folding CDS ECK2191 ccmC ccmC yejT -!- yejU b2199 2293605 2294342 - (no change) JW2187 2298917 2299654 - t heme exporter subunit -!- membrane component of ABC superfamily interacts with CcmE to deliver heme E 10339610 -!- 12196152 -!- 14532274 -!- 21413853 -!- 95362656 -!- 7635817 Integral Membrane Protein heteromultimer; CcmABC ABC transporter (b2201-b2200-b2199) -!- heteromultimer; CcmABCDEFGH cytochrome c biogenesis system (b2194-b2195-b2196-b2197-b2198-b2199-b2200-b2201) 9.B.14; The Putative Heme Exporter Protein (HEP) Family 6 6 in "COG0755;ABC-type transport system involved in cytochrome c biogenesis, permease component" PF01578;Cytochrome C assembly protein;1.3e-61;codon 5-184 TIGR01191;ccmC: heme exporter protein CcmC;2.8e-135;codon 45-225 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0017004 cytochrome biogenesis -!- GO:0006457 protein folding CDS ECK2192 ccmB ccmB yejV b2200 2294384 2295046 - (no change) JW2188 2299696 2300358 - t heme exporter subunit -!- membrane component of ABC superfamily E 10339610 -!- 12196152 -!- 95362656 -!- 9716493 -!- 7635817 Integral Membrane Protein heteromultimer; CcmABC ABC transporter (b2201-b2200-b2199) -!- heteromultimer; CcmABCDEFGH cytochrome c biogenesis system (b2194-b2195-b2196-b2197-b2198-b2199-b2200-b2201) 6 6 in "COG2386;ABC-type transport system involved in cytochrome c biogenesis, permease component" PF03379;CcmB protein;9.9e-129;codon 3-217 TIGR01190;ccmB: heme exporter protein CcmB;1.1e-145;codon 6-216 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0017004 cytochrome biogenesis -!- GO:0006457 protein folding CDS ECK2193 ccmA ccmA yejW b2201 2295043 2295666 - start codon change JW5366 2300355 2300978 - t heme exporter subunit -!- ATP-binding component of ABC superfamily E 10339610 -!- 12196152 -!- 95362656 -!- 7635817 Cytoplasmic heteromultimer; CcmABC ABC transporter (b2201-b2200-b2199) -!- heteromultimer; CcmABCDEFGH cytochrome c biogenesis system (b2194-b2195-b2196-b2197-b2198-b2199-b2200-b2201) "COG4133;ABC-type transport system involved in cytochrome c biogenesis, ATPase component" 52540; P-loop containing nucleotide triphosphate hydrolases PF00005;ABC transporter;1.8e-55;codon 27-202 TIGR01189;ccmA: heme exporter protein CcmA;8.1e-135;codon 2-199 GO:0005737 cytoplasm GO:0017004 cytochrome biogenesis -!- GO:0006457 protein folding CDS ECK2194 napC napC yejX b2202 2295679 2296281 - (no change) JW2190 2300991 2301593 - c "nitrate reductase, cytochrome c-type,periplasmic" E 96228696 -!- 99395037 -!- 8039676 Membrane Anchored heteromultimer; periplasmic nitrate reductase (b2202-b2206-b2203) -!- heteromultimer; periplasmic nitrate reductase (b2206-b2203-b2202-b2205-b2204) "COG3005;Nitrate/TMAO reductases, membrane-bound tetraheme cytochrome c subunit" 48695; Multiheme cytochromes "PF03264;NapC/NirT cytochrome c family, N-termin;2.4e-128;codon 20-193" TIGR02161;napC_nirT: periplasmic nitrate (or nitrite);3.5e-143;codon 10-194 GO:0019866 inner membrane GO:0009061 anaerobic respiration -!- GO:0017004 cytochrome biogenesis GO:0009054 electron acceptor activity CDS ECK2195 napB napB yejY b2203 2296291 2296740 - start codon change JW5367 2301603 2302052 - c "nitrate reductase, small, cytochrome C550 subunit, periplasmic" E 10234835 -!- 96228696 -!- 99395037 -!- 8039676 Periplasmic heteromultimer; molybdoprotein complex (b2203-b2206-b0784) -!- heteromultimer; periplasmic nitrate reductase (b2202-b2206-b2203) -!- heteromultimer; periplasmic nitrate reductase (b2206-b2203-b2202-b2205-b2204) 1-34 149 48695; Multiheme cytochromes PF03892;Nitrate reductase cytochrome c-type subunit;1.5e-51;codon 13-155 GO:0042597 periplasmic space GO:0009061 anaerobic respiration -!- GO:0017004 cytochrome biogenesis GO:0009054 electron acceptor activity CDS ECK2196 napH napH yejZ b2204 2296737 2297600 - (no change) JW2192 2302049 2302912 - c ferredoxin-type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB) E 14674886 -!- 96228696 Integral Membrane Protein "heteromultimer; NapGH, alternative quinol dehydrogenase (b2204-b2205) -!- heteromultimer; periplasmic nitrate reductase (b2206-b2203-b2202-b2205-b2204)" 5 4 COG0348;Polyferredoxin 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;0.0004;codon 253-276 "TIGR02163;napH_: ferredoxin-type protein, NapH/MauN fa;2.2e-184;codon 24-279" GO:0009061 anaerobic respiration GO:0009055 electron carrier activity CDS ECK2197 napG napG yojA -!- yojB b2205 2297587 2298282 - (no change) JW2193 2302899 2303594 - c ferredoxin-type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB) E 14674886 -!- 96228696 "heteromultimer; NapGH, alternative quinol dehydrogenase (b2204-b2205) -!- heteromultimer; periplasmic nitrate reductase (b2206-b2203-b2202-b2205-b2204)" COG1145;Ferredoxin 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;2.8e-05;codon 54-77 -!- PF00037;4Fe-4S binding domain;0.0021;codon 179-204 TIGR00397;mauM_napG: MauM/NapG family ferredoxin;2.4e-76;codon 8-223 -!- TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;0.017;codon 9-41 GO:0009061 anaerobic respiration GO:0009055 electron carrier activity CDS ECK2198 napA napA yojC -!- yojD -!- yojE b2206 2298289 2300775 - (no change) JW2194 2303601 2306087 - e "nitrate reductase, periplasmic, large subunit" E 10234835 -!- 96228696 -!- 99395037 Periplasmic 1.7.99.4 heteromultimer; molybdoprotein complex (b2203-b2206-b0784) -!- heteromultimer; periplasmic nitrate reductase (b2202-b2206-b2203) -!- heteromultimer; periplasmic nitrate reductase (b2206-b2203-b2202-b2205-b2204) 1-21 "COG0243;Anaerobic dehydrogenases, typically selenocysteine-containing" "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3" PF04879;Molybdopterin oxidoreductase Fe4S4 do;2.2e-23;codon 39-93 -!- PF00384;Molybdopterin oxidoreductase;1.7e-137;codon 96-568 -!- PF01568;Molydopterin dinucleotide binding dom;2.2e-43;codon 714-822 "TIGR01706;NAPA: periplasmic nitrate reductase, l;0;codon 2-828 -!- TIGR01409;TAT_signal_seq: Tat (twin-arginine tra;3.1e-06;codon 3-31" GO:0042597 periplasmic space GO:0009061 anaerobic respiration GO:0009054 electron acceptor activity CDS ECK2199 napD napD yojF b2207 2300772 2301035 - (no change) JW2195 2306084 2306347 - f assembly protein for periplasmic nitrate reductase E 96228696 -!- 99395037 Cytoplasmic COG3062;Uncharacterized protein involved in formation of periplasmic nitrate reductase PF03927;NapD protein;4.5e-43;codon 3-82 GO:0042597 periplasmic space GO:0009061 anaerobic respiration -!- GO:0006464 protein modification CDS ECK2200 napF napF yojG b2208 2301025 2301519 - (no change) JW2196 2306337 2306831 - c "ferredoxin-type protein, predicted role in electron transfer to periplasmic nitrate reductase (NapA)" C 96228696 Cytoplasmic COG1145;Ferredoxin 54862; 4Fe-4S ferredoxins PF00037;4Fe-4S binding domain;0.0011;codon 30-53 -!- PF00037;4Fe-4S binding domain;0.00085;codon 62-85 -!- PF00037;4Fe-4S binding domain;3.8e-07;codon 134-157 TIGR00402;napF: ferredoxin-type protein NapF;3.6e-120;codon 7-157 GO:0009061 anaerobic respiration GO:0009055 electron carrier activity CDS ECK2201 eco eco eti b2209 2301927 2302415 + (no change) JW2197 2307239 2307727 + r "ecotin, a serine protease inhibitor" E 91177925 -!- 92071946 -!- 10843853 -!- 11513582 -!- 1879537 -!- 2007606 -!- 7757004 -!- 8156987 -!- 8931142 -!- 9154920 -!- 9298646 Periplasmic monomeric multimer; ecotin homodimer; serine protease inhibitor (b2209) 1-20 162 1N8O COG4574;Serine protease inhibitor ecotin "49772; Ecotin, trypsin inhibitor" PF03974;Ecotin;4e-145;codon 1-160 GO:0042597 periplasmic space CDS ECK2202 mqo mqo yojH b2210 2303130 2304776 - (no change) JW2198 2308442 2310088 - e "malate dehydrogenase, FAD/NAD(P)-binding domain" E 20545431 Periplasmic 1.1.99.16 1-21 COG0579;Predicted dehydrogenase 51905; FAD/NAD(P)-binding domain PF06039;Malate:quinone oxidoreductase (Mqo);0;codon 28-518 TIGR01320;mal_quin_oxido: malate:quinone-oxidore;1.3e-281;codon 32-516 GO:0006099 tricarboxylic acid cycle CDS ECK2203 yojI yojI yojJ b2211 2304994 2306637 - (no change) JW2199 2310306 2311949 - pt fused predicted multidrug transport subunits of ABC superfamily: membrane component -!- ATP-binding component C Integral Membrane Protein 5 6 "fused predicted multidrug transport protein, ABC superfamily: membrane component (aa1-306) -!- atp_binding component (aa307-547)" "COG4615;ABC-type siderophore export system, fused ATPase and permease components" 52540; P-loop containing nucleotide triphosphate hydrolases PF00664;ABC transporter transmembrane region;0.008;codon 15-279 -!- PF00005;ABC transporter;6e-42;codon 349-525 TIGR01194;cyc_pep_trnsptr: cyclic peptide trans;1.4e-88;codon 2-533 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2204 alkB alkB aidD b2212 2306713 2307363 - (no change) JW2200 2312025 2312675 - e oxidative demethylase of N1-methyladenine or N3-methylcytosine DNA lesions acts in repair of alkylated DNA E 12226668 -!- 12517444 -!- 12862460 -!- 14527653 -!- 87057220 -!- 88151899 -!- 92017669 -!- 3536913 -!- 3887409 -!- 7928996 Cytoplasmic Fe2+ COG3145;Alkylated DNA repair protein PF03171;2OG-Fe(II) oxygenase superfamily;6.7e-07;codon 113-213 TIGR00568;alkb: alkylated DNA repair protein AlkB;2.1e-119;codon 21-189 GO:0005737 cytoplasm GO:0006281 DNA repair CDS ECK2205 ada ada b2213 2307363 2308427 - (no change) JW2201 2312675 2313739 - r fused DNA-binding transcriptional dual regulator -!- O6-methylguanine-DNA methyltransferase DNA repair E 91073391 -!- 93272965 -!- 94252990 Cytoplasmic 2.1.1.63 AraC/XylS ada-alkB -!- aidB -!- alkA fused: transcriptional regulator of DNA repair (aa1-183) -!- O6-methylguanine-DNA methyltransferase (aa189-354) COG2169;Adenosine deaminase -!- COG0350;Methylated DNA-protein cysteine methyltransferase "46689; Homeodomain-like -!- 57884; N-ada DNA repair protein, N-terminal domain (N-Ada 10) -!- 46767; Methylated DNA-protein cysteine methyltransferase, C-terminal domain -!- 53155; Methylated DNA-protein cysteine methyltransferase domain" "PF02805;Metal binding domain of Ada;3.5e-46;codon 10-75 -!- PF00165;Bacterial regulatory helix-turn-helix;2.8e-14;codon 89-133 -!- PF00165;Bacterial regulatory helix-turn-helix;1.1e-05;codon 136-182 -!- PF02870;6-O-methylguanine DNA methyltransferase, ribonuclease-like domain;1.8e-26;codon 188-266 -!- PF01035;6-O-methylguanine DNA methyltransferase, DNA binding domain;3e-58;codon 268-353" TIGR00589;ogt: methylated-DNA--protein-cysteine methyl;1.6e-58;codon 269-348 GO:0005737 cytoplasm GO:0006281 DNA repair -!- GO:0006350 transcription GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity CDS ECK2206 yojL yojL apbE -!- yojK b2214 2308501 2309556 - (no change) JW5368 2313813 2314868 - lp predicted thiamine biosynthesis lipoprotein C Inner membrane Lipoprotein regulated by attenuation (yojL) COG1477;Membrane-associated lipoprotein involved in thiamine biosynthesis PF02424;ApbE family;1.5e-172;codon 13-332 GO:0009228 thiamin biosynthesis CDS ECK2207 ompC ompC meoA -!- par b2215 2309668 2310771 - (no change) JW2203 2314980 2316083 - t outer membrane porin protein C outer membrane protein 1b E 91008984 -!- 91278079 -!- 92165726 -!- 2997131 -!- 6297988 -!- 6304064 -!- 9298646 -!- 9629924 Outer Membrane B-barrel protein 1.B.1; The General Bacterial Porin (GBP) Family 1-21 367 COG3203;Outer membrane protein (porin) 56935; Porins PF00267;Gram-negative porin;2.1e-201;codon 27-367 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) misc_RNA ECK2208 micF micF stc -!- IS113 b4439 2311106 2311198 + (no change) JWR0043 2316418 2316510 + n regulatory sRNA antisense translational regulator of ompF -!- stress response E 15063850 -!- 20485613 -!- 21488538 -!- 2436145 -!- 94327469 -!- 95020599 -!- 96079513 CDS ECK2209 rcsD rcsD yojN -!- yojP -!- yojQ b2216 2311510 2314182 + (no change) JW2204 2316822 2319494 + r phosphotransfer intermediate protein in two-component regulatory system with RcsBC repressor in colanic capsule biosynthesis E 11758943 -!- 12864862 -!- 21206231 -!- 2404948 -!- 7984428 Membrane Anchored fhlDC COG0642;Signal transduction histidine kinase -!- COG2198;FOG: HPt domain "47226; Histidine-containing phosphotransfer domain, HPT domain -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase" "PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;7.4e-12;codon 565-677 -!- PF01627;Hpt domain;4.2e-15;codon 809-885" GO:0006464 protein modification CDS ECK2210 rcsB rcsB b2217 2314199 2314849 + (no change) JW2205 2319511 2320161 + r DNA-binding response regulator in two-component regulatory system with RcsC and YojN E 11758943 -!- 12864862 -!- 20032358 -!- 20167175 -!- 21450811 -!- 90130299 -!- 92048476 -!- 9209051 -!- 92283751 -!- 2404948 -!- 8366025 Cytoplasmic heteromultimer; RcsB transcriptional activator (b1951-b2217) -!- monomeric multimer; RcsB (b2217) LuxR/UhpA flhDC -!- ftsAZ -!- osmC -!- rcsA -!- wza-wzb-b2060-wcaA-wcaB -!- cpsBG COG2197;Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain 52172; CheY-like "PF00072;Response regulator receiver domain;2.8e-32;codon 4-128 -!- PF00196;Bacterial regulatory proteins, luxR fami;1.4e-21;codon 148-205" GO:0030113 capsule (sensu Bacteria) -!- GO:0005737 cytoplasm GO:0009242 colanic acid biosynthesis -!- GO:0006350 transcription "GO:0016563 transcriptional activator activity -!- GO:0016564 transcriptional repressor activity -!- GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2211 rcsC rcsC b2218 2315049 2317850 - (no change) JW5917 2320361 2320735 - pseudogene r hybrid sensory kinase in two-component regulatory system with RcsB and YojN cpsBG CDS ECK2211 rcsC rcsC b2218 2315049 2317850 - (no change) JW5920 2322075 2324498 - pseudogene r hybrid sensory kinase in two-component regulatory system with RcsB and YojN cpsBG CDS ECK2211 rcsC rcsC b2218 2315049 2317850 - (no change) JW5920+JW5917 2320361 2324498 - ancestral gene -!- IS is inserted in strain W3110. b2218 is split into JW5370 & JW2206 in strain W -!- intact b2218 is found in strain MG r hybrid sensory kinase in two-component regulatory system with RcsB and YojN E 11758943 -!- 12864862 -!- 14651646 -!- 20032358 -!- 21450811 -!- 88227838 -!- 90130299 -!- 92048476 -!- 9209051 -!- 2404948 -!- 8366025 Integral Membrane Protein 3 2 cpsBG fused hybrid sensory histidine kinase: sensory histidine kinase (aa1-677) -!- response regulator (aa806-993) COG0642;Signal transduction histidine kinase -!- COG0784;FOG: CheY-like receiver 47384; Homodimeric domain of signal transducing histidine kinase -!- 52172; CheY-like -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase GO:0009274 cell wall (sensu Bacteria) -!- GO:0030113 capsule (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009242 colanic acid biosynthesis -!- GO:0006464 protein modification "GO:0042280 cell surface antigen activity, host-interacting" CDS ECK2212 atoS atoS b2219 2318065 2319891 + (no change) JW2213 2324713 2326539 + r sensory histidine kinase in two-component regulatory system with AtoC E 15522865 -!- 12897016 -!- 8346225 Integral Membrane Protein 3 2 in atoDAEB COG1012;NAD-dependent aldehyde dehydrogenases -!- COG0642;Signal transduction histidine kinase 47384; Homodimeric domain of signal transducing histidine kinase -!- 55785; PYP-like sensor domain -!- 55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase "PF00672;HAMP domain;3e-10;codon 192-259 -!- PF00989;PAS domain;2.2e-15;codon 262-325 -!- PF00512;His Kinase A (phosphoacceptor) domain;2.3e-20;codon 388-453 -!- PF02518;Histidine kinase-, DNA gyrase B-, and HSP90;1.1e-35;codon 495-601" TIGR00229;sensory_box: PAS domain S-box;7.1e-17;codon 258-380 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0019395 fatty acid oxidation -!- GO:0006464 protein modification CDS ECK2213 atoC atoC Az -!- az b2220 2319888 2321273 + (no change) JW2214 2326536 2327921 + r "fused response regulator of ato opeon, in two-component system with AtoS: response regulator -!- sigma54 interaction protein" E 2883171 -!- 73032600 -!- 87083402 -!- 8346225 Cytoplasmic EBP atoDAE fused regulator: response regulator (aa1-125) -!- sigma54 interaction protein (aa145-461) "COG2204;Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains" 52172; CheY-like -!- 52540; P-loop containing nucleotide triphosphate hydrolases "PF00072;Response regulator receiver domain;2.4e-39;codon 5-124 -!- PF00158;Sigma-54 interaction domain;2.8e-158;codon 145-366 -!- PF02954;Bacterial regulatory protein, Fis fam;2.6e-15;codon 414-454" "TIGR01199;HTH_fis: Helix-turn-helix domain, fis-type;1.3e-16;codon 414-456" GO:0005737 cytoplasm GO:0019395 fatty acid oxidation -!- GO:0006596 polyamine biosynthesis -!- GO:0006350 transcription GO:0016563 transcriptional activator activity CDS ECK2214 atoD atoD b2221 2321469 2322131 + (no change) JW2215 2328117 2328779 + c "acetyl-CoA:acetoacetyl-CoA transferase, alpha subunit" E 73032600 -!- 87083402 Cytoplasmic 2.8.3.8 heteromultimer; acetoacetyl-CoA transferase (b2222-b2221) -!- monomeric multimer; alpha complex (b2221) 1K6D "COG1788;Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit" 53316; Glutaconate-CoA transferase subunits PF01144;Coenzyme A transferase;9.4e-95;codon 5-216 GO:0019395 fatty acid oxidation CDS ECK2215 atoA atoA b2222 2322131 2322781 + (no change) JW2216 2328779 2329429 + c "acetyl-CoA:acetoacetyl-CoA transferase, beta subunit" E 73032600 -!- 87083402 Cytoplasmic 2.8.3.8 heteromultimer; acetoacetyl-CoA transferase (b2222-b2221) -!- monomeric multimer; beta complex (b2222) "COG2057;Acyl CoA:acetate/3-ketoacid CoA transferase, beta subunit" 53316; Glutaconate-CoA transferase subunits PF01144;Coenzyme A transferase;1.1e-65;codon 4-198 GO:0019395 fatty acid oxidation CDS ECK2216 atoE atoE b2223 2322778 2324100 + (no change) JW2217 2329426 2330748 + t short chain fatty acid transporter E 73032600 -!- 87083402 Integral Membrane Protein 11 9 out COG2031;Short chain fatty acids transporter PF02667;Short chain fatty acid transporter;0;codon 1-440 TIGR00366;TIGR00366: conserved hypothetical protein T;0;codon 4-428 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0019395 fatty acid oxidation CDS ECK2217 atoB atoB b2224 2324131 2325315 + (no change) JW2218 2330779 2331963 + c acetyl-CoA acetyltransferase E 73032600 -!- 87083402 2.3.1.9 monomeric multimer; acetyl-CoA acetyltransferase (b2224) COG0183;Acetyl-CoA acetyltransferase 53901; Thiolase-like "PF00108;Thiolase, N-terminal domain;1.5e-164;codon 1-263 -!- PF02803;Thiolase, C-terminal domain;7.4e-80;codon 270-392" TIGR01930;AcCoA-C-Actrans: acetyl-CoA acyltrans;8e-210;codon 6-391 GO:0019395 fatty acid oxidation CDS ECK2218 yfaP yfaP b2225 2325389 2326165 - (no change) JW2219 2332037 2332813 - o conserved protein C Periplasmic COG4676;Uncharacterized protein conserved in bacteria CDS ECK2219 yfaQ yfaQ b2226 2326170 2327819 - (no change) JW2220 2332818 2334467 - o predicted protein C Periplasmic ECK2220 yfaS yfaS b4500 2327820 2332424 - pseudogene; interrupted by in-frame stop JW2222+JW2221 2334468 2339072 - ancestral gene su predicted protein (pseudogene) C Periplasmic PF01835;Alpha-2-macroglobulin family N-terminal regi;6.3e-62;codon 222-480 -!- PF07703;Alpha-2-macroglobulin family N-terminal regi;1.9e-23;codon 628-779 CDS ECK2220 yfaS yfaS_1 b2228 2328321 2332424 - pseudogene fragment -!- start codon change JW2222 2334969 2339072 - pseudogene su "predicted protein, N-ter fragment (pseudogene)" C CDS ECK2220 yfaS yfaS_2 yfaR b2227 2327820 2328305 - pseudogene fragment -!- (no change) JW2221 2334468 2334953 - pseudogene su "predicted protein, C-ter fragment (pseudogene)" C CDS ECK2221 yfaT yfaT b2229 2332358 2332981 - start codon change JW2223 2339006 2339629 - o predicted protein C Periplasmic PF06672;Protein of unknown function (DUF1175);8.2e-190;codon 10-216 CDS ECK2222 yfaA yfaA pufY b2230 2332978 2334666 - start codon change JW2224 2339626 2341314 - o predicted protein C 1-46 regulated by attenuation (yfaA-yfaT) CDS ECK2223 gyrA gyrA hisW -!- nalA -!- parD -!- nfxA -!- norA b2231 2334815 2337442 - (no change) JW2225 2341463 2344090 - e "DNA gyrase (type II topoisomerase), subunit A" E 91139640 -!- 91205604 -!- 92283777 -!- 1850970 -!- 1850972 -!- 2168148 -!- 2548439 -!- 2828631 -!- 2830458 -!- 2834621 -!- 3029031 -!- 3031051 -!- 9278055 Cytoplasmic 5.99.1.3 heteromultimer; DNA gyrase (b2231-b3699) "COG0188;Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit" 56719; Type II DNA topoisomerase "PF00521;DNA gyrase/topoisomerase IV, subunit A;0;aa 32-514 -!- 6 of PF03989;DNA gyrase C-terminal domain, beta-propeller;1.1e-13;aa 537-586 -!- 5e-15;aa 587-639 -!- 6.2e-09;aa 643-690 -!- 1.6e-16;aa 691-740 -!- 1.8e-14;aa 741-791 -!- 1.1e-13;aa 792-841" "TIGR01063;gyrA: DNA gyrase, A subunit;0;codon 8-841" GO:0005737 cytoplasm GO:0006261 DNA dependent DNA replication -!- GO:0006350 transcription CDS ECK2224 ubiG ubiG yfaB -!- pufX b2232 2337589 2338311 + (no change) JW2226 2344237 2344959 + e bifunctional 3-demethylubiquinone-9 3-methyltransferase and 2-octaprenyl-6-hydroxy phenol methylase E 88139199 -!- 93123968 -!- 99348293 -!- 1479344 -!- 2834621 Cytoplasmic 2.1.1.64 Zn2+ monomeric multimer; 3-demethylubiquinone 3-methyltransferase / 2-octaprenyl-6-hydroxyphenol methylase (b2232) "COG2227;2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase" 53335; S-adenosyl-L-methionine-dependent methyltransferases TIGR01983;UbiG: ubiquinone biosynthesis O-methyltransf;8e-156;codon 16-234 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration CDS ECK2225 yfaL yfaL yfaF -!- yfaJ -!- yfaK b2233 2338439 2342191 - (no change) JW2227 2345087 2348839 - f adhesin E 15659678 Periplasmic 1-28 "COG3468;Type V secretory pathway, adhesin AidA" 51126; Pectin lyase-like PF02415;Chlamydia polymorphic membrane protein;13;codon 67-82 -!- PF05594;Haemagluttinin repeat;5;codon 74-186 -!- PF02415;Chlamydia polymorphic membrane protein;8;codon 97-118 -!- PF02415;Chlamydia polymorphic membrane protein;0.0016;codon 127-145 -!- PF02415;Chlamydia polymorphic membrane protein;6.1;codon 159-178 -!- PF02415;Chlamydia polymorphic membrane protein;0.029;codon 186-211 -!- PF02415;Chlamydia polymorphic membrane protein;0.014;codon 228-246 -!- PF05594;Haemagluttinin repeat;5.8;codon 331-429 -!- PF05594;Haemagluttinin repeat;2.6;codon 666-772 -!- PF03212;Pertactin;0.00013;codon 793-915 -!- PF03797;Autotransporter beta-domain;1.4e-35;codon 981-1241 4 of TIGR01376;Chlamydial polymorphic outer membrane protein repeat: 0.39;aa 94-123 -!- .0014;aa 124-151 -!- 0.51;aa 156-184 -!- 0.0006;aa 227-251 -!- TIGR01414;outer membrane autotransporter barrel domain;3.5e-108;aa 806-1250 CDS ECK2226 nrdA nrdA dnaF b2234 2342887 2345172 + (no change) JW2228 2349535 2351820 + e "ribonucleoside diphosphate reductase 1, alpha subunit" E 91242422 -!- 93043591 -!- 93323110 -!- 2663852 -!- 3287341 -!- 3894026 -!- 6087316 -!- 8052308 -!- 9309223 Cytoplasmic 1.17.4.1 Mg2+ heteromultimer; ribonucleoside-diphosphate reductase / CDP reductase / UDP reductase / ADP reductase / GDP reductase (b2234-b2235) -!- monomeric multimer; B1 protein (b2234) regulated by attenuation (nrdA) 3R1R "COG0209;Ribonucleotide reductase, alpha subunit" "48168; R1 subunit of ribonucleotide reductase, N-terminal domain -!- 51998; PFL-like glycyl radical enzymes" "PF03477;ATP cone domain;2e-21;codon 5-94 -!- PF00317;Ribonucleotide reductase, all-alpha d;8.4e-24;codon 141-220 -!- PF02867;Ribonucleotide reductase, barrel doma;2.2e-280;codon 222-736" "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK2227 nrdB nrdB ftsB b2235 2345406 2346536 + (no change) JW2229 2352054 2353184 + c "ribonucleoside diphosphate reductase 1, beta subunit, ferritin-like" E 90202752 -!- 93043591 -!- 93323110 -!- 11315567 -!- 2190093 -!- 3511029 -!- 6087316 -!- 8331655 -!- 8805591 -!- 9309223 -!- 9558317 -!- 9692970 Cytoplasmic 1.17.4.1 Mg2+ heteromultimer; ribonucleoside-diphosphate reductase / CDP reductase / UDP reductase / ADP reductase / GDP reductase (b2234-b2235) -!- monomeric multimer; B2 protein (b2235) 1MXR "COG0208;Ribonucleotide reductase, beta subunit" 47240; Ferritin-like "PF00268;Ribonucleotide reductase, small chain;1.4e-174;codon 16-339" "GO:0015949 nucleobase, nucleoside and nucleotide interconversion" CDS ECK2228 yfaE yfaE b2236 2346536 2346790 + (no change) JW2230 2353184 2353438 + pc predicted 2Fe-2S cluster-containing protein C Cytoplasmic COG0633;Ferredoxin 54292; 2Fe-2S ferredoxin-like PF00111;2Fe-2S iron-sulfur cluster binding domain;2.1e-14;codon 4-78 CDS ECK2229 inaA inaA yfaG b2237 2346844 2347494 - (no change) JW2231 2353492 2354142 - d conserved protein pH-inducible -!- involved in stress response C 92165728 -!- 1537798 -!- 6087316 Cytoplasmic 56112; Protein kinase-like (PK-like) PF06293;Lipopolysaccharide kinase (Kdo/WaaP) family;4.1e-98;codon 11-213 CDS ECK2230 yfaH yfaH b2238 2347709 2347915 + (no change) JW2232 2354357 2354563 + d conserved protein C Cytoplasmic COG0583;Transcriptional regulator 53850; Periplasmic binding protein-like II CDS ECK2231 glpQ glpQ b2239 2347957 2349033 - (no change) JW2233 2354605 2355681 - e periplasmic glycerophosphodiester phosphodiesterase E 91238712 -!- 92210583 -!- 1851953 -!- 3329281 Periplasmic 3.1.4.46 Ca2+ "monomeric multimer; glycerophosphoryl diester phosphodiesterase, periplasmic (b2239)" 1-25 358 1T8Q COG0584;Glycerophosphoryl diester phosphodiesterase PF03009;Glycerophosphoryl diester phosphodiesterase;5.7e-114;codon 36-350 GO:0042597 periplasmic space GO:0006071 glycerol metabolism CDS ECK2232 glpT glpT b2240 2349038 2350396 - (no change) JW2234 2355686 2357044 - t sn-glycerol-3-phosphate transporter E 3329281 -!- 92210583 -!- 3141744 Integral Membrane Protein 2.A.1; The Major Facilitator Superfamily (MFS) 12 12 in COG2271;Sugar phosphate permease PF07690;Major Facilitator Superfamily;1.1e-49;codon 34-409 TIGR00712;glpT: glycerol-3-phosphate transporter;0;codon 1-440 -!- TIGR00881;2A0104: phosphoglycerate transporter protein;2.9e-244;codon 35-417 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration -!- GO:0006071 glycerol metabolism CDS ECK2233 glpA glpA b2241 2350669 2352297 + (no change) JW2235 2357317 2358945 + e "sn-glycerol-3-phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)-binding" E 82007833 -!- 88227815 -!- 92210583 -!- 3286606 Cytoplasmic 1.1.99.5 "heteromultimer; glycerol-3-phosphate-dehydrogenase, anaerobic (b2241-b2242-b2243)" COG0578;Glycerol-3-phosphate dehydrogenase "51905; FAD/NAD(P)-binding domain -!- 54373; FAD-linked reductases, C-terminal domain" PF01266;FAD dependent oxidoreductase;4.6e-72;codon 10-368 -!- PF04324;BFD-like [2Fe-2S] binding domain;1.7e-18;codon 431-487 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration -!- GO:0006071 glycerol metabolism GO:0009053 electron donor activity CDS ECK2234 glpB glpB psi-51 b2242 2352287 2353546 + (no change) JW2236 2358935 2360194 + m "sn-glycerol-3-phosphate dehydrogenase (anaerobic), membrane anchor subunit" E 82007833 -!- 88227815 -!- 92210583 -!- 3286606 Cytoplasmic "heteromultimer; glycerol-3-phosphate-dehydrogenase, anaerobic (b2241-b2242-b2243)" COG3075;Anaerobic glycerol-3-phosphate dehydrogenase 51905; FAD/NAD(P)-binding domain PF06982;Anaerobic glycerol-3-phosphate dehydrogenase;1.2e-271;codon 35-411 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration -!- GO:0006071 glycerol metabolism GO:0009053 electron donor activity CDS ECK2235 glpC glpC b2243 2353543 2354733 + (no change) JW2237 2360191 2361381 + e "sn-glycerol-3-phosphate dehydrogenase (anaerobic), small subunit" E 82007833 -!- 88227815 -!- 92210583 -!- 3286606 Cytoplasmic 1.1.99.5 "heteromultimer; glycerol-3-phosphate-dehydrogenase, anaerobic (b2241-b2242-b2243)" COG0247;Fe-S oxidoreductase 46548; alpha-helical ferredoxin PF00037;4Fe-4S binding domain;0.002;codon 49-72 -!- PF02754;Cysteine-rich domain;1.2e-09;codon 186-249 -!- PF02754;Cysteine-rich domain;4.9e-17;codon 315-377 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009061 anaerobic respiration -!- GO:0006071 glycerol metabolism GO:0009053 electron donor activity CDS ECK2236 yfaD yfaD b2244 2354926 2355825 + (no change) JW2238 2361574 2362473 + d conserved protein C Cytoplasmic regulated by attenuation (yfaD) 48452; TPR-like "PF04754;Putative transposase, YhgA-like;1.7e-213;codon 2-278" TIGR01784;T_den_put_tspse: conserved hypothetic;1.4e-59;codon 9-298 CDS ECK2237 ypaA ypaA b4543 2355838 2356023 + pseudogene -!- new JW5964 2362486 2362671 + "pseudogene, split by terminal codon (yfaD)" su predicted protein (pseudogene) C CDS ECK2238 yfaU yfaU b2245 2356064 2356867 - (no change) JW2239 2362712 2363515 - pe "predicted 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase" C 12454498 Cytoplasmic "COG3836;2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase" 51621; Phosphoenolpyruvate/pyruvate domain PF03328;HpcH/HpaI aldolase/citrate lyase family;1.5e-118;codon 19-246 CDS ECK2239 yfaV yfaV b2246 2356885 2358174 - start codon change JW2240 2363533 2364822 - pt predicted transporter C Integral Membrane Protein 12 12 in PF07690;Major Facilitator Superfamily;1.4e-48;codon 34-402 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane CDS ECK2240 yfaW yfaW b2247 2358231 2359448 - (no change) JW2241 2364879 2366096 - pe predicted enolase C Cytoplasmic COG4948;L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily 51604; Enolase C-terminal domain-like -!- 54826; Enolase N-terminal domain-like PF02746;Mandelate racemase / muconate lactonizing en;0.00012;codon 50-161 -!- PF01188;Mandelate racemase / muconate lactonizing en;3.1e-07;codon 164-402 CDS ECK2241 yfaX yfaX b2248 2359451 2360233 - (no change) JW2242 2366099 2366881 - pr predicted DNA-binding transcriptional regulator C Cytoplasmic COG1414;Transcriptional regulator 46785; Winged helix PF01614;Bacterial transcriptional regulator;1e-86;codon 63-248 "GO:0006350 transcription -!- GO:0006355 regulation of transcription, DNA-dependent" CDS ECK2242 yfaY yfaY b2249 2360453 2361655 - (no change) JW2243 2367101 2368303 - d conserved protein molybdopterin biosynthesis C Cytoplasmic COG1058;Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA 53218; Molybdenum cofactor biosynthesis proteins PF00994;Probable molybdopterin binding domain;2.9e-06;codon 2-127 TIGR00177;molyb_syn: molybdenum cofactor synthesis d;5e-34;codon 1-167 -!- TIGR00200;cinA_nterm: competence/damage-inducible pr;9.5e-195;codon 1-399 CDS ECK2243 yfaZ yfaZ b2250 2361755 2362297 - start codon change JW5371 2368403 2368945 - pt predicted outer membrane porin protein C 1-28 regulated by attenuation (yfaZ) 56935; Porins PF07437;YfaZ precursor;2.5e-131;codon 8-187 GO:0009274 cell wall (sensu Bacteria) -!- GO:0009279 external outer membrane (sensu Gram-negative Bacteria) CDS ECK2244 yfaO yfaO b2251 2362576 2363001 + (no change) JW2245 2369224 2369649 + pe predicted NUDIX hydrolase C Cytoplasmic COG0494;NTP pyrophosphohydrolases including oxidative damage repair enzymes 55811; Nudix PF00293;NUDIX domain;1.6e-24;codon 2-141 CDS ECK2245 ais ais b2252 2363040 2363642 - (no change) JW2246 2369688 2370290 - d conserved protein induced by aluminum C 53254; Phosphoglycerate mutase-like CDS ECK2246 yfbE yfbE arnB -!- pmrH b2253 2363932 2365089 + start codon change JW5372 2370580 2371737 + e "uridine 5'-(beta-1-threo-pentapyranosyl-4-ulose diphosphate) aminotransferase, PLP-dependent" E 12704196 Cytoplasmic 53383; PLP-dependent transferases PF01041;DegT/DnrJ/EryC1/StrS aminotransferase;2.8e-195;codon 21-385 CDS ECK2247 yfbF yfbF pmrF -!- ORF2 b2254 2365093 2366061 + (no change) JW2248 2371741 2372709 + e undecaprenyl phosphate-L-Ara4FN transferase inner membrane protein E 15695810 Integral Membrane Protein 2 2 in COG0463;Glycosyltransferases involved in cell wall biogenesis 53448; Nucleotide-diphospho-sugar transferases PF00535;Glycosyl transferase;2.4e-34;codon 11-175 CDS ECK2248 yfbG yfbG arnA -!- pmrI -!- SAF b2255 2366061 2368043 + (no change) JW2249 2372709 2374691 + e fused UDP-L-Ara4N formyltransferase -!- UDP-GlcA C-4'-decarboxylase E 11706007 -!- 12704196 -!- 15491143 Cytoplasmic 2.1.2.- -!- 4.1.1.35 fused: UDP-4-amino-4-deoxy-1-arabinose formyl transferase (aa1-305) -!- UDPglucuronate decarboxylase (aa312-660) COG0223;Methionyl-tRNA formyltransferase -!- COG0451;Nucleoside-diphosphate-sugar epimerases 50486; FMT C-terminal domain-like -!- 53328; Formyltransferase -!- 51735; NAD(P)-binding Rossmann-fold domains "PF00551;Formyl transferase;3.5e-16;codon 1-177 -!- PF02911;Formyl transferase, C-terminal domain;2.2e-34;codon 202-297" CDS ECK2249 yfbH yfbH b2256 2368040 2368930 + (no change) JW2250 2374688 2375578 + o conserved protein C Cytoplasmic COG0726;Predicted xylanase/chitin deacetylase PF01522;Polysaccharide deacetylase;7.3e-06;codon 8-170 CDS ECK2250 arnT arnT yfbI b2257 2368930 2370582 + (no change) JW2251 2375578 2377230 + e 4-amino-4-deoxy-L-arabinose transferase lipid A modification E 11535604 -!- 11970957 Integral Membrane Protein 13 12 COG1807;4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family PF02366;Dolichyl-phosphate-mannose-prote in mannosylt;2.6e-70;codon 3-237 GO:0006950 response to stress CDS ECK2251 yfbW yfbW b4544 2370579 2370914 + new JW2252 2377227 2377562 + o conserved protein C Integral Membrane Protein out 103481; Multidrug resistance efflux transporter EmrE PF00893;DUF7: Integral membrane protein;0.0037;codon 1-100 GO:0016021 integral to membrane CDS ECK2252 yfbJ yfbJ b2258 2370914 2371300 + start codon change JW5373 2377562 2377948 + pm predicted inner membrane protein C Integral Membrane Protein 4 4 in PF00892;DUF6: Integral membrane protein;0.27;codon 3-121 CDS ECK2253 pmrD pmrD b2259 2371294 2371560 - start codon change JW2254 2377942 2378208 - pt polymyxin resistance protein B E 96015440 -!- 15569938 Cytoplasmic GO:0042493 response to drug CDS ECK2254 menE menE b2260 2371670 2373025 - (no change) JW2255 2378318 2379673 - e o-succinylbenzoate-CoA ligase E 96186953 -!- 8626063 Cytoplasmic 6.2.1.26 Mg2+ monomeric multimer; O-succinylbenzoic acid-CoA ligase (b2260) COG0318;Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II 56801; Firefly luciferase-like PF00501;AMP-binding enzyme;1.8e-68;codon 29-382 TIGR01923;menE: O-succinylbenzoate-CoA ligase;2.7e-131;codon 29-443 GO:0009061 anaerobic respiration CDS ECK2255 menC menC b2261 2373022 2373984 - (no change) JW2256 2379670 2380632 - e o-succinylbenzoyl-CoA synthase E 6337125 -!- 93328700 -!- 10194342 -!- 10978150 -!- 8335646 Cytoplasmic 4.2.1.- 1FHU COG1441;O-succinylbenzoate synthase 51604; Enolase C-terminal domain-like -!- 54826; Enolase N-terminal domain-like PF01188;Mandelate racemase / muconate lactonizing en;7.8e-05;codon 98-319 TIGR01927;menC_gamma/gm+: o-succinylbenzoic acid;4.5e-197;codon 7-306 GO:0009061 anaerobic respiration CDS ECK2256 menB menB b2262 2373984 2374841 - (no change) JW2257 2380632 2381489 - e dihydroxynaphthoic acid synthetase E 1629162 -!- 9325429 -!- 6754698 -!- 6454056 Cytoplasmic 4.1.3.36 COG0447;Dihydroxynaphthoic acid synthase 52096; ClpP/crotonase PF00378;Enoyl-CoA hydratase/isomerase family;1.6e-72;codon 35-206 TIGR01929;menB: naphthoate synthase;2e-228;codon 22-281 GO:0009061 anaerobic respiration CDS ECK2257 yfbB yfbB b2263 2374856 2375614 - (no change) JW2258 2381504 2382262 - pe predicted peptidase C Cytoplasmic S33 family; unassigned peptidases (YfbB protein) COG0596;Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) 53474; alpha/beta-Hydrolases PF00561;alpha/beta hydrolase fold;3.9e-06;codon 40-248 CDS ECK2258 menD menD b2264 2375611 2377281 - (no change) JW5374 2382259 2383929 - e bifunctional 2-oxoglutarate decarboxylase and SHCHC synthase E 6337125 -!- 89327151 -!- 93094143 -!- 1459959 -!- 2666397 Cytoplasmic 4.1.1.71 -!- 2.5.1.64 "COG1165;2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase" 52518; Thiamin diphosphate-binding fold (THDP-binding) "PF02776;Thiamine pyrophosphate enzyme, N-termina;0.00078;codon 8-178" "TIGR00173;menD: 2-succinyl-6-hydroxy-2,4-cyclohexadien;1.5e-290;codon 1-556" GO:0009061 anaerobic respiration CDS ECK2259 menF menF yfbA b2265 2377370 2378665 - start codon change JW2260 2384018 2385313 - e isochorismate synthase 2 menaquinone biosynthesis E 9150206 -!- 96140724 -!- 2666397 -!- 7984428 -!- 8549818 -!- 8764478 Cytoplasmic 5.4.4.2 Mg2+ "monomeric multimer; isochorismate synthase, menaquinone-specific (b2265)" 56322; ADC synthase PF00425;chorismate_bind: chorismate binding enzyme;9.7e-118;codon 168-427 TIGR00543;isochor_syn: isochorismate synthases;1.6e-53;codon 36-424 -!- TIGR00564;trpE_most: anthranilate synthase component;5.3e-08;codon 46-430 -!- TIGR00565;trpE_proteo: anthranilate synthase componen;0.00031;codon 1-429 GO:0009061 anaerobic respiration CDS ECK2260 elaB elaB yfbD b2266 2378744 2379049 - (no change) JW2261 2385392 2385697 - o conserved protein C Membrane Anchored COG4575;Uncharacterized conserved protein PF05957;Bacterial protein of unknown function (DUF88;1.7e-50;codon 7-101 CDS ECK2261 elaA elaA yfbC b2267 2379104 2379565 - (no change) JW2262 2385752 2386213 - pe predicted acyltransferase with acyl-CoA N-acyltransferase domain C Cytoplasmic COG2153;Predicted acyltransferase 55729; Acyl-CoA N-acyltransferases (Nat) PF00583;Acetyltransferase (GNAT) family;9.9e-12;codon 51-130 CDS ECK2262 elaC elaC ecoZ -!- rnz -!- zipD b2268 2379630 2380547 + start codon change JW2263 2386278 2387195 + e binuclear zinc phosphodiesterase E 12029081 Cytoplasmic Zn2+ monomeric multimer; binuclear zinc phosphodiesterase (b2268) 56281; Metallo-hydrolase/oxidoreductase PF00753;Metallo-beta-lactamase superfamily;6.5e-12;codon 24-254 CDS ECK2263 elaD elaD b2269 2380735 2381946 + (no change) JW5840 2387383 2388594 + pe predicted enzyme C Cytoplasmic 54001; Cysteine proteinases "PF02902;Ulp1 protease family, C-terminal cataly;7.8e-42;codon 149-358" CDS ECK2264 yfbK yfbK b2270 2382017 2383744 - (no change) JW2265 2388665 2390392 - d conserved protein C Membrane Lipoprotein 1-63 COG2304;Uncharacterized protein containing a von Willebrand factor type A (vWA) domain 53300; Integrin A (or I) domain PF00092;von Willebrand factor type A domain;1.5e-25;codon 216-386 CDS ECK2265 yfbL yfbL b2271 2383882 2384853 + start codon change JW2266 2390530 2391501 + pe predicted peptidase C M28A family; unassigned peptidases (YfbL protein) COG2234;Predicted aminopeptidases 53187; Zn-dependent exopeptidases PF04389;Peptidase family M28;3.4e-18;codon 108-311 CDS ECK2266 yfbM yfbM b2272 2384956 2385459 + (no change) JW2267 2391604 2392107 + o predicted protein C Cytoplasmic 1RYL CDS ECK2267 yfbN yfbN b2273 2385732 2386448 - (no change) JW2268 2392380 2393096 - d predicted protein C Cytoplasmic 46934; UBA-like CDS ECK2268 yfbO yfbO b2274 2386603 2387079 + (no change) JW2269 2393251 2393727 + o predicted protein C Cytoplasmic CDS ECK2269 yfbP yfbP b2275 2387135 2387986 + (no change) JW2270 2393783 2394634 + d predicted protein C Cytoplasmic 48452; TPR-like CDS ECK2270 nuoN nuoN b2276 2388070 2389347 - (no change) JW2271 2394718 2395995 - m "NADH:ubiquinone oxidoreductase, membrane subunit N" "NADH dehydrogenase I, complex I" E 93259946 -!- 93389724 -!- 94209210 -!- 98256007 -!- 7690854 Integral Membrane Protein heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family 14 14 out COG1007;NADH:ubiquinone oxidoreductase subunit 2 (chain N) 52518; Thiamin diphosphate-binding fold (THDP-binding) PF00361;NADH-Ubiquinone/plastoquinone (complex I);9.2e-105;codon 62-357 TIGR01770;NDH_I_N: proton-translocating NADH-quinone o;1.3e-187;codon 1-415 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK2271 nuoM nuoM nuoA b2277 2389534 2391063 - (no change) JW2272 2396182 2397711 - m "NADH:ubiquinone oxidoreductase, membrane subunit M" "NADH dehydrogenase I, complex I, contains the ubiquinone-binding site, is homologus to antiporters, and is implicated in proton pumping" E 93259946 -!- 93389724 -!- 94209210 -!- 98256007 -!- 7690854 -!- 8366049 Integral Membrane Protein heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family 14 14 out COG1008;NADH:ubiquinone oxidoreductase subunit 4 (chain M) PF00361;NADH-Ubiquinone/plastoquinone (complex I);5.3e-80;codon 133-428 TIGR01972;NDH_I_M: proton-translocating NADH-quinone o;1.7e-293;codon 3-500 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK2272 nuoL nuoL b2278 2391227 2393068 - (no change) JW2273 2397875 2399716 - m "NADH:ubiquinone oxidoreductase, membrane subunit L" "NADH dehydrogenase I, complex I, facilitates the uptake of Na(+) and is implicated in proton pumping" E 93259946 -!- 93389724 -!- 94209210 -!- 98256007 -!- 7690854 Integral Membrane Protein heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family 18 16 out "COG1009;NADH:ubiquinone oxidoreductase subunit 5 (chain L)/Multisubunit Na+/H+ antiporter, MnhA subunit" PF00662;NADH-Ubiquinone oxidoreductase (complex;2.8e-30;codon 61-122 -!- PF00361;NADH-Ubiquinone/plastoquinone (complex;6.7e-126;codon 133-421 TIGR01974;NDH_I_L: proton-translocating NADH-quinone o;0;codon 2-610 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK2273 nuoK nuoK b2279 2393065 2393367 - (no change) JW2274 2399713 2400015 - m "NADH:ubiquinone oxidoreductase, membrane subunit K" "NADH dehydrogenase I, complex I" E 93259946 -!- 93389724 -!- 94209210 -!- 98256007 -!- 7690854 Integral Membrane Protein heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family 3 3 in COG0713;NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) PF00420;NADH-ubiquinone/plastoquinone oxidoreduct;6.1e-32;codon 6-100 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK2274 nuoJ nuoJ b2280 2393364 2393918 - (no change) JW2275 2400012 2400566 - m "NADH:ubiquinone oxidoreductase, membrane subunit J" "NADH dehydrogenase I, complex I" E 93259946 -!- 93389724 -!- 94209210 -!- 98256007 -!- 7690854 Integral Membrane Protein heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family 5 5 in COG0839;NADH:ubiquinone oxidoreductase subunit 6 (chain J) PF00499;NADH-ubiquinone/plastoquinone oxidoreduct;2e-15;codon 1-160 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK2275 nuoI nuoI b2281 2393930 2394472 - (no change) JW2276 2400578 2401120 - c "NADH:ubiquinone oxidoreductase, chain I" "NADH dehydrogenase I, complex I" E 93259946 -!- 93389724 -!- 94209210 -!- 98256007 -!- 7690854 -!- 9298646 Cytoplasmic 1.6.5.3 heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) -!- heteromultimer; connecting fragment of NADH dehydrogenase I (b2281-b2286-b2287) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family COG1143;Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) PF00037;4Fe-4S binding domain;0.00011;codon 53-76 -!- PF00037;4Fe-4S binding domain;2.6e-08;codon 92-115 "TIGR01971;NuoI: NADH-quinone oxidoreductase, chain I;8.1e-83;codon 16-137" GO:0005737 cytoplasm GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK2276 nuoH nuoH b2282 2394487 2395464 - (no change) JW2277 2401135 2402112 - m "NADH:ubiquinone oxidoreductase, membrane subunit H" "NADH dehydrogenase I, complex I" E 93259946 -!- 93389724 -!- 94209210 -!- 98256007 -!- 7690854 Integral Membrane Protein heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family 8 8 out COG1005;NADH:ubiquinone oxidoreductase subunit 1 (chain H) PF00146;NADH dehydrogenase;6.1e-179;codon 13-321 GO:0009274 cell wall (sensu Bacteria) -!- GO:0019866 inner membrane GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK2277 nuoG nuoG b2283 2395461 2398193 - (no change) JW2278 2402109 2404841 - c "NADH:ubiquinone oxidoreductase, chain G" "NADH dehydrogenase I, complex I" E 93259946 -!- 93389724 -!- 94209210 -!- 98256007 -!- 7690854 -!- 8157582 -!- 9298646 Cytoplasmic 1.6.5.3 heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) -!- heteromultimer; soluble NADH dehydrogenase fragment (b2283-b2284-b2285) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family "50692; ADC-like -!- 53706; Formate dehydrogenase/DMSO reductase, domains 1-3 -!- 54292; 2Fe-2S ferredoxin-like -!- 54862; 4Fe-4S ferredoxins" PF00111;2Fe-2S iron-sulfur cluster binding dom;5.9e-13;codon 6-75 -!- PF04879;Molybdopterin oxidoreductase Fe4S4 dom;4.1e-15;codon 223-277 "TIGR01973;NuoG: NADH-quinone oxidoreductase, chain G;0;codon 6-657" GO:0005737 cytoplasm GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK2278 nuoF nuoF ygfQ -!- nuoB b2284 2398240 2399577 - (no change) JW2279 2404888 2406225 - c "NADH:ubiquinone oxidoreductase, chain F" "NADH dehydrogenase I, complex I" E 93259946 -!- 93389724 -!- 94209210 -!- 98256007 -!- 7690854 -!- 8157582 -!- 8366049 Cytoplasmic 1.6.5.3 heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) -!- heteromultimer; soluble NADH dehydrogenase fragment (b2283-b2284-b2285) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family "COG1894;NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit" PF01512;Respiratory-chain NADH dehydrogenase;2e-181;codon 33-295 "TIGR01959;nuoF_fam: NADH-quinone oxidoreductase, F sub;0;codon 12-423" GO:0005737 cytoplasm GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK2279 nuoE nuoE b2285 2399574 2400074 - (no change) JW2280 2406222 2406722 - c "NADH:ubiquinone oxidoreductase, chain E" "NADH dehydrogenase I, complex I" E 93259946 -!- 98256007 -!- 7690854 -!- 8157582 Cytoplasmic 1.6.5.3 heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) -!- heteromultimer; soluble NADH dehydrogenase fragment (b2283-b2284-b2285) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family COG1905;NADH:ubiquinone oxidoreductase 24 kD subunit 52833; Thioredoxin-like PF01257;Respiratory-chain NADH dehydrogenase;3.2e-109;codon 12-166 "TIGR01958;nuoE_fam: NADH-quinone oxidoreductase, E sub;1.4e-76;codon 21-166" GO:0005737 cytoplasm GO:0009060 aerobic respiration -!- GO:0009061 anaerobic respiration GO:0009053 electron donor activity CDS ECK2280 nuoC nuoC nuoCD -!- nuoD b2286 2400077 2401879 - (no change) JW5375 2406725 2408527 - c "NADH:ubiquinone oxidoreductase, chain C,D" "NADH dehydrogenase I, complex I" E 93259946 -!- 98256007 -!- 7690854 -!- 8157582 Cytoplasmic 1.6.5.3 heteromultimer; NADH dehydrogenase I (b2288-b2282-b2280-b2279-b2278-b2277-b2276-b2285-b 2284-b2283-b2287-b2286-b2281) -!- heteromultimer; connecting fragment of NADH dehydrogenase I (b2281-b2286-b2287) 3.D.1; The Proton-translocating NADH Dehydrogenase (NDH) Family COG0852;NADH:ubiquinone oxidoreductase 27 kD subunit -!- COG0649;NADH:ubiquinone oxidoreductase 49 kD subunit 7 "56762; Nickel-iron hydrogenase, large subunit" "PF00329;Respiratory-chain NADH dehydrogenase,;3.4e-41;codon 113-181 -!- PF00346;Respiratory-chain NADH dehydrogenase,;3.2e-189;codon 329-600" "TIGR01961;NuoC_fam: NADH (or F420