Spreadsheet: b3f8ac35-901a-4aaa-aad7-c36103c75610
Sheet: master_RM_RM.FinalScoresAndAnno

Table S1. List of 821 target genes subject to eSGA screens
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Genea | Bnumb | Jwnumc | Essentialityd | Localizatione | Categoryf | Pathwayg | Description | Comments | [NAME] | Orphan genesi | Predicted COG category for orphansj | YFP expressionk | YFP Expression (Number of Molecules / cell)l | Donor query strainm | Recipient strainn | Number of gene pairs [NAME] | Number of gene Pairs tested (30 kbp Linkage removed)p | Number of gene Pairs (|E-score >2|)q | Aggravating (E-score ≤ - 2)r | Alleviating (E-score ≥ 2)s | Donor query strain | Recipient strain | Number of gene pairs tested | Number of gene Pairs tested (30 kbp Linkage removed) | Number of gene Pairs (|E-score >2|) | Aggravating | Alleviating
aaeA | b3241 | JW3210 | non-essential | IM | PREDICTED | PROTEIN.SECRETION | p.hydroxybenzoic.acid.efflux.system.component | [NAME] and AaeB for a complex which is described as Aromatic Carboxylic Acid Efflux Transport in EcoCyc. [NAME] is annotated in GOA GO:0009306-protein secretion, because IPR006143 Secretion_HlyD. | V | -- | -- | -- | -- | Y | -- | 690 | 678 | 214 | 119 | 95 | Y | Y | 599 | 588 | 241 | 170 | 71
aaeB | b3240 | JW3209 | non-essential | IM | PREDICTED | PROTEIN.SECRETION | p.hydroxybenzoic.acid.efflux.system.component | [NAME] and AaeB for a complex which is described as Aromatic Carboxylic Acid Efflux Transport in EcoCyc. [NAME] is annotated in GOA GO:0009306-protein secretion, because IPR006143 Secretion_HlyD. | S | -- | -- | -- | -- | Y | Y | 793 | 780 | 378 | 208 | 170 | Y | Y | 610 | 599 | 323 | 178 | 145
accA | b0185 | JW0180 | essential | CY | CORE | FAS | acetyl.CoA.carboxylase.carboxytransferase.alpha.subunit | -- | I | -- | -- | -- | -- | Y | -- | 708 | 694 | 211 | 70 | 141 | Y | -- | 589 | 579 | 161 | 137 | 24
accB | b3255 | JW3223 | essential | CY | CORE | FAS | acetyl.CoA.carboxylase.BCCP.subunit | -- | I | -- | -- | -- | -- | Y | -- | 690 | 680 | 408 | 292 | 116 | Y | -- | 626 | 619 | 396 | 261 | 135
accC | b3256 | JW3224 | essential | CY | CORE | FAS | acetyl.CoA.carboxylase.biotin.carboxylase.subunit | -- | I | -- | -- | -- | -- | Y | Y | 519 | 509 | 260 | 72 | 188 | Y | Y | 336 | 328 | 207 | 85 | 122
accD | b2316 | JW2313 | essential | CY | CORE | FAS | acetyl.CoA.carboxylase.beta.carboxyltranferase.subunit | -- | I | -- | -- | -- | -- | Y | -- | 706 | 695 | 217 | 3 | 214 | Y | -- | 22 | 22 | 5 | 1 | 4
[NAME] | b2296 | JW2293 | non-essential | CY | FUNCTION-UNCERTAIN | NA | acetate.kinase.A.and.propionate.kinase.2 | acetate.kinase.A.and.propionate.kinase.2 | C | -- | -- | Y | 201.673 | Y | Y | 724 | 716 | 439 | 319 | 120 | Y | Y | 153 | 152 | 113 | 96 | 17
acpP | b1094 | JW1080 | essential | CY | CORE | FAS | acyl.carrier.protein.ACP | -- | IQ | -- | -- | -- | -- | Y | Y | 818 | 797 | 460 | 168 | 292 | Y | Y | 609 | 591 | 409 | 245 | 164
acpS | b2563 | JW2547 | essential | CY | CORE | FAS | holo.acyl.carrier.protein.synthase.1 | -- | I | -- | -- | Y | 11.815 | Y | Y | 797 | 794 | 278 | 88 | 190 | Y | Y | 648 | 646 | 354 | 168 | 186
acpT | b3475 | JW3440 | non-essential | CY | CORE | PHOSPHOLIPIDS,FAS | holo.acyl.carrier.protein.synthase.2 | AcpT is a holo-[acyl carrier protein] synthase 2. A yejM null mutation is lethal [ De08  ]. Overexpression of acpT as well as the temperature sensitivity of yejMG570A mutants [ De08  , Nurminen97  , Hirvas97  ]. This suppression does not require phosphopantetheinyl transferase activity because a mutant lacking this activity was still able to suppress the temperature sensitivity of the yejMG570A mutant [ De08  ]. A yejMG570A mutant retaining its N-terminal membrane domain but lacking its C-terminal periplasmic domain, is temperature sensitive, is more sensitive to rifampicin and erythromycin, and is defective for Lipid A synthesis [ De08  , Nurminen97  , Hirvas97  ]. | H | -- | -- | -- | -- | -- | Y | 387 | 384 | 92 | 53 | 39 | -- | Y | 223 | 221 | 82 | 41 | 41
acrA | b0463 | JW0452 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system | -- | M | -- | -- | -- | -- | Y | Y | 795 | 786 | 363 | 86 | 277 | Y | Y | 595 | 587 | 188 | 97 | 91
acrB | b0462 | JW0451 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.protein | -- | - | -- | -- | -- | -- | Y | Y | 796 | 784 | 315 | 109 | 206 | Y | Y | 553 | 542 | 273 | 119 | 154
acrD | b2470 | JW2454 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | aminoglycoside.multidrug.efflux.system | -- | V | -- | -- | -- | -- | Y | Y | 793 | 791 | 475 | 346 | 129 | Y | Y | 522 | 521 | 299 | 175 | 124
acrE | b3265 | JW3233 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | cytoplasmic.membrane.lipoprotein | -- | M | -- | -- | -- | -- | Y | Y | 784 | 775 | 231 | 65 | 166 | Y | Y | 633 | 625 | 233 | 59 | 174
acrF | b3266 | JW3234 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.protein | -- | V | -- | -- | -- | -- | Y | Y | 779 | 770 | 286 | 163 | 123 | Y | Y | 637 | 629 | 272 | 159 | 113
agaS | b3136 | JW3105 | non-essential | -- | FUNCTION-UNCERTAIN | NA | tagatose.6.phosphate.ketose.aldose.isomerase | tagatose.6.phosphate.ketose.aldose.isomerase | M | -- | -- | -- | -- | -- | Y | 329 | 328 | 269 | 183 | 86 | -- | Y | 134 | 134 | 100 | 74 | 26
aidB | b4187 | JW5867 | non-essential | -- | CORE | FAD | isovaleryl.CoA.dehydrogenase | -- | I | -- | -- | Y | 26.165 | Y | Y | 320 | 315 | 105 | 58 | 47 | Y | Y | 265 | 260 | 108 | 65 | 43
alr | b4053 | JW4013 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS | alanine.racemase.1.PLP.binding.biosynthetic | E. coli has two alanine racemase, the constitutive Alr and the metabolically regulated DadX. Alr is the minor racemase, being much less abundant than derepressed DadX [PMID:3920477,PMID:8335265]. Potential SSL between them | M | -- | -- | Y | 8.011 | -- | Y | 497 | 491 | 200 | 137 | 63 | Y | Y | 327 | 325 | 168 | 109 | 59
amiA | b2435 | JW2428 | non-essential | -- | CORE | CELL.DIVISION | N.acetylmuramoyl.l.alanine.amidase.I | E. coli contains three N-acetylmuramyl-L-alanine amidases named AmiA, B, and C involved in cell division by splitting the murein septum [PMID:11454209] | M | -- | -- | -- | -- | Y | Y | 778 | 771 | 374 | 264 | 110 | Y | Y | 244 | 241 | 101 | 50 | 51
amiB | b4169 | JW4127 | non-essential | -- | CORE | CELL.DIVISION | N.acetylmuramoyl.l.alanine.amidase.II | E. coli contains three N-acetylmuramyl-L-alanine amidases named AmiA, B, and C involved in cell division by splitting the murein septum [PMID:11454209] | M | -- | -- | Y | 0.371 | Y | Y | 815 | 789 | 194 | 102 | 92 | Y | Y | 608 | 591 | 212 | 145 | 67
amiC | b2817 | JW5449 | non-essential | PE | CORE | CELL.DIVISION | N.acetylmuramoyl.L.alanine.amidase | E. coli contains three N-acetylmuramyl-L-alanine amidases named AmiA, B, and C involved in cell division by splitting the murein septum [PMID:11454209] | M | -- | -- | -- | -- | Y | Y | 517 | 515 | 185 | 54 | 131 | Y | Y | 307 | 305 | 145 | 74 | 71
ampC | b4150 | JW4111 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | beta.lactamase.D.alanine.carboxypeptidase | One of two beta.lactamase.D.alanine.carboxypeptidase (ampH and ampC) [TO_CONFIRM]. The ampC ?-lactamase gene encodes a serine cephalosporinase [PMID:6795623]. AmpC is also believed to have an additional function as a peptidoglycan hydrolyzing enzyme [PMID:8288112] | V | -- | -- | -- | -- | Y | Y | 801 | 775 | 156 | 48 | 108 | Y | Y | 150 | 143 | 40 | 18 | 22
ampD | b0110 | JW0106 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS | N.acetyl.anhydromuranmyl.L.alanine.amidase | ampD is a member of the ampDE operon. AmpD is a cytosolic N-acetylmuramyl-L-alanine amidase responsible for breakdown of anhMurNAc-tri-, tetra-, and pentapeptides to release the peptides for recycling [PMID:7925310] | V | -- | -- | -- | -- | Y | Y | 794 | 774 | 176 | 71 | 105 | Y | Y | 650 | 639 | 222 | 129 | 93
ampG | b0433 | JW0423 | non-essential | IM | CORE | CELL.WALL.BIOGENESIS | muropeptide.transporter | AmpG is a member of the major facilitator superfamily of transporters, and together with AmpD, is essential for induction of the AmpC ?-lactamase and is involved in the recycling of cell wall peptides [PMID:8559061] | GEPR | -- | -- | -- | -- | Y | Y | 793 | 772 | 190 | 69 | 121 | Y | Y | 608 | 593 | 181 | 71 | 110
ampH | b0376 | JW5052 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | beta.lactamase.D.alanine.carboxypeptidase | One of two beta.lactamase.D.alanine.carboxypeptidase (ampH and ampC) [TO_CONFIRM]. AmpH may influence or contain a weak DD-carboxypeptidase activity [PMID:14769329] | V | -- | -- | -- | -- | Y | Y | 809 | 802 | 213 | 82 | 131 | Y | Y | 663 | 656 | 208 | 100 | 108
ansB | b2957 | JW2924 | non-essential | PE | FUNCTION-UNCERTAIN | NA | periplasmic.L.asparaginase.II | periplasmic.L.asparaginase.II | EJ | -- | -- | -- | -- | -- | Y | 369 | 367 | 245 | 185 | 60 | -- | Y | 197 | 195 | 109 | 85 | 24
appB | b0979 | JW0961 | non-essential | IM | FUNCTION-UNCERTAIN | NA | cytochrome.bd.II.oxidase.subunit.II | -- | C | -- | -- | -- | -- | -- | Y | 389 | 384 | 131 | 75 | 56 | -- | Y | 180 | 180 | 76 | 46 | 30
appC | b0978 | JW0960 | non-essential | IM | FUNCTION-UNCERTAIN | NA | cytochrome.bd.II.oxidase.subunit.I | -- | C | -- | -- | Y | 3.091 | -- | Y | 391 | 386 | 170 | 131 | 39 | -- | Y | 201 | 200 | 97 | 65 | 32
arcB | b3210 | JW5536 | non-essential | IM | FUNCTION-UNCERTAIN | NA | hybrid.sensory.histidine.kinase.in.two.component.regulatory.system.with.[NAME] | Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | T | -- | -- | Y | 55.757 | Y | Y | 731 | 715 | 363 | 264 | 99 | Y | Y | 501 | 488 | 319 | 188 | 131
arnT | b2257 | JW2251 | non-essential | IM | CORE | LPS.AND.ECA | 4.amino.4.deoxy.L.arabinose.transferase | LPS levels in the outer membrane are lowered in asmA null mutants [ Deng96  ]. So it might participate in LPS and/or Outer membrane assembly and/or [NAME], check interactions wityh BamABCD | M | -- | -- | -- | -- | -- | Y | 377 | 370 | 138 | 53 | 85 | Y | Y | 206 | 201 | 83 | 24 | 59
asmA | b2064 | JW2049 | non-essential | PE | FUNCTION-UNCERTAIN | LPS.AND.ECA | predicted.assembly.protein | The OmpF assembly step that is affected by this suppression occurs in the outer membrane [ Deng96  ]. LPS levels in the outer membrane are lowered in asmA null mutants [ Deng96  ] | M | -- | -- | Y | 1.707 | Y | Y | 814 | 784 | 250 | 105 | 145 | Y | Y | 646 | 621 | 414 | 222 | 192
avtA | b3572 | JW5652 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS | valine.pyruvate.aminotransferase | Is commonly classified in L-alanine biosynthesis. But L-alanine is a precursor for D-alanine which is needed for peptidoglycan assembly | E | -- | -- | -- | -- | Y | Y | 523 | 520 | 130 | 68 | 62 | Y | Y | 336 | 333 | 141 | 69 | 72
bacA | b3057 | [NAME] | non-essential | IM | CORE | ISOPRENOIDS.BIOSYNTHESIS,CELL.WALL.BIOGENESIS | undecaprenyl.pyrophosphate.phosphatase | ybjG, bacA and pgpB are links between isoprenoids and cell.wall biogenesis as they provide  'undecaprenyl phosphate' [EC:3.6.1.27]  which is essential for the synthesis of peptidoglycan via MraY. However all BacA, YbjG, PgpB, and YeiU conduct EC:3.6.1.27. Simultaneous inactivation of bacA, ybjG, and pgpB is lethal [PMID:15778224]. PgpB also conducts EC:3.6.1.26 as well as PgpA, but they may not be the principal enzymes responsible for EC:3.6.1.26. Expression of C55PP activity from one of the three genes ybjG, bacA, and pgpB appears to be sufficient for synthesis of undecaprenyl phosphate and survival [ El05  ] | V | -- | -- | -- | -- | Y | Y | 810 | 803 | 228 | 79 | 149 | Y | Y | 672 | 665 | 328 | 118 | 210
bcr | b2182 | JW5363 | non-essential | IM | PREDICTED | RESPONSE.TO.ANTIBIOTIC | bicyclomycin.multidrug.efflux.system | [NAME] is a probable multidrug efflux protein, expression of which has been shown to confer resistance to bicyclomycin [ Bentley93  ] and sulfathiazole [ Vedantam98  ]. [NAME] is a member of the major facilitator superfamily and has been proposed to function as a drug/proton antiporter [ Paulsen93  ]. | GEPR | -- | -- | -- | -- | -- | Y | 393 | 389 | 136 | 89 | 47 | -- | Y | 209 | 208 | 95 | 48 | 47
bcsA | b3533 | JW5665 | non-essential | IM | CORE | CELL.SHAPE | cellulose.synthase.catalytic.subunit | BcsA, BcsB, BcsZ and BcsC are involved in biosynthesis of cellulose, a characteristic of the rdar morphotype [ Zogaj01  ]. Besides thin aggregative fimbriae, cellulose is the second the second component of the extracellular matrix of the multicellular morphotype (rdar) | M | -- | -- | -- | -- | Y | Y | 790 | 776 | 254 | 142 | 112 | Y | Y | 153 | 153 | 81 | 43 | 38
bcsB | b3532 | JW3500 | essential | IM | CORE | CELL.SHAPE | regulator.of.cellulose.synthase.cyclic.di.GMP.binding | BcsA, BcsB, BcsZ and BcsC are involved in biosynthesis of cellulose, a characteristic of the rdar morphotype [ Zogaj01  ]. Besides thin aggregative fimbriae, cellulose is the second the second component of the extracellular matrix of the multicellular morphotype (rdar) | - | -- | -- | -- | -- | Y | Y | 795 | 779 | 269 | 82 | 187 | Y | Y | 626 | 616 | 421 | 196 | 225
bcsC | b3530 | JW5942 | non-essential | OM | CORE | CELL.SHAPE | cellulose.synthase.subunit | BcsA, BcsB, BcsZ and BcsC are involved in biosynthesis of cellulose, a characteristic of the rdar morphotype [ Zogaj01  ]. Besides thin aggregative fimbriae, cellulose is the second the second component of the extracellular matrix of the multicellular morphotype (rdar) | R | -- | -- | Y | 2.848 | -- | Y | 376 | 367 | 104 | 45 | 59 | -- | Y | 218 | 215 | 71 | 39 | 32
betT | b0314 | JW0306 | non-essential | IM | CORE | PHOSPHOLIPIDS | choline.transporter.of.high.affinity | Choline transporter Choline is a key component of phospholipids | M | -- | -- | -- | -- | Y | -- | 709 | 707 | 218 | 67 | 151 | Y | Y | 618 | 616 | 198 | 82 | 116
bglH | b3720 | JW3698 | non-essential | OM | PREDICTED | NA | carbohydrate.specific.outer.membrane.porin.cryptic | carbohydrate.specific.outer.membrane.porin.cryptic | G | -- | -- | -- | -- | -- | Y | 393 | 390 | 160 | 89 | 71 | -- | Y | 203 | 201 | 118 | 80 | 38
birA | b3973 | JW3941 | essential | CY | CORE | FAS | bifunctional.biotin.acetylCoA.carboxylase.holoenzyme.synthetase.and.DNA.binding.transcriptional.repressor.bio.5.AMP.binding | -- | HK | -- | -- | Y | 9.329 | Y | Y | 805 | 799 | 251 | 158 | 93 | Y | Y | 608 | 603 | 302 | 200 | 102
blc | b4149 | JW4110 | non-essential | -- | FUNCTION-UNCERTAIN | CELL.ENVELOPE.INTEGRITY | outer.membrane.lipoprotein.lipocalin | Structural analysis of the purified Blc protein suggest a possible role for the outer membrane [NAME] in membrane repair or maintenance requiring lipid storage or transport [PMID:15044022] Hu et al (2009) have PPI of Blc and 'fabD_b1092 Malonyl-CoA-[acyl-carrier-protein] transacylase'. Structural analysis of the purified Blc protein suggest a possible role for the outer membrane [NAME] in membrane repair or maintenance requiring lipid storage or transport [ Campanacci04  ] | M | -- | -- | -- | -- | Y | Y | 812 | 786 | 178 | 45 | 133 | Y | Y | 232 | 223 | 62 | 19 | 43
blr | b4409 | JW5963 | non-essential | -- | FUNCTION-UNCERTAIN | NA | beta.lactam.resistance.membrane.protein | This proteins could form another class called 'Response.to.drugs' or 'Cell.proliferation', perhaps together with 'Biofilm.formation' | - | -- | -- | -- | -- | Y | -- | 696 | 686 | 427 | 268 | 159 | Y | Y | 602 | 593 | 489 | 407 | 82
btuB | b3966 | JW3938 | non-essential | OM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | vitamin.B12.cobalamin.outer.membrane.transporter | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | H | -- | -- | -- | -- | Y | -- | 690 | 685 | 246 | 123 | 123 | Y | Y | 549 | 546 | 415 | 297 | 118
btuC | b1711 | JW1701 | non-essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | vitamin.B12.transporter.subunit.membrane.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | H | -- | -- | -- | -- | -- | Y | 349 | 345 | 123 | 59 | 64 | Y | Y | 176 | 174 | 101 | 42 | 59
btuD | b1709 | JW1699 | non-essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | vitamin.B12.transporter.subunit.ATP.binding.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | H | -- | -- | -- | -- | -- | Y | 367 | 363 | 170 | 116 | 54 | -- | Y | 175 | 173 | 78 | 48 | 30
btuF | b0158 | JW0154 | non-essential | PE | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | vitamin.B12.transporter.subunit.periplasmic.binding.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | -- | -- | Y | Y | 798 | 781 | 268 | 104 | 164 | Y | Y | 627 | 612 | 273 | 168 | 105
caiA | b0039 | JW0038 | non-essential | CY | FUNCTION-UNCERTAIN | FAD | crotonobetaine.reductase.subunit.II.FAD.binding | L-Carnitine is essential for transport of activated fatty acids across the inner membrane. The carnitine pathway may play more than one role in the cell: generation of an osmoprotectant and generation of an external electron acceptor in anaerobic respiration [ECOCYC].  E. coli uses two operons, the caiTABCDE operon and the fixABCX operon, for anaerobic carnitine metabolism. [NAME] is proposed to function as an L-carnitine/gamma-butyrobetaine exchanger (antiporter) according to the substrate/product antiport principle [PMID:12163501] | I | -- | -- | -- | -- | Y | -- | 692 | 684 | 356 | 264 | 92 | -- | -- | -- | -- | -- | -- | --
caiC | b0037 | JW0036 | non-essential | CY | FUNCTION-UNCERTAIN | FAD | predicted.crotonobetaine.CoA.ligase.carnitine.CoA.ligase | L-Carnitine is essential for transport of activated fatty acids across the inner membrane. The carnitine pathway may play more than one role in the cell: generation of an osmoprotectant and generation of an external electron acceptor in anaerobic respiration [ECOCYC].  E. coli uses two operons, the caiTABCDE operon and the fixABCX operon, for anaerobic carnitine metabolism. [NAME] is proposed to function as an L-carnitine/gamma-butyrobetaine exchanger (antiporter) according to the substrate/product antiport principle [PMID:12163501] | IQ | -- | -- | -- | -- | Y | Y | 768 | 757 | 237 | 82 | 155 | Y | Y | 608 | 601 | 215 | 84 | 131
caiD | b0036 | JW0035 | non-essential | CY | FUNCTION-UNCERTAIN | FAD | crotonobetainyl.CoA.hydratase | L-Carnitine is essential for transport of activated fatty acids across the inner membrane. The carnitine pathway may play more than one role in the cell: generation of an osmoprotectant and generation of an external electron acceptor in anaerobic respiration [ECOCYC].  E. coli uses two operons, the caiTABCDE operon and the fixABCX operon, for anaerobic carnitine metabolism. [NAME] is proposed to function as an L-carnitine/gamma-butyrobetaine exchanger (antiporter) according to the substrate/product antiport principle [PMID:12163501] | I | -- | -- | -- | -- | Y | -- | 686 | 678 | 555 | 507 | 48 | -- | -- | -- | -- | -- | -- | --
caiE | b0035 | JW5004 | non-essential | CY | FUNCTION-UNCERTAIN | FAD | predicted.acyl.transferase | The function of the CaiE protein is currently unknown. Overproduction of CaiE appears to stimulate carnitine racemase activity of CaiD and carnitine dehydratase activity of CaiB, leading to the hypothesis that CaiE may be involved in the synthesis or activation of an unknown cofactor required for these activities [ Eichler94  ]. | R | -- | -- | -- | -- | -- | Y | 392 | 383 | 158 | 88 | 70 | -- | Y | 212 | 208 | 71 | 29 | 42
caiT | b0040 | JW0039 | non-essential | IM | CORE | FAD | predicted.transporter | L-Carnitine is essential for transport of activated fatty acids across the inner membrane. The carnitine pathway may play more than one role in the cell: generation of an osmoprotectant and generation of an external electron acceptor in anaerobic respiration [ECOCYC].  E. coli uses two operons, the caiTABCDE operon and the fixABCX operon, for anaerobic carnitine metabolism. [NAME] is proposed to function as an L-carnitine/gamma-butyrobetaine exchanger (antiporter) according to the substrate/product antiport principle [PMID:12163501] | M | -- | -- | -- | -- | Y | Y | 818 | 808 | 342 | 138 | 204 | Y | Y | 657 | 650 | 283 | 126 | 157
[NAME] | b2197 | JW2185 | non-essential | CY | FUNCTION-UNCERTAIN | CHAPERONES | periplasmic.heme.chaperone | periplasmic.heme.chaperone responsible for shuttling heme from the CcmABCDE protoheme IX ABC transport complex to the CcmEFGH holocytochrome c synthetase for attachment to c-type cytochromes | O | -- | -- | -- | -- | -- | Y | 392 | 387 | 99 | 54 | 45 | -- | Y | 213 | 211 | 81 | 37 | 44
cdh | b3918 | JW3889 | non-essential | CY | CORE | LPS.AND.ECA | CDP.diacylglycerol.phosphotidylhydrolase | -- | I | -- | -- | -- | -- | Y | Y | 471 | 467 | 151 | 63 | 88 | Y | Y | 295 | 292 | 140 | 43 | 97
cedA | b1731 | JW1720 | non-essential | CY | FUNCTION-UNCERTAIN | CELL.DIVISION | cell.division.modulator | CedA appears to be involved in the regulation of cell division in a wild-type or dnaA mutant strain [PMID:9427399] -- | - | -- | -- | Y | 7.844 | Y | Y | 816 | 809 | 215 | 135 | 80 | Y | Y | 219 | 218 | 111 | 58 | 53
cfa | b1661 | JW1653 | non-essential | CY | CORE | PHOSPHOLIPIDS | cyclopropane.fatty.acyl.phospholipid.synthase.unsaturated.phospholipid.methyltransferase | -- | M | -- | -- | -- | -- | Y | Y | 523 | 518 | 287 | 141 | 146 | Y | Y | 354 | 350 | 165 | 95 | 70
cheA | b1888 | JW1877 | non-essential | CY | FUNCTION-UNCERTAIN | NA | fused.chemotactic.sensory.histidine.kinase.in.two.component.regulatory.system.with.CheB.and.CheY.sensory.histidine.kinase.signal.sensing.protein | -- | NT | -- | -- | -- | -- | -- | Y | 486 | 478 | 195 | 141 | 54 | Y | Y | 278 | 276 | 131 | 81 | 50
cheB | [NAME] | [NAME] | non-essential | CY | FUNCTION-UNCERTAIN | NA | fused.chemotaxis.regulator.protein.glutamate.methylesterase.in.two.component.regulatory.system.with.[NAME] | -- | NT | -- | -- | -- | -- | -- | Y | 355 | 348 | 217 | 179 | 38 | Y | Y | 180 | 179 | 103 | 75 | 28
cheR | b1884 | JW1873 | non-essential | CY | FUNCTION-UNCERTAIN | NA | chemotaxis.regulator.protein.glutamate.methyltransferase | -- | NT | -- | -- | -- | -- | Y | Y | 796 | 784 | 231 | 142 | 89 | Y | Y | 157 | 156 | 66 | 33 | 33
cheW | b1887 | JW1876 | non-essential | CY | FUNCTION-UNCERTAIN | NA | purine.binding.chemotaxis.protein | -- | NT | -- | -- | Y | 0.437 | Y | Y | 530 | 522 | 223 | 163 | 60 | Y | Y | 352 | 349 | 179 | 133 | 46
cheY | b1882 | JW1871 | non-essential | CY | FUNCTION-UNCERTAIN | NA | chemotaxis.regulator.transmitting.signal.to.flagellar.motor.component | -- | T | -- | -- | Y | 11.765 | Y | Y | 807 | 795 | 289 | 141 | 148 | Y | Y | 212 | 208 | 112 | 62 | 50
cheZ | b1881 | JW1870 | non-essential | CY | FUNCTION-UNCERTAIN | NA | chemotaxis.regulator.protein.phosphatase.for.CheY | -- | NT | -- | -- | -- | -- | Y | Y | 794 | 782 | 376 | 232 | 144 | Y | Y | 152 | 151 | 54 | 14 | 40
chiA | b3338 | JW3300 | non-essential | EC | FUNCTION-UNCERTAIN | NA | periplasmic.endochitinase | periplasmic.endochitinase | - | -- | -- | -- | -- | -- | Y | 367 | 358 | 163 | 123 | 40 | Y | Y | 198 | 196 | 94 | 74 | 20
cirA | b2155 | JW2142 | non-essential | OM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | ferric.iron.catecholate.outer.membrane.transporter | [NAME] is a TonB dependent iron-siderophore complex uptake receptor (EcoCyc) | P | -- | -- | Y | 0.378 | -- | Y | 344 | 341 | 84 | 29 | 55 | -- | Y | 186 | 183 | 62 | 15 | 47
cld | b2027 | JW5836 | non-essential | IM | CORE | LPS.AND.ECA | regulator.of.length.of.O.antigen.component.of.lipopolysaccharide.chains | In E. coli strains O8 and O9, the orthologous Cld (Wzz) protein was shown to control the length of the O-antigen component of lipopolysaccharide [ Franco96  , Amor97  ]. Regulation of O-antigen chain length is required for virulence of Salmonella typhimurium [ Murray03  ]. E. coli [NAME] does not produce O-antigen. | M | -- | -- | -- | -- | Y | Y | 768 | 743 | 316 | 222 | 94 | Y | Y | 516 | 500 | 318 | 209 | 109
cls | b1249 | JW1241 | non-essential | IM | CORE | PHOSPHOLIPIDS | cardiolipin.synthase.1 | -- | I | -- | -- | -- | -- | Y | Y | 815 | 806 | 267 | 77 | 190 | Y | Y | 588 | 580 | 332 | 140 | 192
cmr | b0842 | JW0826 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.protein | The MdfA protein, also known as Cmr, is a multidrug efflux protein belonging to the major facilitator superfamily (MFS) [ Paulsen96a  ]. Overexpression of MdfA has demonstrated that it confers resistance to tetracycline, chloramphenicol, erythromycin, some aminoglycosides and fluoroquinolones, and organic cations such as ethidium bromide [ Edgar97  ]. | GEPR | -- | -- | -- | -- | -- | Y | 362 | 360 | 101 | 37 | 64 | -- | Y | 195 | 194 | 53 | 26 | 27
coaD | b3634 | JW3609 | essential | CY | CORE | PANTOTHENATE.AND.COA.BIOSYNTHESIS | pantetheine.phosphate.adenylyltransferase | -- | H | -- | -- | -- | -- | Y | Y | 481 | 466 | 214 | 91 | 123 | Y | Y | 306 | 294 | 193 | 122 | 71
coaE | b0103 | JW0100 | non-essential | CY | CORE | PANTOTHENATE.AND.COA.BIOSYNTHESIS | [NAME] | -- | H | -- | -- | -- | -- | Y | -- | 685 | 673 | 230 | 132 | 98 | -- | -- | -- | -- | -- | -- | --
cpsB | b2049 | JW2034 | non-essential | CY | CORE | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | mannose.1.phosphate.guanyltransferase | -- | GM | -- | -- | -- | -- | -- | Y | 393 | 383 | 166 | 69 | 97 | Y | Y | 222 | 216 | 83 | 37 | 46
cpsG | b2048 | JW2033 | non-essential | CY | CORE | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | phosphomannomutase | -- | G | -- | -- | -- | -- | -- | Y | 487 | 465 | 259 | 97 | 162 | Y | Y | 296 | 283 | 148 | 86 | 62
cpxP | b3913 | JW5558 | non-essential | PE | CORE | CHAPERONES | periplasmic.protein.combats.stress | CpxP is involved in resistance to extracytoplasmic stresses [ Danese98  ]. CpxP is a negative regulator of the Cpx response; this feedback regulation occurs via CpxA and may serve to restrict the response to a limited period of time [ Raivio99  ]. Envelope perturbation inhibits the CpxP-mediated inhibition of CpxA signaling [ DiGiuseppe03  ]. CpxP may also act as a chaperone [ DiGiuseppe03  ]. Check genetic interactions with DegP. | -- | -- | -- | -- | -- | -- | Y | 389 | 385 | 121 | 60 | 61 | -- | Y | 214 | 211 | 95 | 64 | 31
cpxR | b3912 | JW3883 | non-essential | CY | CORE | CHAPERONES | DNA.binding.response.regulator.in.two.component.regulatory.system.with.CpxA | The sensor protein CpxA is part of the two-component CpxA/CpxR signal transduction system. The system senses and responds to aggregated and misfolded proteins in the bacterial envelope. The precise physiological role of this system has not been identified, although it appears to be involved in several diverse cell processes. Among these is the temperature-independent, positive regulation of degP gene expression which is a periplasmic protease. The CpxA/R system may play a key role in an extensive stress response network in which the unifying element is coordination of protein turnover and energy conservation. [ De99b  , Dong93a  , Danese95  , Mileykovsk97  , Weber88  , Albin86  ]. Check genetic interactions with DegP. | TK | -- | -- | Y | 33.164 | Y | -- | 676 | 672 | 278 | 155 | 123 | -- | -- | -- | -- | -- | -- | --
crcA | b0622 | JW0617 | non-essential | OM | CORE | PHOSPHOLIPIDS,LPS.AND.ECA | palmitoyl.transferase.for.Lipid.A | Escherichia coli homolog (crcA/pagP) encode an unusual enzyme of lipid A biosynthesis localized in the outer membrane. PagP transfers a palmitate residue from the sn-1 position of a phospholipid to the N-linked hydroxymyristate on the proximal unit of lipid A (or its precursors) [PMID:11013210] | - | -- | -- | -- | -- | Y | Y | 784 | 773 | 212 | 96 | 116 | Y | Y | 605 | 595 | 259 | 80 | 179
crcB | b0624 | JW0619 | non-essential | IM | FUNCTION-UNCERTAIN | CHROMOSOME.SEGREGATION | predicted.inner.membrane.protein.associated.with.chromosome.condensation | Link between LPS and Chromosome.segregation. PagP (crcA), cspE, and crcB are involved in resistance to camphor-induced chromosome decondensation [PMID:8844142,PMID:12904550], and crcA is also involved in transfer of palmitate from a phospholipid (sn-1 position) to lipid A or to a lipid A precursor [PMID:11013210] -- | D | -- | -- | -- | -- | -- | Y | 387 | 382 | 144 | 89 | 55 | -- | Y | 185 | 184 | 90 | 58 | 32
csgE | b1039 | JW1022 | non-essential | CY | FUNCTION-UNCERTAIN | PROTEIN.SECRETION | predicted.transport.protein | Curli Secretion and Assembly Complex (CsgG, CsgE, CsgF) | - | -- | -- | -- | -- | Y | Y | 798 | 786 | 247 | 96 | 151 | Y | Y | 139 | 137 | 51 | 17 | 34
csgF | b1038 | JW1021 | non-essential | -- | FUNCTION-UNCERTAIN | PROTEIN.SECRETION | predicted.transport.protein | Curli Secretion and Assembly Complex (CsgG, CsgE, CsgF) An insertion in the csgF gene abolishes the formation of curli, although csgA, which encodes one of the structural subunits of curli, continues to be expressed [ Hammar95  ]. A csgF mutant is able to extracellularly complement curli formation in a csgA mutant, arguing that CsgF is not involved in CsgA secretion, but in curli nucleation [ Chapman02  ]. This proteins could form another class called 'Cell.motility' or 'Cell.proliferation', perhaps together with 'Biofilm.formation' | - | -- | -- | -- | -- | -- | Y | 499 | 492 | 132 | 52 | 80 | -- | Y | 339 | 334 | 159 | 75 | 84
[NAME] | b1037 | JW1020 | non-essential | -- | FUNCTION-UNCERTAIN | PROTEIN.SECRETION | outer.membrane.lipoprotein | Curli Secretion and Assembly Complex (CsgG, CsgE, CsgF) An insertion in the csgF gene abolishes the formation of curli, although csgA, which encodes one of the structural subunits of curli, continues to be expressed [ Hammar95  ]. A csgF mutant is able to extracellularly complement curli formation in a csgA mutant, arguing that CsgF is not involved in CsgA secretion, but in curli nucleation [ Chapman02  ]. This proteins could form another class called 'Cell.motility' or 'Cell.proliferation', perhaps together with 'Biofilm.formation' | M | -- | -- | Y | 2.845 | Y | Y | 797 | 784 | 216 | 97 | 119 | Y | Y | 589 | 580 | 194 | 114 | 80
csrA | b2696 | JW2666 | essential | CY | FUNCTION-UNCERTAIN | CELL.SHAPE | pleiotropic.regulatory.protein.for.carbon.source.metabolism | A csrA mutation affects cell adherence and cell size [PMID:8393005], although EcoCyc description is more focused on it function as a regulator of carbohydrate metabolism that affects glycogen biosynthesis [NAME], | T | -- | -- | Y | 473.979 | Y | Y | 784 | 779 | 214 | 98 | 116 | Y | Y | 612 | 607 | 220 | 91 | 129
cusA | b0575 | JW0564 | non-essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | copper.silver.efflux.system.membrane.component | CusA is a member of the Resistance-Nodulation-Cell Division (RND) [NAME] and is involved in the detoxification of copper and silver ions in E. coli as part of the CusCFBA copper/silver efflux system [ Silver03 ] | P | -- | -- | -- | -- | -- | Y | 386 | 373 | 255 | 141 | 114 | -- | Y | 187 | 182 | 126 | 104 | 22
cusB | b0574 | JW0563 | non-essential | PE | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | copper.silver.efflux.system.membrane.fusion.protein | CusA is a member of the Resistance-Nodulation-Cell Division (RND) [NAME] and is involved in the detoxification of copper and silver ions in E. coli as part of the CusCFBA copper/silver efflux system [ Silver03 ] | - | -- | -- | -- | -- | -- | Y | 390 | 377 | 125 | 73 | 52 | -- | Y | 193 | 187 | 90 | 55 | 35
cusC | b0572 | JW0561 | non-essential | OM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | copper.silver.efflux.system.outer.membrane.component | CusA is a member of the Resistance-Nodulation-Cell Division (RND) [NAME] and is involved in the detoxification of copper and silver ions in E. coli as part of the CusCFBA copper/silver efflux system [ Silver03 ] | MU | -- | -- | -- | -- | Y | Y | 798 | 780 | 257 | 119 | 138 | Y | Y | 131 | 128 | 62 | 39 | 23
[NAME] | b0573 | JW0562 | non-essential | PE | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | periplasmic.copper.binding.protein | CusA is a member of the Resistance-Nodulation-Cell Division (RND) [NAME] and is involved in the detoxification of copper and silver ions in E. coli as part of the CusCFBA copper/silver efflux system [ Silver03 ] | S | -- | -- | -- | -- | Y | Y | 794 | 776 | 212 | 93 | 119 | Y | Y | 121 | 117 | 50 | 32 | 18
cyaR | b4438 | UNKW3110 | unknown | -- | FUNCTION-UNCERTAIN | NA | -- | Small RNA. [NAME] is a small RNA that promotes degradation of the ompX [ [NAME]  , De09  ]. [NAME] expression is also upregulated by the alternative sigma factor of the envelope stress response, ?E [ Johansen08 ]. | -- | -- | -- | -- | -- | Y | -- | 663 | 648 | 362 | 241 | 121 | -- | -- | -- | -- | -- | -- | --
cycA | b4208 | JW4166 | non-essential | IM | CORE | CELL.WALL.BIOGENESIS | D.alanine.D.serine.glycine.transporter | CycA is a serine/alanine/glycine APC transporter. Mutants defective in cycA show decreased transport of glycine, D-serine and D-alanine and are resistant to D-cycloserine inhibition [ Ghrist95  , Robbins73  ] | E | -- | -- | -- | -- | -- | Y | 494 | 488 | 166 | 98 | 68 | -- | Y | 319 | 315 | 155 | 83 | 72
cydA | b0733 | JW0722 | essential | IM | FUNCTION-UNCERTAIN | NA | cytochrome.d.terminal.oxidase.subunit.I | CydA contains the heme b558 component of cytochrome bd-I [ Green84a  ]. This protein could form another class called 'Energetic.metabolism' | C | -- | -- | Y | 485.087 | Y | -- | 710 | 695 | 329 | 40 | 289 | Y | Y | 565 | 553 | 156 | 76 | 80
cydB | b0734 | JW0723 | non-essential | IM | FUNCTION-UNCERTAIN | NA | cytochrome.d.terminal.oxidase.subunit.II | -- | C | -- | -- | -- | -- | Y | Y | 783 | 770 | 327 | 148 | 179 | Y | Y | 620 | 608 | 225 | 100 | 125
cydC | b0886 | JW0869 | essential | IM | FUNCTION-UNCERTAIN | NA | fused.cysteine.transporter.subunits.of.ABC.superfamily.membrane.component.ATP.binding.component | The cydDC operon encodes two ATP-binding cassette (ABC) transporter proteins that are most closely similar to ABC transporters involved in export [ [NAME]  ]. Deletion studies have shown that both of these proteins are essential for functional cytochrome bd and cytochrome c [ Georgiou87  , Poole94  ].  This protein could form another class called 'Energetic.metabolism' | CO | -- | -- | Y | 16.468 | -- | Y | 457 | 455 | 242 | 187 | 55 | Y | Y | 279 | 278 | 191 | 135 | 56
cyoA | [NAME] | JW0422 | non-essential | IM | FUNCTION-UNCERTAIN | NA | cytochrome.o.ubiquinol.oxidase.subunit.II | -- | C | -- | -- | -- | -- | Y | Y | 791 | 771 | 238 | 137 | 101 | Y | Y | 136 | 130 | 92 | 63 | 29
cyoB | b0431 | JW0421 | non-essential | IM | FUNCTION-UNCERTAIN | NA | cytochrome.o.ubiquinol.oxidase.subunit.I | -- | C | -- | -- | -- | -- | Y | Y | 784 | 765 | 222 | 92 | 130 | Y | Y | 676 | 661 | 246 | 131 | 115
cyoC | b0430 | JW0420 | non-essential | IM | FUNCTION-UNCERTAIN | NA | cytochrome.o.ubiquinol.oxidase.subunit.III | -- | C | -- | -- | Y | 46.768 | Y | -- | 677 | 661 | 172 | 57 | 115 | Y | Y | 600 | 586 | 131 | 30 | 101
cyoD | b0429 | JW0419 | non-essential | IM | FUNCTION-UNCERTAIN | NA | cytochrome.o.ubiquinol.oxidase.subunit.IV | -- | C | -- | -- | Y | 114.088 | Y | -- | 676 | 659 | 201 | 59 | 142 | Y | Y | 654 | 639 | 85 | 23 | 62
dacA | b0632 | JW0627 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | D.alanyl.D.alanine.carboxypeptidase.penicillin.binding.protein.5 | DacA(PBP5), DacC(PBP6A) and [NAME]) are isozymes (D.alanyl.D.alanine.carboxypeptidase) | M | -- | -- | Y | 5.122 | Y | Y | 526 | 517 | 166 | 113 | 53 | Y | Y | 330 | 323 | 203 | 148 | 55
dacB | b3182 | JW3149 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | D.alanyl.D.alanine.carboxypeptidase | dacB catalyzes both D-alanyl-D-alanine carboxypeptidase and D-alanyl-D-alanine endopeptidase activities, whereas yfeB is a predicted penicillin-binding protein 4B with EPase and/or Cpase activities [PMID:16402224]. Check for SSL between dacB and yfeW | M | -- | -- | Y | 1.177 | Y | Y | 816 | 799 | 211 | 94 | 117 | Y | Y | 691 | 677 | 336 | 244 | 92
dacC | b0839 | JW0823 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | D.alanyl.[NAME] | DacA(PBP5), DacC(PBP6A) and [NAME]) are isozymes (D.alanyl.D.alanine.carboxypeptidase) | M | -- | -- | -- | -- | Y | Y | 514 | 511 | 184 | 103 | 81 | Y | Y | 241 | 240 | 125 | 52 | 73
[NAME] | b2010 | JW5329 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | D.alanyl.[NAME] | DacA(PBP5), DacC(PBP6A) and [NAME]) are isozymes (D.alanyl.D.alanine.carboxypeptidase) | M | -- | -- | -- | -- | Y | Y | 797 | 784 | 255 | 139 | 116 | Y | Y | 231 | 224 | 90 | 39 | 51
dadX | b1190 | JW1179 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS | alanine.racemase.2.PLP.binding | E. coli has two alanine racemase, the constitutive Alr and the metabolically regulated DadX. Alr is the minor racemase, being much less abundant than derepressed DadX [PMID:3920477,PMID:8335265]. Potential SSL between them | M | -- | -- | Y | 10.883 | Y | Y | 806 | 791 | 243 | 132 | 111 | Y | Y | 654 | 641 | 235 | 75 | 160
[NAME] | b3388 | JW3351 | non-essential | EC | FUNCTION-UNCERTAIN | CELL.DIVISION | predicted.protein | [NAME] is a non-essential cell division protein; it contains a C-terminal SPOR domain which targets the protein to the septal ring [PMID:19684127 ]. Overexpression of damX induces cell filamentation [PMID:7603433]. A damX deletion strain in otherwise wild-type background shows no obvious defect; however, in combination with an ftsN or dedD allele shows a synthetic phenotype [PMID:19684127] -- | S | -- | -- | -- | -- | Y | Y | 789 | 784 | 488 | 331 | 157 | Y | Y | 134 | 134 | 94 | 70 | 24
dcrB | b3472 | JW5682 | non-essential | PE | FUNCTION-UNCERTAIN | NA | periplasmic.protein | periplasmic.protein | - | -- | -- | Y | 5.115 | -- | Y | 393 | 390 | 128 | 61 | 67 | -- | Y | 218 | 216 | 88 | 37 | 51
ddg | b2378 | JW2375 | non-essential | IM | CORE | LPS.AND.ECA | palmitoleoyl.acyl.carrier.protein.ACP.dependent.acyltransferase | -- | M | -- | -- | -- | -- | Y | Y | 519 | 517 | 136 | 92 | 44 | Y | Y | 356 | 354 | 173 | 90 | 83
ddlA | b0381 | JW0372 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS | D.alanine.D.alanine.ligase.A | There are two distinct D-alanine-D-alanine ligase activites in E. coli DdlA and DdlB [PMID:1993184], look for SSL between them. | M | -- | -- | Y | 25.582 | Y | Y | 817 | 807 | 173 | 77 | 96 | Y | Y | 577 | 567 | 207 | 127 | 80
ddlB | b0092 | JW0090 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS | D.alanine.D.alanine.ligase | There are two distinct D-alanine-D-alanine ligase activites in E. coli DdlA and DdlB [PMID:1993184], look for SSL between them. | M | -- | -- | -- | -- | Y | -- | 701 | 688 | 304 | 224 | 80 | Y | -- | 97 | 93 | 65 | 19 | 46
ddpA | b1487 | JW5240 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | D.ala.D.a.la.transporter.subunit.periplasmic.binding.component.of.ABC.superfamily | Riley et al annotated ddp- proteins as a D.ala.D.ala. ABC transporter | E | -- | -- | Y | 14 | Y | Y | 795 | 783 | 350 | 184 | 166 | Y | Y | 153 | 151 | 66 | 32 | 34
ddpB | b1486 | JW1481 | non-essential | IM | CORE | CELL.WALL.BIOGENESIS | D.ala.D.ala.transporter.subunit.membrane.component.of.ABC.superfamily | Riley et al annotated ddp- proteins as a D.ala.D.ala. ABC transporter | EP | -- | -- | -- | -- | Y | Y | 750 | 738 | 193 | 55 | 138 | Y | Y | 242 | 240 | 106 | 30 | 76
ddpC | b1485 | [NAME] | non-essential | IM | CORE | CELL.WALL.BIOGENESIS | D.ala.D.ala.transporter.subunit.membrane.component.of.ABC.superfamily | Riley et al annotated ddp- proteins as a D.ala.D.ala. ABC transporter | EP | -- | -- | -- | -- | Y | Y | 805 | 792 | 245 | 79 | 166 | -- | Y | 213 | 210 | 92 | 44 | 48
ddpD | b1484 | JW1479 | non-essential | -- | CORE | CELL.WALL.BIOGENESIS | D.ala.D.ala.transporter.subunit.ATP.binding.component.of.ABC.superfamily | Riley et al annotated ddp- proteins as a D.ala.D.ala. ABC transporter | EP | -- | -- | -- | -- | -- | Y | 378 | 372 | 112 | 49 | 63 | Y | Y | 170 | 168 | 92 | 36 | 56
ddpF | b1483 | JW1478 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS | D.ala.D.ala.transporter.subunit.ATP.binding.component.of.ABC.superfamily | Riley et al annotated ddp- proteins as a D.ala.D.ala. ABC transporter | EP | -- | -- | -- | -- | -- | Y | 390 | 384 | 93 | 41 | 52 | Y | Y | 217 | 215 | 69 | 33 | 36
ddpX | b1488 | JW1483 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS | D.ala.D.ala.dipeptidase.Zn.dependent | ddpX(VanX) is a D-Ala-D-Ala dipeptidase, which catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide required for wild-type peptidoglycan biosynthesis [PMID:9751644] and may be involved in murein recycling [PMID:9751644]. Is in an operon with other ddp- genes, thus may be coupled to recycle D-ala (guess by [NAME]) | M | -- | -- | -- | -- | Y | Y | 808 | 797 | 244 | 94 | 150 | Y | Y | 611 | 605 | 194 | 93 | 101
degP | b0161 | JW0157 | non-essential | PE | CORE | PROTEIN.SECRETION,CHAPERONES | serine.endoprotease.protease.Do.membrane.associated | surA genetically interacts with (degP/skp) and double mutant surA ppiD was reprted as synthetic lethal [PMID:9670013]. However, in [PMID:16267292] mutations involving four E. coli PPIases (FkpA, PpiA, PpiD, and SurA) showed that no single or double mutants were shown to have growth defects. Three triple mutants shown growth defects, while one does not, and the quadruple mutant had the most pronounced defect. -- | O | -- | -- | -- | -- | Y | -- | 697 | 683 | 192 | 59 | 133 | Y | Y | 668 | 656 | 245 | 42 | 203
dgkA | b4042 | JW4002 | non-essential | IM | CORE | PHOSPHOLIPIDS | diacylglycerol.kinase | DgkA phosphorylates diacylglycerol yielding 1,2-diacylglycerol-3-phosphate (EC:2.7.1.107), relatively at the same level than cdsA (SSL's between them??). This is part of the biosynthesis of phosphatidic acid, however DgkA represents only a minor route in phosphatidic acid biosynthesis [EcoCyc] -- | M | -- | -- | -- | -- | Y | Y | 804 | 795 | 264 | 115 | 149 | Y | Y | 232 | 231 | 90 | 38 | 52
dicF | b1574 | UNKW3110 | unknown | -- | CORE | CELL.DIVISION | -- | Small RNA. The DicF RNA acts to inhibit cell division [ Bouche89  ]. DicF causes inhibition of the formation of the constriction and the separation of the replicated chromosomes into the daughter nucleoids [ Tetart92  ]. DicF RNA interferes with FtsZ mRNA translation [ Tetart92a  ]; DicF may bind to and occlude the ribosome binding site on the FtsZ mRNA [ Tetart92a  ]. | -- | -- | -- | -- | -- | Y | -- | 677 | 667 | 423 | 323 | 100 | Y | -- | 540 | 534 | 380 | 325 | 55
[NAME] | b4136 | JW5734 | non-essential | IM | FUNCTION-UNCERTAIN | NA | fused.thiol.disulfide.interchange.protein.activator.of.DsbC.conserved.protein | -- | OC | -- | -- | -- | -- | Y | -- | 677 | 666 | 246 | 135 | 111 | Y | -- | 588 | 578 | 195 | 141 | 54
dppA | b3544 | JW3513 | non-essential | PE | CORE | OLIGOPEPTIDE.TRANSPORT | dipeptide.transporter.periplasmic.binding.component.of.ABC.superfamily | -- | E | -- | -- | Y | 0.294 | -- | Y | 314 | 308 | 132 | 86 | 46 | Y | Y | 172 | 170 | 115 | 78 | 37
dppB | b3543 | JW3512 | non-essential | IM | CORE | OLIGOPEPTIDE.TRANSPORT | dipeptide.transporter.membrane.component.of.ABC.superfamily | -- | EP | -- | -- | -- | -- | -- | Y | 394 | 388 | 103 | 55 | 48 | -- | Y | 209 | 207 | 79 | 47 | 32
dppC | b3542 | JW3511 | non-essential | IM | CORE | OLIGOPEPTIDE.TRANSPORT | dipeptide.transporter.membrane.component.of.ABC.superfamily | -- | EP | -- | -- | -- | -- | Y | Y | 797 | 783 | 233 | 87 | 146 | Y | Y | 143 | 143 | 88 | 59 | 29
[NAME] | b3541 | JW3510 | non-essential | -- | CORE | OLIGOPEPTIDE.TRANSPORT | dipeptide.transporter.ATP.binding.component.of.ABC.superfamily | -- | EP | -- | -- | -- | -- | -- | Y | 388 | 381 | 236 | 206 | 30 | -- | Y | 184 | 182 | 134 | 116 | 18
dppF | b3540 | JW3509 | non-essential | CY | CORE | OLIGOPEPTIDE.TRANSPORT | dipeptide.transporter.ATP.binding.component.of.ABC.superfamily | -- | E | -- | -- | -- | -- | Y | Y | 784 | 770 | 310 | 195 | 115 | Y | Y | 110 | 110 | 68 | 65 | 3
dsbA | b3860 | JW3832 | non-essential | PE | CORE | CHAPERONES | periplasmic.protein.disulfide.isomerase.I | The dsbA gene codes for a protein that is a disulfide catalyst. The protein itself has a disulfide bond that is transferred catalytically to folding proteins in the periplasm. The disulfide oxidoreductase is capable of oxidizing proteins very rapidly. The oxidoreductase requires the dsbB protein for reoxidation [ Bardwell94  , Grauschopf95  , Kishigami95  , Guilhot95  , Akiyama92  , Metheringh95  ]. | OC | -- | -- | Y | 8.972 | -- | Y | 380 | 376 | 98 | 54 | 44 | -- | Y | 196 | 195 | 71 | 36 | 35
dsbB | b1185 | JW5182 | non-essential | IM | FUNCTION-UNCERTAIN | CHAPERONES | oxidoreductase.that.catalyzes.reoxidation.of.DsbA.protein.disulfide.isomerase.I | The dsbB gene codes for a transmembrane protein that is responsible for reoxidizing the dsbA-encoded disulfide oxidoreductase. It is believed that the dsbB protein acts by transferring disulfide bonds directly to the oxidoreductase. DsbB is then oxidized by either ubiquinone, under aerobic conditions, or menaquinone, under anaerobic conditions [ Jander94  , Missiakas93  , Bardwell93  , Bardwell94  , Kishigami95  , Kadokura00  ]. | O | -- | -- | -- | -- | Y | -- | 684 | 674 | 417 | 314 | 103 | Y | -- | 618 | 609 | 337 | 277 | 60
dsbC | b2893 | JW2861 | non-essential | PE | FUNCTION-UNCERTAIN | CHAPERONES | protein.disulfide.isomerase.II | The gene dsbC encodes both a disulfide isomerase and an oxidoreductase in addition to its chaperone activity. The isomerase activity appears to be the major function of the protein. [ Bardwell94  , Zapun95  , Frishman96  , Chen99  ] | O | -- | -- | Y | 1.016 | Y | -- | 682 | 677 | 329 | 202 | 127 | -- | -- | -- | -- | -- | -- | --
dsbG | b0604 | JW0597 | non-essential | PE | CORE | CHAPERONES | periplasmic.disulfide.isomerase.thiol.disulphide.oxidase | The periplasmic transpeptidases YbiS, ErfK and [NAME] are substrates of DsbG [ Depuydt09  ]. DsbG also acts as a disulfide isomerase which has narrower substrate specificity than the isomerase encoded by the dsbC gene [ Bessette99  ] | O | -- | -- | Y | 15.511 | -- | Y | 392 | 378 | 165 | 113 | 52 | -- | Y | 199 | 191 | 85 | 38 | 47
dut | b3640 | JW3615 | essential | CY | CORE | CHROMOSOME.SEGREGATION | deoxyuridinetriphosphatase | Link between Chromosomal.segregation and several cell.envelope.biogenesis processes. Dut interacts aggravating with a number of proteins (degP, ftsK, ligA, phoU, polA, recA, tdk, ung, [NAME], xerD, xthA) see [NAME] for details. dut mutants fail to replicate the chromosomal terminus, resulting in the accumulation of subchromosomal fragments containing an origin of replication [ Kouzminova06  ]. | F | -- | -- | Y | 119.921 | Y | -- | 611 | 589 | 378 | 323 | 55 | -- | -- | -- | -- | -- | -- | --
dxr | b0173 | JW0168 | essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS | 1.deoxy.D.xylulose.5.phosphate.reductoisomerase | -- | I | -- | -- | -- | -- | Y | Y | 818 | 798 | 203 | 99 | 104 | Y | Y | 670 | 652 | 266 | 157 | 109
[NAME] | b0420 | JW0410 | essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS | 1.deoxyxylulose.5.phosphate.synthase.thiamine.requiring.FAD.requiring | -- | HI | -- | -- | Y | 59.694 | Y | Y | 521 | 508 | 219 | 67 | 152 | Y | Y | 312 | 304 | 172 | 118 | 54
ecnA | b4410 | JW5737 | non-essential | -- | FUNCTION-UNCERTAIN | NA | entericidin.A.membrane.lipoprotein.antidote.entericidin.B | EcnAB form a linked toxin-antitoxin "addiction module" which functions to regulate programmed bacterial cell death under high osmolarity conditions. The entericidin A lipoprotein (EcnA) functions as an antidote to the bacteriolytic entericidin B lipoprotein [ Bishop98  ]. So this proteins could form a separate class 'Cell.killing', but here I'm just wondering if they do have SSL's | - | -- | -- | -- | -- | Y | Y | 809 | 785 | 274 | 128 | 146 | Y | Y | 214 | 207 | 67 | 36 | 31
ecnB | b4411 | JW4108 | non-essential | -- | FUNCTION-UNCERTAIN | NA | entericidin.B.membrane.lipoprotein | EcnAB form a linked toxin-antitoxin "addiction module" which functions to regulate programmed bacterial cell death under high osmolarity conditions. The entericidin A lipoprotein (EcnA) functions as an antidote to the bacteriolytic entericidin B lipoprotein [ Bishop98  ]. So this proteins could form a separate class 'Cell.killing', but here I'm just wondering if they do have SSL's | - | -- | -- | -- | -- | Y | Y | 524 | 505 | 127 | 71 | 56 | Y | Y | 337 | 328 | 163 | 83 | 80
emrA | b2685 | JW2660 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system | -- | - | -- | -- | -- | -- | -- | Y | 391 | 387 | 185 | 116 | 69 | Y | Y | 196 | 192 | 106 | 62 | 44
emrB | b2686 | JW2661 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.protein | -- | GEPR | -- | -- | -- | -- | Y | -- | 652 | 646 | 206 | 18 | 188 | Y | Y | 640 | 634 | 582 | 551 | 31
emrD | [NAME] | JW5634 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.protein | -- | - | -- | -- | -- | -- | -- | Y | 367 | 366 | 119 | 49 | 70 | -- | Y | 213 | 212 | 85 | 48 | 37
emrK | b2368 | JW2365 | non-essential | -- | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | EmrKY.TolC.multidrug.resistance.efflux.pump.membrane.fusion.protein.component | -- | V | -- | -- | -- | -- | -- | Y | 365 | 363 | 146 | 46 | 100 | -- | Y | 204 | 203 | 92 | 30 | 62
emrY | b2367 | JW2364 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | predicted.multidrug.efflux.system | -- | - | -- | -- | -- | -- | -- | Y | 393 | 391 | 89 | 47 | 42 | -- | Y | 219 | 218 | 71 | 34 | 37
emtA | b1193 | JW5821 | non-essential | -- | CORE | CELL.DIVISION,CELL.SHAPE,CELL.WALL.BIOGENESIS | lytic.murein.endotransglycosylase.E | Is one of six major lytic murein endotransglycosylases (slt, mltD, mltB, mltA, emtA, mltC) expressed in Escherichia coli, allowing for cell enlargement and division and also for localized opening of the peptidoglycan layer to allow the export of bulky compounds such as DNA, toxins, flagella, and fimbrial proteins [PMID:9642199]. | M | -- | -- | -- | -- | Y | Y | 808 | 793 | 360 | 164 | 196 | Y | Y | 159 | 154 | 61 | 32 | 29
eno | b2779 | JW2750 | essential | CY | FUNCTION-UNCERTAIN | NA | enolase | Enolase catalyzes the interconversion of 2-phosphoglycerate and phosphoenolpyruvate. It is also a component of the degradosome, a complex that degrades [NAME] | G | -- | -- | Y | 567.312 | Y | -- | 666 | 664 | 311 | 113 | 198 | Y | Y | 567 | 565 | 187 | 105 | 82
entA | b0596 | JW0588 | non-essential | CY | CORE | CHORISMATE.DEGRADATION | 2.3.dihydro.2.3.dihydroxybenzoate.dehydrogenase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | IQR | -- | -- | -- | -- | -- | Y | 370 | 360 | 127 | 75 | 52 | -- | Y | 218 | 212 | 68 | 54 | 14
entB | b0595 | JW0587 | non-essential | CY | CORE | CHORISMATE.DEGRADATION | isochorismatase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | Q | -- | -- | -- | -- | Y | Y | 794 | 778 | 194 | 77 | 117 | Y | Y | 575 | 564 | 185 | 124 | 61
entC | b0593 | JW0585 | non-essential | PE | CORE | CHORISMATE.DEGRADATION | isochorismate.synthase.1 | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | HQ | -- | -- | -- | -- | -- | Y | 389 | 377 | 154 | 58 | 96 | -- | Y | 199 | 194 | 91 | 53 | 38
entD | b0583 | JW5085 | essential | CY | CORE | CHORISMATE.DEGRADATION | phosphopantetheinyltransferase.component.of.enterobactin.synthase.multienzyme.complex | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | Q | -- | -- | -- | -- | Y | -- | 205 | 202 | 77 | 58 | 19 | Y | -- | 143 | 141 | 69 | 52 | 17
entE | b0594 | JW0586 | non-essential | CY | CORE | CHORISMATE.DEGRADATION | 2.3.dihydroxybenzoate.AMP.ligase.component.of.enterobactin.synthase.multienzyme.complex | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | Q | -- | -- | Y | 33.049 | Y | Y | 787 | 772 | 307 | 99 | 208 | Y | Y | 625 | 613 | 191 | 65 | 126
entF | b0586 | JW0578 | non-essential | -- | CORE | CHORISMATE.DEGRADATION | enterobactin.synthase.multienzyme.complex.component.ATP.dependent | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | Q | -- | -- | Y | 32.275 | Y | Y | 794 | 773 | 291 | 118 | 173 | Y | Y | 645 | 633 | 509 | 463 | 46
envC | [NAME] | JW5646 | non-essential | -- | CORE | CELL.DIVISION | protease.with.a.role.in.cell.division | FtsA and ZipA initially associate with FtsZ, followed by addition of FtsEX, FtsK, FtsQ, FtsL/FtsB, FtsW, FtsI, FtsN and AmiC, and EnvC apparently in this defined order guided by PPIs to form complexes for the divisome [PMID:17326815] -- | D | -- | -- | -- | -- | Y | Y | 425 | 410 | 224 | 143 | 81 | Y | Y | 196 | 186 | 114 | 79 | 35
eptA | b4114 | JW5730 | non-essential | IM | PREDICTED | CELL.DIVISION,CELL.SHAPE | predicted.metal.dependent.hydrolase | The YjdB protein can be found in the membrane in a complex with ZipA and an unidentified 24 [NAME] protein [ Stenberg05  ]. | R | -- | -- | -- | -- | -- | Y | 387 | 386 | 110 | 48 | 62 | -- | Y | 204 | 203 | 57 | 26 | 31
era | b2566 | JW2550 | essential | CY | FUNCTION-UNCERTAIN | CELL.DIVISION,CHROMOSOME.SEGREGATION | membrane.associated.16S.rRNA.binding.GTPase | Mutants that are partially defective in Era GTPase activity or that are reduced in the synthesis of wild-type Era become arrested in the cell cycle at the predivisional two-cell stage. The partially defective Era GTPase mutation (era1) suppresses several temperature-sensitive lethal alleles that affect chromosome replication and chromosome partitioning but not cell division. Our results suggest that Era plays an important role in cell cycle progression at a specific point in the cycle, after chromosome partitioning but before cytokinesis [PMID:9515700] | R | -- | -- | Y | 0.779 | Y | -- | 673 | 671 | 237 | 76 | 161 | Y | Y | 555 | 553 | 317 | 119 | 198
[NAME] | b0982 | JW5132 | non-essential | CY | FUNCTION-UNCERTAIN | LPS.AND.ECA | phosphotyrosine.protein.phosphatase | In contrast to the related phosphatase, Wzb, [NAME] has minimal effect on biosynthesis of colanic acid [ Vincent00  ]. Perhaps related with yccZ_b0983. Seven gene products (YmcD, [NAME], YmcB, [NAME], [NAME], [NAME], and Etk) in E. coli O127:H6  are required for the production of the G4C capsule polysaccharide [ Peleg05  ]. That operon may not be expressed in E. coli [NAME], because the promoter region that was mapped in E. coli O127:H6 is inactivated in E. coli K12 by the insertion of an IS1 element 15 bp upstream of the YmcD translation start site [ Peleg05  ]. Also GO:0006464.protein.modification.process | G | -- | -- | -- | -- | Y | -- | 683 | 673 | 371 | 297 | 74 | Y | -- | 86 | 86 | 57 | 52 | 5
exbB | b3006 | JW2974 | non-essential | IM | CORE | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | membrane.spanning.protein.in.TonB.ExbB.ExbD.complex | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | U | -- | -- | -- | -- | Y | Y | 783 | 778 | 414 | 189 | 225 | Y | Y | 615 | 612 | 229 | 68 | 161
exbD | b3005 | JW2973 | non-essential | IM | CORE | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | membrane.spanning.protein.in.TonB.ExbB.ExbD.complex | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | U | -- | -- | -- | -- | Y | Y | 784 | 779 | 223 | 80 | 143 | Y | Y | 634 | 630 | 264 | 122 | 142
fabA | b0954 | JW0937 | essential | CY | CORE | FAS | beta.hydroxydecanoyl.thioester.dehydrase | -- | I | -- | -- | Y | 610.512 | Y | Y | 477 | 471 | 179 | 109 | 70 | Y | Y | 283 | 280 | 172 | 143 | 29
fabB | b2323 | JW2320 | essential | CY | CORE | FAS | 3.oxoacyl.acyl.carrier.protein.synthase.I | -- | IQ | -- | -- | Y | 162.983 | Y | -- | 691 | 676 | 215 | 79 | 136 | Y | Y | 612 | 600 | 218 | 72 | 146
fabD | b1092 | JW1078 | essential | CY | CORE | FAS | malonyl.CoA.acyl.carrier.protein.transacylase | -- | I | -- | -- | Y | 5.316 | Y | Y | 752 | 733 | 311 | 68 | 243 | Y | Y | 44 | 42 | 15 | 5 | 10
fabF | b1095 | JW1081 | non-essential | CY | CORE | FAS | 3.oxoacyl.acyl.carrier.protein.synthase.II | -- | IQ | -- | -- | Y | 73.676 | Y | Y | 738 | 718 | 192 | 91 | 101 | Y | Y | 666 | 648 | 178 | 73 | 105
fabG | b1093 | JW1079 | essential | CY | CORE | FAS | 3.oxoacyl.acyl.carrier.protein.reductase | -- | IQR | -- | -- | -- | -- | Y | Y | 523 | 510 | 228 | 49 | 179 | Y | Y | 318 | 308 | 142 | 62 | 80
fabH | b1091 | JW1077 | non-essential | CY | CORE | FAS | 3.oxoacyl.acyl.carrier.protein.synthase.III | -- | I | -- | -- | Y | 84.754 | Y | Y | 795 | 774 | 445 | 243 | 202 | Y | Y | 601 | 583 | 278 | 121 | 157
fabI | b1288 | JW1281 | essential | CY | CORE | FAS | enoyl.acyl.carrier.protein.reductase.NADH.dependent | -- | I | -- | -- | Y | 342.234 | Y | Y | 816 | 809 | 268 | 74 | 194 | Y | Y | 183 | 180 | 120 | 86 | 34
fabR | b3963 | JW3935 | non-essential | CY | CORE | FAS | DNA.binding.transcriptional.repressor | -- | - | -- | -- | Y | 23.345 | Y | Y | 462 | 457 | 150 | 86 | 64 | Y | Y | 287 | 283 | 121 | 93 | 28
[NAME] | b0180 | JW0175 | essential | CY | CORE | FAS | 3R.hydroxymyristol.acyl.carrier.protein.dehydratase | -- | I | -- | -- | Y | 169.29 | Y | Y | 796 | 780 | 224 | 60 | 164 | Y | Y | 610 | 598 | 186 | 152 | 34
fadA | b3845 | JW5578 | non-essential | CY | CORE | FAD | 3.ketoacyl.CoA.thiolase.thiolase.I | -- | I | -- | -- | Y | 2.905 | Y | Y | 461 | 455 | 162 | 127 | 35 | Y | Y | 304 | 300 | 151 | 117 | 34
fadB | b3846 | JW3822 | non-essential | CY | CORE | FAD | fused.3.hydroxybutyryl.CoA.epimerase.and.delta.3.cis.delta.2.trans.enoyl.CoA.isomerase.and.enoyl.CoA.hydratase.3.hydroxyacyl.CoA.dehydrogenase | -- | I | -- | -- | Y | 2.077 | Y | Y | 484 | 477 | 148 | 51 | 97 | Y | Y | 292 | 288 | 140 | 87 | 53
fadD | b1805 | JW1794 | non-essential | CY | CORE | FAD | acyl.CoA.synthetase.long.chain.fatty.acid.CoA.ligase | -- | IQ | -- | -- | -- | -- | Y | Y | 526 | 520 | 199 | 83 | 116 | Y | Y | 300 | 299 | 140 | 55 | 85
fadE | b0221 | JW5020 | non-essential | IM | CORE | FAD | acyl.coenzyme.A.dehydrogenase | -- | I | -- | -- | Y | 11.891 | Y | Y | 812 | 803 | 203 | 74 | 129 | Y | Y | 625 | 618 | 237 | 122 | 115
fadL | b2344 | JW2341 | non-essential | OM | CORE | FAS | long.chain.fatty.acid.outer.membrane.transporter | [NAME] is an outer membrane protein involved with the uptake of long-chain fatty acids [ Kumar93  ]. | I | -- | -- | -- | -- | -- | Y | 391 | 386 | 107 | 31 | 76 | Y | Y | 212 | 209 | 84 | 39 | 45
fcl | b2052 | JW2037 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | bifunctional.GDP.fucose.synthetase.GDP.4.dehydro.6.deoxy.D.mannose.epimerase.and.GDP.4.dehydro.6.L.deoxygalactose.reductase | Predicted by [NAME] et al as participating in M-antigen biosynthesis [PMID:8759852]. Fcl(WcaG) probably involved in the biosynthesis of the slime polysaccharide colanic acid, probably at the level of synthesis of nucleotide sugar precursors of CA [PMID:8759852]. Later characterized as the bifunctional enzyme that catalyzes the two-step synthesis of GDP-fucose from GDP-4-dehydro-6-deoxy-D-mannose via a GDP-4-dehydro-6-L-deoxygalactose intermediate [PMID:9473059] | MG | -- | -- | -- | -- | -- | Y | 383 | 372 | 211 | 117 | 94 | Y | Y | 224 | 219 | 109 | 46 | 63
fdrA | b0518 | JW0506 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.acyl.CoA.synthetase.with.NAD.P.binding.Rossmann.fold.domain | predicted.acyl.CoA.synthetase.with.NAD.P.binding.Rossmann.fold.domain | C | -- | -- | -- | -- | -- | Y | 395 | 392 | 126 | 56 | 70 | -- | Y | 200 | 198 | 100 | 75 | 25
fecA | b4291 | JW4251 | non-essential | OM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | KpLE2.phage.like.element.ferric.citrate.outer.membrane.transporter | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | -- | -- | Y | -- | 685 | 675 | 293 | 172 | 121 | -- | -- | -- | -- | -- | -- | --
fecB | b4290 | JW4250 | non-essential | PE | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | KpLE2.phage.like.element.iron.dicitrate.transporter.subunit.periplasmic.binding.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | -- | -- | Y | Y | 792 | 781 | 207 | 155 | 52 | Y | Y | 103 | 102 | 58 | 37 | 21
fecC | b4289 | JW4249 | non-essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | KpLE2.phage.like.element.iron.dicitrate.transporter.subunit.membrane.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | -- | -- | Y | Y | 785 | 776 | 348 | 243 | 105 | Y | Y | 106 | 106 | 61 | 32 | 29
fecD | b4288 | JW4248 | non-essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | KpLE2.phage.like.element.iron.dicitrate.transporter.subunit.membrane.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | -- | -- | Y | Y | 792 | 782 | 315 | 194 | 121 | Y | Y | 152 | 151 | 71 | 43 | 28
fecE | [NAME] | [NAME] | non-essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | KpLE2.phage.like.element.iron.dicitrate.transporter.subunit.ATP.binding.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | PH | -- | -- | -- | -- | Y | Y | 794 | 784 | 246 | 134 | 112 | Y | Y | 144 | 143 | 43 | 21 | 22
fepA | b0584 | JW5086 | non-essential | OM | CORE | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | iron.enterobactin.outer.membrane.transporter | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | -- | -- | Y | Y | 791 | 770 | 229 | 99 | 130 | Y | Y | 614 | 599 | 195 | 111 | 84
fepB | b0592 | JW0584 | non-essential | PE | CORE | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | iron.enterobactin.transporter.subunit.periplasmic.binding.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | Y | 8.456 | Y | Y | 790 | 773 | 330 | 67 | 263 | -- | Y | 125 | 122 | 57 | 35 | 22
fepC | b0588 | JW0580 | non-essential | CY | CORE | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | iron.enterobactin.transporter.subunit.ATP.binding.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | PH | -- | -- | -- | -- | Y | Y | 798 | 780 | 348 | 75 | 273 | Y | Y | 146 | 144 | 77 | 17 | 60
fepD | b0590 | JW0582 | non-essential | IM | CORE | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | iron.enterobactin.transporter.subunit.membrane.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | -- | -- | Y | -- | 680 | 665 | 216 | 36 | 180 | Y | Y | 533 | 524 | 218 | 32 | 186
fepE | b0587 | JW0579 | non-essential | IM | CORE | CHORISMATE.DEGRADATION | regulator.of.length.of.O.antigen.component.of.lipopolysaccharide.chains | FepE is a link between Enterobactin and O-antigen. A fepE homolog in Salmonella typhimurium has been shown to be responsible for very long O antigen polymerization in lipopolysaccharide [PMID:12603743] Is a link between Enterobactin and O-antigen. A fepE homolog in Salmonella typhimurium has been shown to be responsible for very long O antigen polymerization in lipopolysaccharide [PMID:12603743]. 'Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS | M | -- | -- | -- | -- | -- | Y | 485 | 473 | 144 | 79 | 65 | Y | Y | 344 | 340 | 153 | 76 | 77
fepG | b0589 | JW0581 | non-essential | IM | CORE | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | iron.enterobactin.transporter.subunit.membrane.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | -- | -- | Y | Y | 787 | 769 | 393 | 58 | 335 | Y | Y | 610 | 598 | 293 | 53 | 240
fes | b0585 | JW0576 | non-essential | CY | CORE | CHORISMATE.DEGRADATION | enterobactin.ferric.enterobactin.esterase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | P | -- | -- | -- | -- | Y | Y | 805 | 783 | 293 | 181 | 112 | Y | Y | 137 | 134 | 95 | 76 | 19
ffh | b2610 | JW5414 | essential | CY | CORE | PROTEIN.SECRETION | Signal.Recognition.Particle.SRP.component.with.4.5S.RNA.ffs | For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | -- | -- | Y | Y | 717 | 712 | 234 | 84 | 150 | Y | Y | 583 | 580 | 316 | 285 | 31
fhuA | b0150 | JW0146 | non-essential | OM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | ferrichrome.outer.membrane.transporter | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | Y | 3.905 | Y | Y | 794 | 780 | 115 | 20 | 95 | Y | Y | 556 | 547 | 237 | 53 | 184
fhuB | b0153 | JW0149 | non-essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | fused.iron.hydroxamate.transporter.subunits.of.ABC.superfamily.membrane.components | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | -- | -- | -- | Y | 325 | 313 | 133 | 76 | 57 | Y | Y | 121 | 115 | 58 | 46 | 12
fhuC | b0151 | JW0147 | non-essential | -- | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | iron.hydroxamate.transporter.subunit.ATP.binding.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | PH | -- | -- | Y | 11.085 | Y | Y | 792 | 777 | 341 | 222 | 119 | Y | Y | 169 | 165 | 55 | 21 | 34
fhuD | b0152 | JW0148 | non-essential | PE | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | iron.hydroxamate.transporter.subunit.periplasmic.binding.component.of.ABC.superfamily | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | P | -- | -- | -- | -- | Y | Y | 764 | 749 | 329 | 134 | 195 | Y | Y | 51 | 49 | 26 | 18 | 8
fhuE | b1102 | JW1088 | non-essential | OM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | ferric.rhodotorulic.acid.outer.membrane.transporter | FhuE is a protein which serves as a receptor for ferric-coprogen and ferric-rhodotorulic acid [ Sauer87  ] | P | -- | -- | -- | -- | -- | Y | 391 | 378 | 168 | 110 | 58 | -- | Y | 180 | 174 | 109 | 84 | 25
fimC | b4316 | JW4279 | non-essential | PE | CORE | CHAPERONES | chaperone.periplasmic | Might be interesting to see if has SSL's with other chaperones. FimC is a member of the periplasmic chaperone family which functions in the chaperone-usher pathway and is indispensable in the biogenesis of the type 1 pilus fiber of Escherichia coli [ Jones93b  ]. | NU | -- | -- | -- | -- | Y | Y | 811 | 803 | 242 | 105 | 137 | Y | Y | 304 | 304 | 88 | 28 | 60
fimD | b4317 | JW5780 | non-essential | OM | FUNCTION-UNCERTAIN | NA | outer.membrane.usher.protein.type.1.fimbrial.synthesis | [NAME] (2009) provided GC evidences clustering sfm- and fim- genes in fimbria related module | NU | -- | -- | Y | 0.387 | -- | Y | 353 | 350 | 172 | 142 | 30 | -- | Y | 174 | 174 | 101 | 83 | 18
fiu | b0805 | JW0790 | non-essential | OM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | predicted.iron.outer.membrane.transporter | YbiL is an integral outer membrane protein whose expression is stimulated by growth under iron limitation [ Molloy00  ]. putative outer membrane receptor for iron transport (EcoCyc) | P | -- | -- | -- | -- | -- | Y | 391 | 388 | 119 | 54 | 65 | -- | Y | 190 | 188 | 102 | 39 | 63
flgA | b1072 | JW1059 | non-essential | PE | FUNCTION-UNCERTAIN | NA | assembly.protein.for.flagellar.basal.body.periplasmic.P.ring | -- | NO | -- | -- | -- | -- | -- | Y | 361 | 352 | 180 | 91 | 89 | -- | Y | 202 | 194 | 72 | 43 | 29
flgJ | b1081 | JW1068 | non-essential | PE | CORE | CELL.DIVISION,CELL.SHAPE,CELL.WALL.BIOGENESIS | muramidase | The C-terminal half of FlgJ has homology to autolytic murmidases and has peptidoglycan-hydrolyzing activity [PMID:10049388]. This muramidase domain locally digests the peptidoglycan layer to allow rod formation in the periplasm, and is required for L ring and hook formation of bacterial flagellum [PMID:11554792]. Apart of being part of the Flagellum machinery, the C-terminal half of FlgJ has homology to autolytic murmidases [ Dijkstra96a  ] and has peptidoglycan-hydrolyzing activity [ Nambu99  ]. This muramidase domain locally digests the peptidoglycan layer to allow rod formation in the periplasm, and is required for L ring and hook formation [ Hirano01  ] | NUMO | -- | -- | -- | -- | -- | Y | 393 | 382 | 105 | 39 | 66 | Y | Y | 220 | 214 | 80 | 35 | 45
fliL | b1944 | JW1928 | non-essential | IM | FUNCTION-UNCERTAIN | NA | [NAME] | -- | N | -- | -- | -- | -- | Y | -- | 681 | 680 | 526 | 444 | 82 | -- | -- | -- | -- | -- | -- | --
fliN | b1946 | JW1930 | non-essential | IM | FUNCTION-UNCERTAIN | NA | flagellar.motor.switching.and.energizing.component | -- | NU | -- | -- | Y | 0.153 | Y | -- | 691 | 690 | 359 | 251 | 108 | -- | -- | -- | -- | -- | -- | --
[NAME] | b1948 | JW1932 | non-essential | IM | FUNCTION-UNCERTAIN | NA | [NAME] | -- | NU | -- | -- | -- | -- | Y | -- | 690 | 689 | 311 | 168 | 143 | Y | -- | 662 | 661 | 243 | 106 | 137
fliR | b1950 | JW1934 | non-essential | IM | FUNCTION-UNCERTAIN | NA | [NAME] | -- | NU | -- | -- | -- | -- | Y | -- | 684 | 683 | 236 | 134 | 102 | Y | -- | 623 | 623 | 202 | 89 | 113
folA | b0048 | JW0047 | essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | dihydrofolate.reductase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | H | -- | -- | Y | 37.932 | Y | Y | 792 | 782 | 279 | 98 | 181 | Y | Y | 571 | 564 | 329 | 224 | 105
folC | b2315 | JW2312 | essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | bifunctional.folylpolyglutamate.synthase.and.dihydrofolate.synthase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | H | -- | -- | Y | 15.213 | Y | Y | 788 | 775 | 379 | 141 | 238 | Y | Y | 156 | 153 | 97 | 62 | 35
folD | b0529 | JW0518 | essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | bifunctional.5.10.methylene.tetrahydrofolate.dehydrogenase.and.5.10.methylene.tetrahydrofolate.cyclohydrolase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | H | -- | -- | -- | -- | Y | Y | 794 | 783 | 252 | 70 | 182 | Y | Y | 582 | 575 | 202 | 133 | 69
folE | b2153 | JW2140 | essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | GTP.cyclohydrolase.I | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | H | -- | -- | -- | -- | Y | Y | 792 | 782 | 299 | 120 | 179 | Y | Y | 623 | 617 | 375 | 203 | 172
folM | b1606 | JW1598 | non-essential | CY | FUNCTION-UNCERTAIN | NA | [NAME] | [NAME] | - | -- | -- | -- | -- | -- | Y | 394 | 392 | 113 | 49 | 64 | -- | Y | 198 | 197 | 78 | 39 | 39
frdA | b4154 | JW4115 | non-essential | PE | FUNCTION-UNCERTAIN | NA | fumarate.reductase.anaerobic.catalytic.and.NAD.flavoprotein.subunit | -- | C | -- | -- | -- | -- | -- | Y | 359 | 341 | 158 | 115 | 43 | -- | Y | 193 | 183 | 93 | 65 | 28
frdB | b4153 | JW4114 | non-essential | PE | FUNCTION-UNCERTAIN | NA | fumarate.reductase.anaerobic.Fe.S.subunit | -- | C | -- | -- | -- | -- | Y | Y | 794 | 768 | 367 | 276 | 91 | Y | Y | 131 | 121 | 64 | 48 | 16
frdC | b4152 | JW4113 | non-essential | IM | FUNCTION-UNCERTAIN | NA | fumarate.reductase.anaerobic.membrane.anchor.subunit | -- | C | -- | -- | -- | -- | Y | Y | 791 | 765 | 346 | 250 | 96 | Y | Y | 611 | 591 | 315 | 189 | 126
frdD | b4151 | JW4112 | non-essential | IM | FUNCTION-UNCERTAIN | NA | fumarate.reductase.anaerobic.membrane.anchor.subunit | -- | C | -- | -- | -- | -- | Y | Y | 777 | 754 | 449 | 316 | 133 | Y | Y | 120 | 112 | 62 | 51 | 11
frlB | b3371 | JW5700 | non-essential | CY | FUNCTION-UNCERTAIN | NA | fructoselysine.6.P.deglycase | fructoselysine.6.P.deglycase | M | -- | -- | -- | -- | Y | Y | 790 | 785 | 179 | 77 | 102 | Y | Y | 662 | 658 | 378 | 226 | 152
ftsA | b0094 | JW0092 | essential | CY | CORE | CELL.DIVISION,CELL.SHAPE | ATP.binding.cell.division.protein.involved.in.recruitment.of.FtsK.to.Z.ring | FtsA and ZipA initially associate with FtsZ, followed by addition of FtsEX, FtsK, FtsQ, FtsL/FtsB, FtsW, FtsI, FtsN and AmiC, and EnvC apparently in this defined order guided by PPIs to form complexes for the divisome [PMID:17326815] -- | D | -- | -- | Y | 58.922 | Y | Y | 471 | 457 | 189 | 105 | 84 | Y | Y | 285 | 277 | 172 | 117 | 55
ftsB | b2748 | JW2718 | essential | -- | CORE | CELL.DIVISION | cell.division.protein | Depletion of FtsB results in abnormal filamentous morphology, but does not cause a defect in segregation of replicated DNA [PMID:11972052 ]. FtsQ, FtsL and [NAME] form a complex in vivo even in the absence of FtsK and thus independently of their localization to the septal region [PMID:15165235 ]. -- | D | -- | -- | -- | -- | Y | -- | 216 | 214 | 111 | 98 | 13 | Y | -- | 165 | 163 | 104 | 96 | 8
ftsE | b3463 | JW3428 | essential | IM | CORE | CELL.DIVISION | predicted.transporter.subunit.ATP.binding.component.of.ABC.superfamily | Functional link (potential). ftsE and ftsX (Cell.division) are located in an operon with the ftsY (SRP, Protein.secretion via the Sec-system). FtsA and ZipA initially associate with FtsZ, followed by addition of FtsEX, FtsK, FtsQ, FtsL/FtsB, FtsW, FtsI, FtsN and AmiC, and EnvC apparently in this defined order guided by PPIs to form complexes for the divisome [PMID:17326815] -- | D | -- | -- | -- | -- | -- | Y | 381 | 377 | 235 | 141 | 94 | -- | Y | 198 | 195 | 162 | 145 | 17
ftsH | b3178 | JW3145 | essential | IM | CORE | PROTEASE,CELL.DIVISION | protease.ATP.dependent.zinc.metallo | FtsH is a zinc-dependent metalloendoprotease required for survival [ Jayasekera00  ]. Cells lacking functional FtsH fail to septate, instead forming multinucleate filaments [ Santos75  ]. Loss of FtsH or its ATPase activity results in "stop-transfer defects," or mislocalization of protein segments that are normally anchored in the membranes or transported out of the cell [ Akiyama94a  ]. This may relate to the role of FtsH in maintenance of proper membrane structures and LPS production, possibly based on degradation of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC/EnvA) [PMID:10048027] -- | O | -- | -- | Y | 83.183 | Y | Y | 485 | 472 | 198 | 99 | 99 | Y | Y | 317 | 308 | 176 | 151 | 25
ftsK | b0890 | JW0873 | essential | IM | CORE | CELL.DIVISION,CHROMOSOME.SEGREGATION | DNA.binding.membrane.protein.required.for.chromosome.resolution.and.partitioning | Link between Cell.division and Chromosome.segregation.The FtsK protein is very large, and its membrane and cytoplasmic domains appear to have to separable functions during cell division [PMID:15522074]. The N-terminal domain is Trans-IM and Periplasmic and is sufficient for targetting FtsK to the septum and for its function in cell division [PMID:9721304], whereas the C-terminal domain is cytoplasmic and involved in septation and chromosome partitioning [PMID:9723927]. The C-terminal portion of FtsK is required for XerC and XerD resolution of chromosome dimers. -- | D | -- | -- | Y | 4.585 | Y | Y | 772 | 763 | 302 | 95 | 207 | Y | Y | 255 | 254 | 146 | 79 | 67
ftsL | b0083 | JW0081 | essential | IM | CORE | CELL.DIVISION | [NAME] | FtsQ, FtsL and [NAME] form a complex in vivo even in the absence of FtsK and thus independently of their localization to the septal region [PMID:15165235 ]. -- | D | -- | -- | -- | -- | -- | Y | 386 | 372 | 179 | 95 | 84 | Y | Y | 215 | 207 | 133 | 72 | 61
ftsQ | b0093 | JW0091 | essential | IM | CORE | CELL.DIVISION | membrane.anchored.protein.involved.in.growth.of.wall.at.septum | FtsQ is an essential cell division protein that is required throughout the process of septum formation (EcoCyc). FtsQ, FtsL and [NAME] form a complex in vivo even in the absence of FtsK and thus independently of their localization to the septal region [PMID:15165235 ]. -- | M | -- | -- | -- | -- | Y | -- | 582 | 572 | 240 | 136 | 104 | Y | -- | 75 | 73 | 57 | 47 | 10
ftsW | b0089 | JW0087 | essential | IM | CORE | CELL.DIVISION,CELL.SHAPE | integral.membrane.protein.involved.in.stabilizing.FstZ.ring.during.cell.division | FtsA and ZipA initially associate with FtsZ, followed by addition of FtsEX, FtsK, FtsQ, FtsL/FtsB, FtsW, FtsI, FtsN and AmiC, and EnvC apparently in this defined order guided by PPIs to form complexes for the divisome [PMID:17326815] -- | D | -- | -- | -- | -- | Y | -- | 707 | 694 | 330 | 216 | 114 | Y | -- | 95 | 90 | 41 | 33 | 8
ftsX | b3462 | JW3427 | essential | IM | CORE | CELL.DIVISION | predicted.transporter.subunit.membrane.component.of.ABC.superfamily | Functional link (potential). ftsE and ftsX (Cell.division) are located in an operon with the ftsY (SRP, Protein.secretion via the Sec-system). FtsA and ZipA initially associate with FtsZ, followed by addition of FtsEX, FtsK, FtsQ, FtsL/FtsB, FtsW, FtsI, FtsN and AmiC, and EnvC apparently in this defined order guided by PPIs to form complexes for the divisome [PMID:17326815] -- | D | -- | -- | Y | 28.608 | Y | Y | 786 | 772 | 358 | 133 | 225 | Y | Y | 614 | 603 | 304 | 241 | 63
ftsY | b3464 | JW3429 | essential | IM | CORE | PROTEIN.SECRETION | fused.Signal.Recognition.Particle.SRP.receptor.membrane.binding.protein.conserved.protein | Functional link (potential). ftsE and ftsX (Cell.division) are located in an operon with the ftsY (SRP, Protein.secretion via the Sec-system). Or a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | -- | -- | Y | -- | 692 | 678 | 294 | 136 | 158 | Y | Y | 583 | 574 | 196 | 75 | 121
ftsZ | b0095 | JW0093 | essential | IM | CORE | CELL.DIVISION,CELL.SHAPE | GTP.binding.tubulin.like.cell.division.protein | FtsA and ZipA initially associate with FtsZ, followed by addition of FtsEX, FtsK, FtsQ, FtsL/FtsB, FtsW, FtsI, FtsN and AmiC, and EnvC apparently in this defined order guided by PPIs to form complexes for the divisome [PMID:17326815] -- | D | -- | -- | -- | -- | Y | Y | 811 | 794 | 345 | 77 | 268 | Y | Y | 206 | 197 | 112 | 79 | 33
galE | b0759 | JW0742 | non-essential | CY | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | UDP.galactose.4.epimerase | -- | M | -- | -- | -- | -- | Y | Y | 515 | 509 | 129 | 74 | 55 | Y | Y | 373 | 369 | 134 | 79 | 55
galF | b2042 | JW2027 | non-essential | CY | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.subunit.with.GalU | -- | M | -- | -- | Y | 231.012 | Y | Y | 529 | 500 | 168 | 115 | 53 | Y | Y | 365 | 337 | 126 | 74 | 52
galK | b0757 | JW0740 | non-essential | CY | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | galactokinase | -- | G | -- | -- | -- | -- | Y | Y | 813 | 801 | 197 | 75 | 122 | Y | Y | 636 | 627 | 223 | 111 | 112
galT | b0758 | JW0741 | non-essential | -- | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | galactose.1.phosphate.uridylyltransferase | -- | C | -- | -- | -- | -- | Y | Y | 787 | 775 | 377 | 163 | 214 | Y | Y | 210 | 206 | 78 | 52 | 26
[NAME] | b1236 | JW1224 | non-essential | CY | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | glucose.1.phosphate.uridylyltransferase | -- | M | -- | -- | -- | -- | Y | Y | 810 | 797 | 423 | 179 | 244 | Y | Y | 628 | 619 | 299 | 107 | 192
gcvB | b4443 | UNKW3110 | unknown | -- | CORE | OLIGOPEPTIDE.TRANSPORT | -- | Small RNA. GcvB regulates expression of the periplasmic transporter components DppA and OppA [ Urbanowski00  ] | -- | -- | -- | -- | -- | Y | -- | 624 | 609 | 324 | 228 | 96 | Y | -- | 518 | 505 | 305 | 260 | 45
ggt | [NAME] | JW3412 | non-essential | PE | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | gamma.glutamyltranspeptidase | A mutant exhibits increased glutathione efflux, compared to wild type [ Suzuki87  ], and increased resistance to osmotic stress [ Smirnova01  ] | E | -- | -- | Y | 3.027 | Y | Y | 786 | 771 | 359 | 197 | 162 | Y | Y | 673 | 661 | 403 | 220 | 183
[NAME] | b3740 | JW3718 | non-essential | CY | FUNCTION-UNCERTAIN | CELL.DIVISION | methyltransferase.SAM.dependent.methyltransferase.glucose.inhibited.cell.division.protein | GidA  [PMID:9603884] and gidB [PMID:6185823] were suggested to be involved in cell division. It has been cited that disruption of gidA in E.coli affects cell division but only when cells are grown on glucose [PMID:6185823](don't have access to the full paper). However the main roles of gidA and gidB have been described in tRNA-modification pathways and it was not clear the apparent relationship with cell division. -- | M | -- | -- | Y | 12.989 | -- | Y | 395 | 393 | 144 | 58 | 86 | -- | Y | 219 | 217 | 112 | 67 | 45
glf | b2036 | JW2021 | non-essential | CY | CORE | LPS.AND.ECA | UDP.galactopyranose.mutase.FAD.NAD.P.binding | -- | M | -- | -- | Y | 192.91 | Y | -- | 223 | 200 | 99 | 88 | 11 | Y | -- | 184 | 162 | 97 | 71 | 26
glgA | b3429 | JW3392 | non-essential | CY | FUNCTION-UNCERTAIN | NA | glycogen.synthase | Glycogen is a glucose-containing polysaccharide, comprised of approximately 95% ?-1,4 linkages and 5% ?-1,6 branch glucosyl linkages, The biosynthetic pathways comprises glgA, glgB and glgC. | G | -- | -- | -- | -- | Y | Y | 798 | 790 | 303 | 138 | 165 | Y | Y | 156 | 156 | 68 | 33 | 35
glgB | b3432 | JW3395 | non-essential | CY | FUNCTION-UNCERTAIN | NA | 1.4.alpha.glucan.branching.enzyme | Glycogen is a glucose-containing polysa | G | -- | -- | -- | -- | Y | Y | 794 | 782 | 299 | 178 | 121 | Y | Y | 154 | 150 | 52 | 30 | 22
glgC | b3430 | JW3393 | non-essential | CY | FUNCTION-UNCERTAIN | NA | glucose.1.phosphate.adenylyltransferase | Glycogen is a glucose-containing polysaccharide, comprised of approximately 95% ?-1,4 linkages and 5% ?-1,6 branch glucosyl linkages, The biosynthetic pathways comprises glgA, glgB and glgC | G | -- | -- | Y | 1.458 | Y | Y | 795 | 786 | 250 | 114 | 136 | Y | Y | 670 | 663 | 273 | 168 | 105
glmM | b3176 | JW3143 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS,LPS.AND.ECA | phosphoglucosamine.mutase | Link between Cell.wall.biogenesis, LPS and ECA because is a precursor step in the biosynthesis of precursors of lipid A (LPS), lipid II (peptidoglycan) and lipid III (ECA) | G | -- | -- | Y | 146.558 | Y | -- | 236 | 232 | 205 | 172 | 33 | Y | -- | 179 | 176 | 145 | 142 | 3
glmS | b3729 | JW3707 | essential | CY | CORE | CELL.WALL.BIOGENESIS,LPS.AND.ECA | L.glutamine.D.fructose.6.phosphate.aminotransferase | Link between Cell.wall.biogenesis, LPS and ECA because is a precursor step in the biosynthesis of precursors of lipid A (LPS), lipid II (peptidoglycan) and lipid III (ECA) | M | -- | -- | -- | -- | Y | Y | 792 | 785 | 470 | 190 | 280 | Y | Y | 639 | 633 | 432 | 301 | 131
glmU | b3730 | JW3708 | essential | CY | CORE | CELL.WALL.BIOGENESIS,LPS.AND.ECA | fused.N.acetyl.glucosamine.1.phosphate.uridyltransferase.glucosamine.1.phosphate.acetyl.transferase | Link between Cell.wall.biogenesis, LPS and ECA because is a precursor key step in the biosynthesis of precursors of lipid A (LPS), lipid II (peptidoglycan) and lipid III (ECA) | M | -- | -- | Y | 42.07 | Y | Y | 787 | 781 | 293 | 95 | 198 | Y | Y | 621 | 615 | 282 | 177 | 105
glpA | b2241 | JW2235 | non-essential | CY | CORE | PHOSPHOLIPIDS | sn.glycerol.3.phosphate.dehydrogenase.anaerobic.large.subunit.FAD.NAD.P.binding | Optimal intracellular levels of glycerol-3-phosphate are maintained for biosynthesis of phospholipids. There are two glycerol 3-phosphate dehydrogenase, GlpD (aerobic) and GlpABC (anaerobic). The glpTQ operon, which encodes glycerol-3-phosphate transporter and phosphodiesterase is adjacent to glpABC. The two operons are divergently transcribed; the operators to which GlpR binds overlap the ,glpA promoter [ Yang97  ]. . Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | C | -- | -- | -- | -- | Y | -- | 684 | 671 | 327 | 263 | 64 | -- | -- | -- | -- | -- | -- | --
glpB | b2242 | JW2236 | non-essential | CY | CORE | PHOSPHOLIPIDS | sn.glycerol.3.phosphate.dehydrogenase.anaerobic.membrane.anchor.subunit | Optimal intracellular levels of glycerol-3-phosphate are maintained for biosynthesis of phospholipids.  There are two glycerol 3-phosphate dehydrogenase, GlpD (aerobic) and GlpABC (anaerobic). The glpTQ operon, which encodes glycerol-3-phosphate transporter and phosphodiesterase is adjacent to glpABC. The two operons are divergently transcribed; the operators to which GlpR binds overlap the ,glpA promoter [ Yang97  ]. . Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | E | -- | -- | -- | -- | Y | -- | 675 | 662 | 437 | 349 | 88 | Y | -- | 546 | 535 | 479 | 465 | 14
glpD | b3426 | JW3389 | non-essential | CY | CORE | PHOSPHOLIPIDS | sn.glycerol.3.phosphate.dehydrogenase.aerobic.FAD.NAD.P.binding | Optimal intracellular levels of glycerol-3-phosphate are maintained for biosynthesis of phospholipids.  There are two glycerol 3-phosphate dehydrogenase, GlpD (aerobic) and GlpABC (anaerobic). The glpTQ operon, which encodes glycerol-3-phosphate transporter and phosphodiesterase is adjacent to glpABC. The two operons are divergently transcribed; the operators to which GlpR binds overlap the ,glpA promoter [ Yang97  ]. . Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | C | -- | -- | Y | 70.686 | Y | -- | 689 | 679 | 397 | 330 | 67 | -- | -- | -- | -- | -- | -- | --
glpF | b3927 | JW3898 | non-essential | IM | CORE | PHOSPHOLIPIDS | glycerol.facilitator | The glycerol facilitator, GlpF, allows the facilitated diffusion of glycerol across the inner membrane for utilization inside the cell. Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes.. Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | G | -- | -- | -- | -- | Y | -- | 681 | 677 | 151 | 38 | 113 | Y | Y | 633 | 629 | 231 | 41 | 190
glpK | b3926 | JW3897 | non-essential | CY | CORE | PHOSPHOLIPIDS | glycerol.kinase | Converts glycerol+ATP to sn-glycerol-3P. . Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | C | -- | -- | -- | -- | Y | -- | 687 | 683 | 374 | 299 | 75 | Y | -- | 489 | 485 | 322 | 289 | 33
glpQ | b2239 | JW2233 | non-essential | PE | CORE | PHOSPHOLIPIDS | periplasmic.glycerophosphodiester.phosphodiesterase | Converts glycerophosphodiester+H2O to sn-glycerol-3P and alcohol. Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | C | -- | -- | -- | -- | -- | Y | 389 | 382 | 148 | 69 | 79 | -- | Y | 196 | 192 | 106 | 53 | 53
glpT | b2240 | JW2234 | non-essential | IM | CORE | PHOSPHOLIPIDS | sn.glycerol.3.phosphate.transporter | GlpT is the major E. coli uptake system for glycerol-3-phosphate (EcoCyc). Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | G | -- | -- | -- | -- | -- | Y | 394 | 387 | 147 | 62 | 85 | -- | Y | 219 | 215 | 86 | 39 | 47
gmd | b2053 | JW2038 | non-essential | CY | CORE | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | GDP.D.mannose.dehydratase.NAD.P.binding | -- | M | -- | -- | -- | -- | Y | Y | 467 | 439 | 179 | 136 | 43 | Y | Y | 264 | 243 | 124 | 72 | 52
gmhB | b0200 | JW0196 | non-essential | CY | CORE | LPS.AND.ECA | D.D.heptose.1.7.bisphosphate.phosphatase | -- | E | -- | -- | -- | -- | Y | Y | 807 | 789 | 250 | 102 | 148 | Y | Y | 128 | 121 | 63 | 41 | 22
gpsA | b3608 | JW3583 | essential | CY | CORE | PHOSPHOLIPIDS | glycerol.3.phosphate.dehydrogenase.NAD | -- | C | -- | -- | Y | 26.034 | Y | -- | 219 | 207 | 125 | 61 | 64 | Y | -- | 163 | 153 | 108 | 49 | 59
[NAME] | b4143 | JW4103 | non-essential | CY | CORE | CHAPERONES | Cpn60.chaperonin.GroEL.large.subunit.of.[NAME] | -- | O | -- | -- | -- | -- | Y | -- | 683 | 668 | 347 | 269 | 78 | -- | -- | -- | -- | -- | -- | --
gspA | b3323 | JW3285 | non-essential | CY | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | general.secretory.pathway.component.cryptic | general.secretory.pathway.component.cryptic | - | -- | -- | -- | -- | -- | Y | 388 | 377 | 252 | 206 | 46 | Y | Y | 184 | 181 | 141 | 125 | 16
gspC | b3324 | JW3286 | non-essential | -- | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | general.secretory.pathway.component.cryptic | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | U | -- | -- | -- | -- | Y | Y | 786 | 770 | 194 | 91 | 103 | Y | Y | 110 | 107 | 44 | 33 | 11
gspD | b3325 | JW5707 | non-essential | OM | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | general.secretory.pathway.component.cryptic | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | NU | -- | -- | -- | -- | Y | Y | 790 | 773 | 258 | 119 | 139 | Y | Y | 135 | 132 | 79 | 50 | 29
gspE | b3326 | JW3288 | non-essential | CY | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | general.secretory.pathway.component.cryptic | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | NU | -- | -- | -- | -- | Y | Y | 791 | 775 | 321 | 190 | 131 | Y | Y | 100 | 99 | 57 | 35 | 22
gspF | b3327 | JW3289 | non-essential | IM | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | general.secretory.pathway.component.cryptic | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | NU | -- | -- | -- | -- | -- | Y | 393 | 382 | 97 | 45 | 52 | Y | Y | 218 | 214 | 74 | 37 | 37
gspG | b3328 | JW3290 | non-essential | -- | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | pseudopilin.cryptic.general.secretion.pathway | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | NU | -- | -- | -- | -- | Y | Y | 793 | 778 | 241 | 136 | 105 | Y | Y | 600 | 591 | 300 | 248 | 52
gspH | b3329 | JW3291 | non-essential | -- | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | predicted.general.secretory.pathway.component.cryptic | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | NU | -- | -- | -- | -- | Y | -- | 689 | 673 | 201 | 103 | 98 | Y | Y | 552 | 539 | 192 | 172 | 20
gspI | b3330 | JW5706 | non-essential | -- | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | general.secretory.pathway.component.cryptic | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | NU | -- | -- | -- | -- | Y | Y | 792 | 775 | 241 | 147 | 94 | Y | Y | 155 | 152 | 74 | 49 | 25
[NAME] | b3331 | JW3293 | non-essential | IM | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | predicted.general.secretory.pathway.component.cryptic | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | U | -- | -- | -- | -- | Y | Y | 789 | 772 | 273 | 107 | 166 | Y | Y | 109 | 108 | 55 | 18 | 37
gspK | b3332 | JW3294 | non-essential | -- | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | general.secretory.pathway.component.cryptic | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | U | -- | -- | -- | -- | Y | -- | 691 | 675 | 333 | 123 | 210 | -- | -- | -- | -- | -- | -- | --
gspL | b3333 | JW5705 | non-essential | -- | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | general.secretory.pathway.component.cryptic | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | U | -- | -- | -- | -- | -- | Y | 391 | 380 | 77 | 43 | 34 | Y | Y | 218 | 215 | 77 | 33 | 44
gspM | b3334 | JW5704 | non-essential | IM | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | general.secretory.pathway.component.cryptic | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | - | -- | -- | -- | -- | -- | Y | 355 | 345 | 139 | 73 | 66 | Y | Y | 177 | 174 | 79 | 56 | 23
gspO | b3335 | JW3297 | non-essential | IM | FUNCTION-UNCERTAIN | CRYPTIC.SECRETORY.PATHWAY | bifunctional.prepilin.leader.peptidase.and.methylase | Wild-type E.coli K-12 does not secrete proteins into the extracellular medium under standard growth conditions. Divergent transcription of the two gsp- operons is silenced by the nucleoid-structuring protein H-NS that can be turned on upon deprivation of H-NS using moderate-copy-number plasmids, e.g. expressing endochitinase ChiA [PMID:11118204]. [NAME] found a weak expression of gsp- genes in Biofilms (M3D microarrays database) and [NAME] ([NAME] (2009)) shown three Z- scores >= 3 but all for different proteins and none was significant (>= 0.7). LCMS shows no hits. [NAME] found that by sequence gsp- proteins are similar to "IV pilus assembly and DNA-uptake by transformation proteins" -- | NOU | -- | -- | -- | -- | Y | Y | 813 | 796 | 203 | 90 | 113 | Y | Y | 666 | 654 | 367 | 162 | 205
gutQ | b2708 | JW5431 | non-essential | CY | CORE | LPS.AND.ECA | predicted.phosphosugar.binding.protein | -- | RM | -- | -- | -- | -- | Y | Y | 808 | 803 | 288 | 144 | 144 | Y | Y | 591 | 587 | 311 | 129 | 182
hemX | b3803 | JW3775 | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.uroporphyrinogen.III.methylase | Poorly characterized proteins HemY and HemX suggested to be a uroporphyrinogen III methylase [PMID:3062586]. Check patterns of SSL | H | -- | -- | Y | 5.416 | -- | Y | 392 | 384 | 130 | 56 | 74 | Y | Y | 211 | 207 | 82 | 37 | 45
hemY | [NAME] | JW3774 | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.protoheme.IX.synthesis.protein | Poorly characterized proteins HemY and HemX suggested to be a uroporphyrinogen III methylase [PMID:3062586]. Check patterns of SSL | H | -- | -- | Y | 1.869 | Y | Y | 521 | 507 | 156 | 92 | 64 | Y | Y | 328 | 316 | 140 | 83 | 57
[NAME] | b4175 | JW4133 | non-essential | -- | CORE | PROTEASE,CELL.DIVISION | modulator.for.HflB.protease.specific.for.phage.lambda.cII.repressor | The HflK-HflC (HflKC) complex interacts with FtsH and regulates (inhibits) proteolysis by FtsH of SecY (Sec- protein secretion system) [PMID:9159109] -- | O | -- | -- | Y | 2.243 | -- | Y | 391 | 375 | 120 | 40 | 80 | Y | Y | 203 | 195 | 74 | 27 | 47
[NAME] | b4174 | JW4132 | non-essential | -- | CORE | PROTEASE,CELL.DIVISION | modulator.for.HflB.protease.specific.for.phage.lambda.cII.repressor | The HflK-HflC (HflKC) complex interacts with FtsH and regulates (inhibits) proteolysis by FtsH of SecY (Sec- protein secretion system) [PMID:9159109] -- | O | -- | -- | Y | 67.602 | Y | Y | 777 | 750 | 366 | 162 | 204 | Y | Y | 519 | 500 | 332 | 190 | 142
hflX | b4173 | JW4131 | non-essential | CY | FUNCTION-UNCERTAIN | CELL.DIVISION | predicted.GTPase | HflX(hflA) Shows a SSL interaction with ftsH(hflB) upon lysogeny_by_lambda_phage [PMID:2939254], and its co-operon partners [NAME] inhibit proteolysis by FtsH of SecY. hflX was first identified as involved in lysogenization by coliphage lambda, but later was shown it has no role in lambda lysogeny or in transposition [PMID:19181811]. [NAME] (2009) has no clear clues. [NAME] predicts this gene can be also functionaly related with ftsH (see EcoliSick SSL reference). -- | R | -- | -- | -- | -- | -- | Y | 383 | 365 | 180 | 138 | 42 | Y | Y | 170 | 161 | 103 | 94 | 9
hlpA | b0178 | JW0173 | non-essential | OM | CORE | PROTEIN.SECRETION,CHAPERONES | periplasmic.chaperone | surA genetically interacts with (degP/skp) and double mutant surA ppiD was reprted as synthetic lethal [PMID:9670013]. However, in [PMID:16267292] mutations involving four E. coli PPIases (FkpA, PpiA, PpiD, and SurA) showed that no single or double mutants were shown to have growth defects. Three triple mutants shown growth defects, while one does not, and the quadruple mutant had the most pronounced defect. -- | - | -- | -- | Y | 20.347 | -- | Y | 483 | 468 | 164 | 97 | 67 | Y | Y | 163 | 157 | 85 | 56 | 29
hofC | b0106 | JW0102 | non-essential | IM | FUNCTION-UNCERTAIN | PROTEIN.SECRETION | assembly.protein.in.type.IV.pilin.biogenesis.transmembrane.protein | hofC is a homolog of pilC from Pseudomonas aeruginosa which is involved in type-IV pilus assembly [PMID:10633126] Annotated as participating in secretion of pili components. What about secretion of other proteins? Look for SSL | NU | -- | -- | -- | -- | Y | Y | 814 | 796 | 148 | 50 | 98 | Y | Y | 667 | 652 | 288 | 64 | 224
hsrA | b3754 | JW3733 | non-essential | IM | PREDICTED | RESPONSE.TO.ANTIBIOTIC | predicted.multidrug.or.homocysteine.efflux.system | [NAME], Phylogenetic profiles with mdtD (Multidrug efflux system protein), and same GC-module than ent- proteins. Based on sequence similarity, YieO may function as a proton-driven drug efflux system (EcoCyc, nor reference). | - | -- | -- | -- | -- | -- | Y | 392 | 388 | 130 | 60 | 70 | -- | Y | 205 | 203 | 88 | 44 | 44
htrE | b0139 | JW0135 | non-essential | OM | PREDICTED | NA | predicted.outer.membrane.usher.protein | predicted.outer.membrane.usher.protein | NU | -- | -- | Y | 1.275 | -- | Y | 394 | 385 | 120 | 47 | 73 | -- | Y | 220 | 216 | 79 | 32 | 47
htrL | b3618 | JW5644 | non-essential | CY | FUNCTION-UNCERTAIN | LPS.AND.ECA | predicted.protein | HtrL is involved in lipopolysaccharide biosynthesis [EcoCyc]. [NAME] [NAME] no data about LPS | - | -- | -- | Y | 11.33 | Y | Y | 813 | 787 | 306 | 195 | 111 | Y | Y | 663 | 644 | 362 | 214 | 148
idi | b2889 | JW2857 | non-essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS | isopentenyl.diphosphate.isomerase | Isoprenoids are relevant for the E. coli cell envelope biogenesis mainly because they are precursors of both peptidoglycan (Lipid II) and K-antigen (undecaprenyl moiety) | I | -- | -- | -- | -- | Y | -- | 217 | 216 | 116 | 109 | 7 | Y | -- | 151 | 150 | 112 | 94 | 18
imp | b0054 | JW0053 | essential | OM | CORE | LPS.AND.ECA | exported.protein.required.for.envelope.biosynthesis.and.integrity | Imp (LptD) has been genetically and biochemically characterized as part of an ABC transporter LptBFGC complex required for the outer membrane sorting of lipopolysaccharides has been reported [PMID:19500581,PMID:18375759]. Disruption of the pathway at any step after [NAME] leads to indistinguishable phenotypes: in all cases, LPS accumulates in the outer leaflet of the IM. Therefore, we cannot conduct epistasis analysis to determine exact pathway order. We can only rely on the information about the cellular location of these proteins to predict temporal order in the pathway as follows: MsbA followed by a complex of LptB, [NAME], [NAME] and LptG, followed by LptA and finally by a complex of LptD and LptE [PMID:19633680] | M | -- | -- | -- | -- | Y | Y | 751 | 741 | 248 | 134 | 114 | Y | Y | 546 | 539 | 312 | 179 | 133
iscS | b2530 | JW2514 | non-essential | CY | FUNCTION-UNCERTAIN | NA | cysteine.desulfurase.tRNA.sulfurtransferase.PLP.dependent | Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | E | -- | -- | Y | 826.119 | Y | Y | 764 | 759 | 476 | 292 | 184 | Y | Y | 106 | 105 | 74 | 60 | 14
ispA | b0421 | JW0411 | essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS,CELL.WALL.BIOGENESIS | geranyltranstransferase | GO database has only ispU and bacA as Cell wall related. However ispA is the immediate step before ispU and the B. subtilis ortholog was demonstrated to synthetically interact alleviating with ftsZ in a cell wall dependent way [PMID:19212404] | H | -- | -- | Y | 22.682 | Y | Y | 817 | 797 | 255 | 57 | 198 | Y | Y | 557 | 541 | 338 | 170 | 168
ispB | b3187 | JW3154 | essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS | octaprenyl.diphosphate.synthase | -- | H | -- | -- | -- | -- | Y | -- | 223 | 219 | 123 | 104 | 19 | Y | -- | 172 | 168 | 118 | 89 | 29
ispD | b2747 | JW2717 | essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS | 4.diphosphocytidyl.2C.methyl.D.erythritol.synthase | -- | I | -- | -- | -- | -- | -- | Y | 385 | 382 | 174 | 59 | 115 | Y | Y | 216 | 214 | 136 | 71 | 65
ispE | b1208 | JW1199 | essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS | 4.diphosphocytidyl.2.C.methylerythritol.kinase | -- | I | -- | -- | Y | 8.579 | Y | Y | 523 | 514 | 230 | 116 | 114 | Y | Y | 312 | 309 | 201 | 144 | 57
ispF | b2746 | JW2716 | essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS | 2C.methyl.D.erythritol.2.4.cyclodiphosphate.synthase | -- | I | -- | -- | Y | 36.76 | Y | Y | 782 | 775 | 249 | 108 | 141 | Y | Y | 259 | 256 | 175 | 129 | 46
ispG | b2515 | [NAME] | essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS | 1.hydroxy.2.methyl.2.E.butenyl.4.diphosphate.synthase | -- | I | -- | -- | Y | 39.344 | Y | Y | 807 | 801 | 324 | 157 | 167 | Y | Y | 229 | 227 | 135 | 74 | 61
ispH | b0029 | JW0027 | essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS | 1.hydroxy.2.methyl.2.E.butenyl.4.diphosphate.reductase.4Fe.4S.protein | -- | IM | -- | -- | Y | 30.665 | Y | Y | 818 | 807 | 314 | 141 | 173 | Y | Y | 255 | 251 | 144 | 86 | 58
ispU | b0174 | JW0169 | essential | CY | CORE | ISOPRENOIDS.BIOSYNTHESIS,CELL.WALL.BIOGENESIS | undecaprenyl.pyrophosphate.synthase | GO database has only ispU and bacA as Cell wall related. However ispA is the immediate step before ispU and the B. subtilis ortholog was demonstrated to synthetically interact alleviating with ftsZ in a cell wall dependent way [PMID:19212404] | I | -- | -- | Y | 21.068 | Y | Y | 514 | 498 | 200 | 99 | 101 | Y | Y | 348 | 338 | 201 | 88 | 113
kdsA | b1215 | [NAME] | essential | CY | CORE | LPS.AND.ECA | 3.deoxy.D.manno.octulosonate.8.phosphate.synthase | -- | M | -- | -- | Y | 94.955 | Y | Y | 815 | 803 | 412 | 164 | 248 | Y | Y | 655 | 649 | 403 | 257 | 146
kdsB | b0918 | JW0901 | essential | CY | CORE | LPS.AND.ECA | 3.deoxy.manno.octulosonate.cytidylyltransferase | -- | M | -- | -- | Y | 35.914 | Y | Y | 524 | 519 | 203 | 118 | 85 | Y | Y | 335 | 332 | 214 | 131 | 83
kdsC | b3198 | JW3165 | non-essential | CY | CORE | LPS.AND.ECA | 3.deoxy.D.manno.octulosonate.8.phosphate.phosphatase | -- | R | -- | -- | Y | 36.695 | Y | Y | 799 | 782 | 239 | 109 | 130 | Y | Y | 678 | 664 | 431 | 270 | 161
[NAME] | [NAME] | JW3164 | non-essential | CY | CORE | LPS.AND.ECA | D.arabinose.5.phosphate.isomerase | -- | RM | -- | -- | Y | 15.163 | Y | Y | 708 | 693 | 329 | 213 | 116 | Y | Y | 514 | 501 | 311 | 251 | 60
kdtA | b3633 | JW3608 | essential | IM | CORE | LPS.AND.ECA | 3.deoxy.D.manno.octulosonic.acid.transferase.KDO.transferase | -- | M | -- | -- | Y | 10.62 | Y | Y | 808 | 784 | 339 | 84 | 255 | Y | Y | 632 | 611 | 414 | 263 | 151
kefA | b0465 | JW0454 | non-essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | fused.conserved.protein.mechanosensitive.channel.protein | MscK, MscS, [NAME] and [NAME] are potassium-dependent mechanosensitive (MS) channels each with different conductance. Interesting to look for SSL among them. Mutation, deletion, and complementation studies using patch clamp conductance measurements have characterized two E.coli genes that are required for MscS activity: yggB and kefA. Deletion of yggB in kefA-deletion mutants eliminates all MscS activity and complementation with [NAME] (MscS) on a moderate copy number plasmid restores MscS activity (EcoCyc). | M | -- | -- | -- | -- | Y | Y | 792 | 783 | 237 | 111 | 126 | Y | Y | 589 | 581 | 216 | 83 | 133
lamB | b4036 | JW3996 | non-essential | OM | CORE | CELL.ENVELOPE.INTEGRITY | maltose.outer.membrane.porin.maltoporin | -- | G | -- | -- | -- | -- | Y | Y | 785 | 778 | 247 | 98 | 149 | Y | Y | 627 | 624 | 276 | 69 | 207
ldcA | b1192 | JW1181 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS | L.D.carboxypeptidase.A | [NAME] is an L,D-carboxypeptidase that has an essential function in murein (peptidoglycan) recycling/turnover [PMID:10428950] | V | -- | -- | -- | -- | Y | Y | 779 | 765 | 326 | 196 | 130 | Y | Y | 134 | 130 | 86 | 37 | 49
lepA | b2569 | JW2553 | non-essential | CY | FUNCTION-UNCERTAIN | NA | GTP.binding.membrane.protein | GTP.binding.membrane.protein | M | -- | -- | Y | 64.087 | -- | Y | 339 | 336 | 208 | 158 | 50 | -- | Y | 149 | 147 | 70 | 55 | 15
lepB | b2568 | JW2552 | essential | IM | CORE | PROTEIN.SECRETION | leader.peptidase.signal.peptidase.I | LepB is the signal peptidase of Sec- and Tat- systems [PMID:19270402] Signal peptidase catalyzes the cleavage of the amino-terminal leader peptide from secretory proteins [EcoCyc] | U | -- | -- | -- | -- | Y | -- | 219 | 219 | 97 | 70 | 27 | Y | -- | 164 | 164 | 101 | 65 | 36
lgt | b2828 | JW2796 | essential | IM | CORE | PHOSPHOLIPIDS | phosphatidylglycerol.prolipoprotein.diacylglyceryl.transferase | Assays have shown it to be involved in the lipid modification of prolipoprotein by transferring the sn-1,2-diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine [ Sankaran94  ] | M | -- | -- | -- | -- | Y | -- | 216 | 215 | 97 | 73 | 24 | Y | -- | 168 | 167 | 94 | 54 | 40
lnt | b0657 | JW0654 | essential | IM | CORE | PHOSPHOLIPIDS,PROTEIN.SECRETION | apolipoprotein.N.acyltransferase | Lnt(CutE) is a link between Phospholipods and Protein.secretion (lipoproteins). Aminoacylation of lipoproteins bound for the outer membrane is required for proper localization of these lipoproteins via the [NAME] pathway [PMID:12198129]. CutE can utilize the phospholipids phosphatidylethanolamine, phosphatidylglycerol, or cardiolipin in vitro [PMID:2032623] | M | -- | -- | -- | -- | Y | Y | 479 | 474 | 192 | 63 | 129 | Y | Y | 293 | 290 | 146 | 83 | 63
lolA | b0891 | JW0874 | essential | PE | CORE | PROTEIN.SECRETION,CHAPERONES | chaperone.for.lipoproteins | Initially all Lol- system was classsified as 'Chaperones', but actually only LolA is chaperone -- | M | -- | -- | Y | 2.87 | Y | Y | 525 | 522 | 257 | 132 | 125 | Y | Y | 324 | 324 | 200 | 136 | 64
lolB | b1209 | JW1200 | essential | -- | CORE | PROTEIN.SECRETION | chaperone.for.lipoproteins | Initially all Lol- system was classsified as 'Chaperones', but actually only LolA is chaperone -- | M | -- | -- | -- | -- | Y | Y | 816 | 803 | 261 | 44 | 217 | Y | Y | 108 | 106 | 63 | 32 | 31
lolC | b1116 | JW5161 | essential | IM | CORE | PROTEIN.SECRETION | outer.membrane.specific.lipoprotein.transporter.subunit.membrane.component.of.ABC.superfamily | Initially all Lol- system was classsified as 'Chaperones', but actually only LolA is chaperone -- | M | -- | -- | -- | -- | Y | Y | 796 | 780 | 354 | 137 | 217 | Y | Y | 656 | 642 | 397 | 206 | 191
[NAME] | b1117 | JW5162 | essential | IM | CORE | PROTEIN.SECRETION | outer.membrane.specific.lipoprotein.transporter.subunit.ATP.binding.component.of.ABC.superfamily | Initially all Lol- system was classsified as 'Chaperones', but actually only LolA is chaperone -- | V | -- | -- | Y | 56.729 | Y | Y | 484 | 473 | 188 | 73 | 115 | Y | Y | 283 | 276 | 183 | 90 | 93
lolE | b1118 | JW1104 | essential | IM | CORE | PROTEIN.SECRETION | outer.membrane.specific.lipoprotein.transporter.subunit.membrane.component.of.ABC.superfamily | Initially all Lol- system was classsified as 'Chaperones', but actually only LolA is chaperone -- | M | -- | -- | -- | -- | Y | Y | 815 | 799 | 328 | 78 | 250 | Y | Y | 635 | 621 | 302 | 196 | 106
lpcA | b0222 | JW0212 | non-essential | CY | CORE | LPS.AND.ECA | D.sedoheptulose.7.phosphate.isomerase | -- | G | -- | -- | -- | -- | Y | Y | 745 | 736 | 231 | 40 | 191 | Y | Y | 633 | 629 | 185 | 100 | 85
lpp | b1677 | JW1667 | non-essential | -- | CORE | CELL.ENVELOPE.INTEGRITY | murein.lipoprotein | -- | M | -- | -- | -- | -- | -- | Y | 485 | 481 | 186 | 48 | 138 | Y | Y | 324 | 320 | 77 | 40 | 37
lpxA | b0181 | JW0176 | essential | CY | CORE | LPS.AND.ECA | UDP.N.acetylglucosamine.acetyltransferase | -- | M | -- | -- | -- | -- | Y | Y | 746 | 728 | 198 | 34 | 164 | Y | Y | 535 | 528 | 171 | 80 | 91
[NAME] | b0182 | JW0177 | essential | CY | CORE | LPS.AND.ECA | tetraacyldisaccharide.1.P.synthase | -- | M | -- | -- | Y | 13.028 | Y | Y | 816 | 798 | 354 | 101 | 253 | Y | Y | 639 | 623 | 319 | 144 | 175
lpxC | b0096 | [NAME] | essential | CY | CORE | LPS.AND.ECA | UDP.3.O.acyl.N.acetylglucosamine.deacetylase | -- | M | -- | -- | -- | -- | Y | Y | 814 | 797 | 349 | 59 | 290 | Y | Y | 556 | 549 | 210 | 133 | 77
lpxD | b0179 | JW0174 | essential | CY | CORE | LPS.AND.ECA | UDP.3.O.3.hydroxymyristoyl.glucosamine.N.acyltransferase | -- | M | -- | -- | Y | 96.296 | Y | Y | 794 | 777 | 349 | 84 | 265 | Y | Y | 644 | 631 | 290 | 196 | 94
lpxH | b0524 | JW0513 | essential | CY | CORE | LPS.AND.ECA | UDP.2.3.diacylglucosamine.pyrophosphatase | -- | S | -- | -- | Y | 5.421 | Y | Y | 523 | 520 | 192 | 93 | 99 | Y | Y | 265 | 262 | 159 | 116 | 43
lpxK | b0915 | JW0898 | essential | IM | CORE | LPS.AND.ECA | lipid.A.4.kinase | -- | M | -- | -- | -- | -- | Y | Y | 814 | 804 | 271 | 68 | 203 | Y | Y | 589 | 583 | 299 | 112 | 187
lpxL | b1054 | JW1041 | non-essential | IM | CORE | LPS.AND.ECA | lauryl.acyl.carrier.protein.ACP.dependent.acyltransferase | -- | M | -- | -- | -- | -- | Y | -- | 101 | 97 | 69 | 48 | 21 | Y | -- | 68 | 65 | 40 | 33 | 7
lpxM | b1855 | JW1844 | non-essential | IM | CORE | LPS.AND.ECA | myristoyl.acyl.carrier.protein.ACP.dependent.acyltransferase | -- | M | -- | -- | Y | 24.963 | Y | Y | 524 | 519 | 216 | 180 | 36 | Y | Y | 338 | 336 | 133 | 89 | 44
lspA | b0027 | JW0025 | essential | IM | CORE | PROTEIN.SECRETION | prolipoprotein.signal.peptidase.signal.peptidase.II | LspA, also called Signal peptidase (SPase) is a membrane-bound peptidase that cleaves the signal sequence from preproteins at the periplasmic face of the membrane [PMID:18078384]. For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | E | -- | -- | -- | -- | Y | Y | 483 | 474 | 213 | 61 | 152 | Y | Y | 291 | 287 | 145 | 90 | 55
macA | b0878 | JW0862 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | macrolide.transporter.subunit.membrane.fusion.protein.MFP.component | MacAB, also known as YbjYZ, probably forms a complex with outer membrane protein TolC to confer macrolide resistance via active drug efflux (EcoCyc) | M | -- | -- | Y | 0.251 | Y | Y | 781 | 773 | 341 | 167 | 174 | Y | Y | 165 | 165 | 57 | 26 | 31
macB | b0879 | JW0863 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | fused.macrolide.transporter.subunits.of.ABC.superfamily.ATP.binding.component.membrane.component | MacAB, also known as YbjYZ, probably forms a complex with outer membrane protein TolC to confer macrolide resistance via active drug efflux (EcoCyc) | V | -- | -- | -- | -- | -- | Y | 393 | 391 | 108 | 24 | 84 | Y | Y | 199 | 199 | 93 | 40 | 53
manA | b1613 | JW1605 | non-essential | CY | CORE | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | mannose.6.phosphate.isomerase | Link between Cell.wall.biogenesis, LPS and ECA because is a precursor step in the biosynthesis of precursors of lipid A (LPS), lipid II (peptidoglycan) and lipid III (ECA) | G | -- | -- | Y | 22.119 | Y | -- | 681 | 672 | 295 | 160 | 135 | -- | -- | -- | -- | -- | -- | --
manX | b1817 | JW1806 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS,[NAME],M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | fused.mannose.specific.PTS.enzymes.IIA.component.IIB.component | Link between Cell.wall.biogenesis, LPS and ECA because is a precursor step in the biosynthesis of precursors of lipid A (LPS), lipid II (peptidoglycan) and lipid III (ECA) | G | -- | -- | Y | 57.951 | Y | -- | 622 | 616 | 302 | 206 | 96 | -- | -- | -- | -- | -- | -- | --
manY | b1818 | JW1807 | non-essential | IM | CORE | CELL.WALL.BIOGENESIS,[NAME],M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | mannose.specific.enzyme.IIC.component.of.PTS | Link between Cell.wall.biogenesis, LPS and ECA because is a precursor step in the biosynthesis of precursors of lipid A (LPS), lipid II (peptidoglycan) and lipid III (ECA) | G | -- | -- | Y | 197.264 | Y | -- | 604 | 598 | 365 | 294 | 71 | -- | -- | -- | -- | -- | -- | --
manZ | b1819 | JW1808 | non-essential | IM | CORE | CELL.WALL.BIOGENESIS,[NAME],M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | mannose.specific.enzyme.IID.component.of.[NAME] | Link between Cell.wall.biogenesis, LPS and ECA because is a precursor step in the biosynthesis of precursors of lipid A (LPS), lipid II (peptidoglycan) and lipid III (ECA) | G | -- | -- | -- | -- | Y | -- | 678 | 672 | 311 | 205 | 106 | -- | -- | -- | -- | -- | -- | --
maoC | b1387 | JW1382 | non-essential | CY | CORE | FAD | fused.aldehyde.dehydrogenase.enoyl.CoA.hydratase | -- | I | -- | -- | -- | -- | Y | Y | 749 | 736 | 260 | 122 | 138 | Y | Y | 581 | 570 | 243 | 179 | 64
mdlA | b0448 | JW0438 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | fused.predicted.multidrug.transporter.subunits.of.ABC.superfamily.ATP.binding.components | Based on sequence similarity these proteins may function as an ATP-dependent drug efflux pumps (EcoCyc). [NAME] is a transcriptional regulator related with the increase in resistance to antibiotics and is expressed constitutively. [NAME] have shown that this regulator activates the transcription of mdlA gene and that it is forms three complexes in the promoter region, suggesting the existence of multiple [NAME] binding sites [ Bennik00 ]. | V | -- | -- | Y | 1.871 | -- | Y | 392 | 381 | 131 | 76 | 55 | -- | Y | 193 | 186 | 99 | 65 | 34
mdlB | b0449 | JW5061 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | fused.predicted.multidrug.transporter.subunits.of.ABC.superfamily.ATP.binding.components | Based on sequence similarity these proteins may function as an ATP-dependent drug efflux pumps (EcoCyc). [NAME] is a transcriptional regulator related with the increase in resistance to antibiotics and is expressed constitutively. [NAME] have shown that this regulator activates the transcription of mdlA gene and that it is forms three complexes in the promoter region, suggesting the existence of multiple [NAME] binding sites [ Bennik00 ]. | V | -- | -- | Y | 5.423 | -- | Y | 363 | 352 | 163 | 100 | 63 | -- | Y | 188 | 182 | 109 | 69 | 40
mdoB | b4359 | JW5794 | non-essential | IM | CORE | PHOSPHOLIPIDS | phosphoglycerol.transferase.I | Javier classified mdo* enzymes originally as Cell.wall because participae in 'oligosaccharides' of periplasm, butr they actually are involved metabolism of Membrane-derived oligosaccharides (MDO) which is more related with phospholipids [NAME] is an enzyme catalyzing transfer of phosphoglycerol residues from phosphatidylglycerol to membrane-derived oligosaccharides or to synthetic beta-glucoside acceptors. The products are sn-1,2-diglyceride and beta-glucoside-6-phosphoglycerol [PMID:6296144] | M | -- | -- | -- | -- | Y | -- | 707 | 702 | 153 | 41 | 112 | Y | Y | 593 | 588 | 275 | 198 | 77
mdoC | b1047 | JW1034 | non-essential | IM | CORE | PHOSPHOLIPIDS | membrane.protein.required.for.modification.of.periplasmic.glucan | Javier classified mdo* enzymes originally as Cell.wall because participae in 'oligosaccharides' of periplasm, butr they actually are involved metabolism of Membrane-derived oligosaccharides (MDO) which is more related with phospholipids [NAME] is an enzyme catalyzing transfer of phosphoglycerol residues from phosphatidylglycerol to membrane-derived oligosaccharides or to synthetic beta-glucoside acceptors. The products are sn-1,2-diglyceride and beta-glucoside-6-phosphoglycerol [PMID:6296144] | - | -- | -- | -- | -- | Y | Y | 524 | 517 | 180 | 117 | 63 | Y | Y | 220 | 216 | 123 | 74 | 49
[NAME] | b1048 | JW1035 | non-essential | PE | CORE | PHOSPHOLIPIDS | glucan.biosynthesis.protein.periplasmic | Javier classified mdo* enzymes originally as Cell.wall because participation in 'oligosaccharides' of periplasm, butr they actually are involved metabolism of Membrane-derived oligosaccharides (MDO) which is more related with phospholipids [NAME] is an enzyme catalyzing transfer of phosphoglycerol residues from phosphatidylglycerol to membrane-derived oligosaccharides or to synthetic beta-glucoside acceptors. The products are sn-1,2-diglyceride and beta-glucoside-6-phosphoglycerol [PMID:6296144] | P | -- | -- | -- | -- | Y | Y | 766 | 753 | 317 | 210 | 107 | Y | Y | 536 | 526 | 276 | 157 | 119
mdoH | b1049 | JW1037 | non-essential | IM | CORE | PHOSPHOLIPIDS | glucan.biosynthesis.glycosyl.transferase | Javier classified mdo* enzymes originally as Cell.wall because participae in 'oligosaccharides' of periplasm, butr they actually are involved metabolism of Membrane-derived oligosaccharides (MDO) which is more related with phospholipids [NAME] is an enzyme catalyzing transfer of phosphoglycerol residues from phosphatidylglycerol to membrane-derived oligosaccharides or to synthetic beta-glucoside acceptors. The products are sn-1,2-diglyceride and beta-glucoside-6-phosphoglycerol [PMID:6296144] | M | -- | -- | Y | 30.192 | -- | Y | 379 | 374 | 124 | 41 | 83 | Y | Y | 176 | 173 | 108 | 37 | 71
mdtA | b2074 | JW5338 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.subunit.A | The mdtABCD (yegMNOB) genes were found to constitute a multidrug resistance cluster which is regulated by the response regulator BaeR [ Baranova02  ]. These genes code for an RND-type drug exporter, MdtABC, which confers resistance against bile salt derivatives, sodium dodecyl sulfate (SDS) and novobiocin. MdtABC also has an absolute requirement for the multifunctional outer membrane channel TolC for its function (EcoCyc) | M | -- | -- | Y | 1.805 | -- | Y | 376 | 368 | 130 | 100 | 30 | Y | Y | 203 | 199 | 80 | 57 | 23
[NAME] | b2075 | JW2060 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.subunit.B | The mdtABCD (yegMNOB) genes were found to constitute a multidrug resistance cluster which is regulated by the response regulator BaeR [ Baranova02  ]. These genes code for an RND-type drug exporter, MdtABC, which confers resistance against bile salt derivatives, sodium dodecyl sulfate (SDS) and novobiocin. MdtABC also has an absolute requirement for the multifunctional outer membrane channel TolC for its function (EcoCyc) | V | -- | -- | -- | -- | Y | Y | 796 | 777 | 422 | 174 | 248 | Y | Y | 169 | 165 | 69 | 26 | 43
mdtC | b2076 | JW2061 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.subunit.C | The mdtABCD (yegMNOB) genes were found to constitute a multidrug resistance cluster which is regulated by the response regulator BaeR [ Baranova02  ]. These genes code for an RND-type drug exporter, MdtABC, which confers resistance against bile salt derivatives, sodium dodecyl sulfate (SDS) and novobiocin. MdtABC also has an absolute requirement for the multifunctional outer membrane channel TolC for its function (EcoCyc) | V | -- | -- | -- | -- | -- | Y | 391 | 384 | 145 | 53 | 92 | Y | Y | 205 | 202 | 74 | 31 | 43
mdtD | b2077 | JW2062 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.protein | The mdtABCD (yegMNOB) genes were found to constitute a multidrug resistance cluster which is regulated by the response regulator BaeR [ Baranova02  ]. These genes code for an RND-type drug exporter, MdtABC, which confers resistance against bile salt derivatives, sodium dodecyl sulfate (SDS) and novobiocin. MdtABC also has an absolute requirement for the multifunctional outer membrane channel TolC for its function (EcoCyc). | - | -- | -- | -- | -- | -- | Y | 392 | 385 | 159 | 45 | 114 | -- | Y | 208 | 203 | 72 | 27 | 45
[NAME] | b3513 | JW3481 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.resistance.efflux.transporter | [NAME] has similarity to AcrA, but production of [NAME] does not suppress an acrA mutant defect in efflux function with AcrB [ Elkins03  ]. An N-terminal [NAME] fragment can be substituted for an N-terminal fragment of AcrA, indicating that the AcrA C terminus is required for proper function with AcrB [ Elkins03  ]. [NAME] is a component of the MdtEF multidrug transporter.TolC is required for proper MdtEF transporter function [ Zgurskaya00 ]. | M | -- | -- | Y | 0.875 | Y | -- | 688 | 680 | 212 | 77 | 135 | Y | Y | 674 | 666 | 412 | 186 | 226
[NAME] | b3514 | JW3482 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.transporter.RpoS.dependent | [NAME] has similarity to AcrA, but production of [NAME] does not suppress an acrA mutant defect in efflux function with AcrB [ Elkins03  ]. An N-terminal [NAME] fragment can be substituted for an N-terminal fragment of AcrA, indicating that the AcrA C terminus is required for proper function with AcrB [ Elkins03  ]. [NAME] is a component of the MdtEF multidrug transporter.TolC is required for proper MdtEF transporter function [ Zgurskaya00 ]. | V | -- | -- | -- | -- | Y | Y | 769 | 759 | 259 | 132 | 127 | Y | Y | 144 | 142 | 56 | 20 | 36
mdtH | b1065 | JW1052 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | predicted.drug.efflux.system | Overexpression of the cloned yceL gene in a drug-sensitive background strain resulted in a two-fold increase in resistance to norfloxacin and enoxacin [ Nishino01  ]. | - | -- | -- | -- | -- | -- | Y | 394 | 383 | 133 | 54 | 79 | -- | Y | 208 | 200 | 79 | 29 | 50
mdtI | b1599 | JW1591 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.transporter | The products of mdtJI are considered two-component-type, Small Multidrug Resistance (SMR) family, proton-dependent, transporter proteins [ Paulsen96  , Jack00  ]. Sequence analysis and gene fusion studies indicate that MdtJ and [NAME] are homologous, oppositely oriented proteins. Drug-resistance studies indicate that overexpression of mdtJI in an expression vector conferred increased resistance to deoxycholate (4-fold), nalidixic acid (2-fold), fosfomycin (2-fold), and SDS ( 2-fold) [ Nishino01 ]. | P | -- | -- | -- | -- | -- | Y | 396 | 395 | 294 | 134 | 160 | -- | Y | 218 | 218 | 113 | 60 | 53
[NAME] | b1600 | JW1592 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.transporter | The products of mdtJI are considered two-component-type, Small Multidrug Resistance (SMR) family, proton-dependent, transporter proteins [ Paulsen96  , Jack00  ]. Sequence analysis and gene fusion studies indicate that MdtJ and [NAME] are homologous, oppositely oriented proteins. Drug-resistance studies indicate that overexpression of mdtJI in an expression vector conferred increased resistance to deoxycholate (4-fold), nalidixic acid (2-fold), fosfomycin (2-fold), and SDS ( 2-fold) [ Nishino01 ]. | P | -- | -- | -- | -- | -- | Y | 396 | 395 | 195 | 111 | 84 | -- | Y | 207 | 207 | 84 | 44 | 40
[NAME] | b1663 | JW1655 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.transporter | YdhE is a member of the MATE family of multidrug efflux transporters [ Brown99a  ]. Expression of the cloned ydhE gene conferred increased resistance to norfloxacin, ciprofloxacin, acriflavine, and tetraphenylphosphonium [ Morita98 ]. | V | -- | -- | -- | -- | -- | Y | 388 | 385 | 188 | 122 | 66 | -- | Y | 188 | 186 | 111 | 77 | 34
[NAME] | b3710 | JW3688 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.protein | The YidY protein is, based on sequence similarity and hydropathy analysis, a member of the major facilitator superfamily (MFS) [ Paulsen00  ]. Overexpression of the cloned yidY gene in a drug sensitive background strain resulted in a four-fold increase in resistance to chloramphenicol, ethidium bromide and TPP [ Nishino01  ]. | - | -- | -- | -- | -- | -- | Y | 395 | 392 | 157 | 61 | 96 | -- | Y | 221 | 218 | 76 | 25 | 51
mepA | [NAME] | JW2325 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | murein.DD.endopeptidase | mepA and pbpG are isozymes, check for SSL between them | M | -- | -- | -- | -- | Y | Y | 814 | 799 | 297 | 144 | 153 | Y | Y | 622 | 611 | 379 | 247 | 132
metK | b2942 | JW2909 | essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | methionine.adenosyltransferase.1 | In EcoCyc MetK is not part of the ubiquinone-8 biosynthesis but it provides S-adenosyl-L-methionine which used as substrate by many enzymes in this pathway | H | -- | -- | Y | 347.042 | Y | Y | 477 | 474 | 202 | 62 | 140 | Y | Y | 271 | 268 | 164 | 94 | 70
micA | b4442 | UNKW3110 | unknown | -- | CORE | CELL.ENVELOPE.INTEGRITY | -- | Small RNA. MicA is a small RNA that binds as an antisense RNA to the translation initiation region of ompA mRNA, blocking ribosome binding and downregulating OmpA expression. A micA deletion mutant is sensitive to cell envelope stress [ Hobbs10 ].  Interesting to look for SSL between B4442 and ompA | -- | -- | -- | -- | -- | Y | -- | 683 | 667 | 196 | 115 | 81 | Y | -- | 579 | 565 | 269 | 201 | 68
micC | b4427 | UNKW3110 | unknown | -- | CORE | CELL.ENVELOPE.INTEGRITY | -- | Small RNA. MicC is a small RNA that regulates expression of OmpC at the post-transcriptional level [ [NAME]  , Urban07  ]. | -- | -- | -- | -- | -- | Y | -- | 655 | 641 | 400 | 333 | 67 | Y | -- | 521 | 510 | 374 | 319 | 55
micF | [NAME] | UNKW3110 | unknown | -- | CORE | CELL.ENVELOPE.INTEGRITY,RESPONSE.TO.ANTIBIOTIC,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | -- | Small RNA. The MicF RNA [ Andersen87  ] is an antisense regulator of the translation of OmpF porin [ Andersen89  ] and the stability of OmpF mRNA [ Andersen89  , Deighan00  ]. MicF binds to OmpF mRNA [ Andersen90  ] and represses production of OmpF in response to environmental and/or stress conditions, including conditions of high osmolarity [ Aiba87  , Andersen89  ], low or moderate osmolarity [ Ramani94  ], heat [ Andersen89  ], ethanol [ Andersen89  ], salicylate [ Rosner91  , Ramani01  ], paraquat [ Chou93  ], and membrane perturbation [ Inoue97  ]. MicF activity has been implicated in resistance to antibiotic drugs [ Cohen88  , Hooper92  , Cambau93  , Chou93  , Ariza95  , [NAME]  , Balague01  ]. Interesting to look for SSL between [NAME] (microRNA) and ompF | -- | -- | -- | -- | -- | Y | -- | 676 | 660 | 245 | 170 | 75 | Y | -- | 545 | 534 | 355 | 276 | 79
minC | b1176 | JW1165 | non-essential | CY | CORE | CELL.DIVISION | cell.division.inhibitor | There are at least three model for action of [NAME], but in all three MinCD form a complex for acting together, and separate from MinE see review [PMID:17326815]. According to the nucleoid segregation model, the replication cycle produces a medial, nucleoid-free interstice that permits FtsZ assembly and cell division. Genetic data suggest that the division inhibitors MinC and MinD, which are concentrated at the cell poles, and the DNA-associated proteins SlmA in E. coli and Noc in B. subtilis, function in concert to ensure that FtsZ assembly is restricted to the DNA-free space at midcell [PMID:18396093]. -- | D | -- | -- | -- | -- | -- | Y | 503 | 495 | 144 | 72 | 72 | Y | Y | 307 | 302 | 112 | 61 | 51
minD | b1175 | JW1164 | essential | CY | CORE | CELL.DIVISION | membrane.ATPase.of.the.MinC.MinD.MinE.system | There are at least three model for action of [NAME], but in all three MinCD form a complex for acting together, and separate from MinE see review [PMID:17326815]. According to the nucleoid segregation model, the replication cycle produces a medial, nucleoid-free interstice that permits FtsZ assembly and cell division. Genetic data suggest that the division inhibitors MinC and MinD, which are concentrated at the cell poles, and the DNA-associated proteins SlmA in E. coli and Noc in B. subtilis, function in concert to ensure that FtsZ assembly is restricted to the DNA-free space at midcell [PMID:18396093]. -- | D | -- | -- | -- | -- | Y | Y | 781 | 770 | 477 | 194 | 283 | Y | Y | 507 | 499 | 321 | 241 | 80
minE | b1174 | JW1163 | essential | CY | CORE | CELL.DIVISION | cell.division.topological.specificity.factor | There are at least three model for action of [NAME], but in all three MinCD form a complex for acting together, and separate from MinE see review [PMID:17326815]. According to the nucleoid segregation model, the replication cycle produces a medial, nucleoid-free interstice that permits FtsZ assembly and cell division. Genetic data suggest that the division inhibitors MinC and MinD, which are concentrated at the cell poles, and the DNA-associated proteins SlmA in E. coli and Noc in B. subtilis, function in concert to ensure that FtsZ assembly is restricted to the DNA-free space at midcell [PMID:18396093]. -- | D | -- | -- | -- | -- | Y | -- | 683 | 674 | 249 | 137 | 112 | Y | -- | 629 | 622 | 342 | 290 | 52
mipA | b1782 | JW1771 | non-essential | OM | CORE | CELL.WALL.BIOGENESIS | scaffolding.protein.for.murein.synthesizing.machinery | MipA, MltA-interacting protein, is scaffolding protein that forms a trimer with PBP1B, a murein polymerase, and MltA, a murein hydrolase PMID:10037771] | M | -- | -- | -- | -- | -- | Y | 491 | 490 | 174 | 104 | 70 | -- | Y | 308 | 308 | 151 | 120 | 31
mltA | b2813 | JW2784 | non-essential | -- | CORE | CELL.DIVISION,CELL.SHAPE,CELL.WALL.BIOGENESIS | membrane.bound.lytic.murein.transglycosylase.A | Is one of six major lytic murein endotransglycosylases (slt, mltD, mltB, mltA, emtA, mltC) expressed in Escherichia coli, allowing for cell enlargement and division and also for localized opening of the peptidoglycan layer to allow the export of bulky compounds such as DNA, toxins, flagella, and fimbrial proteins [PMID:9642199]. | M | -- | -- | Y | 1.732 | Y | Y | 798 | 796 | 181 | 66 | 115 | Y | Y | 638 | 636 | 285 | 149 | 136
mltB | b2701 | JW2671 | non-essential | PE | CORE | CELL.DIVISION,CELL.SHAPE,CELL.WALL.BIOGENESIS | membrane.bound.lytic.murein.transglycosylase.B | Is one of six major lytic murein endotransglycosylases (slt, mltD, mltB, mltA, emtA, mltC) expressed in Escherichia coli, allowing for cell enlargement and division and also for localized opening of the peptidoglycan layer to allow the export of bulky compounds such as DNA, toxins, flagella, and fimbrial proteins [PMID:9642199]. | M | -- | -- | Y | 0.157 | Y | Y | 810 | 805 | 342 | 211 | 131 | Y | Y | 628 | 623 | 317 | 254 | 63
mltC | b2963 | JW5481 | non-essential | OM | CORE | CELL.DIVISION,CELL.SHAPE,CELL.WALL.BIOGENESIS | membrane.bound.lytic.murein.transglycosylase.C | Is one of six major lytic murein endotransglycosylases (slt, mltD, mltB, mltA, emtA, mltC) expressed in Escherichia coli, allowing for cell enlargement and division and also for localized opening of the peptidoglycan layer to allow the export of bulky compounds such as DNA, toxins, flagella, and fimbrial proteins [PMID:9642199]. | M | -- | -- | -- | -- | Y | Y | 797 | 793 | 268 | 107 | 161 | Y | Y | 600 | 596 | 305 | 199 | 106
mltD | b0211 | [NAME] | non-essential | -- | CORE | CELL.DIVISION,CELL.SHAPE,CELL.WALL.BIOGENESIS | predicted.membrane.bound.lytic.murein.transglycosylase.D | Is one of six major lytic murein endotransglycosylases (slt, mltD, mltB, mltA, emtA, mltC) expressed in Escherichia coli, allowing for cell enlargement and division and also for localized opening of the peptidoglycan layer to allow the export of bulky compounds such as DNA, toxins, flagella, and fimbrial proteins [PMID:9642199]. | M | -- | -- | Y | 0.772 | Y | Y | 810 | 798 | 262 | 146 | 116 | Y | Y | 601 | 594 | 231 | 125 | 106
motA | b1890 | JW1879 | non-essential | IM | FUNCTION-UNCERTAIN | NA | proton.conductor.component.of.flagella.motor | MotA and MotB comprise the stator element of the flagellar motor complex (EcoCyc) | N | -- | -- | -- | -- | Y | Y | 786 | 776 | 477 | 294 | 183 | Y | Y | 133 | 131 | 77 | 43 | 34
[NAME] | b1889 | JW1878 | non-essential | IM | FUNCTION-UNCERTAIN | NA | protein.that.enables.flagellar.motor.rotation | MotA and MotB comprise the stator element of the flagellar motor complex (EcoCyc) | N | -- | -- | -- | -- | Y | Y | 704 | 695 | 400 | 248 | 152 | Y | Y | 166 | 164 | 72 | 43 | 29
mpaA | b1326 | JW1319 | non-essential | -- | PREDICTED | CELL.WALL.BIOGENESIS | murein.peptide.amidase.A | Probably involved in recycling of peptidoglycan YcjG is an L-Ala-D/L-Glu epimerase that may play a role in the metabolism of murein peptide [EcoCyc]. MpaA is a murein peptide amidase that may act with YcjG in murein recycling [PMID:12511517].  [NAME] info related with this. | E | -- | -- | -- | -- | Y | Y | 797 | 792 | 273 | 102 | 171 | Y | Y | 625 | 621 | 301 | 75 | 226
mpl | b4233 | JW4192 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS | UDP.N.acetylmuramate.L.alanyl.gamma.D.glutamyl.meso.diaminopimelate.ligase | The mpl gene encodes UDP-N-acetylmuramate:L-alanyl-?-D-glutamyl-meso-diaminopimelate ligase, which acts in murein recycling by allowing ligation of the tripeptide L-Ala-D-Glu-mesoA2pm with UDP-MurNAc and reincorporation into peptidoglycan. L-Ala-D-Glu-mesoA2pm is released while remodelling the cell wall during growth [PMID:8808921]. Overexpression of mpl can complement the conditional growth defect of a murC mutant [PMID:17384195] -- | M | -- | -- | -- | -- | Y | Y | 817 | 809 | 147 | 59 | 88 | Y | Y | 676 | 668 | 398 | 270 | 128
mppA | b1329 | JW1322 | non-essential | PE | CORE | OLIGOPEPTIDE.TRANSPORT,CELL.WALL.BIOGENESIS | murein.tripeptide.L.ala.gamma.D.glutamyl.meso.DAP.transporter.subunit.periplasmic.binding.component.of.ABC.superfamily | OppA is the periplasmic substrate-binding component of the oligopeptide ABC transporter, however MppA can replace OppA as a periplasmic-binding component of the transporter when it binds murein tripeptides [PMID:9495761]. The system has been observed to function in oligopeptide uptake, as well as recycling of cell wall peptides [PMID:3301822]. [NAME] (2009) shown GC-based functional inferences of MppA  with both opp- and dpp-(dipeptide transport) systems, suggesting interacts with both. Thus may be interesting if these two systems show SSL's | E | -- | -- | -- | -- | Y | Y | 815 | 810 | 247 | 87 | 160 | Y | Y | 248 | 246 | 91 | 46 | 45
mraY | b0087 | JW0085 | essential | IM | CORE | CELL.WALL.BIOGENESIS | phospho.N.acetylmuramoyl.pentapeptide.transferase | 7th step in biosynthesis of Lipid II (peptidoglycan) | M | -- | -- | -- | -- | Y | Y | 525 | 510 | 201 | 108 | 93 | Y | Y | 305 | 297 | 179 | 87 | 92
[NAME] | b3396 | JW3359 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | fused.penicillin.binding.protein.1a.murein.transglycosylase.murein.transpeptidase | There are four PBP transglycosilases in E. coli (mtgA, pbpC, mrcB, [NAME]) | M | -- | -- | Y | 1.429 | Y | Y | 674 | 670 | 294 | 170 | 124 | Y | Y | 580 | 577 | 249 | 154 | 95
mrcB | b0149 | JW0145 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | fused.glycosyl.transferase.transpeptidase | There are four PBP transglycosilases in E. coli (mtgA, pbpC, mrcB, [NAME]) | M | -- | -- | Y | 0.945 | Y | Y | 816 | 802 | 229 | 57 | 172 | Y | Y | 622 | 612 | 202 | 64 | 138
mrdA | b0635 | JW0630 | essential | PE | CORE | CELL.SHAPE,CELL.WALL.BIOGENESIS | transpeptidase.involved.in.peptidoglycan.synthesis.penicillin.binding.protein.2 | Both mrdA(pbpA;pbp2) and mrdB(rodB) are involved in both cell.shape and cell.wall.biogenesis. SSL's couldn't be determined by eSGA because are neighbor genes | M | -- | -- | -- | -- | Y | Y | 810 | 798 | 345 | 103 | 242 | Y | Y | 257 | 250 | 116 | 44 | 72
mrdB | b0634 | JW0629 | essential | IM | CORE | CELL.SHAPE,CELL.WALL.BIOGENESIS | cell.wall.shape.determining.protein | Both mrdA(pbpA;pbp2) and mrdB(rodB) are involved in both cell.shape and cell.wall.biogenesis. SSL's couldn't be determined by eSGA because are neighbor genes | D | -- | -- | -- | -- | Y | -- | 222 | 217 | 158 | 104 | 54 | Y | -- | 168 | 163 | 111 | 85 | 26
mreB | b3251 | [NAME] | essential | CY | CORE | CELL.DIVISION,CHROMOSOME.SEGREGATION,CELL.SHAPE,CELL.WALL.BIOGENESIS | cell.wall.structural.complex.MreBCD.actin.like.component.MreB | Link between Cell.shape, Cell.wall.biogenesis, and Chromosome.segregation. MreB is responsible for proper chromosome segregation and movement. MreC is also believed to interact with [NAME] (PBP2), which is responsible for lateral wall peptidoglycan synthesis, suggesting a role for the MreBCD complex in directing peptidoglycan formation through this interaction [PMID:15612918] -- | D | -- | -- | Y | 210.659 | -- | Y | 276 | 271 | 123 | 77 | 46 | Y | Y | 198 | 195 | 152 | 95 | 57
mreC | b3250 | JW3219 | essential | -- | CORE | CELL.DIVISION,CHROMOSOME.SEGREGATION,CELL.SHAPE,CELL.WALL.BIOGENESIS | cell.wall.structural.complex.MreBCD.transmembrane.component.MreC | Link between Cell.shape, Cell.wall.biogenesis, and Chromosome.segregation. MreB is responsible for proper chromosome segregation and movement. MreC is also believed to interact with [NAME] (PBP2), which is responsible for lateral wall peptidoglycan synthesis, suggesting a role for the MreBCD complex in directing peptidoglycan formation through this interaction [PMID:15612918] -- | M | -- | -- | -- | -- | Y | Y | 476 | 465 | 221 | 118 | 103 | Y | Y | 284 | 275 | 178 | 127 | 51
mreD | b3249 | JW3218 | essential | IM | CORE | CELL.DIVISION,CHROMOSOME.SEGREGATION,CELL.SHAPE,CELL.WALL.BIOGENESIS | cell.wall.structural.complex.MreBCD.transmembrane.component.MreD | Link between Cell.shape, Cell.wall.biogenesis, and Chromosome.segregation. MreB is responsible for proper chromosome segregation and movement. MreC is also believed to interact with [NAME] (PBP2), which is responsible for lateral wall peptidoglycan synthesis, suggesting a role for the MreBCD complex in directing peptidoglycan formation through this interaction [PMID:15612918] -- | M | -- | -- | -- | -- | Y | Y | 800 | 787 | 395 | 134 | 261 | Y | Y | 537 | 529 | 278 | 158 | 120
[NAME] | b0914 | JW0897 | essential | IM | CORE | PHOSPHOLIPIDS,LPS.AND.ECA | fused.lipid.transporter.subunits.of.ABC.superfamily.membrane.component.ATP.binding.component | MsbA is a key transporter of Lipid A across the IM [PMID:9575204] presumably coordinated with the Lpt- system. Disruption of the pathway at any step after [NAME] leads to indistinguishable phenotypes: in all cases, LPS accumulates in the outer leaflet of the IM. Therefore, we cannot conduct epistasis analysis to determine exact pathway order. We can only rely on the information about the cellular location of these proteins to predict temporal order in the pathway as follows: MsbA followed by a complex of LptB, [NAME], [NAME] and LptG, followed by LptA and finally by a complex of LptD and LptE [PMID:19633680]. It has also been suggested to be the flippase of phospholipids (glycerophospholipids) [PMID:9575204], and depletion or loss of function of MsbA results in the accumulation of lipid A and phospholipids in the inner membrane of E. coli [PMID:9575204,PMID: 11278265]. However, recently MsbA was demonstrated to don't be required for phospholipid transport in Neisseria meningitidis [PMID:16123038]. Thus it's role as flippase of phospholipids is not so clear. | V | -- | -- | Y | 24.296 | Y | -- | 687 | 676 | 191 | 51 | 140 | Y | -- | 30 | 30 | 22 | 12 | 10
mscL | b3291 | JW3252 | non-essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | mechanosensitive.channel | MscK, mscS, [NAME] and [NAME] are potassium-dependent mechanosensitive (MS) channels each with different conductance. Interesting to look for SSL among them. Mutation, deletion, and complementation studies using patch clamp conductance measurements have characterized two E.coli genes that are required for MscS activity: yggB and kefA. Deletion of yggB in kefA-deletion mutants eliminates all MscS activity and complementation with [NAME] on a moderate copy number plasmid restores MscS activity (EcoCyc) | M | -- | -- | -- | -- | Y | Y | 787 | 771 | 366 | 100 | 266 | Y | Y | 129 | 129 | 39 | 21 | 18
mscS | b2924 | JW2891 | non-essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | mechanosensitive.channel | MscK, mscS, [NAME] and [NAME] are potassium-dependent mechanosensitive (MS) channels each with different conductance. Interesting to look for SSL among them. Mutation, deletion, and complementation studies using patch clamp conductance measurements have characterized two E.coli genes that are required for MscS activity: yggB and kefA. Deletion of yggB in kefA-deletion mutants eliminates all MscS activity and complementation with [NAME] on a moderate copy number plasmid restores MscS activity (EcoCyc) | M | -- | -- | -- | -- | Y | Y | 800 | 794 | 227 | 109 | 118 | Y | Y | 656 | 650 | 298 | 176 | 122
mtgA | b3208 | JW3175 | non-essential | PE | CORE | CELL.DIVISION,CELL.WALL.BIOGENESIS | biosynthetic.peptidoglycan.transglycosylase | There are four PBP transglycosilases in E. coli (mtgA, pbpC, mrcB, [NAME]). MtgA interacts with Penicillin-Binding Protein 3 (FtsI), FtsW, and FtsN [PMID:18165305] | M | -- | -- | -- | -- | Y | Y | 800 | 783 | 260 | 131 | 129 | Y | Y | 596 | 585 | 286 | 177 | 109
mtr | b3161 | JW3130 | non-essential | IM | FUNCTION-UNCERTAIN | NA | tryptophan.transporter.of.high.affinity | Mtr is one of three known transporters for tryptophan in E. coli, the others being TnaB and AroP. Mtr is a high affinity transporter for tryptophan (Km of about 2 ?M) [ Brown70  ], and is also able to transport indole [ Yanofsky91  ]. | E | -- | -- | -- | -- | -- | Y | 363 | 358 | 161 | 70 | 91 | -- | Y | 199 | 197 | 81 | 41 | 40
mukB | b0924 | JW0907 | essential | CY | CORE | CELL.DIVISION,CHROMOSOME.SEGREGATION | [NAME] | The MukB protein is involved in chromosome condensation and partitioning. The MukEF complex appears to compete with DNA for binding to MukB. The fully assembled MukBEF complex is unable to bind DNA; addition of MukEF to DNA-bound MukB displaces MukB from the DNA [PMID:16982609]. Supressors of the mukB null mutant phenotype have been isolated with [NAME], smbA, msmA, msmB, msmC, smbB, crcA, cspE, crcB, topA, and gyrB (see EcoCyc for refs) -- | D | -- | -- | Y | 37.896 | -- | Y | 388 | 383 | 178 | 78 | 100 | -- | Y | 203 | 199 | 118 | 70 | 48
murA | b3189 | JW3156 | essential | CY | CORE | CELL.WALL.BIOGENESIS | UDP.N.acetylglucosamine.1.carboxyvinyltransferase | 1st step in biosynthesis of Lipid II (peptidoglycan) | M | -- | -- | Y | 50.691 | Y | Y | 791 | 776 | 357 | 122 | 235 | Y | Y | 184 | 179 | 113 | 68 | 45
murB | b3972 | JW3940 | essential | CY | CORE | CELL.WALL.BIOGENESIS | UDP.N.acetylenolpyruvoylglucosamine.reductase.FAD.binding | 2nd step in biosynthesis of Lipid II (peptidoglycan) | M | -- | -- | Y | 18.166 | Y | Y | 803 | 797 | 318 | 85 | 233 | Y | Y | 575 | 572 | 238 | 176 | 62
murC | b0091 | JW0089 | essential | CY | CORE | CELL.WALL.BIOGENESIS | UDP.N.acetylmuramate.L.alanine.ligase | 3rd step in biosynthesis of Lipid II (peptidoglycan) along MurI | M | -- | -- | -- | -- | Y | Y | 800 | 783 | 315 | 58 | 257 | Y | Y | 637 | 629 | 266 | 130 | 136
murD | b0088 | JW0086 | essential | CY | CORE | CELL.WALL.BIOGENESIS | UDP.N.acetylmuramoyl.L.alanine.D.glutamate.ligase | 4th step in biosynthesis of Lipid II (peptidoglycan) | M | -- | -- | -- | -- | Y | Y | 812 | 795 | 398 | 53 | 345 | Y | Y | 637 | 624 | 284 | 142 | 142
murE | b0085 | JW0083 | essential | CY | CORE | CELL.WALL.BIOGENESIS | UDP.N.acetylmuramoyl.L.alanyl.D.glutamate.meso.diaminopimelate.ligase | 5th step in biosynthesis of Lipid II (peptidoglycan) | M | -- | -- | Y | 31.722 | Y | Y | 814 | 797 | 302 | 78 | 224 | Y | Y | 592 | 582 | 262 | 133 | 129
murF | b0086 | JW0084 | essential | CY | CORE | CELL.WALL.BIOGENESIS | UDP.N.acetylmuramoyl.tripeptide.D.alanyl.D.alanine.ligase | 6th step in biosynthesis of Lipid II (peptidoglycan) | M | -- | -- | Y | 19.117 | -- | Y | 391 | 377 | 184 | 62 | 122 | Y | Y | 216 | 211 | 138 | 107 | 31
murG | b0090 | JW0088 | essential | IM | CORE | CELL.WALL.BIOGENESIS | N.acetylglucosaminyl.transferase | 8th step in biosynthesis of Lipid II (peptidoglycan) | M | -- | -- | Y | 12.39 | Y | Y | 800 | 784 | 324 | 60 | 264 | Y | Y | 621 | 611 | 239 | 155 | 84
murI | b3967 | JW5550 | essential | CY | CORE | CELL.WALL.BIOGENESIS | glutamate.racemase | 3rd step in biosynthesis of Lipid II (peptidoglycan) along [NAME] | M | -- | -- | Y | 13.395 | Y | Y | 523 | 518 | 240 | 118 | 122 | Y | Y | 256 | 255 | 153 | 129 | 24
mviN | b1069 | JW1056 | essential | IM | CORE | CELL.WALL.BIOGENESIS | predicted.inner.membrane.protein | MviN ([NAME]) was determined by genetic and biochemical data as required for peptidoglycan biosynthesis and was suggested as the flippase of Lipid II [PMID:18832143]. The gene encoding [NAME] is essential in E. coli and has four homologs in B. subtilis, including SpoVB, which can compensate for cross-species knockouts. SpoVB has been reported to be necessary for spore cortex peptidoglycan synthesis during sporulation. However B. subtilis strains lacking these four proteins have no defects in growth, indicating that they likely do not serve as lipid II flippases in this organism [PMID:19666716]. or that there are other genes that can buffer their lost in B. subtilis. | R | -- | -- | -- | -- | Y | -- | 702 | 682 | 316 | 171 | 145 | Y | -- | 628 | 612 | 286 | 180 | 106
nanA | b3225 | JW3194 | non-essential | CY | FUNCTION-UNCERTAIN | NA | N.acetylneuraminate.lyase | Sialic acids are nine-carbon keto sugars that mediate a variety of cell-cell and cell-molecule interactions in eukaryotes and can be utilized by pathogens to evade the host immune response. Other bacteria, including E. coli K-12, can utilize N-acetylneuraminate, the most common form of sialic acid, as a sole source of carbon [ Vimr85  , Plumbridge99  ]. | EM | -- | -- | -- | -- | Y | Y | 790 | 776 | 326 | 123 | 203 | Y | Y | 642 | 629 | 284 | 190 | 94
nanE | b3223 | JW3192 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.N.acetylmannosamine.6.P.epimerase | Sialic acids are nine-carbon keto sugars that mediate a variety of cell-cell and cell-molecule interactions in eukaryotes and can be utilized by pathogens to evade the host immune response. Other bacteria, including E. coli K-12, can utilize N-acetylneuraminate, the most common form of sialic acid, as a sole source of carbon [ Vimr85  , Plumbridge99  ]. | G | -- | -- | Y | 6.814 | -- | Y | 393 | 382 | 110 | 58 | 52 | -- | Y | 216 | 206 | 81 | 46 | 35
nanK | b3222 | JW5538 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.N.acetylmannosamine.kinase | Sialic acids are nine-carbon keto sugars that mediate a variety of cell-cell and cell-molecule interactions in eukaryotes and can be utilized by pathogens to evade the host immune response. Other bacteria, including E. coli K-12, can utilize N-acetylneuraminate, the most common form of sialic acid, as a sole source of carbon [ Vimr85  , Plumbridge99  ]. | KG | -- | -- | -- | -- | Y | Y | 793 | 778 | 310 | 163 | 147 | Y | Y | 690 | 678 | 246 | 86 | 160
napD | b2207 | JW2195 | non-essential | CY | FUNCTION-UNCERTAIN | NA | assembly.protein.for.periplasmic.nitrate.reductase | assembly.protein.for.periplasmic.nitrate.reductase | P | -- | -- | Y | 1.045 | -- | Y | 395 | 393 | 155 | 63 | 92 | -- | Y | 216 | 215 | 91 | 33 | 58
nfrA | b0568 | JW0557 | non-essential | OM | FUNCTION-UNCERTAIN | NA | bacteriophage.N4.receptor.outer.membrane.subunit | Isolation of spontaneous N4 bacteriophage-resistant mutants of E. coli K-12 strain SC1100, cloning of the affected genes, and subsequent complementation experiments revealed that nfrA is important in N4 adsorption. | R | -- | -- | Y | 1.075 | -- | Y | 390 | 382 | 186 | 79 | 107 | -- | Y | 201 | 199 | 117 | 57 | 60
nfrB | b0569 | JW0558 | non-essential | IM | FUNCTION-UNCERTAIN | NA | bacteriophage.N4.receptor.inner.membrane.subunit | Isolation of spontaneous N4 bacteriophage-resistant mutants of E. coli K-12 strain SC1100, cloning of the affected genes, and subsequent complementation experiments revealed that nfrB is important in N4 adsorption. | - | -- | -- | Y | 2.786 | -- | Y | 392 | 382 | 93 | 31 | 62 | -- | Y | 209 | 204 | 82 | 35 | 47
nlpB | b2477 | JW2462 | non-essential | -- | CORE | PROTEIN.SECRETION | [NAME] | For a review of OM biogenesis see [PMID:19270402] -- | M | -- | -- | -- | -- | Y | Y | 798 | 797 | 281 | 125 | 156 | Y | Y | 610 | 610 | 332 | 198 | 134
nlpC | b1708 | JW1698 | non-essential | PE | FUNCTION-UNCERTAIN | CELL.WALL.BIOGENESIS | predicted.lipoprotein | [NAME] of Escherichia coli exhibits high sequence similarity to the p60 proteins of [NAME] species and to CwlF of Bacillus subtilis. In B.subtilis, [NAME] is a cell wall hydrolase involved in the cell separation process [PMID:9573210] Check SSLs vs. Cell.wall.biogenesis to see is is like the B. subtilis homolog. The NlpC lipoprotein of Escherichia coli exhibits high sequence similarity to the p60 proteins of [NAME] species and to CwlF of Bacillus subtilis [ Ishikawa98a  ]. In B.subtilis, [NAME] is a cell wall hydrolase involved in the cell separation process [ Ishikawa98a  ].  [NAME] et [NAME] show operon rearrangements with murI, lpxB, wcaL, arnC; and PhilProfile and GeneFusion with spr which is also in the EMAP. pbpG(PBP7) acts as a multicopy suppressor of spr deletion mutations when its D-alanyl-D-alanine endopeptidase activity is intact [ Hara96  ]. | M | -- | -- | -- | -- | Y | Y | 818 | 809 | 283 | 123 | 160 | Y | Y | 202 | 201 | 107 | 47 | 60
nlpD | b2742 | JW2712 | non-essential | -- | FUNCTION-UNCERTAIN | CELL.DIVISION | predicted.outer.membrane.lipoprotein | NlpD is thought to function in cell division [EcoCyc]. An NlpD-Mcherry fusion protein localises to the septal ring division site. envC nlpD double null mutants show significant defects in cell separation resulting in very long chain formation due to a defect in septal peptidoglycan splitting [PMID:19525345] | M | -- | -- | -- | -- | Y | Y | 811 | 805 | 251 | 73 | 178 | Y | Y | 644 | 639 | 282 | 110 | 172
nlpE | b0192 | JW0188 | non-essential | PE | FUNCTION-UNCERTAIN | NA | lipoprotein.involved.with.copper.homeostasis.and.adhesion | NlpE is an outer membrane lipoprotein [ Snyder95  ]. Activation of the Cpx signaling pathway in response to surface interactions such as adhesion requires NlpE [ Otto02  ], while activation in response to envelope stress does not require NlpE [ DiGiuseppe03  ]. This proteins could form another class called 'Cell.proliferation', perhaps together with 'Biofilm.formation' | MP | -- | -- | -- | -- | Y | Y | 814 | 797 | 191 | 47 | 144 | Y | Y | 579 | 565 | 233 | 108 | 125
nudD | b2051 | JW5335 | non-essential | CY | FUNCTION-UNCERTAIN | CELL.WALL.BIOGENESIS,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | GDP.mannose.mannosyl.hydrolase | Predicted by [NAME] et al as participating in M-antigen biosynthesis [PMID:8759852]. BudD(WcaH,Gmm). EcoCyc: GDP-mannose mannosyl hydrolase (GDPMH) is able to hydrolyze both GDP-mannose and GDP-glucose. Its biological role is as yet unknown, though it may participate in the regulation of cell wall biosynthesis by influencing the cell concentration of GDP-mannose or GDP-glucose [PMID:7592609]. Uniprot: same about cell wall and might also be involved in the biosynthesis of the slime polysaccharide colanic acid, probably at the level of synthesis of nucleotide sugar precursors of CA [PMID:8759852] | LR | -- | -- | -- | -- | Y | Y | 528 | 499 | 206 | 62 | 144 | Y | Y | 359 | 334 | 118 | 48 | 70
ompA | b0957 | JW0940 | non-essential | OM | CORE | CELL.ENVELOPE.INTEGRITY | outer.membrane.protein.A.3a.II*.G.d | micA is a small RNA that binds as an antisense RNA to the translation initiation region of ompA mRNA, blocking ribosome binding and downregulating OmpA expression. A micA deletion mutant is sensitive to cell envelope stress [ Hobbs10 ].  Interesting to look for SSL between B4442 and ompA | M | -- | -- | -- | -- | Y | Y | 745 | 735 | 288 | 159 | 129 | Y | Y | 551 | 546 | 179 | 65 | 114
ompC | b2215 | JW2203 | non-essential | OM | CORE | CELL.ENVELOPE.INTEGRITY | outer.membrane.porin.protein.C | -- | M | -- | -- | Y | 0.824 | Y | Y | 814 | 809 | 268 | 135 | 133 | Y | Y | 192 | 192 | 119 | 67 | 52
ompF | b0929 | JW0912 | non-essential | OM | CORE | CELL.ENVELOPE.INTEGRITY | outer.membrane.porin.1a.[NAME].F | The MicF RNA [ Andersen87  ] is an antisense regulator of the translation of OmpF porin [ Andersen89  ] and the stability of OmpF mRNA [ Andersen89  , Deighan00  ]. MicF binds to OmpF mRNA [ Andersen90  ] and represses production of OmpF in response to environmental and/or stress conditions, including conditions of high osmolarity [ Aiba87  , Andersen89  ], low or moderate osmolarity [ Ramani94  ], heat [ Andersen89  ], ethanol [ Andersen89  ], salicylate [ Rosner91  , Ramani01  ], paraquat [ Chou93  ], and membrane perturbation [ Inoue97  ]. MicF activity has been implicated in resistance to antibiotic drugs [ Cohen88  , Hooper92  , Cambau93  , Chou93  , Ariza95  , [NAME]  , Balague01  ]. Interesting to look for SSL between [NAME] (microRNA) and ompF | M | -- | -- | -- | -- | Y | Y | 809 | 799 | 297 | 86 | 211 | Y | Y | 642 | 634 | 231 | 67 | 164
ompG | b1319 | JW1312 | non-essential | OM | FUNCTION-UNCERTAIN | NA | outer.membrane.porin | OmpG is an efficient, nonspecific channel for mono-, di, and trisaccharides with sizes less than 600 Daltons although liposome swelling assays have demonstrated that OmpG is capable of transporting large solutes [ Fajardo98  ]. ompG expression in E. coli K-12 occurs only due to rare chromosomal mutations [ Misra89  , [NAME]. | - | -- | -- | -- | -- | -- | Y | 395 | 387 | 141 | 55 | 86 | -- | Y | 199 | 195 | 82 | 49 | 33
ompL | b3875 | JW3846 | non-essential | OM | FUNCTION-UNCERTAIN | NA | predicted.outer.membrane.porin.L | OmpL is a member of the OmpG porin Family. It has been shown to localize to the outer membrane and exhibits porin type properties allowing a non-specific group of solutes smaller than 600 Daltons to pass into and out of the periplasm. [ Dartigalon00  ] | - | -- | -- | -- | -- | -- | Y | 388 | 388 | 209 | 156 | 53 | -- | Y | 203 | 203 | 122 | 96 | 26
ompN | b1377 | JW1371 | non-essential | OM | FUNCTION-UNCERTAIN | NA | outer.membrane.pore.protein.N.non.specific | Check SSL's with 'Biofilm.formation' related genes because M3D data shows that ompN is more expressed during Biofilm formation conditions [jdime_observations]. Although under typical laboratory growth conditions OmpN is not highly expressed, when overexpressed it operates as a ion porin with single-channel conductance properties similar to those of OmpC [Prilipov98]. | M | -- | -- | -- | -- | Y | Y | 727 | 716 | 268 | 144 | 124 | Y | Y | 610 | 600 | 310 | 153 | 157
ompT | b0565 | JW0554 | non-essential | OM | FUNCTION-UNCERTAIN | NA | DLP12.prophage.outer.membrane.protease.VII.outer.membrane.protein.3b | OmpT is an outer membrane protease with specificity for paired basic residues [ Sugimura88  ]. OmpT is active under extreme denaturing conditions and shows a preference for denatured substrates [ White95a  ]. It is responsible for hydrolysis of the antimicrobial peptide protamine [ Stumpe98  ] and is a virulence determinant in urinary tract infections [ [NAME]  ].  Could for another class called 'Protein.degradation' | M | -- | -- | -- | -- | Y | Y | 479 | 472 | 145 | 92 | 53 | Y | Y | 277 | 274 | 126 | 68 | 58
ompW | b1256 | JW1248 | non-essential | OM | FUNCTION-UNCERTAIN | CELL.ENVELOPE.INTEGRITY | outer.membrane.protein.W | OmpW is a receptor for Colicin S4 in the Colicin S4 Transport System along TolA, TolQ, TolR, TolB, [NAME], and Pal proteins -- | M | -- | -- | -- | -- | Y | Y | 818 | 807 | 202 | 78 | 124 | Y | Y | 685 | 675 | 287 | 68 | 219
ompX | b0814 | JW0799 | non-essential | OM | FUNCTION-UNCERTAIN | NA | outer.membrane.protein | Deletion of ompX leads to an increase in cell-surface contact in fimbriated strains of E. coli, and production of type 1 fimbriae is upregulated. Furthermore, ompX mutants show impaired motility, increased EPS production, and increased tolerance to SDS and hydrophobic antibiotics. In nonfimbriated strains, deletion of ompX led to a decrease in cell surface contact [ Otto04  ]. So this proteins could form a separate class 'Biofilm.formation', but here I'm just wondering if they do have SSL's | M | -- | -- | -- | -- | -- | Y | 486 | 482 | 275 | 188 | 87 | Y | Y | 285 | 282 | 163 | 131 | 32
omrA | [NAME] | UNKW3110 | unknown | -- | CORE | CELL.ENVELOPE.INTEGRITY | -- | Small RNA. OmrA is a small RNA of approximately 88 nt in length [ Argaman01  , Wassarman01  ] that is involved in regulating the protein composition of the outer membrane [ Guillier06  ]. OmrA was shown to negatively regulate the levels of ompT, cirA, fecA, fepA [ Guillier06  ] and ompR [ Guillier08  ] | -- | -- | -- | -- | -- | Y | -- | 688 | 673 | 235 | 142 | 93 | Y | -- | 630 | 616 | 293 | 231 | 62
oppA | b1243 | JW1235 | non-essential | PE | CORE | OLIGOPEPTIDE.TRANSPORT,CELL.WALL.BIOGENESIS | oligopeptide.transporter.subunit.periplasmic.binding.component.of.ABC.superfamily | OppA is the periplasmic substrate-binding component of the oligopeptide ABC transporter, however MppA can replace OppA as a periplasmic-binding component of the transporter when it binds murein tripeptides [PMID:9495761]. The system has been observed to function in oligopeptide uptake, as well as recycling of cell wall peptides [PMID:3301822]. [NAME] (2009) shown GC-based functional inferences of MppA  with both opp- and dpp-(dipeptide transport) systems, suggesting interacts with both. Thus may be interesting if these two systems show SSL's | E | -- | -- | -- | -- | Y | Y | 786 | 776 | 357 | 143 | 214 | Y | Y | 637 | 629 | 219 | 68 | 151
oppB | b1244 | JW1236 | non-essential | IM | CORE | OLIGOPEPTIDE.TRANSPORT,CELL.WALL.BIOGENESIS | oligopeptide.transporter.subunit.membrane.component.of.ABC.superfamily | OppA is the periplasmic substrate-binding component of the oligopeptide ABC transporter, however MppA can replace OppA as a periplasmic-binding component of the transporter when it binds murein tripeptides [PMID:9495761]. The system has been observed to function in oligopeptide uptake, as well as recycling of cell wall peptides [PMID:3301822]. [NAME] (2009) shown GC-based functional inferences of MppA  with both opp- and dpp-(dipeptide transport) systems, suggesting interacts with both. Thus may be interesting if these two systems show SSL's | EP | -- | -- | -- | -- | -- | Y | 360 | 353 | 218 | 199 | 19 | Y | Y | 163 | 160 | 94 | 79 | 15
oppC | b1245 | JW1237 | non-essential | IM | CORE | OLIGOPEPTIDE.TRANSPORT,CELL.WALL.BIOGENESIS | oligopeptide.transporter.subunit.membrane.component.of.ABC.superfamily | OppA is the periplasmic substrate-binding component of the oligopeptide ABC transporter, however MppA can replace OppA as a periplasmic-binding component of the transporter when it binds murein tripeptides [PMID:9495761]. The system has been observed to function in oligopeptide uptake, as well as recycling of cell wall peptides [PMID:3301822]. [NAME] (2009) shown GC-based functional inferences of MppA  with both opp- and dpp-(dipeptide transport) systems, suggesting interacts with both. Thus may be interesting if these two systems show SSL's | EP | -- | -- | -- | -- | Y | Y | 711 | 701 | 370 | 274 | 96 | Y | Y | 140 | 137 | 78 | 51 | 27
oppD | b1246 | JW1238 | non-essential | -- | CORE | OLIGOPEPTIDE.TRANSPORT,CELL.WALL.BIOGENESIS | oligopeptide.transporter.subunit.ATP.binding.component.of.ABC.superfamily | OppA is the periplasmic substrate-binding component of the oligopeptide ABC transporter, however MppA can replace OppA as a periplasmic-binding component of the transporter when it binds murein tripeptides [PMID:9495761]. The system has been observed to function in oligopeptide uptake, as well as recycling of cell wall peptides [PMID:3301822]. [NAME] (2009) shown GC-based functional inferences of MppA  with both opp- and dpp-(dipeptide transport) systems, suggesting interacts with both. Thus may be interesting if these two systems show SSL's | EP | -- | -- | -- | -- | Y | Y | 792 | 782 | 276 | 172 | 104 | Y | Y | 617 | 608 | 342 | 231 | 111
oppF | b1247 | JW1239 | non-essential | IM | CORE | OLIGOPEPTIDE.TRANSPORT,CELL.WALL.BIOGENESIS | oligopeptide.transporter.subunit.ATP.binding.component.of.ABC.superfamily | OppA is the periplasmic substrate-binding component of the oligopeptide ABC transporter, however MppA can replace OppA as a periplasmic-binding component of the transporter when it binds murein tripeptides [PMID:9495761]. The system has been observed to function in oligopeptide uptake, as well as recycling of cell wall peptides [PMID:3301822]. [NAME] (2009) shown GC-based functional inferences of MppA  with both opp- and dpp-(dipeptide transport) systems, suggesting interacts with both. Thus may be interesting if these two systems show SSL's | E | -- | -- | -- | -- | Y | Y | 716 | 708 | 389 | 281 | 108 | Y | Y | 162 | 158 | 95 | 47 | 48
osmB | b1283 | JW1275 | non-essential | PE | CORE | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | [NAME] | The lipoprotein osmB gene of Escherichia coli has been shown to be inducible by both osmotic stress [ Jung89  ] and growth phase signals [ Jung90  ]. | - | -- | -- | -- | -- | -- | Y | 395 | 388 | 167 | 130 | 37 | -- | Y | 203 | 200 | 78 | 38 | 40
osmC | b1482 | JW1477 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | osmotically.inducible.stress.inducible.membrane.protein | Expression of osmC is growth phase-regulated and osmotically inducible [ Gutierrez91  , Bouvier98  ]. osmC mutants show increased sensitivity to oxidative stress [ Conter01  ] | O | -- | -- | Y | 1.205 | Y | Y | 752 | 741 | 213 | 79 | 134 | Y | Y | 710 | 701 | 298 | 73 | 225
osmY | b4376 | JW4338 | non-essential | PE | CORE | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | periplasmic.protein | Mutation of osmY resulted in increases sensitivity to hyperosmotic stress [ Yim92  ]. Expression of osmY is induced under conditions of hyperosmotic stress [ Barron86  ]. | R | -- | -- | Y | 15.707 | -- | Y | 351 | 346 | 143 | 98 | 45 | -- | Y | 175 | 172 | 70 | 41 | 29
oxyS | b4458 | UNKW3110 | unknown | -- | FUNCTION-UNCERTAIN | NA | -- | -- | -- | -- | -- | -- | -- | Y | -- | 691 | 675 | 238 | 143 | 95 | Y | -- | 536 | 525 | 385 | 330 | 55
paaA | b1388 | JW1383 | non-essential | CY | CORE | FAD | predicted.multicomponent.oxygenase.reductase.subunit.for.phenylacetic.acid.degradation | -- | S | -- | -- | Y | 2.214 | -- | Y | 390 | 382 | 116 | 50 | 66 | -- | Y | 201 | 197 | 85 | 47 | 38
paaB | b1389 | JW1384 | non-essential | -- | CORE | FAD | predicted.multicomponent.oxygenase.reductase.subunit.for.phenylacetic.acid.degradation | -- | Q | -- | -- | -- | -- | -- | Y | 395 | 387 | 121 | 46 | 75 | -- | Y | 214 | 212 | 77 | 28 | 49
paaC | b1390 | JW1385 | non-essential | CY | CORE | FAD | predicted.multicomponent.oxygenase.reductase.subunit.for.phenylacetic.acid.degradation | -- | S | -- | -- | -- | -- | -- | Y | 392 | 384 | 94 | 36 | 58 | Y | Y | 199 | 196 | 85 | 55 | 30
paaD | b1391 | JW5217 | non-essential | -- | CORE | FAD | predicted.multicomponent.oxygenase.reductase.subunit.for.phenylacetic.acid.degradation | -- | R | -- | -- | Y | 0.487 | -- | Y | 392 | 384 | 115 | 53 | 62 | Y | Y | 209 | 205 | 79 | 28 | 51
paaE | b1392 | JW1387 | non-essential | CY | CORE | FAD | predicted.multicomponent.oxygenase.reductase.subunit.for.phenylacetic.acid.degradation | -- | C | -- | -- | -- | -- | -- | Y | 369 | 362 | 198 | 129 | 69 | Y | Y | 195 | 192 | 117 | 59 | 58
paaF | b1393 | JW1388 | non-essential | IM | CORE | FAD | enoyl.CoA.hydratase.isomerase | -- | I | -- | -- | Y | 0.699 | Y | Y | 797 | 784 | 245 | 148 | 97 | Y | Y | 150 | 147 | 48 | 23 | 25
paaG | b1394 | JW1389 | non-essential | CY | CORE | FAD | acyl.CoA.hydratase | -- | I | -- | -- | -- | -- | Y | Y | 795 | 782 | 362 | 194 | 168 | Y | Y | 155 | 153 | 71 | 33 | 38
paaH | b1395 | JW1390 | non-essential | CY | CORE | FAD | 3.hydroxybutyryl.CoA.dehydrogenase | -- | I | -- | -- | -- | -- | Y | Y | 785 | 772 | 398 | 278 | 120 | Y | Y | 115 | 112 | 92 | 83 | 9
paaJ | b1397 | JW1392 | non-essential | CY | CORE | FAD | predicted.beta.ketoadipyl.CoA.thiolase | -- | I | -- | -- | -- | -- | Y | Y | 800 | 787 | 233 | 65 | 168 | Y | Y | 661 | 650 | 221 | 57 | 164
paaK | b1398 | JW5218 | non-essential | CY | CORE | FAD | phenylacetyl.CoA.ligase | -- | H | -- | -- | Y | 0.05 | Y | Y | 789 | 775 | 302 | 184 | 118 | Y | Y | 142 | 138 | 79 | 51 | 28
pabB | b1812 | JW1801 | non-essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | aminodeoxychorismate.synthase.subunit.I | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | EH | -- | -- | -- | -- | -- | Y | 393 | 389 | 161 | 75 | 86 | Y | Y | 208 | 208 | 84 | 47 | 37
pabC | b1096 | JW1082 | non-essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | 4.amino.4.deoxychorismate.lyase.component.of.para.aminobenzoate.synthase.multienzyme.complex | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | EH | -- | -- | -- | -- | Y | Y | 791 | 772 | 466 | 320 | 146 | Y | Y | 175 | 170 | 90 | 58 | 32
pal | b0741 | JW0731 | non-essential | OM | CORE | CELL.ENVELOPE.INTEGRITY | peptidoglycan.associated.outer.membrane.lipoprotein | -- | M | -- | -- | -- | -- | -- | Y | 478 | 473 | 223 | 128 | 95 | Y | Y | 263 | 261 | 148 | 101 | 47
panB | b0134 | JW0130 | non-essential | CY | CORE | PANTOTHENATE.AND.COA.BIOSYNTHESIS | 3.methyl.2.oxobutanoate.hydroxymethyltransferase | -- | H | -- | -- | -- | -- | Y | Y | 751 | 741 | 238 | 114 | 124 | Y | Y | 176 | 173 | 107 | 61 | 46
panC | b0133 | JW0129 | non-essential | CY | CORE | PANTOTHENATE.AND.COA.BIOSYNTHESIS | pantothenate.synthetase | -- | H | -- | -- | Y | 53.307 | -- | Y | 385 | 376 | 126 | 66 | 60 | -- | Y | 204 | 201 | 118 | 74 | 44
panD | b0131 | JW0127 | non-essential | -- | CORE | PANTOTHENATE.AND.COA.BIOSYNTHESIS | aspartate.1.decarboxylase | Aspartate 1-decarboxylase is responsible for the synthesis of ?-alanine, which is needed in the biosynthesis of pantothenate. | H | -- | -- | -- | -- | Y | Y | 803 | 793 | 199 | 82 | 117 | Y | Y | 144 | 143 | 63 | 33 | 30
panE | b0425 | JW0415 | non-essential | CY | CORE | PANTOTHENATE.AND.COA.BIOSYNTHESIS | 2.dehydropantoate.reductase.NADPH.specific | -- | H | -- | -- | -- | -- | Y | Y | 797 | 778 | 321 | 196 | 125 | Y | Y | 109 | 102 | 63 | 45 | 18
panF | b3258 | JW3226 | non-essential | IM | FUNCTION-UNCERTAIN | PANTOTHENATE.AND.COA.BIOSYNTHESIS | pantothenate.sodium.symporter | PanF is a pantothenate transporter which probably functions as a panthothenate/proton symporte | H | -- | -- | -- | -- | -- | Y | 393 | 385 | 150 | 104 | 46 | -- | Y | 197 | 191 | 104 | 77 | 27
parE | b3030 | JW2998 | essential | CY | FUNCTION-UNCERTAIN | NA | DNA.topoisomerase.IV.subunit.B | ParE is the drug target of ciprofloxacin, enoxacin, nalidixic_acid and norfloxacin | L | -- | -- | Y | 9.1 | -- | Y | 393 | 387 | 177 | 78 | 99 | -- | Y | 216 | 212 | 133 | 112 | 21
pbpC | b2519 | JW2503 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | fused.transglycosylase.transpeptidase | There are four PBP transglycosilases in E. coli (mtgA, pbpC, mrcB, [NAME]) | M | -- | -- | -- | -- | Y | Y | 519 | 515 | 245 | 147 | 98 | Y | Y | 338 | 335 | 182 | 122 | 60
pbpG | b2134 | JW5355 | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | D.alanyl.D.alanine.endopeptidase | mepA and pbpG are isozymes, check for SSL between them | M | -- | -- | Y | 1.067 | Y | Y | 816 | 809 | 219 | 81 | 138 | Y | Y | 605 | 600 | 290 | 162 | 128
pgpA | b0418 | JW0408 | non-essential | IM | CORE | PHOSPHOLIPIDS | phosphatidylglycerophosphatase.A | -- | I | -- | -- | -- | -- | Y | Y | 816 | 798 | 296 | 91 | 205 | Y | Y | 637 | 622 | 239 | 77 | 162
pgpB | b1278 | JW1270 | non-essential | IM | CORE | PHOSPHOLIPIDS,CELL.WALL.BIOGENESIS | phosphatidylglycerophosphatase.B | ybjG, bacA and pgpB are links between isoprenoids and cell.wall biogenesis as they provide  'undecaprenyl phosphate' [EC:3.6.1.27]  which is essential for the synthesis of peptidoglycan via MraY. However all BacA, YbjG, PgpB, and YeiU conduct EC:3.6.1.27. Simultaneous inactivation of bacA, ybjG, and pgpB is lethal [PMID:15778224]. PgpB also conducts EC:3.6.1.26 as well as PgpA, but they may not be the principal enzymes responsible for EC:3.6.1.26. Expression of C55PP activity from one of the three genes ybjG, bacA, and pgpB appears to be sufficient for synthesis of undecaprenyl phosphate and survival [ El05  ] | I | -- | -- | -- | -- | Y | Y | 525 | 517 | 200 | 129 | 71 | Y | Y | 227 | 223 | 135 | 106 | 29
pgsA | b1912 | JW1897 | essential | IM | CORE | PHOSPHOLIPIDS | phosphatidylglycerophosphate.synthetase | -- | I | -- | -- | Y | 25.135 | Y | Y | 746 | 735 | 230 | 98 | 132 | Y | Y | 563 | 555 | 361 | 346 | 15
phoE | b0241 | JW0231 | non-essential | OM | CORE | CELL.ENVELOPE.INTEGRITY | outer.membrane.phosphoporin.protein.E | -- | M | -- | -- | -- | -- | Y | Y | 813 | 807 | 260 | 108 | 152 | Y | Y | 565 | 560 | 345 | 195 | 150
pldA | b3821 | JW3794 | non-essential | OM | FUNCTION-UNCERTAIN | PHOSPHOLIPIDS,FAS | outer.membrane.phospholipase.A | PldA hydrolyzes phospholipids forming lysophospholipids and fatty acids which perturb the lipid bilayer, allowing for the semispecific secretion of bacteriocins [ Snijder99  ]. | M | -- | -- | Y | 2.796 | -- | Y | 394 | 387 | 264 | 206 | 58 | -- | Y | 202 | 200 | 139 | 102 | 37
pldB | b3825 | JW5584 | non-essential | IM | CORE | PHOSPHOLIPIDS | lysophospholipase.L.2 | -- | I | -- | -- | Y | 8.065 | -- | Y | 481 | 470 | 205 | 138 | 67 | -- | Y | 336 | 329 | 142 | 75 | 67
plsB | b4041 | JW4001 | essential | CY | CORE | PHOSPHOLIPIDS | glycerol.3.phosphate.O.acyltransferase | -- | I | -- | -- | Y | 41.199 | Y | Y | 812 | 803 | 245 | 93 | 152 | Y | Y | 167 | 167 | 80 | 40 | 40
plsC | b3018 | [NAME] | essential | IM | CORE | PHOSPHOLIPIDS | 1.acyl.sn.glycerol.3.phosphate.acyltransferase | -- | I | -- | -- | -- | -- | Y | Y | 509 | 506 | 218 | 153 | 65 | Y | Y | 324 | 322 | 190 | 131 | 59
[NAME] | b1090 | JW5156 | non-essential | -- | CORE | PHOSPHOLIPIDS,FAS | fatty.acid.phospholipid.synthesis.protein | Involvement of the YneS(B. subtilis)/YgiH(E. coli) and [NAME] proteins in phospholipid biosynthesis in both Bacillus subtilis and [NAME]]. We found that plsB is essential for E. coli growth, indicating that PlsB plays an important role in 1-acyl-G3P synthesis in E. coli. We also found, that the simultaneous inactivation of [NAME] and ygiH was impossible, revealing important roles for [NAME] and YgiH in E. coli growth, possibly by regulating the intracellular concentration of acyl-ACP [PMID:17645809]. In E. coli the first step in [NAME] biosynthesis is catalyzed by PlsB. A new two-step pathway catalyzed by [NAME] and PlsY proteins for the initiation of phospholipid formation in Streptococcus pneumoniae has been reported [PMID:17308305]. B. subtilis ortholog of S. pneumoniae PlsY, YneS, is required for [NAME] acyltransferase activity, together with PlsX. The B. subtilis genome lacks plsB, and we show in vivo that the [NAME]/Y pathway is indeed essential for the growth of bacteria lacking plsB [PMID:17645809]. In E. coli, PlsB plays a principal role in 1-acyl-G3P synthesis and is also essential for bacterial growth. [NAME] and [NAME] ortholog) also, however, play important roles in E. coli growth, possibly by regulating the intracellular concentration of acyl-ACP [PMID:17645809] but actual role was not determined. Check for SSL's between PlsB and (plsX or ygiH) | I | -- | -- | Y | 18.22 | Y | Y | 482 | 469 | 137 | 84 | 53 | Y | Y | 287 | 280 | 119 | 76 | 43
ppiD | b0441 | JW0431 | non-essential | PE | CORE | PROTEIN.SECRETION,CHAPERONES | peptidyl.prolyl.cis.trans.isomerase.rotamase.D | surA genetically interacts with (degP/skp), and double mutant surA ppiD was reprted as synthetic lethal [PMID:9670013]. However, in [PMID:16267292] mutations involving four E. coli PPIases (FkpA, PpiA, PpiD, and SurA) showed that no single or double mutants were shown to have growth defects. Three triple mutants shown growth defects, while one does not, and the quadruple mutant had the most pronounced defect. -- | O | -- | -- | -- | -- | -- | Y | 395 | 382 | 106 | 46 | 60 | Y | Y | 209 | 201 | 99 | 44 | 55
pppA | b2972 | JW2939 | non-essential | IM | FUNCTION-UNCERTAIN | NA | bifunctional.prepilin.leader.peptidase.and.methylase | bifunctional.prepilin.leader.peptidase.and.methylase | NOU | -- | -- | -- | -- | -- | Y | 390 | 389 | 151 | 81 | 70 | -- | Y | 219 | 218 | 98 | 55 | 43
prc | b1830 | JW1819 | non-essential | OM | CORE | PROTEASE,CELL.DIVISION,CELL.WALL.BIOGENESIS | carboxy.terminal.protease.for.penicillin.binding.protein.3 | Protease for a number of proteins inluding FtsI(PBP3) which also participated in regulation of cell.shape. [NAME] may have some redundancy with [NAME], [NAME] and [NAME], as they were able to suppress the deleterious effects of losing Prc [PMID:8576052], but neither of these proteins was included in the CE-EMAP | M | -- | -- | -- | -- | Y | -- | 688 | 681 | 432 | 309 | 123 | Y | Y | 91 | 87 | 64 | 38 | 26
psd | b4160 | JW4121 | essential | -- | CORE | PHOSPHOLIPIDS | phosphatidylserine.decarboxylase | -- | I | -- | -- | -- | -- | Y | -- | 220 | 216 | 64 | 34 | 30 | Y | -- | 170 | 166 | 67 | 41 | 26
pssA | b2585 | JW2569 | essential | CY | CORE | PHOSPHOLIPIDS | phosphatidylserine.synthase.CDP.diacylglycerol.serine.O.phosphatidyltransferase | -- | I | -- | -- | Y | 94.049 | Y | -- | 235 | 232 | 210 | 191 | 19 | Y | -- | 192 | 189 | 158 | 153 | 5
pta | b2297 | JW2294 | non-essential | CY | FUNCTION-UNCERTAIN | NA | phosphate.acetyltransferase | Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | CR | -- | -- | Y | 62.472 | Y | Y | 714 | 705 | 342 | 247 | 95 | Y | Y | 436 | 430 | 303 | 204 | 99
ptsH | b2415 | JW2408 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS,[NAME],M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | phosphohistidinoprotein.hexose.phosphotransferase.component.of.PTS.system.Hpr | Link between Cell.wall.biogenesis, LPS and ECA because is a precursor step in the biosynthesis of precursors of lipid A (LPS), lipid II (peptidoglycan) and lipid III (ECA) | G | -- | -- | -- | -- | Y | -- | 682 | 677 | 544 | 487 | 57 | -- | -- | -- | -- | -- | -- | --
ptsI | b2416 | JW2409 | non-essential | CY | CORE | CELL.WALL.BIOGENESIS,[NAME],M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | PEP.protein.phosphotransferase.of.PTS.system.enzyme.I | Link between Cell.wall.biogenesis, LPS and ECA because is a precursor step in the biosynthesis of precursors of lipid A (LPS), lipid II (peptidoglycan) and lipid III (ECA) | G | -- | -- | -- | -- | Y | -- | 689 | 684 | 484 | 366 | 118 | -- | -- | -- | -- | -- | -- | --
purB | b1131 | JW1117 | essential | CY | FUNCTION-UNCERTAIN | NA | adenylosuccinate.lyase | Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | F | -- | -- | Y | 100.924 | Y | Y | 798 | 788 | 264 | 89 | 175 | Y | Y | 639 | 632 | 343 | 216 | 127
rfaB | b3628 | JW3603 | non-essential | CY | CORE | LPS.AND.ECA | UDP.D.galactose.glucosyl.lipopolysaccharide.1.6.D.galactosyltransferase | -- | M | -- | -- | -- | -- | Y | Y | 518 | 501 | 252 | 133 | 119 | Y | Y | 335 | 323 | 162 | 91 | 71
[NAME] | b3621 | JW3596 | non-essential | CY | CORE | LPS.AND.ECA | ADP.heptose.LPS.heptosyl.transferase.I | -- | M | -- | -- | -- | -- | Y | Y | 786 | 762 | 465 | 170 | 295 | Y | Y | 609 | 589 | 291 | 124 | 167
rfaD | b3619 | JW3594 | non-essential | CY | CORE | LPS.AND.ECA | ADP.L.glycero.D.mannoheptose.6.epimerase.NAD.P.binding | -- | MG | -- | -- | Y | 147.463 | Y | Y | 732 | 710 | 523 | 141 | 382 | Y | Y | 320 | 305 | 211 | 175 | 36
rfaE | b3052 | JW3024 | non-essential | CY | CORE | LPS.AND.ECA | fused.heptose.7.phosphate.kinase.heptose.1.phosphate.adenyltransferase | -- | M | -- | -- | -- | -- | Y | Y | 777 | 771 | 384 | 199 | 185 | Y | Y | 613 | 607 | 403 | 268 | 135
rfaF | b3620 | JW3595 | non-essential | CY | CORE | LPS.AND.ECA | ADP.heptose.LPS.heptosyltransferase.II | -- | M | -- | -- | -- | -- | Y | Y | 797 | 771 | 323 | 154 | 169 | Y | Y | 621 | 601 | 239 | 106 | 133
rfaG | b3631 | JW3606 | non-essential | CY | CORE | LPS.AND.ECA | glucosyltransferase.I | -- | M | -- | -- | -- | -- | Y | Y | 529 | 509 | 249 | 136 | 113 | Y | Y | 352 | 335 | 192 | 115 | 77
rfaI | b3627 | JW3602 | non-essential | CY | CORE | LPS.AND.ECA | UDP.D.galactose.glucosyl.lipopolysaccharide.alpha.1.3.D.galactosyltransferase | -- | M | -- | -- | -- | -- | -- | Y | 464 | 449 | 173 | 103 | 70 | -- | Y | 305 | 292 | 132 | 93 | 39
rfaJ | b3626 | JW3601 | non-essential | CY | CORE | LPS.AND.ECA | UDP.D.glucose.galactosyl.lipopolysaccharide.glucosyltransferase | -- | M | -- | -- | -- | -- | -- | Y | 502 | 484 | 179 | 119 | 60 | Y | Y | 341 | 325 | 158 | 113 | 45
rfaK | b3623 | JW3598 | essential | -- | CORE | LPS.AND.ECA | lipopolysaccharide.core.biosynthesis | -- | M | -- | -- | -- | -- | Y | -- | 698 | 676 | 240 | 111 | 129 | Y | -- | 564 | 549 | 251 | 145 | 106
rfaL | b3622 | JW3597 | non-essential | IM | CORE | LPS.AND.ECA | O.antigen.ligase | -- | M | -- | -- | -- | -- | -- | Y | 484 | 466 | 145 | 55 | 90 | Y | Y | 355 | 339 | 212 | 41 | 171
rfaP | b3630 | JW3605 | non-essential | CY | CORE | LPS.AND.ECA | kinase.that.phosphorylates.core.heptose.of.lipopolysaccharide | -- | - | -- | -- | -- | -- | Y | Y | 805 | 781 | 353 | 115 | 238 | Y | Y | 602 | 587 | 296 | 130 | 166
rfaQ | b3632 | JW3607 | non-essential | CY | CORE | LPS.AND.ECA | lipopolysaccharide.core.biosynthesis.protein | -- | M | -- | -- | -- | -- | Y | Y | 797 | 774 | 209 | 91 | 118 | Y | Y | 639 | 621 | 311 | 143 | 168
rfaS | b3629 | JW3604 | non-essential | CY | FUNCTION-UNCERTAIN | LPS.AND.ECA | lipopolysaccharide.core.biosynthesis.protein | rfaS(waaS) encodes a protein necessary for the attachment of [NAME] to the LPS core by a linkage to the KDOII residue [PMID:7504166] | - | -- | -- | -- | -- | -- | Y | 360 | 351 | 183 | 109 | 74 | Y | Y | 200 | 194 | 112 | 58 | 54
rfaY | b3625 | JW3600 | non-essential | CY | CORE | LPS.AND.ECA | lipopolysaccharide.core.biosynthesis.protein | -- | - | -- | -- | -- | -- | Y | Y | 485 | 468 | 318 | 245 | 73 | Y | Y | 283 | 270 | 191 | 147 | 44
rfaZ | b3624 | JW3599 | non-essential | CY | FUNCTION-UNCERTAIN | LPS.AND.ECA | lipopolysaccharide.core.biosynthesis.protein | rfaZ(WaaZ) is involved in the nonstoichiometric addition of 3-deoxy-D-manno-oct-2-ulosonic acid III (KDOIII) to the KDOII residue of the inner lipopolysaccharide core [PMID:12591884]. An waaZ mutation does not cause an O antigen attachment defect [PMID:1385388] | - | -- | -- | -- | -- | Y | Y | 796 | 774 | 236 | 99 | 137 | Y | Y | 634 | 614 | 232 | 87 | 145
rfbA | b2039 | JW2024 | non-essential | CY | CORE | LPS.AND.ECA | glucose.1.phosphate.thymidylyltransferase | -- | M | -- | -- | -- | -- | Y | Y | 525 | 496 | 164 | 97 | 67 | Y | Y | 335 | 310 | 152 | 100 | 52
rfbB | b2041 | JW2026 | non-essential | CY | CORE | LPS.AND.ECA | dTDP.glucose.4.6.dehydratase.NAD.P.binding | -- | M | -- | -- | -- | -- | Y | Y | 518 | 490 | 171 | 85 | 86 | Y | Y | 324 | 302 | 137 | 71 | 66
rfbC | b2038 | JW2023 | non-essential | CY | CORE | LPS.AND.ECA | dTDP.4.deoxyrhamnose.3.5.epimerase | -- | - | -- | -- | -- | -- | Y | Y | 529 | 501 | 199 | 145 | 54 | Y | Y | 341 | 318 | 184 | 118 | 66
rfbD | b2040 | JW2025 | non-essential | CY | CORE | LPS.AND.ECA | dTDP.4.dehydrorhamnose.reductase.subunit.NAD.P.binding.of.dTDP.L.rhamnose.synthase | -- | M | -- | -- | Y | 50.046 | Y | Y | 531 | 502 | 150 | 82 | 68 | Y | Y | 366 | 342 | 131 | 76 | 55
rfbX | b2037 | JW2022 | non-essential | IM | CORE | LPS.AND.ECA | predicted.polisoprenol.linked.O.antigen.transporter | Wzx(WzxC) should not be confused with the homologous RfbX O-antigen flippase, also known as [NAME] or WzxB. The wzx gene is located in a gene cluster responsible for production of extracellular colanic acid [ Stevenson96  ]. Colanic acid or M-antigen is an extracellular polysaccharide possibly important in cell survival outside of a host. Based on sequence similarity to RfbX, [NAME] has been proposed to function as a colanic acid export system [Stevenson96]. Check for SSL between rfbX(WzxB) and WzxC | R | -- | -- | -- | -- | Y | Y | 527 | 499 | 162 | 47 | 115 | Y | Y | 379 | 352 | 146 | 44 | 102
rfe | b3784 | JW3758 | non-essential | IM | CORE | LPS.AND.ECA | UDP.GlcNAc.undecaprenylphosphate.GlcNAc.1.phosphate.transferase | Rfe is a key step incorporating UDP-N-acetyl-glucosamine into ECA biosyntheses. Also RffE incorporates UDP-N-acetyl-glucosamine  in an earlier step of the same pathway. | M | -- | -- | -- | -- | Y | Y | 796 | 778 | 300 | 191 | 109 | Y | Y | 198 | 192 | 106 | 53 | 53
rffA | b3791 | JW3765 | non-essential | CY | CORE | LPS.AND.ECA | TDP.4.oxo.6.deoxy.D.glucose.transaminase | -- | M | -- | -- | -- | -- | Y | Y | 530 | 517 | 290 | 212 | 78 | Y | Y | 337 | 328 | 204 | 148 | 56
[NAME] | b3790 | JW5597 | non-essential | -- | CORE | LPS.AND.ECA | TDP.fucosamine.acetyltransferase | -- | KR | -- | -- | -- | -- | Y | Y | 819 | 801 | 245 | 69 | 176 | Y | Y | 662 | 648 | 187 | 75 | 112
rffD | b3787 | JW5599 | non-essential | CY | CORE | LPS.AND.ECA | UDP.N.acetyl.D.mannosaminuronic.acid.dehydrogenase | -- | M | -- | -- | -- | -- | Y | Y | 808 | 791 | 207 | 56 | 151 | Y | Y | 711 | 696 | 244 | 88 | 156
rffE | b3786 | JW5600 | non-essential | CY | CORE | LPS.AND.ECA | UDP.N.acetyl.glucosamine.2.epimerase | -- | M | -- | -- | -- | -- | -- | Y | 496 | 484 | 143 | 74 | 69 | -- | Y | 350 | 342 | 156 | 76 | 80
rffG | b3788 | JW5598 | non-essential | CY | CORE | LPS.AND.ECA | dTDP.glucose.4.6.dehydratase | -- | M | -- | -- | -- | -- | Y | Y | 813 | 796 | 222 | 115 | 107 | Y | Y | 282 | 272 | 107 | 24 | 83
rffH | b3789 | JW3763 | non-essential | CY | CORE | LPS.AND.ECA | glucose.1.phosphate.thymidylyltransferase | -- | M | -- | -- | -- | -- | Y | Y | 529 | 516 | 223 | 114 | 109 | Y | Y | 350 | 339 | 120 | 55 | 65
rffM | b3794 | JW3770 | non-essential | CY | CORE | LPS.AND.ECA | UDP.N.acetyl.D.mannosaminuronic.acid.transferase | -- | M | -- | -- | -- | -- | Y | Y | 475 | 461 | 182 | 85 | 97 | Y | Y | 274 | 264 | 112 | 61 | 51
rffT | b4404 | JW5596 | non-essential | CY | CORE | LPS.AND.ECA | TDP.Fuc4NAc.lipidIIFuc4NAc.transferase | -- | -- | -- | -- | -- | -- | Y | -- | 708 | 691 | 182 | 69 | 113 | Y | Y | 636 | 620 | 300 | 213 | 87
rhsA | b3593 | JW3566 | non-essential | -- | PREDICTED | NA | [NAME].RshA | rhs- proteins were added to the CE-eMAP because are potential trans-outer membrane beta-barrels. There are five homologous rhs loci [ Sadosky89  ] that encode hydrophilic proteins with repetitive sequence elements and divergent C-termini [ Feulner90  ]. RhsA, RhsB, and RhsC define one subfamily, and RhsD and RhsE define a second subfamily of Rhs elements [ Sadosky91  ]. | M | -- | -- | -- | -- | -- | Y | 392 | 386 | 120 | 71 | 49 | -- | Y | 209 | 207 | 85 | 41 | 44
rhsD | b0497 | [NAME] | non-essential | OM | PREDICTED | NA | [NAME] | rhs- proteins were added to the CE-eMAP because are potential trans-outer membrane beta-barrels. There are five homologous rhs loci [ Sadosky89  ] that encode hydrophilic proteins with repetitive sequence elements and divergent C-termini [ Feulner90  ]. RhsA, RhsB, and RhsC define one subfamily, and RhsD and RhsE define a second subfamily of Rhs elements [ Sadosky91  ]. | M | -- | -- | -- | -- | Y | Y | 777 | 768 | 299 | 123 | 176 | Y | Y | 577 | 571 | 240 | 120 | 120
rhsE | b1456 | JW1451 | non-essential | CY | PREDICTED | NA | rhsE.element.core.protein.RshE | rhs- proteins were added to the CE-eMAP because are potential trans-outer membrane beta-barrels. There are five homologous rhs loci [ Sadosky89  ] that encode hydrophilic proteins with repetitive sequence elements and divergent C-termini [ Feulner90  ]. RhsA, RhsB, and RhsC define one subfamily, and RhsD and RhsE define a second subfamily of Rhs elements [ Sadosky91  ]. | -- | -- | -- | -- | -- | -- | Y | 396 | 393 | 137 | 53 | 84 | -- | Y | 209 | 208 | 77 | 31 | 46
rlpA | b0633 | JW0628 | non-essential | -- | PREDICTED | CELL.WALL.BIOGENESIS | minor.lipoprotein | [NAME] in the same neighborhood with several 'Cell.wall.biogenesis' related proteins. So chech SSL's with them. RlpA is one of two (along with RlpB) so-called rare lipoproteins in Escherichia coli. An RlpA-RFP fusion protein accumulates at cell division sites, but is also localized elsewhere in the cell envelope. Deletion of rlpA does not result in cell growth or division defects [PMID:19684127] | M | -- | -- | -- | -- | Y | Y | 478 | 471 | 161 | 94 | 67 | Y | Y | 300 | 294 | 102 | 52 | 50
rlpB | b0641 | JW0636 | essential | PE | CORE | LPS.AND.ECA | minor.lipoprotein | RlpB (LptE) has been genetically and biochemically characterized as part of an ABC transporter LptBFGC complex required for the outer membrane sorting of lipopolysaccharides has been reported [PMID:19500581,PMID:18375759]. Disruption of the pathway at any step after [NAME] leads to indistinguishable phenotypes: in all cases, LPS accumulates in the outer leaflet of the IM. Therefore, we cannot conduct epistasis analysis to determine exact pathway order. We can only rely on the information about the cellular location of these proteins to predict temporal order in the pathway as follows: MsbA followed by a complex of LptB, [NAME], [NAME] and LptG, followed by LptA and finally by a complex of LptD and LptE [PMID:19633680] | M | -- | -- | -- | -- | Y | Y | 737 | 727 | 223 | 48 | 175 | Y | Y | 128 | 124 | 80 | 52 | 28
rmf | b0953 | JW0936 | non-essential | CY | FUNCTION-UNCERTAIN | NA | ribosome.modulation.factor | [NAME] interacts Aggravating with ompC (PMID:9792800). Expression of rmf is induced at the transition from exponential growth to stationary phase or during slow growth; rmf expression appears to be inversely proportional to the growth rate [ Yamagishi93  ] | J | -- | -- | -- | -- | Y | Y | 761 | 751 | 249 | 143 | 106 | Y | Y | 69 | 69 | 40 | 24 | 16
rne | b1084 | [NAME] | essential | IM | FUNCTION-UNCERTAIN | NA | fused.ribonucleaseE.endoribonuclease.RNA.binding.protein.RNA.degradosome.binding.protein | Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | J | -- | -- | -- | -- | Y | -- | 695 | 678 | 182 | 57 | 125 | Y | Y | 575 | 561 | 126 | 117 | 9
rof | b0189 | JW0184 | non-essential | CY | CORE | CELL.DIVISION | modulator.of.Rho.dependent.transcription.termination | rof is a multicopy suppressor of temperature-sensitive alleles of genes such as ftsA, ftsQ, groEL, grpE, a malE-minE fusion allele [ Pichoff98  ] | K | -- | -- | -- | -- | -- | Y | 362 | 349 | 211 | 132 | 79 | Y | Y | 180 | 172 | 63 | 41 | 22
[NAME] | b3186 | JW3153 | essential | CY | FUNCTION-UNCERTAIN | NA | 50S.ribosomal.subunit.protein.[NAME] | Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | J | -- | -- | -- | -- | Y | -- | 678 | 665 | 217 | 102 | 115 | Y | Y | 629 | 616 | 269 | 232 | 37
rplW | b3318 | JW3280 | essential | CY | FUNCTION-UNCERTAIN | NA | 50S.ribosomal.subunit.protein.[NAME] | Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | J | -- | -- | -- | -- | -- | Y | 386 | 375 | 230 | 111 | 119 | -- | Y | 196 | 192 | 151 | 122 | 29
rpmA | b3185 | JW3152 | essential | CY | FUNCTION-UNCERTAIN | NA | 50S.ribosomal.subunit.protein.L27 | Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | J | -- | -- | -- | -- | -- | Y | 392 | 382 | 215 | 116 | 99 | -- | Y | 219 | 212 | 141 | 106 | 35
rpoE | b2573 | JW2557 | essential | CY | FUNCTION-UNCERTAIN | NA | RNA.polymerase.sigma.24.sigma.E.factor | RpoE interacts Aggravating with ompC (PMID:15774872) upon exposure to zinc | K | -- | -- | -- | -- | Y | -- | 664 | 661 | 221 | 49 | 172 | -- | -- | -- | -- | -- | -- | --
rpoS | [NAME] | JW5437 | non-essential | CY | CORE | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | RNA.polymerase.sigma.S.sigma.38.factor | rpoS encodes the alternative sigma factor ?S, a subunit of RNA polymerase that acts as the master regulator of the general stress response in E. coli (EcoCyc). [NAME] negatively regulates expression of M-antigen genes [ | K | -- | -- | -- | -- | Y | Y | 789 | 784 | 277 | 142 | 135 | Y | Y | 563 | 559 | 344 | 174 | 170
rssA | b1234 | JW1222 | non-essential | CY | FUNCTION-UNCERTAIN | NA | conserved.protein | An rssA mutant does not exhibit a defect in SprE or [NAME] regulation [ Ruiz01  ]. | R | -- | -- | Y | 13.06 | Y | Y | 784 | 770 | 241 | 121 | 120 | Y | Y | 137 | 134 | 37 | 22 | 15
rybB | b4417 | UNKW3110 | unknown | -- | FUNCTION-UNCERTAIN | CELL.ENVELOPE.INTEGRITY | -- | Small RNA. [NAME] is a small RNA 81 nt in length [ Vogel03  ].A rybB deletion mutant is less sensitive to cell envelope stress than wild type [ Hobbs10 ]. | -- | -- | -- | -- | -- | Y | -- | 670 | 657 | 342 | 271 | 71 | Y | -- | 548 | 539 | 447 | 415 | 32
sapA | b1294 | JW1287 | non-essential | PE | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | predicted.antimicrobial.peptide.transporter.subunit.periplasmic.binding.component.of.ABC.superfamily | SapABCDF (Sensitive to antimicrobial peptides) is a member of the ATP Binding Cassette (ABC) transporter superfamily [ [NAME]  ]. Disruption of the sap gene results in increased susceptibility to endogenous antimicrobial peptides, such as protamine, mellitin, defensins and human neutrophil granules. This suggests that the SapABCDF system may be involved in uptake of these peptides as part of a defense degradation system [ ParraLopez93  ] | E | -- | -- | Y | 3.547 | Y | Y | 779 | 771 | 245 | 105 | 140 | Y | Y | 82 | 81 | 45 | 29 | 16
sapB | b1293 | JW1286 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | predicted.antimicrobial.peptide.transporter.subunit.membrane.component.of.ABC.superfamily | SapABCDF (Sensitive to antimicrobial peptides) is a member of the ATP Binding Cassette (ABC) transporter superfamily [ [NAME]  ]. Disruption of the sap gene results in increased susceptibility to endogenous antimicrobial peptides, such as protamine, mellitin, defensins and human neutrophil granules. This suggests that the SapABCDF system may be involved in uptake of these peptides as part of a defense degradation system [ ParraLopez93  ] | V | -- | -- | -- | -- | Y | Y | 791 | 783 | 250 | 60 | 190 | Y | Y | 632 | 626 | 218 | 102 | 116
sapC | b1292 | JW1285 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | predicted.antimicrobial.peptide.transporter.subunit.membrane.component.of.ABC.superfamily | SapABCDF (Sensitive to antimicrobial peptides) is a member of the ATP Binding Cassette (ABC) transporter superfamily [ [NAME]  ]. Disruption of the sap gene results in increased susceptibility to endogenous antimicrobial peptides, such as protamine, mellitin, defensins and human neutrophil granules. This suggests that the SapABCDF system may be involved in uptake of these peptides as part of a defense degradation system [ ParraLopez93  ] | V | -- | -- | -- | -- | Y | -- | 685 | 677 | 182 | 57 | 125 | -- | -- | -- | -- | -- | -- | --
sapD | b1291 | JW1284 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | predicted.antimicrobial.peptide.transporter.subunit.ATP.binding.component.of.ABC.superfamily | SapABCDF (Sensitive to antimicrobial peptides) is a member of the ATP Binding Cassette (ABC) transporter superfamily [ [NAME]  ]. Disruption of the sap gene results in increased susceptibility to endogenous antimicrobial peptides, such as protamine, mellitin, defensins and human neutrophil granules. This suggests that the SapABCDF system may be involved in uptake of these peptides as part of a defense degradation system [ ParraLopez93  ] | V | -- | -- | -- | -- | Y | Y | 794 | 786 | 321 | 98 | 223 | Y | Y | 570 | 565 | 195 | 86 | 109
sapF | b1290 | JW1283 | non-essential | CY | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | predicted.antimicrobial.peptide.transporter.subunit.ATP.binding.component.of.ABC.superfamily | SapABCDF (Sensitive to antimicrobial peptides) is a member of the ATP Binding Cassette (ABC) transporter superfamily [ [NAME]  ]. Disruption of the sap gene results in increased susceptibility to endogenous antimicrobial peptides, such as protamine, mellitin, defensins and human neutrophil granules. This suggests that the SapABCDF system may be involved in uptake of these peptides as part of a defense degradation system [ ParraLopez93  ] | V | -- | -- | Y | 7.617 | Y | Y | 783 | 775 | 391 | 130 | 261 | Y | Y | 125 | 125 | 55 | 24 | 31
sbmA | b0377 | [NAME] | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.transporter | SbmA has a SSL interaction with TolC [EcoCyc]. Seems that the only reason to be included in the EMAP -- | I | -- | -- | -- | -- | -- | Y | 388 | 382 | 89 | 50 | 39 | Y | Y | 213 | 207 | 76 | 37 | 39
secA | b0098 | [NAME] | essential | IM | CORE | PROTEIN.SECRETION | preprotein.translocase.subunit.ATPase | For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | Y | 71.319 | Y | Y | 747 | 731 | 202 | 69 | 133 | Y | Y | 649 | 636 | 230 | 164 | 66
secB | b3609 | JW3584 | non-essential | CY | CORE | PROTEIN.SECRETION,CHAPERONES | protein.export.chaperone | For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | Y | 672.937 | Y | Y | 807 | 784 | 303 | 138 | 165 | Y | Y | 212 | 204 | 114 | 48 | 66
[NAME] | b0408 | JW0398 | essential | IM | CORE | PROTEIN.SECRETION | SecYEG.protein.translocase.auxillary.subunit | For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | -- | -- | Y | Y | 752 | 736 | 226 | 63 | 163 | Y | Y | 652 | 638 | 268 | 236 | 32
secE | b3981 | JW3944 | essential | IM | CORE | PROTEIN.SECRETION | preprotein.translocase.membrane.subunit | For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | -- | -- | Y | -- | 697 | 692 | 234 | 120 | 114 | Y | -- | 629 | 625 | 198 | 107 | 91
secF | b0409 | JW0399 | essential | IM | CORE | PROTEIN.SECRETION | SecYEG.protein.translocase.auxillary.subunit | For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | -- | -- | Y | -- | 703 | 689 | 280 | 173 | 107 | Y | -- | 588 | 576 | 382 | 319 | 63
secG | b3175 | JW3142 | non-essential | IM | CORE | PROTEIN.SECRETION | preprotein.translocase.membrane.subunit | For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | -- | -- | Y | Y | 791 | 776 | 308 | 165 | 143 | Y | Y | 180 | 176 | 93 | 36 | 57
secM | b0097 | JW5007 | essential | PE | CORE | PROTEIN.SECRETION | regulator.of.secA.translation | SecM regulates production of co-translated SecA; reduced secretion of SecM acts as a "sensor" that stimulates translation of the SecA translocation factor [PMID:9748461] -- | - | -- | -- | -- | -- | Y | -- | 698 | 685 | 277 | 167 | 110 | Y | -- | 82 | 81 | 30 | 16 | 14
secY | b3300 | JW3262 | essential | IM | CORE | PROTEIN.SECRETION | preprotein.translocase.membrane.subunit | For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | -- | -- | Y | Y | 786 | 770 | 323 | 100 | 223 | Y | Y | 672 | 662 | 353 | 173 | 180
sfmC | b0531 | JW0520 | non-essential | PE | FUNCTION-UNCERTAIN | NA | pilin.chaperone.periplasmic | [NAME] (2009) provided GC evidences clustering sfm- and fim- genes in fimbria related module | NU | -- | -- | -- | -- | -- | Y | 393 | 391 | 104 | 44 | 60 | -- | Y | 214 | 213 | 83 | 38 | 45
[NAME] | b0532 | JW0521 | non-essential | OM | FUNCTION-UNCERTAIN | NA | predicted.outer.membrane.export.usher.protein | [NAME] (2009) provided GC evidences clustering sfm- and fim- genes in fimbria related module | NU | -- | -- | -- | -- | -- | Y | 390 | 388 | 162 | 65 | 97 | -- | Y | 218 | 216 | 89 | 34 | 55
sgrS | b4577 | UNKW3110 | unknown | -- | FUNCTION-UNCERTAIN | NA | -- | -- | -- | -- | -- | -- | -- | Y | -- | 693 | 684 | 316 | 261 | 55 | -- | -- | -- | -- | -- | -- | --
slp | b3506 | JW3474 | non-essential | -- | FUNCTION-UNCERTAIN | NA | outer.membrane.lipoprotein | outer.membrane.lipoprotein | M | -- | -- | -- | -- | -- | Y | 388 | 385 | 136 | 91 | 45 | -- | Y | 207 | 206 | 130 | 100 | 30
slt | b4392 | JW4355 | non-essential | PE | CORE | CELL.DIVISION,CELL.SHAPE,CELL.WALL.BIOGENESIS | lytic.murein.transglycosylase.soluble | Is one of six major lytic murein endotransglycosylases (slt, mltD, mltB, mltA, emtA, mltC) expressed in Escherichia coli, allowing for cell enlargement and division and also for localized opening of the peptidoglycan layer to allow the export of bulky compounds such as DNA, toxins, flagella, and fimbrial proteins [PMID:9642199]. | M | -- | -- | -- | -- | Y | Y | 818 | 816 | 182 | 66 | 116 | Y | Y | 618 | 617 | 408 | 242 | 166
slyB | b1641 | JW1633 | non-essential | -- | FUNCTION-UNCERTAIN | NA | outer.membrane.lipoprotein | Dnase I footprinting assays show slyB is directly regulated by PhoP [ Minagawa03  ]  which activates transcription of a large collection of genes involved in Mg2+ homeostasis, resistance to antimicrobial peptides, acid resistance, and LPS modification [ Kato99b  , [NAME]  , Miyashiro07  ]. | M | -- | -- | -- | -- | Y | Y | 811 | 799 | 204 | 86 | 118 | Y | Y | 301 | 299 | 120 | 24 | 96
smpA | [NAME] | JW2598 | non-essential | -- | CORE | PROTEIN.SECRETION | small.membrane.lipoprotein | For a review of OM biogenesis see [PMID:19270402] -- | J | -- | -- | -- | -- | -- | Y | 390 | 388 | 129 | 58 | 71 | -- | Y | 216 | 214 | 99 | 60 | 39
sohA | b3129 | JW3098 | non-essential | CY | FUNCTION-UNCERTAIN | CELL.DIVISION | predicted.regulator | SohA Interacts aggravating with degP (PMID:2407727). Overproduction of PrlF yields a growth defect and increased export of a reporter protein[ Kiino90  ] | K | -- | -- | -- | -- | Y | Y | 790 | 784 | 393 | 198 | 195 | Y | Y | 142 | 142 | 97 | 83 | 14
spoT | b3650 | JW3625 | essential | CY | FUNCTION-UNCERTAIN | NA | bifunctional.p.ppGpp.synthetase.II.and.guanosine.3.5.bis.pyrophosphate.3.pyrophosphohydrolase | Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | TK | -- | -- | Y | 29.004 | -- | Y | 392 | 383 | 319 | 275 | 44 | -- | Y | 223 | 217 | 197 | 191 | 6
spr | b2175 | JW2163 | non-essential | -- | FUNCTION-UNCERTAIN | NA | predicted.peptidase.outer.membrane.lipoprotein | [NAME] (2009) predicted Spr interacting with YafL by all four GC methods. YafL was predicted involved in 'FAS' etc. Penicillin binding protein 7 acts as a multicopy suppressor of spr deletion mutations when its D-alanyl-D-alanine endopeptidase activity is intact [ Hara96a  ]. Chech their SSL's | M | -- | -- | -- | -- | Y | Y | 811 | 802 | 190 | 65 | 125 | Y | Y | 242 | 240 | 86 | 26 | 60
spy | b1743 | JW1732 | non-essential | PE | FUNCTION-UNCERTAIN | CELL.ENVELOPE.INTEGRITY | envelope.stress.induced.periplasmic.protein | [NAME] (2009) predicted Spy in the same neighbothood of several other (cell-envelope) stress response related proteins. Expression of spy is regulated by the Cpx envelope stress response as well as by the BaeSR two-component response regulator [ Raffa02  ] | UNTP | -- | -- | Y | 0.158 | -- | Y | 502 | 501 | 131 | 60 | 71 | Y | Y | 320 | 320 | 164 | 66 | 98
sugE | b4148 | JW5738 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.protein | SugE is a member of the SMR family of proton-dependent drug efflux transporters [ Paulsen96  ]. The function of SugE is not known, but expression of the sugE  gene has been shown to suppress a groEL chaperonin mutant [ Greener93  ]. Overproduction of SugE results in decreased sensitivity to some quaternary ammonium compounds, compared to wild type [ Chung02  ]. | P | -- | -- | -- | -- | -- | Y | 360 | 342 | 176 | 110 | 66 | -- | Y | 173 | 168 | 71 | 37 | 34
sulA | b0958 | [NAME] | non-essential | IM | CORE | CELL.DIVISION | SOS.cell.division.inhibitor | Induction of the SulA(SfiA) protein is sufficient to cause inhibition of division as part of the SOS response. Mutations in the ftsZ(sfiB) gene can suppress IPTG-induced SfiA-mediated inhibition of division. At higher SfiA concentrations, however, even sfiB mutants cease division; an additional mutation genetically inseparable from sfiB restores normal division. These observations reinforce the hypothesis that the SfiB protein, probably required for cell septation, is the target of action of the SfiA division inhibitor [PMID:6087326] -- | D | -- | -- | Y | 1.571 | Y | Y | 531 | 525 | 182 | 70 | 112 | Y | Y | 364 | 360 | 146 | 59 | 87
surA | b0053 | JW0052 | non-essential | PE | CORE | PROTEIN.SECRETION,CHAPERONES | peptidyl.prolyl.cis.trans.isomerase.PPIase | surA genetically interacts with (degP/skp)  , and double mutant surA ppiD was reprted as synthetic lethal [PMID:9670013]. However, in [PMID:16267292] mutations involving four E. coli PPIases (FkpA, PpiA, PpiD, and SurA) showed that no single or double mutants were shown to have growth defects. Three triple mutants shown growth defects, while one does not, and the quadruple mutant had the most pronounced defect. -- | O | -- | -- | Y | 6.869 | Y | -- | 647 | 639 | 290 | 194 | 96 | Y | Y | 148 | 148 | 19 | 3 | 16
tap | b1885 | JW1874 | non-essential | IM | FUNCTION-UNCERTAIN | NA | [NAME].IV | -- | NT | -- | -- | -- | -- | -- | Y | 393 | 385 | 148 | 95 | 53 | Y | Y | 185 | 184 | 105 | 62 | 43
tar | b1886 | JW1875 | non-essential | IM | FUNCTION-UNCERTAIN | NA | methyl.accepting.chemotaxis.protein.II | -- | NT | -- | -- | Y | 0.334 | Y | Y | 783 | 772 | 306 | 144 | 162 | Y | Y | 665 | 659 | 248 | 103 | 145
tatA | b3836 | JW3813 | non-essential | -- | CORE | PROTEIN.SECRETION | TatABCE.protein.translocation.system.subunit | For a review of Tat-system see [PMID:19270402]. The secreted peptide binds The TatBC-substrate complex (first TatC) then associates with TatA in a Delta_p-dependent step. This association appears to persist until the substrate molecule has been transported across the membrane. Signal peptide is cleaved by LepB. TatE shares overlapping functions with TatA [PMID:9649434] -- | U | -- | -- | Y | 297.63 | Y | Y | 801 | 788 | 210 | 77 | 133 | Y | Y | 197 | 194 | 75 | 38 | 37
tatB | b3838 | JW5580 | non-essential | -- | CORE | PROTEIN.SECRETION | TatABCE.protein.translocation.system.subunit | For a review of Tat-system see [PMID:19270402]. The secreted peptide binds The TatBC-substrate complex (first TatC) then associates with TatA in a Delta_p-dependent step. This association appears to persist until the substrate molecule has been transported across the membrane. Signal peptide is cleaved by LepB. TatE shares overlapping functions with TatA [PMID:9649434] -- | U | -- | -- | Y | 28.014 | Y | Y | 518 | 509 | 148 | 33 | 115 | Y | Y | 306 | 301 | 142 | 61 | 81
tatC | b3839 | JW3815 | non-essential | IM | CORE | PROTEIN.SECRETION | TatABCE.protein.translocation.system.subunit | For a review of Tat-system see [PMID:19270402]. The secreted peptide binds The TatBC-substrate complex (first TatC) then associates with TatA in a Delta_p-dependent step. This association appears to persist until the substrate molecule has been transported across the membrane. Signal peptide is cleaved by LepB. TatE shares overlapping functions with TatA [PMID:9649434] -- | U | -- | -- | -- | -- | Y | Y | 517 | 508 | 174 | 92 | 82 | Y | Y | 320 | 316 | 153 | 91 | 62
[NAME] | b0627 | JW0622 | non-essential | -- | CORE | PROTEIN.SECRETION | TatABCE.protein.translocation.system.subunit | For a review of Tat-system see [PMID:19270402]. The secreted peptide binds The TatBC-substrate complex (first TatC) then associates with TatA in a Delta_p-dependent step. This association appears to persist until the substrate molecule has been transported across the membrane. Signal peptide is cleaved by LepB. TatE shares overlapping functions with TatA [PMID:9649434] -- | U | -- | -- | Y | 27.157 | Y | Y | 793 | 785 | 270 | 197 | 73 | Y | Y | 589 | 585 | 284 | 82 | 202
tig | b0436 | JW0426 | non-essential | CY | CORE | PROTEIN.SECRETION | peptidyl.prolyl.cis.trans.isomerase.trigger.factor | GO:0015031.protein.transport | O | -- | -- | Y | 729.704 | Y | -- | 210 | 205 | 39 | 9 | 30 | Y | -- | 156 | 154 | 49 | 21 | 28
tolA | b0739 | JW0729 | non-essential | IM | CORE | CELL.ENVELOPE.INTEGRITY | membrane.anchored.protein.in.TolA.TolQ.TolR.complex | -- | M | -- | -- | -- | -- | -- | Y | 453 | 446 | 171 | 74 | 97 | Y | Y | 269 | 264 | 164 | 85 | 79
tolB | b0740 | JW5100 | non-essential | PE | CORE | CELL.ENVELOPE.INTEGRITY | periplasmic.protein | -- | U | -- | -- | Y | 3.359 | Y | Y | 754 | 740 | 304 | 167 | 137 | Y | Y | 231 | 227 | 105 | 50 | 55
tolC | b3035 | JW5503 | non-essential | OM | CORE | ENTEROBACTIN.AND.METAL.ION.TRANSPORT,RESPONSE.TO.ANTIBIOTIC | transport.channel | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] . MacAB, also known as YbjYZ, probably forms a complex with outer membrane protein TolC to confer macrolide resistance via active drug efflux (EcoCyc) | MU | -- | -- | -- | -- | Y | Y | 749 | 740 | 343 | 209 | 134 | Y | Y | 214 | 211 | 85 | 60 | 25
tolQ | b0737 | JW0727 | non-essential | IM | CORE | CELL.ENVELOPE.INTEGRITY | membrane.spanning.protein.in.TolA.TolQ.TolR.complex | -- | U | -- | -- | -- | -- | -- | Y | 356 | 351 | 182 | 100 | 82 | Y | Y | 167 | 166 | 88 | 55 | 33
tolR | b0738 | JW0728 | non-essential | IM | CORE | CELL.ENVELOPE.INTEGRITY | membrane.spanning.protein.in.TolA.TolQ.TolR.complex | -- | U | -- | -- | -- | -- | -- | Y | 369 | 364 | 179 | 55 | 124 | Y | Y | 186 | 183 | 108 | 41 | 67
tonB | b1252 | JW5195 | non-essential | PE | CORE | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | membrane.spanning.protein.in.TonB.ExbB.ExbD.complex | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-) and [NAME] (fhu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] | M | -- | -- | -- | -- | -- | Y | 465 | 456 | 164 | 80 | 84 | -- | Y | 190 | 185 | 62 | 24 | 38
torD | b0998 | JW0983 | non-essential | CY | FUNCTION-UNCERTAIN | CHAPERONES | chaperone.involved.in.maturation.of.TorA.subunit.of.trimethylamine.N.oxide.reductase.system.I | TorD acts as a private chaperone for TorA, making it competent to receive the molybdenum cofactor; [NAME] was shown to be sufficient for activation of TorA [ Ilbert03  , Genest05  ] | R | -- | -- | -- | -- | -- | Y | 394 | 391 | 108 | 58 | 50 | -- | Y | 191 | 191 | 79 | 48 | 31
torT | b0994 | JW0979 | non-essential | PE | FUNCTION-UNCERTAIN | CHAPERONES | periplasmic.sensory.protein.associated.with.the.TorRS.two.component.regulatory.system | TorT interacts with the periplasmic domain of the two-component sensor protein TorS, and binding of TMAO to TorT may indirectly induce a conformational change in TorS [ Baraquet06  ]. | G | -- | -- | -- | -- | Y | Y | 792 | 785 | 320 | 147 | 173 | Y | Y | 120 | 120 | 72 | 56 | 16
tpx | b1324 | JW1317 | non-essential | CY | FUNCTION-UNCERTAIN | NA | lipid.hydroperoxide.peroxidase | Tpx is a thioredoxin 1  -dependent thiol peroxidase that belongs to the family of atypical 2-Cys peroxidases [ Baker03  , [NAME]  ]. In vivo, [NAME] appears to function as a lipid hydroperoxide peroxidase and acts as the principal antioxidant under anaerobic conditions [ Cha04  ]. | O | -- | -- | -- | -- | -- | Y | 393 | 390 | 119 | 37 | 82 | -- | Y | 204 | 203 | 78 | 40 | 38
treA | b1197 | JW1186 | non-essential | PE | CORE | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | periplasmic.trehalase | E.coli contains two trehalases, one in the periplasm coded for by the treA gene, and one in the cytoplasm coded for by the treF gene. TreA is active under conditions of high osmolarity producing glucose-6P which via trehalose synthesis pathway provides intracellular trehalose to combat high osmolarity. [NAME], Boos87  , Neidhardt96  ] | G | -- | -- | Y | 2.07 | -- | Y | 393 | 382 | 115 | 45 | 70 | -- | Y | 198 | 195 | 96 | 71 | 25
trg | b1421 | [NAME] | non-essential | IM | FUNCTION-UNCERTAIN | NA | methyl.accepting.chemotaxis.protein.III.ribose.and.galactose.sensor.receptor | -- | NT | -- | -- | -- | -- | Y | Y | 791 | 786 | 303 | 136 | 167 | Y | Y | 144 | 144 | 69 | 13 | 56
trxA | b3781 | JW5856 | non-essential | CY | FUNCTION-UNCERTAIN | NA | thioredoxin.1 | -- | OC | -- | -- | Y | 375.299 | Y | Y | 793 | 776 | 260 | 160 | 100 | Y | Y | 168 | 164 | 61 | 30 | 31
tsr | b4355 | JW4318 | non-essential | IM | FUNCTION-UNCERTAIN | NA | methyl.accepting.chemotaxis.protein.I.serine.sensor.receptor | -- | NT | -- | -- | -- | -- | Y | -- | 680 | 674 | 185 | 45 | 140 | Y | Y | 654 | 649 | 394 | 322 | 72
tsx | b0411 | JW0401 | non-essential | OM | FUNCTION-UNCERTAIN | NA | nucleoside.channel.receptor.of.phage.T6.and.colicin.K | Tsx is a protein involved with the permeation of ribo- and deoxy-nucleosides, across the outer membrane of E. coli. It also allows the entry of the antibiotic albicidin, and serves as a receptor for bacteriophage and colicins [ Maier88  ] | M | -- | -- | -- | -- | -- | Y | 388 | 377 | 118 | 79 | 39 | Y | Y | 196 | 188 | 98 | 46 | 52
ttk | b3641 | [NAME] | non-essential | CY | CORE | CELL.DIVISION,CHROMOSOME.SEGREGATION | division.inhibitor | Link between Cell.division and Chromosome.segregation. Parallel to [NAME]. Also potentialy parallel to sulA (SOS response). Z ring assembly is achieved by two partially redundant negative regulatory systems, the Min system and nucleoid occlusion (NO). We identified SlmA (Ttk) as the first NO factor in E. coli that is a DNA-associated division inhibitor that is directly involved in preventing Z ring assembly on portions of the membrane surrounding the nucleoid [PMID:15916962]. lmA min double mutant has a synthetic lethal phenotype [PMID:15916962] | K | -- | -- | -- | -- | Y | Y | 500 | 482 | 174 | 105 | 69 | Y | Y | 327 | 314 | 135 | 88 | 47
ubiA | b4040 | JW4000 | essential | IM | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | p.hydroxybenzoate.octaprenyltransferase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | H | -- | -- | -- | -- | Y | -- | 688 | 680 | 333 | 229 | 104 | -- | -- | -- | -- | -- | -- | --
ubiB | b3835 | JW3812 | essential | IM | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | 2.octaprenylphenol.hydroxylase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | R | -- | -- | -- | -- | Y | Y | 762 | 749 | 324 | 119 | 205 | Y | Y | 558 | 546 | 384 | 281 | 103
ubiC | b4039 | JW5713 | non-essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | chorismate.pyruvate.lyase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | H | -- | -- | Y | 5.586 | Y | Y | 793 | 785 | 206 | 111 | 95 | Y | Y | 167 | 167 | 53 | 25 | 28
ubiD | b3843 | JW3819 | essential | -- | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | 3.octaprenyl.4.hydroxybenzoate.decarboxylase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | H | -- | -- | -- | -- | Y | Y | 794 | 782 | 303 | 125 | 178 | Y | Y | 142 | 141 | 85 | 55 | 30
ubiE | b3833 | JW5581 | non-essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | bifunctional.2.octaprenyl.6.methoxy.1.4.benzoquinone.methylase.and.S.adenosylmethionine.2.DMK.methyltransferase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | H | -- | -- | Y | 0.356 | Y | Y | 784 | 772 | 495 | 204 | 291 | Y | Y | 157 | 156 | 99 | 49 | 50
[NAME] | b0662 | JW0659 | non-essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | 2.octaprenyl.3.methyl.6.methoxy.1.4.benzoquinol.oxygenase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | HC | -- | -- | Y | 18.52 | -- | Y | 395 | 392 | 286 | 89 | 197 | -- | Y | 203 | 202 | 139 | 62 | 77
ubiH | b2907 | JW2875 | non-essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | 2.octaprenyl.6.methoxyphenol.hydroxylase.FAD.NAD.P.binding | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | HC | -- | -- | Y | 12.71 | Y | Y | 767 | 761 | 344 | 166 | 178 | Y | Y | 171 | 170 | 61 | 21 | 40
ubiX | b2311 | JW2308 | non-essential | CY | FUNCTION-UNCERTAIN | CHORISMATE.DEGRADATION | 3.octaprenyl.4.hydroxybenzoate.carboxy.lyase | Chorismate.degradation' is a big superpathway which includes subcategories 'Enterobactin.biosynthesis', 'Tetrahydrofolate.biosynthesis' and 'Ubiquinone.8.biosynthesis'. Only 'Enterobactin.biosynthesis' remained in the core because seems to be related with lenght of O-antigen in LPS (see 'fepE' comments) -- | H | -- | -- | Y | 36.02 | Y | -- | 670 | 661 | 348 | 202 | 146 | Y | Y | 574 | 566 | 271 | 152 | 119
ugd | b2028 | JW2010 | non-essential | CY | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | UDP.glucose.6.dehydrogenase | -- | M | -- | -- | -- | -- | Y | Y | 532 | 510 | 225 | 159 | 66 | Y | Y | 351 | 331 | 160 | 125 | 35
ugpA | b3452 | JW3417 | non-essential | IM | CORE | PHOSPHOLIPIDS | glycerol.3.phosphate.transporter.subunit.membrane.component.of.ABC.superfamily | The UgpABCE glycerol-3-phosphate uptake system is a member of the ATP-Binding Cassette (ABC) Superfamily [ Wu95  ]. Glycerol-3-phosphate can be used as a carbon source and a phosphate source [ Schweizer82  ], and is also an essential intermediate in phospholipid biosynthesis [ Boos98  ]. Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | G | -- | -- | -- | -- | -- | Y | 392 | 385 | 104 | 45 | 59 | -- | Y | 216 | 213 | 84 | 51 | 33
ugpB | b3453 | JW3418 | non-essential | PE | CORE | PHOSPHOLIPIDS | glycerol.3.phosphate.transporter.subunit.periplasmic.binding.component.of.ABC.superfamily | The UgpABCE glycerol-3-phosphate uptake system is a member of the ATP-Binding Cassette (ABC) Superfamily [ Wu95  ]. Glycerol-3-phosphate can be used as a carbon source and a phosphate source [ Schweizer82  ], and is also an essential intermediate in phospholipid biosynthesis [ Boos98  ]. Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | G | -- | -- | Y | 0.661 | -- | Y | 394 | 387 | 124 | 39 | 85 | -- | Y | 220 | 216 | 72 | 30 | 42
ugpC | b3450 | JW3415 | non-essential | CY | CORE | PHOSPHOLIPIDS | glycerol.3.phosphate.transporter.subunit.ATP.binding.component.of.ABC.superfamily | The UgpABCE glycerol-3-phosphate uptake system is a member of the ATP-Binding Cassette (ABC) Superfamily [ Wu95  ]. Glycerol-3-phosphate can be used as a carbon source and a phosphate source [ Schweizer82  ], and is also an essential intermediate in phospholipid biosynthesis [ Boos98  ]. Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | G | -- | -- | -- | -- | -- | Y | 395 | 388 | 178 | 113 | 65 | -- | Y | 201 | 198 | 92 | 69 | 23
ugpE | b3451 | JW3416 | non-essential | IM | CORE | PHOSPHOLIPIDS | glycerol.3.phosphate.transporter.subunit.membrane.component.of.ABC.superfamily | The UgpABCE glycerol-3-phosphate uptake system is a member of the ATP-Binding Cassette (ABC) Superfamily [ Wu95  ]. Glycerol-3-phosphate can be used as a carbon source and a phosphate source [ Schweizer82  ], and is also an essential intermediate in phospholipid biosynthesis [ Boos98  ]. Interesting to look for SSL among several Glycerol-3-P producing/importing genes, including glp- and ugp- genes. | G | -- | -- | -- | -- | -- | Y | 363 | 357 | 197 | 154 | 43 | -- | Y | 188 | 186 | 89 | 55 | 34
uidC | b1615 | JW1607 | non-essential | OM | PREDICTED | NA | predicted.outer.membrane.porin.protein | predicted.outer.membrane.porin.protein | - | -- | -- | -- | -- | -- | Y | 392 | 387 | 171 | 120 | 51 | -- | Y | 198 | 196 | 110 | 71 | 39
vacJ | b2346 | JW2343 | non-essential | -- | CORE | PHOSPHOLIPIDS | predicted.lipoprotein | Recently discovered ABC transport system '[NAME]' that maintains lipid asymmetry in the Gram-negative outer membrane. [NAME] (vacJ), mlaB (yrbB), [NAME] (yrbC), mlaD (yrbD), mlaE (yrbE), and mlaF (yrbF)  [PMID:19383799] | M | -- | -- | -- | -- | -- | Y | 393 | 389 | 141 | 68 | 73 | -- | Y | 218 | 216 | 109 | 53 | 56
wbbH | b2035 | JW2020 | non-essential | IM | CORE | LPS.AND.ECA | O.antigen.polymerase | -- | - | -- | -- | -- | -- | Y | Y | 437 | 422 | 151 | 113 | 38 | Y | Y | 228 | 221 | 131 | 74 | 57
wbbI | b2034 | [NAME] | non-essential | CY | CORE | LPS.AND.ECA | conserved.protein | -- | - | -- | -- | -- | -- | -- | Y | 490 | 465 | 251 | 154 | 97 | -- | Y | 343 | 321 | 174 | 109 | 65
wbbJ | b2033 | JW2018 | non-essential | CY | PREDICTED | LPS.AND.ECA | predicted.acyl.transferase | [NAME] (2009) predicted WbbJ in a module (GC) with several OM biogenesis proteins mainly bases on operon rearrangements, PPI data only with ribosomal proteins. EcoCyc only 'predicted acyl transferase' No more info. | R | -- | -- | -- | -- | -- | Y | 270 | 247 | 115 | 113 | 2 | Y | Y | 252 | 230 | 58 | 58 | --
wbbK | b2032 | JW2017 | non-essential | CY | PREDICTED | LPS.AND.ECA | lipopolysaccharide.biosynthesis.protein | [NAME] (2009) predicted WbbJ in a module (GC) with several OM biogenesis proteins mainly bases on operon rearrangements, PPI data only with ribosomal proteins. EcoCyc only 'predicted lipopolysaccharide biosynthesis protein' No more info. | M | -- | -- | Y | 64.301 | Y | Y | 524 | 498 | 332 | 116 | 216 | Y | Y | 332 | 312 | 167 | 98 | 69
wcaA | b2059 | JW2044 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.glycosyl.transferase | Predicted by [NAME] et al as participating in M-antigen biosynthesis 'Sequential transfer of other sugars' [PMID:8759852] | M | -- | -- | -- | -- | Y | Y | 813 | 777 | 305 | 88 | 217 | Y | Y | 621 | 592 | 246 | 100 | 146
wcaB | b2058 | JW2043 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.acyl.transferase | Predicted by [NAME] et al as participating in M-antigen biosynthesis 'Acetylation' [PMID:8759852] | E | -- | -- | -- | -- | Y | Y | 815 | 779 | 255 | 83 | 172 | Y | Y | 637 | 607 | 334 | 248 | 86
wcaC | b2057 | JW2042 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.glycosyl.transferase | Predicted by [NAME] et al as participating in M-antigen biosynthesis 'Sequential transfer of other sugars' [PMID:8759852] | M | -- | -- | -- | -- | Y | Y | 814 | 779 | 286 | 89 | 197 | Y | Y | 592 | 567 | 379 | 251 | 128
wcaD | b2056 | JW2041 | non-essential | IM | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.colanic.acid.polymerase | Predicted by [NAME] et al as participating in M-antigen biosynthesis 'Polymerization of E-units' [PMID:8759852] | - | -- | -- | -- | -- | -- | Y | 381 | 371 | 145 | 71 | 74 | Y | Y | 218 | 214 | 93 | 35 | 58
wcaE | b2055 | JW2040 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.glycosyl.transferase | Predicted by [NAME] et al as participating in M-antigen biosynthesis 'Sequential transfer of other sugars' [PMID:8759852] | M | -- | -- | -- | -- | -- | Y | 368 | 359 | 171 | 90 | 81 | Y | Y | 216 | 211 | 145 | 55 | 90
wcaF | b2054 | JW2039 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.acyl.transferase | Predicted by [NAME] et al as participating in M-antigen biosynthesis 'Acetylation' [PMID:8759852] | R | -- | -- | -- | -- | -- | Y | 483 | 457 | 191 | 136 | 55 | Y | Y | 297 | 279 | 148 | 85 | 63
wcaI | b2050 | JW2035 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.glycosyl.transferase | Predicted by [NAME] et al as participating in M-antigen biosynthesis 'Sequential transfer of other sugars' [PMID:8759852] | M | -- | -- | -- | -- | Y | Y | 799 | 764 | 336 | 211 | 125 | Y | Y | 217 | 200 | 99 | 60 | 39
wcaJ | b2047 | JW2032 | non-essential | IM | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.UDP.glucose.lipid.carrier.transferase | Predicted by [NAME] et al as participating in M-antigen biosynthesis 'Transfer of Glc-1P to Und-P-carrier' [PMID:8759852] | M | -- | -- | -- | -- | Y | Y | 800 | 767 | 167 | 26 | 141 | Y | Y | 212 | 199 | 60 | 27 | 33
wcaK | b2045 | JW2030 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.pyruvyl.transferase | Annotated in EcoCyc as predicted colanic acid biosynthesis pyruvyl transferase and refers to [NAME] (2006). However [NAME] et al they mention "wcaK is closely related to the E. amylovora EPS gene amsJ, whose function is not known. The only function in the proposed CA biosynthetic pathway that has not yet been at least tentatively assigned is addition of the pyruvyl group to the terminal galactosyl residue of the E-unit side chain ([NAME]. 1); however, wcaK is not homologous to a previously sequenced pyruvylation gene of R. meliloti (24) and so there is no reason to suggest this assignment" | S | -- | -- | -- | -- | Y | Y | 530 | 502 | 147 | 45 | 102 | Y | Y | 383 | 361 | 198 | 36 | 162
wcaL | b2044 | JW2029 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.glycosyl.transferase | Predicted by [NAME] et al as participating in M-antigen biosynthesis [PMID:8759852] | M | -- | -- | -- | -- | Y | Y | 527 | 499 | 151 | 75 | 76 | Y | Y | 361 | 335 | 152 | 95 | 57
wcaM | b2043 | JW2028 | non-essential | CY | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.colanic.acid.biosynthesis.protein | WcaM (orf1.3) and galF were demonstrated by [NAME] et al to be unnecessary for colanic acid production [PMID:8759852]. However GalF provides a precursor for (GalT->GalE->wcaJ). So perhaps wcaM is part of the Colanic acid operon but does not participate in the pathway, chech SSLs | - | -- | -- | -- | -- | Y | Y | 528 | 500 | 195 | 80 | 115 | Y | Y | 341 | 318 | 155 | 88 | 67
wza | b2062 | JW2047 | non-essential | OM | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | lipoprotein.required.for.capsular.polysaccharide.translocation.through.the.outer.membrane | The proteins wzxE, wzyE and wzzE are the flippase, polymerase and lenght-regulator components of the Lipid III (ECA) biosynthesis protein complex [PMID:16816184]. After them Lipid IIIcould be transported via the wzABC translocon [PMID:17086202]. [NAME] predicted 'wzx' as the Exporter of E-unit (M-antigen) to periplasm, [PMID:8759852] but Javier couldn't found a reference clearly probing this. | M | -- | -- | -- | -- | Y | Y | 500 | 475 | 235 | 148 | 87 | Y | Y | 323 | 305 | 212 | 144 | 68
wzb | b2061 | JW2046 | non-essential | CY | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | protein.tyrosine.phosphatase | The proteins wzxE, wzyE and wzzE are the flippase, polymerase and lenght-regulator components of the Lipid III (ECA) biosynthesis protein complex [PMID:16816184]. After them Lipid IIIcould be transported via the wzABC translocon [PMID:17086202]. [NAME] predicted 'wzx' as the Exporter of E-unit (M-antigen) to periplasm, [PMID:8759852] but Javier couldn't found a reference clearly probing this. | T | -- | -- | -- | -- | Y | -- | 705 | 672 | 413 | 354 | 59 | Y | -- | 117 | 103 | 59 | 51 | 8
wzc | b2060 | JW2045 | non-essential | IM | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | protein.tyrosine.kinase | The proteins wzxE, wzyE and wzzE are the flippase, polymerase and lenght-regulator components of the Lipid III (ECA) biosynthesis protein complex [PMID:16816184]. After them Lipid IIIcould be transported via the wzABC translocon [PMID:17086202]. [NAME] predicted 'wzx' as the Exporter of E-unit (M-antigen) to periplasm, [PMID:8759852] but Javier couldn't found a reference clearly probing this. | DM | -- | -- | -- | -- | Y | Y | 792 | 757 | 299 | 102 | 197 | Y | Y | 662 | 632 | 406 | 307 | 99
wzxC | b2046 | [NAME] | non-essential | IM | CORE | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | colanic.acid.exporter | The proteins wzxE, wzyE and wzzE are the flippase, polymerase and lenght-regulator components of the Lipid III (ECA) biosynthesis protein complex [PMID:16816184]. After them Lipid IIIcould be transported via the wzABC translocon [PMID:17086202]. [NAME] predicted wzx(wzxC) as the Exporter of E-unit (M-antigen) to periplasm, [PMID:8759852] but Javier couldn't found a reference clearly probing this. Wzx is an uncharacterized member of the Polysaccharide Transporter (PST) family [ Paulsen97a  ]. Wzx(WzxC) should not be confused with the homologous RfbX O-antigen flippase, also known as [NAME] or [NAME] for SSL between rfbX(WzxB) and WzxC | R | -- | -- | -- | -- | Y | Y | 762 | 728 | 400 | 326 | 74 | Y | Y | 311 | 286 | 150 | 110 | 40
wzxE | b3792 | JW3766 | non-essential | IM | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | O.antigen.translocase | The proteins wzxE, wzyE and wzzE are the flippase, polymerase and lenght-regulator components of the Lipid III (ECA) biosynthesis protein complex [PMID:16816184]. After them Lipid IIIcould be transported via the wzABC translocon [PMID:17086202]. [NAME] predicted 'wzx' as the Exporter of E-unit (M-antigen) to periplasm, [PMID:8759852] but Javier couldn't found a reference clearly probing this. | R | -- | -- | -- | -- | Y | Y | 521 | 509 | 219 | 138 | 81 | Y | Y | 341 | 332 | 163 | 87 | 76
wzyE | b3793 | JW3769 | essential | IM | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.Wzy.protein.involved.in.ECA.polysaccharide.chain.elongation | The proteins wzxE, wzyE and wzzE are the flippase, polymerase and lenght-regulator components of the Lipid III (ECA) biosynthesis protein complex [PMID:16816184]. After them Lipid IIIcould be transported via the wzABC translocon [PMID:17086202]. [NAME] predicted 'wzx' as the Exporter of E-unit (M-antigen) to periplasm, [PMID:8759852] but Javier couldn't found a reference clearly probing this. | - | -- | -- | -- | -- | Y | -- | 709 | 691 | 285 | 213 | 72 | Y | -- | 534 | 519 | 338 | 293 | 45
wzzE | b3785 | JW5601 | non-essential | IM | CORE | LPS.AND.ECA,M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | Entobacterial.Common.Antigen.ECA.polysaccharide.chain.length.modulation.protein | The proteins wzxE, wzyE and wzzE are the flippase, polymerase and lenght-regulator components of the Lipid III (ECA) biosynthesis protein complex [PMID:16816184]. After them Lipid IIIcould be transported via the wzABC translocon [PMID:17086202]. [NAME] predicted 'wzx' as the Exporter of E-unit (M-antigen) to periplasm, [PMID:8759852] but Javier couldn't found a reference clearly probing this. | M | -- | -- | -- | -- | -- | Y | 494 | 483 | 152 | 67 | 85 | Y | Y | 313 | 304 | 140 | 75 | 65
[NAME] | b3811 | JW3784 | non-essential | CY | CORE | CELL.DIVISION,CHROMOSOME.SEGREGATION | site.specific.tyrosine.recombinase | The Xer site-specific recombination system includes [NAME] and XerD, which are two lambda integrase family recombinases and are involved in converting chromosome dimers formed due to homologous recombination into monomers so that segregation of the chromosomes can occur during cell division. The C-terminal portion of FtsK is required for XerC and XerD resolution of chromosome dimers. -- | L | -- | -- | -- | -- | -- | Y | 393 | 383 | 194 | 78 | 116 | -- | Y | 206 | 201 | 124 | 78 | 46
xerD | b2894 | JW2862 | non-essential | CY | CORE | CELL.DIVISION,CHROMOSOME.SEGREGATION | site.specific.tyrosine.recombinase | The Xer site-specific recombination system includes [NAME] and XerD, which are two lambda integrase family recombinases and are involved in converting chromosome dimers formed due to homologous recombination into monomers so that segregation of the chromosomes can occur during cell division. The C-terminal portion of FtsK is required for XerC and XerD resolution of chromosome dimers. -- | L | -- | -- | -- | -- | -- | Y | 392 | 389 | 207 | 92 | 115 | -- | Y | 201 | 200 | 138 | 90 | 48
yaaJ | b0007 | JW0006 | non-essential | IM | PREDICTED | CELL.WALL.BIOGENESIS | predicted.transporter | [NAME] (2009) predicted this gene as 'COG:E:Amino acid transport and metabolism' and GC-data (operon rearrangements) othologs of yaaJ cluster with alanine and peptidoglycan metabolism such as alr, dadX and dadA. Then yaaJ may be related with biosynthesis of peptidoglycan. Based on sequence similarity YaaJ may function as a sodium/alanine symporter [EcoCyc referes to Riley06  ] | E | Y | E | -- | -- | Y | -- | 701 | 696 | 411 | 330 | 81 | Y | -- | 81 | 81 | 54 | 48 | 6
yaaU | b0045 | JW0044 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | G | -- | -- | -- | Y | 394 | 386 | 166 | 101 | 65 | -- | Y | 215 | 211 | 88 | 37 | 51
yadE | b0130 | JW0126 | non-essential | -- | PREDICTED | LPS.AND.ECA | predicted.polysaccharide.deacetylase.lipoprotein | [NAME] (2009) predicted YadE as 'GO:0009103.Lipopolysaccharide biosynthetic process - p=0.8132'. EcoCyc annotates as predicted polysaccharide deacetylase lipoprotein. Presumably is a TOMP | G | Y | M | Y | 1.944 | Y | Y | 812 | 801 | 268 | 114 | 154 | Y | Y | 215 | 214 | 120 | 66 | 54
yaeF | b0193 | JW5016 | non-essential | PE | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | - | Y | L | -- | -- | -- | Y | 390 | 376 | 194 | 120 | 74 | Y | Y | 196 | 184 | 141 | 100 | 41
yaeL | b0176 | JW0171 | essential | IM | FUNCTION-UNCERTAIN | PROTEASE | zinc.metallopeptidase | Upon extracytoplasmic stress, [NAME] and YaeL sequentially catalyze proteolytic cleavage of RseA, thereby relieving repression of sigmaE and activating the sigmaE-mediated stress response [PMIDS:12183369,12183368] YaeL has also been observed to exhibit proteolytic activity toward RpoE and RpoH [ Dartigalon01a  ], and a wide range of other membrane proteins [ Akiyama04  ] | M | -- | -- | -- | -- | Y | -- | 217 | 209 | 75 | 41 | 34 | Y | -- | 174 | 170 | 100 | 34 | 66
yaeT | b0177 | JW0172 | essential | OM | CORE | PROTEIN.SECRETION | conserved.protein | For a review of OM biogenesis see [PMID:19270402] -- | M | -- | -- | -- | -- | Y | Y | 809 | 790 | 465 | 250 | 215 | Y | Y | 279 | 271 | 190 | 121 | 69
yafD | b0209 | JW5017 | non-essential | -- | PREDICTED | CELL.WALL.BIOGENESIS | conserved.protein | [NAME] (2009) predicted YafD as 'COG.M.Cell wall/membrane/envelope biogenesis - p=0.4012', and has similarity with YadD, which is encoded within the panBCD gene cluster [ Merkel96  ] for Panthotenate biosynthesis. So check hits with 'Pantothenate.and.CoA.biosynthesis' | S | Y | M | Y | 7.967 | Y | Y | 813 | 799 | 225 | 81 | 144 | Y | Y | 656 | 643 | 255 | 147 | 108
yafL | b0227 | JW0217 | non-essential | -- | PREDICTED | FAS,CELL.WALL.BIOGENESIS | predicted.lipoprotein.and.C40.family.peptidase | [NAME] (2009) predicted YafL as 'COG.M.Cell wall/membrane/envelope biogenesis - p=0.9817 and 'GO:0008610.Lipid biosynthetic process - p=0.9969' and 'GO:0046677.Response to antibiotic - p=0.8276'. EcoCyc has no information. | M | Y | M | -- | -- | Y | Y | 811 | 804 | 245 | 77 | 168 | Y | Y | 671 | 664 | 238 | 104 | 134
yagG | b0270 | JW0263 | essential | IM | FUNCTION-UNCERTAIN | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | CP4.6.prophage.predicted.sugar.transporter | The YagG protein is an uncharacterized member of the GPH family of galactose-pentose-hexuronide transporters [ Poolman96  ]. Based on sequence similarity, it may function as a proton or other ion-driven sugar uptake system. | G | Y | G | -- | -- | -- | Y | 389 | 388 | 190 | 43 | 147 | -- | Y | 203 | 202 | 104 | 32 | 72
yagX | b0291 | JW0285 | non-essential | OM | PREDICTED | NA | predicted.aromatic.compound.dioxygenase | predicted.aromatic.compound.dioxygenase | - | Y | K G | -- | -- | -- | Y | 394 | 393 | 211 | 74 | 137 | -- | Y | 198 | 197 | 95 | 46 | 49
yahF | b0320 | JW0312 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.acyl.CoA.synthetase.with.NAD.P.binding.domain.and.succinyl.CoA.synthetase.domain | predicted.acyl.CoA.synthetase.with.NAD.P.binding.domain.and.succinyl.CoA.synthetase.domain | C | Y | E | -- | -- | -- | Y | 366 | 365 | 134 | 38 | 96 | -- | Y | 209 | 208 | 77 | 20 | 57
yaiO | b0358 | JW0349 | non-essential | -- | FUNCTION-UNCERTAIN | NA | predicted.protein | Is a TOMP with unknown function. [NAME] (2009) predictions are p<0.1 | - | Y | K | -- | -- | Y | Y | 786 | 779 | 235 | 95 | 140 | Y | Y | 618 | 611 | 256 | 138 | 118
yaiP | b0363 | JW0355 | non-essential | IM | PREDICTED | FAS | predicted.glucosyltransferase | [NAME] (2009) predicted as 'COG:I.Lipid transport and metabolism - p=0.1264'. EcoCyc - nonessential gene of unknown function [ Winterberg05  ]. | M | Y | I | -- | -- | Y | Y | 798 | 791 | 246 | 56 | 190 | Y | Y | 632 | 625 | 275 | 113 | 162
yaiS | b0364 | JW0356 | non-essential | CY | PREDICTED | NA | conserved.protein | [NAME] (2009) predicted YaiS as 'COG.M.Cell wall/membrane/envelope biogenesis  - 0.56'. EcoCyc no info. | S | Y | M | -- | -- | Y | Y | 519 | 515 | 182 | 64 | 118 | Y | Y | 323 | 319 | 129 | 72 | 57
yaiT | b0371 | JW0362 | non-essential | EC | PREDICTED | NA | predicted.protein | predicted.protein | -- | Y | K | -- | -- | -- | Y | 394 | 390 | 210 | 155 | 55 | -- | Y | 203 | 199 | 119 | 98 | 21
yaiU | b0374 | JW5051 | non-essential | OM | PREDICTED | NA | predicted.protein | predicted.protein | -- | Y | L | -- | -- | -- | Y | 392 | 388 | 147 | 66 | 81 | -- | Y | 207 | 203 | 91 | 47 | 44
yajC | b0407 | JW0397 | non-essential | IM | CORE | PROTEIN.SECRETION | SecYEG.protein.translocase.auxillary.subunit | For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | Y | 1538.261 | Y | Y | 790 | 774 | 340 | 131 | 209 | Y | Y | 593 | 582 | 271 | 167 | 104
yajG | b0434 | JW0424 | non-essential | PE | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | M | Y | O | Y | 9.556 | -- | Y | 374 | 361 | 151 | 111 | 40 | -- | Y | 167 | 160 | 102 | 77 | 25
yajI | b0412 | JW5056 | non-essential | PE | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | - | Y | M | -- | -- | Y | Y | 799 | 783 | 284 | 139 | 145 | Y | Y | 154 | 146 | 63 | 27 | 36
yajR | b0427 | JW5059 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | C | -- | -- | -- | Y | 392 | 379 | 174 | 90 | 84 | -- | Y | 193 | 184 | 101 | 66 | 35
ybaL | b0478 | JW0467 | non-essential | IM | PREDICTED | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | predicted.transporter.with.NAD.P.binding.Rossmann.fold.domain | The YbaL protein is an uncharacterised member of the CPA-2 family of monovalent/proton antiporters. Based on sequence similarity YbaL may function as an potassium efflux system. | P | Y | G | -- | -- | -- | Y | 391 | 386 | 91 | 38 | 53 | -- | Y | 203 | 199 | 79 | 41 | 38
ybaT | b0486 | JW0475 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predicted YbaT as GO:0015031-Protein transport - 0.9879. YbaT is a putative amino acid/amine transporter [ Riley06  ] of the APC superfamily. Expression of ybaT was increased in response to acid stress, though whether it has a role in acid resistance has yet to be determined [ Tucker02  ]. ybaT is positively regulated by GadXW which are involved in glutamate-dependent acid resistance [ Tucker03  ]. ybaT is in an operon with cueR which is responsible for copper resistance [ Permina06  ]. | E | Y | G | -- | -- | -- | Y | 393 | 388 | 123 | 53 | 70 | -- | Y | 214 | 209 | 97 | 46 | 51
ybaW | b0443 | JW0433 | non-essential | CY | FUNCTION-UNCERTAIN | FAD,CELL.SHAPE | conserved.protein | [NAME] (2009) predicted  YabW as 'GO:0008360.Regulation of cell shape - 0.9802' but EcoCyc annotates as 'Thioesterase III is a long-chain acyl-CoA thioesterase that is involved in the ?-oxidation of oleic acid' | R | Y | M | -- | -- | -- | Y | 464 | 454 | 147 | 116 | 31 | -- | Y | 154 | 148 | 61 | 43 | 18
ybaY | b0453 | JW0443 | non-essential | PE | PREDICTED | NA | predicted.outer.membrane.lipoprotein | predicted.outer.membrane.lipoprotein | S | Y | M | -- | -- | Y | Y | 772 | 759 | 333 | 235 | 98 | Y | Y | 104 | 101 | 60 | 43 | 17
[NAME] | [NAME] | JW0487 | non-essential | -- | FUNCTION-UNCERTAIN | NA | predicted.protein | Might be used as a negative control. Not sure why this protein was selected. [NAME] (2009) predicted as 'GO:0006260.DNA replication - 0.6163' and 'COG.G.Carbohydrate transport and metabolism - 0.456'. EcoCyc 'No information'. | - | Y | G | -- | -- | Y | Y | 815 | 806 | 247 | 122 | 125 | Y | Y | 591 | 584 | 314 | 154 | 160
ybbW | b0511 | JW0499 | non-essential | IM | PREDICTED | NA | predicted.allantoin.transporter | predicted.allantoin.transporter | FH | Y | F | -- | -- | -- | Y | 394 | 391 | 168 | 115 | 53 | -- | Y | 205 | 203 | 110 | 67 | 43
ybbY | b0513 | JW0501 | non-essential | IM | PREDICTED | NA | predicted.uracil.xanthine.transporter | predicted.uracil.xanthine.transporter | F | Y | I | -- | -- | -- | Y | 394 | 391 | 175 | 92 | 83 | -- | Y | 206 | 204 | 120 | 74 | 46
ybcH | b0567 | JW0556 | non-essential | PE | PREDICTED | CELL.WALL.BIOGENESIS,LPS.AND.ECA | predicted.protein | [NAME] (2009) predict YbcH 'COG.M.Cell wall/membrane/envelope biogenesis - p=0.8768' and 'GO:0009103.Lipopolysaccharide biosynthetic process - p=0.913'. No information in EcoCyc | - | Y | M | -- | -- | Y | Y | 802 | 788 | 220 | 110 | 110 | Y | Y | 582 | 572 | 240 | 138 | 102
ybdA | b0591 | [NAME] | non-essential | IM | CORE | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | predicted.transporter | [NAME], ExbD, and ExbB are core components of several transport systems including those for iron/enterobactin (fep-), Ferric citrate (fec-), [NAME] (fhu-) and vitamin [NAME] (btu-) uptake systems. Only the (TonB-Exb*-Fep*-) and the parallel TolC-YbdA were retained in the CORE. But could be interesting to see if there is crosstalk with other systems involving [NAME]. Enterobactin appears to have more than one mechanism for export to the periplasm, one involving YbdA(EntS), but TolC is the only outer membrane channel that can export enterobactin from the periplasm [PMID:16166532] -- | - | -- | -- | -- | -- | Y | -- | 681 | 664 | 371 | 285 | 86 | -- | -- | -- | -- | -- | -- | --
ybeD | b0631 | JW0626 | non-essential | -- | PREDICTED | CELL.DIVISION,CELL.WALL.BIOGENESIS | conserved.protein | [NAME] (2009) predicted  YbeD as 'COG M Cell wall/membrane/envelope biogenesis p=0.66', '[NAME] division p=0.3281', 'GO-BP GO:0007047 Cell wall organization and biogenesis [NAME]'. EcoCyc 'Conserved protein' | S | Y | M | Y | 213.204 | Y | Y | 816 | 805 | 212 | 27 | 185 | Y | Y | 640 | 632 | 170 | 40 | 130
ybeX | b0658 | JW0655 | non-essential | CY | PREDICTED | NA | predicteed.ion.transport | predicted ion transport protein | P | Y | M | Y | 43.68 | Y | -- | 691 | 683 | 538 | 456 | 82 | Y | -- | 535 | 527 | 350 | 265 | 85
ybfM | b0681 | JW0667 | non-essential | OM | PREDICTED | NA | predicted.outer.membrane.porin | predicted.outer.membrane.porin | - | Y | J L | -- | -- | -- | Y | 386 | 385 | 125 | 72 | 53 | -- | Y | 200 | 199 | 99 | 68 | 31
ybfN | b0682 | JW0668 | non-essential | PE | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | - | Y | J | -- | -- | -- | Y | 395 | 394 | 133 | 43 | 90 | -- | Y | 218 | 217 | 70 | 17 | 53
ybfO | b0703 | JW0692 | non-essential | -- | FUNCTION-UNCERTAIN | NA | conserved.protein.rhs.like | conserved.protein.rhs.like | -- | Y | M | Y | 9.911 | -- | Y | 394 | 394 | 114 | 41 | 73 | -- | Y | 199 | 199 | 80 | 37 | 43
ybgC | b0736 | JW0726 | non-essential | CY | FUNCTION-UNCERTAIN | CELL.ENVELOPE.INTEGRITY | predicted.acyl.CoA.thioesterase | Potential link between Phospholipids and Cell.evelope.integrity. YbgC is a cytoplasmic acyl-ACP thioesterase involved in phospholipid metabolism [ Gully06  ]. [NAME] is a periplasmic protein which interacts with the central domain of TolA [PMID:11994151]. The Tol-Pal system is encoded by two operons, the first one encodes YbgC, TolQ, TolR, TolA, TolB, Pal and [NAME]; and the second from an inner promoter encodes TolB, Pal and YbgF -- | R | Y | J | Y | 32.895 | -- | Y | 380 | 375 | 174 | 111 | 63 | Y | Y | 180 | 178 | 121 | 90 | 31
ybgF | b0742 | [NAME] | non-essential | PE | FUNCTION-UNCERTAIN | CELL.ENVELOPE.INTEGRITY | predicted.protein | [NAME] is a periplasmic protein member of the YbgC-YbgF-TolQ-R-A-B-Pal Cell Envelope Complex, also known as the Tol-Pal system. YbgC is a cytoplasmic acyl-ACP thioesterase involved in phospholipid metabolism [ Gully06  ]. [NAME] is a periplasmic protein which interacts with the central domain of TolA [ Walburger02  ] | S | -- | -- | Y | 0.253 | -- | Y | 390 | 385 | 135 | 82 | 53 | Y | Y | 204 | 202 | 119 | 75 | 44
ybgH | b0709 | JW0699 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | E | Y | K G | -- | -- | -- | Y | 392 | 391 | 97 | 38 | 59 | -- | Y | 202 | 201 | 74 | 41 | 33
[NAME] | b0717 | JW0707 | non-essential | PE | FUNCTION-UNCERTAIN | PROTEIN.SECRETION,CELL.WALL.BIOGENESIS | predicted.assembly.protein | [NAME] (2009) doesn't give a significant label prediction for [NAME], but it was grouped in the '[NAME] related module' of Figure 4F'. [NAME] is annotated in EcoCyc as a 'putative chaperone predicted as an outer membrane porin'. In GOA it is annotated as 'GO:0007047.cell.wall.organization' ,  'GO:0045229:.external.encapsulating.structure.organization' and '[NAME] binding'. I classified as 'Protein.secretion' but might be another function related with Fimbriae | NU | Y | K | -- | -- | Y | Y | 522 | 519 | 146 | 74 | 72 | Y | Y | 283 | 281 | 117 | 68 | 49
ybgQ | b0718 | JW5099 | non-essential | OM | FUNCTION-UNCERTAIN | NA | predicted.outer.membrane.protein | predicted.outer.membrane.protein | NU | Y | U N | -- | -- | -- | Y | 391 | 388 | 127 | 63 | 64 | -- | Y | 182 | 180 | 96 | 64 | 32
ybhG | b0795 | JW0779 | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.membrane.fusion.protein.MFP.component.of.efflux.pump.membrane.anchor | predicted.membrane.fusion.protein.MFP.component.of.efflux.pump.membrane.anchor | M | Y | V | -- | -- | -- | Y | 395 | 392 | 119 | 49 | 70 | -- | Y | 204 | 203 | 85 | 34 | 51
ybhI | b0770 | JW0753 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predicted [NAME] in the same GC module than Citrate metabolic (cit-) genes. [NAME] is predicted to encode a tricarboxylate transporter [ Riley06  ]. | P | Y | C | -- | -- | -- | Y | 383 | 377 | 125 | 81 | 44 | -- | Y | 175 | 174 | 98 | 82 | 16
ybhO | b0789 | JW0772 | non-essential | CY | CORE | PHOSPHOLIPIDS | [NAME] | -- | I | -- | -- | -- | -- | Y | Y | 810 | 804 | 287 | 117 | 170 | Y | Y | 130 | 129 | 59 | 33 | 26
ybiO | b0808 | JW5108 | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.mechanosensitive.channel | Not sure why this protein was selected. [NAME] (2009) predicted as 'GO:0006412.Translation - 0.6606'. EcoCyc '[NAME] exhibits sequence homology to the small mechanosensitive ion channel (MscS) however [NAME] deletion mutants exhibit no detectable phenotype and its function remains unknown [ Levina99  ]'. | M | Y | O | -- | -- | Y | Y | 808 | 802 | 235 | 104 | 131 | Y | Y | 568 | 563 | 290 | 112 | 178
ybiR | b0818 | JW0802 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predicted ybiR as COG-E-Amino acid transport and metabolism - 0.9967. Expression of ybiR was reduced in response to cold shock [ Phadtare04  ]. | P | Y | H | -- | -- | -- | Y | 392 | 388 | 128 | 67 | 61 | -- | Y | 212 | 209 | 58 | 31 | 27
ybiV | b0822 | JW0806 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.hydrolase | predicted.hydrolase | R | -- | -- | Y | 13.503 | Y | Y | 771 | 759 | 208 | 106 | 102 | Y | Y | 599 | 589 | 225 | 75 | 150
ybjG | b0841 | JW5112 | non-essential | IM | CORE | PHOSPHOLIPIDS,CELL.WALL.BIOGENESIS | undecaprenyl.pyrophosphate.phosphatase | ybjG, bacA and pgpB are links between isoprenoids and cell.wall biogenesis as they provide  'undecaprenyl phosphate' [EC:3.6.1.27]  which is essential for the synthesis of peptidoglycan via MraY. However all BacA, YbjG, PgpB, and YeiU conduct EC:3.6.1.27. Simultaneous inactivation of bacA, ybjG, and pgpB is lethal [PMID:15778224]. PgpB also conducts EC:3.6.1.26 as well as PgpA, but they may not be the principal enzymes responsible for EC:3.6.1.26. Expression of C55PP activity from one of the three genes ybjG, bacA, and pgpB appears to be sufficient for synthesis of undecaprenyl phosphate and survival [ El05  ] | I | -- | -- | -- | -- | Y | Y | 524 | 521 | 180 | 107 | 73 | Y | Y | 355 | 353 | 171 | 91 | 80
ybjI | b0844 | JW5113 | non-essential | CY | FUNCTION-UNCERTAIN | NA | conserved.protein | conserved.protein | R | Y | M | Y | 6.345 | -- | Y | 392 | 390 | 119 | 54 | 65 | -- | Y | 220 | 218 | 79 | 25 | 54
ybjJ | b0845 | JW0829 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | T | -- | -- | -- | Y | 390 | 388 | 123 | 72 | 51 | -- | Y | 193 | 191 | 111 | 76 | 35
ybjL | b0847 | JW0831 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predicted [NAME] as COG-E-Amino acid transport and metabolism - 0.9611 OR Multifun-1.7-Central intermediary metabolism - 0.8387, OR GO:0006118 [NAME] transport - 0.9665. GOA has metal ion transporter based on INTERPRO conserved domain | R | Y | E | -- | -- | -- | Y | 389 | 386 | 127 | 62 | 65 | -- | Y | 200 | 198 | 86 | 34 | 52
ybjP | b0865 | JW0849 | non-essential | PE | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | - | Y | E | Y | 0.922 | -- | Y | 391 | 388 | 112 | 49 | 63 | -- | Y | 185 | 185 | 64 | 34 | 30
ycaD | b0898 | JW0881 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | J | -- | -- | -- | Y | 394 | 388 | 129 | 64 | 65 | -- | Y | 196 | 193 | 94 | 45 | 49
ycaI | b0913 | JW5120 | non-essential | IM | PREDICTED | NA | conserved.inner.membrane.protein | conserved.inner.membrane.protein | R | Y | M | -- | -- | -- | Y | 396 | 390 | 111 | 36 | 75 | -- | Y | 216 | 212 | 92 | 38 | 54
ycaM | b0899 | JW5119 | non-essential | IM | PREDICTED | NA | predicted.transporter | YcaM predicted APC amino acid transporter (EcoCyc) | E | Y | O | -- | -- | -- | Y | 390 | 384 | 102 | 36 | 66 | -- | Y | 213 | 210 | 76 | 29 | 47
ycaR | b0917 | JW0900 | non-essential | CY | PREDICTED | FAS | conserved.protein | [NAME] (2009) predicted YcaR as 'GO:0008610.Lipid biosynthetic process - 0.986'. EcoCyc 'no information' | S | Y | M | -- | -- | Y | Y | 778 | 768 | 266 | 123 | 143 | Y | Y | 561 | 554 | 201 | 86 | 115
ycbC | b0920 | JW0903 | non-essential | IM | PREDICTED | CELL.SHAPE,CELL.WALL.BIOGENESIS | conserved.inner.membrane.protein | [NAME] (2009) predict YcbC as COG-M-Cell wall/membrane/envelope biogenesis - 0.3913, GO:0008360-Regulation of cell shape - 0.9839, GO:0009252 - Peptidoglycan biosynthetic process - 0.8034 | S | Y | M | -- | -- | Y | Y | 794 | 784 | 286 | 127 | 159 | Y | Y | 625 | 616 | 204 | 81 | 123
ycbS | b0940 | JW0923 | non-essential | OM | PREDICTED | NA | predicted.outer.membrane.usher.protein | predicted.outer.membrane.usher.protein | NU | Y | U N | -- | -- | -- | Y | 393 | 387 | 154 | 50 | 104 | Y | Y | 203 | 200 | 83 | 36 | 47
yccC | b0981 | JW0964 | non-essential | IM | FUNCTION-UNCERTAIN | LPS.AND.ECA | cryptic.autophosphorylating.protein.tyrosine.kinase.Etk | [NAME] (2009) predicted yccC (etK) in a module with several OM biogenesis proteins mainly by operon rearrangemets and [NAME] profiles with each wcaJ and wzc. In contrast to the related kinase, Wzc, Etk has minimal effect on biosynthesis of colanic acid [ Vincent00  ]. Etk/[NAME]  and Wzb/Wzc forms paralog operons | DM | -- | -- | -- | -- | Y | Y | 819 | 807 | 303 | 137 | 166 | Y | Y | 249 | 245 | 99 | 32 | 67
yccS | b0960 | [NAME] | non-essential | IM | PREDICTED | NA | predicted.inner.membrane.protein | predicted.inner.membrane.protein | S | Y | O L | -- | -- | -- | Y | 388 | 384 | 130 | 72 | 58 | -- | Y | 188 | 188 | 112 | 78 | 34
yccZ | b0983 | JW0966 | non-essential | OM | FUNCTION-UNCERTAIN | LPS.AND.ECA | predicted.exopolysaccharide.export.protein | Perhaps related with etp_b0982. Seven gene products (YmcD, [NAME], YmcB, [NAME], [NAME], [NAME], and Etk) in E. coli O127:H6  are required for the production of the G4C capsule polysaccharide [ Peleg05  ]. That operon may not be expressed in E. coli [NAME], because the promoter region that was mapped in E. coli O127:H6 is inactivated in E. coli K12 by the insertion of an IS1 element 15 bp upstream of the YmcD translation start site [ Peleg05  ] | M | -- | -- | -- | -- | Y | -- | 209 | 207 | 147 | 113 | 34 | Y | -- | 162 | 160 | 126 | 100 | 26
ycdQ | b1022 | JW1007 | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.glycosyl.transferase | The pgaABCD locus is required for the synthesis of a beta-1,6-N-acetylglucosamine residues essential in biofilm formation [ [NAME]  ]. So this proteins could form a separate class 'Biofilm.formation', but here I'm just wondering if they do have SSL's | M | -- | -- | -- | -- | Y | Y | 524 | 517 | 227 | 174 | 53 | Y | Y | 333 | 328 | 216 | 142 | 74
ycdS | b1024 | JW1010 | non-essential | -- | PREDICTED | NA | predicted.outer.membrane.protein | predicted.outer.membrane.protein | - | -- | -- | Y | 1.314 | -- | Y | 393 | 390 | 114 | 39 | 75 | -- | Y | 211 | 209 | 80 | 38 | 42
yceB | b1063 | JW1050 | non-essential | PE | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | - | Y | O | -- | -- | -- | Y | 391 | 382 | 109 | 53 | 56 | Y | Y | 195 | 191 | 90 | 47 | 43
yceG | b1097 | JW1083 | non-essential | -- | PREDICTED | CELL.WALL.BIOGENESIS | predicted.aminodeoxychorismate.lyase | [NAME] (2009) predicted YceG as 'GO:0009252.Peptidoglycan biosynthetic process - p=0.6'. Annotation in EcoCyc states that yceG may be part of a 5-gene operon consisting of the pabC, yceG, tmk, holB, and ycfH genes [ Chaperon05  ]. Functions of these 5 genes are not intuitively related. | R | Y | M | -- | -- | Y | Y | 810 | 790 | 345 | 110 | 235 | Y | Y | 700 | 684 | 293 | 70 | 223
yceK | b1050 | JW5151 | non-essential | -- | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | R | Y | M | -- | -- | -- | Y | 387 | 382 | 252 | 193 | 59 | -- | Y | 178 | 175 | 117 | 99 | 18
ycfL | b1104 | JW1090 | non-essential | -- | PREDICTED | NA | predicted.protein | [NAME] (2009) predicted YfcL as both 'COG.F.Nucleotide transport and metabolism - 1' and 'COG.M.Cell wall/membrane/envelope biogenesis - 0.8943'. Predicted complex and module also show a mixture of these two processes. Look at SSL's with Lipids and Chromosome segregation for dual function | R | Y | M F | -- | -- | Y | Y | 812 | 794 | 270 | 130 | 140 | Y | Y | 162 | 158 | 75 | 43 | 32
ycfM | b1105 | JW5157 | non-essential | -- | PREDICTED | NA | predicted.outer.membrane.lipoprotein | predicted.outer.membrane.lipoprotein | R | Y | M | -- | -- | -- | Y | 389 | 377 | 142 | 69 | 73 | Y | Y | 186 | 178 | 95 | 55 | 40
ycfN | b1106 | JW1092 | non-essential | CY | FUNCTION-UNCERTAIN | NA | thiamin.kinase | thiamin.kinase | M | -- | -- | -- | -- | -- | Y | 392 | 380 | 108 | 50 | 58 | -- | Y | 201 | 193 | 100 | 67 | 33
ycfP | b1108 | JW5158 | non-essential | CY | FUNCTION-UNCERTAIN | NA | conserved.protein | [NAME] (2009) predicted YfcP as 'COG.M.Cell wall/membrane/envelope biogenesis - 0.9423' and shown that YfcP has a PPI with WbbK (LPS biosynthesis). Also show GC hits with YfcL (proximalin chromosome). EcoCyc annotates as 'predicted fimbrial-like adhesin protein' | R | Y | M | Y | 51.647 | Y | Y | 815 | 797 | 265 | 79 | 186 | Y | Y | 200 | 191 | 83 | 57 | 26
ycgR | b1194 | JW1183 | non-essential | -- | FUNCTION-UNCERTAIN | NA | protein.involved.in.flagellar.function | protein.involved.in.flagellar.function | M | -- | -- | -- | -- | -- | Y | 394 | 383 | 122 | 67 | 55 | -- | Y | 190 | 185 | 91 | 40 | 51
ycgV | b1202 | JW1193 | non-essential | EC | PREDICTED | NA | predicted.adhesin | predicted.adhesin | MU | Y | E | Y | 0.341 | -- | Y | 392 | 383 | 199 | 119 | 80 | -- | Y | 187 | 183 | 111 | 72 | 39
ychM | b1206 | JW5189 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predicted YchM as [NAME] transport and metabolism - 0.74. The YchM protein is a putative sulfate transporter belonging to the SulP family of sulfate transporters. YchM may mediate sulfate uptake via sulfate/proton symport (EcoCyc) | P | Y | F | -- | -- | Y | -- | 663 | 652 | 329 | 221 | 108 | -- | -- | -- | -- | -- | -- | --
ychP | [NAME] | [NAME] | non-essential | OM | PREDICTED | NA | predicted.invasin | predicted.invasin | - | Y | C | -- | -- | -- | Y | 393 | 385 | 104 | 36 | 68 | -- | Y | 211 | 207 | 72 | 28 | 44
ycjG | b1325 | JW1318 | non-essential | CY | PREDICTED | CELL.WALL.BIOGENESIS | L.Ala.D.L.Glu.epimerase | Probably involved in recycling of peptidoglycan. YcjG is an L-Ala-D/L-Glu epimerase that may play a role in the metabolism of murein peptide [EcoCyc, nor ref provided]. MpaA is a murein peptide amidase that may act with YcjG in murein recycling [PMID:12511517]. [NAME] [NAME] operon rearrangement with ampH, rffM, rfe and spr | MR | -- | -- | -- | -- | Y | Y | 780 | 775 | 353 | 118 | 235 | Y | Y | 619 | 615 | 262 | 79 | 183
ydcL | b1431 | JW1427 | non-essential | PE | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | - | Y | E | -- | -- | -- | Y | 367 | 365 | 145 | 65 | 80 | -- | Y | 188 | 187 | 100 | 52 | 48
ydcO | b1433 | JW5229 | non-essential | IM | PREDICTED | NA | predicted.benzoate.transporter | predicted.benzoate.transporter | Q | Y | P | -- | -- | -- | Y | 354 | 352 | 252 | 170 | 82 | -- | Y | 173 | 172 | 109 | 72 | 37
yddA | b1496 | JW5242 | non-essential | IM | FUNCTION-UNCERTAIN | NA | fused.predicted.multidrug.transporter.subunits.of.ABC.superfamily.membrane.component.ATP.binding.component | YddA is an inner membrane protein found, in random transposon mutagenesis studies, to be required for growth in optimum (rich medium at 37 degrees C) growth conditions but not under cold conditions (15 degrees C) or in minimal medium [ Serina04  ]. | R | -- | -- | -- | -- | -- | Y | 358 | 353 | 199 | 174 | 25 | -- | Y | 188 | 187 | 125 | 91 | 34
yddB | b1495 | JW1490 | non-essential | OM | PREDICTED | NA | predicted.porin.protein | predicted.porin.protein | - | Y | M | -- | -- | -- | Y | 390 | 384 | 152 | 89 | 63 | -- | Y | 194 | 192 | 103 | 53 | 50
yddL | b1472 | JW1468 | non-essential | OM | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | -- | Y | K | -- | -- | -- | Y | 393 | 387 | 163 | 106 | 57 | Y | Y | 194 | 193 | 91 | 55 | 36
yddW | b1491 | JW1486 | non-essential | PE | PREDICTED | NA | predicted.liprotein | predicted.liprotein | S | Y | E | -- | -- | -- | Y | 385 | 379 | 179 | 123 | 56 | -- | Y | 190 | 188 | 118 | 82 | 36
ydeA | b1528 | JW1521 | non-essential | IM | PREDICTED | NA | predicted.arabinose.transporter | predicted.arabinose.transporter | G | Y | F | -- | -- | -- | Y | 375 | 375 | 243 | 188 | 55 | -- | Y | 200 | 200 | 124 | 100 | 24
ydeE | b1534 | [NAME] | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | K | -- | -- | -- | Y | 387 | 387 | 140 | 80 | 60 | -- | Y | 200 | 200 | 90 | 61 | 29
ydeK | b1510 | JW1503 | non-essential | EC | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | - | Y | L | -- | -- | -- | Y | 390 | 390 | 156 | 69 | 87 | -- | Y | 200 | 200 | 90 | 50 | 40
ydeT | b1505 | [NAME] | non-essential | OM | PREDICTED | NA | predicted.protein | predicted.protein | -- | Y | K | -- | -- | -- | Y | 386 | 381 | 252 | 171 | 81 | -- | Y | 195 | 194 | 135 | 93 | 42
ydfJ | b1543 | JW1536 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | -- | Y | E | -- | -- | -- | Y | 394 | 394 | 126 | 50 | 76 | -- | Y | 218 | 218 | 94 | 62 | 32
ydgA | b1614 | JW1606 | non-essential | CY | FUNCTION-UNCERTAIN | NA | conserved.protein | [NAME] (2009) predicted ydgA as Multifun-1.7-Central intermediary metabolism - 0.7141. Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | S | Y | F | -- | -- | -- | Y | 394 | 389 | 104 | 46 | 58 | Y | Y | 213 | 210 | 89 | 49 | 40
ydgI | b1605 | JW1597 | non-essential | IM | PREDICTED | NA | predicted.arginine.ornithine.antiporter.transporter | [NAME] (2009) predicted [NAME]) as [NAME] acid transport and metabolism - 0.9967. ArcD is an uncharacterized member of the APC family of amino acid transporters. arcD is similar to the arcD gene of Pseudomonas aeruginosa wich encodes an arginine:ornithine antiporter [ Herzberg06  ]. | - | Y | E | -- | -- | -- | Y | 351 | 349 | 231 | 202 | 29 | -- | Y | 173 | 173 | 112 | 101 | 11
ydgR | b1634 | JW1626 | non-essential | IM | FUNCTION-UNCERTAIN | OLIGOPEPTIDE.TRANSPORT | predicted.transporter | In reality this protein was reported as peptide- rather than protein transporter [PMID:17158458] | E | -- | -- | -- | -- | Y | Y | 816 | 803 | 247 | 123 | 124 | Y | Y | 598 | 588 | 371 | 281 | 90
ydhA | b1639 | JW1631 | non-essential | -- | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | R | Y | H | -- | -- | -- | Y | 396 | 391 | 123 | 45 | 78 | -- | Y | 220 | 217 | 80 | 26 | 54
ydhC | b1660 | JW1652 | non-essential | IM | PREDICTED | RESPONSE.TO.ANTIBIOTIC | predicted.transporter | YdhC is an uncharacterized member of the Major Facilitator Superfamily (MFS) [ Marger93  ]. Sequence similarity suggests that it may be involved in drug efflux (EcoCyc) | - | Y | K | -- | -- | -- | Y | 390 | 387 | 137 | 84 | 53 | -- | Y | 182 | 180 | 78 | 45 | 33
ydhJ | b1644 | JW1636 | non-essential | IM | PREDICTED | RESPONSE.TO.ANTIBIOTIC | undecaprenyl.pyrophosphate.phosphatase | [NAME] (2009) predicted ydhJ interacting (GC) with several [NAME] related proteins. GOA annotates as 'GO:0009306.protein.secretion [IEA] presumably because it has PF00529;'. Ecocyc 'No information'. Riley snapshot 'undecaprenyl.pyrophosphate.phosphatase but dont describe why. Other four proteins in EcoCyc are annotated with such activity' | V | -- | -- | -- | -- | Y | Y | 787 | 775 | 365 | 63 | 302 | Y | Y | 622 | 612 | 252 | 56 | 196
ydhK | b1645 | JW1637 | non-essential | IM | PREDICTED | NA | conserved.inner.membrane.protein | conserved.inner.membrane.protein | S | Y | K | -- | -- | -- | Y | 394 | 390 | 174 | 83 | 91 | -- | Y | 200 | 198 | 88 | 46 | 42
ydhO | b1655 | JW5270 | non-essential | PE | PREDICTED | NA | predicted.lipoprotein | [NAME] (2009) predicted YdhO as 'GO:0006412.Translation - 0.8409' presumably because several GC predictions with ribosomal proteins. Ecocyc annotates as predicted lipoprotein but no more information' | M | Y | J | -- | -- | Y | Y | 523 | 517 | 199 | 92 | 107 | Y | Y | 339 | 333 | 164 | 109 | 55
ydhP | b1657 | [NAME] | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | G | Y | C | -- | -- | -- | Y | 395 | 392 | 164 | 82 | 82 | -- | Y | 226 | 224 | 75 | 24 | 51
ydiD | b1701 | JW5910 | non-essential | CY | CORE | FAD | short.chain.acyl.CoA.synthetase.anaerobic | -- | IQ | -- | -- | -- | -- | Y | Y | 817 | 807 | 297 | 97 | 200 | Y | Y | 632 | 623 | 317 | 195 | 122
ydiM | b1690 | JW1680 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | E | -- | -- | -- | Y | 387 | 384 | 119 | 34 | 85 | -- | Y | 209 | 207 | 86 | 21 | 65
ydiN | b1691 | JW5274 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | E | -- | -- | -- | Y | 360 | 357 | 156 | 117 | 39 | -- | Y | 185 | 183 | 89 | 46 | 43
ydiO | b1695 | [NAME] | non-essential | CY | CORE | FAD | predicted.acyl.CoA.dehydrogenase | -- | I | -- | -- | -- | -- | Y | Y | 815 | 807 | 255 | 76 | 179 | Y | Y | 633 | 625 | 284 | 76 | 208
ydiY | b1722 | JW1711 | non-essential | OM | PREDICTED | NA | conserved.protein | conserved.protein | M | Y | G | -- | -- | -- | Y | 391 | 387 | 139 | 86 | 53 | -- | Y | 204 | 202 | 107 | 41 | 66
ydjE | b1769 | JW1758 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | E | -- | -- | -- | Y | 357 | 357 | 236 | 191 | 45 | -- | Y | 172 | 172 | 104 | 71 | 33
ydjK | b1775 | JW5290 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | E | -- | -- | -- | Y | 394 | 394 | 98 | 39 | 59 | -- | Y | 216 | 216 | 64 | 24 | 40
ydjN | b1729 | JW1718 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predicted ydjN as GO:0006865-Amino acid transport - 0.302. EcoCyc annotates as predicted transporter but has no more information. | R | Y | C | -- | -- | -- | Y | 370 | 367 | 151 | 110 | 41 | -- | Y | 197 | 196 | 72 | 32 | 40
yeaN | b1791 | JW1780 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | P | Y | H | -- | -- | -- | Y | 396 | 393 | 144 | 57 | 87 | -- | Y | 203 | 203 | 90 | 55 | 35
yeaV | b1801 | JW5293 | non-essential | IM | PREDICTED | CELL.WALL.BIOGENESIS | predicted.transporter | [NAME] (2009) predicted YeaV as ' COG.M.Cell wall/membrane/envelope biogenesis - 0.8797'. EcoCyc annotates as 'YeaV is an uncharacterized member of the [NAME], [NAME], [NAME] (BCCT) family [ Eichler94  ]' | M | Y | M | -- | -- | Y | Y | 516 | 511 | 190 | 107 | 83 | Y | Y | 334 | 333 | 129 | 76 | 53
yeaY | b1806 | JW1795 | non-essential | -- | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | M | Y | M | -- | -- | -- | Y | 394 | 390 | 159 | 71 | 88 | -- | Y | 205 | 205 | 94 | 41 | 53
yebA | b1856 | JW5304 | non-essential | -- | FUNCTION-UNCERTAIN | CELL.DIVISION,CELL.SHAPE,CELL.WALL.BIOGENESIS | predicted.peptidase | [NAME] (2009) predicted 'GO:Regulation of cell shape - 0.99' and 'COG:Cell wall/membrane/envelope biogenesis - 0.18' . Also GOA has 'GO:0007047.cell.wall.organization' and 'GO:000650.proteolysis'. EcoCyc mention that loss of yebA exacerbates the division phenotype of an envC nlpD double null mutant [PMID:19525345] | M | Y | M | -- | -- | Y | Y | 747 | 738 | 352 | 244 | 108 | Y | Y | 215 | 213 | 151 | 38 | 113
yebQ | b1828 | JW5299 | non-essential | IM | PREDICTED | RESPONSE.TO.ANTIBIOTIC | predicted.transporter | [NAME] (2009) doesn't give a significant label prediction for [NAME], but it was grouped in a GC module with 'bcr' a Bicyclomycin/multidrug efflux system. Based on sequence similarity, it may function as a proton-driven drug efflux system (EcoCyc) | - | Y | L | -- | -- | -- | Y | 391 | 386 | 148 | 92 | 56 | -- | Y | 199 | 199 | 110 | 86 | 24
yedE | b1929 | JW1914 | non-essential | IM | PREDICTED | NA | predicted.inner.membrane.protein | predicted.inner.membrane.protein | R | Y | E | -- | -- | -- | Y | 390 | 385 | 157 | 105 | 52 | -- | Y | 186 | 184 | 111 | 70 | 41
yeeF | b2014 | JW5330 | non-essential | IM | PREDICTED | NA | predicted.amino.acid.transporter | [NAME] (2009) predicted yeeF as COG-E-Amino acid transport and metabolism - 0.8352. [NAME] (2006) annotate YeeF is a putative amino acid transporter [ Riley06  ] of the APC superfamily. | - | Y | E | -- | -- | -- | Y | 392 | 390 | 145 | 77 | 68 | -- | Y | 201 | 200 | 79 | 41 | 38
yeeO | b1985 | JW1965 | non-essential | IM | PREDICTED | RESPONSE.TO.ANTIBIOTIC | predicted.multidrug.efflux.system | predicted.multidrug.efflux.system | V | Y | G | -- | -- | -- | Y | 370 | 370 | 141 | 90 | 51 | -- | Y | 187 | 187 | 102 | 79 | 23
yegE | b2067 | JW2052 | non-essential | IM | PREDICTED | NA | predicted.diguanylate.cyclase.GGDEF.domain.signalling.protein | predicted.diguanylate.cyclase.GGDEF.domain.signalling.protein | T | Y | T | Y | 2.345 | -- | Y | 393 | 383 | 175 | 122 | 53 | -- | Y | 195 | 191 | 112 | 91 | 21
yegT | b2098 | JW2085 | non-essential | IM | PREDICTED | NA | predicted.nucleoside.transporter | predicted.nucleoside.transporter | - | Y | E | -- | -- | -- | Y | 393 | 392 | 119 | 31 | 88 | -- | Y | 213 | 213 | 62 | 22 | 40
yehB | b2109 | JW2096 | non-essential | OM | PREDICTED | NA | predicted.outer.membrane.protein | predicted.outer.membrane.protein | NU | Y | L | -- | -- | -- | Y | 392 | 391 | 189 | 80 | 109 | -- | Y | 211 | 210 | 79 | 39 | 40
yehT | b2125 | JW5352 | non-essential | CY | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | predicted.response.regulator.in.two.component.system.withYehU | Overproduction causes a drug (beta-lactams) resistance phenotype [ Hirakawa03a  , [NAME]  ]. Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | KT | Y | T | -- | -- | Y | Y | 794 | 790 | 319 | 169 | 150 | Y | Y | 578 | 575 | 344 | 246 | 98
yehU | b2126 | [NAME] | non-essential | IM | PREDICTED | FAS,CELL.WALL.BIOGENESIS | [NAME].YehT | [NAME] (2009) predicted yehU as 'GO:0008610.Lipid biosynthetic process - 0.7708' whereas GOA GO:0007047.cell.wall.organization. EcoCyc: YehU and YehT are predicted to function as a histidine kinase/response regulator pair of a two-component signal transduction system. Simultaneous deletion of yehU  and yehT caused no significant difference compared to wild type in a phenotype microarray experiment [ [NAME]  ] | T | Y | H | -- | -- | Y | Y | 812 | 806 | 228 | 68 | 160 | Y | Y | 611 | 606 | 395 | 216 | 179
yeiB | b2152 | JW2139 | non-essential | IM | PREDICTED | NA | conserved.inner.membrane.protein | conserved.inner.membrane.protein | S | Y | H | -- | -- | -- | Y | 393 | 385 | 115 | 55 | 60 | -- | Y | 219 | 213 | 79 | 42 | 37
yeiH | b2158 | JW2145 | non-essential | IM | PREDICTED | NA | conserved.inner.membrane.protein | conserved.inner.membrane.protein | S | Y | L | -- | -- | -- | Y | 395 | 389 | 135 | 41 | 94 | -- | Y | 216 | 211 | 89 | 38 | 51
yeiM | b2164 | JW2151 | non-essential | IM | PREDICTED | NA | predicted.nucleoside.transporter | predicted.nucleoside.transporter | F | Y | F | -- | -- | -- | Y | 391 | 385 | 123 | 68 | 55 | -- | Y | 208 | 204 | 88 | 40 | 48
yeiR | b2173 | JW2161 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.enzyme | Protein of unknown function | R | Y | I | -- | -- | Y | Y | 797 | 787 | 301 | 108 | 193 | Y | Y | 602 | 595 | 350 | 180 | 170
yeiW | b4502 | JW5361 | non-essential | -- | PREDICTED | CELL.WALL.BIOGENESIS | conserved.protein | [NAME] (2009) predicted [NAME] as 'GO:0007047.Cell wall organization and biogenesis - 0.8178' EcoCyc has no information | - | Y | E | -- | -- | Y | Y | 809 | 800 | 374 | 66 | 308 | Y | Y | 587 | 579 | 346 | 135 | 211
yejO | b2190 | JW5839 | non-essential | EC | PREDICTED | NA | [NAME] | [NAME] (2009) predicts YejO involved in 'COG:Replication, recombination and repair' and 'GO:0006310.DNA.recombination' and shows GC interactions with several integrases and other DNA-related machinery. Whereas GOA suggest 'GO:0007155.cell.adhesion' and EcoCyc mentions 'The function of YejO is unknown' | -- | Y | L | -- | -- | Y | Y | 808 | 799 | 270 | 83 | 187 | Y | Y | 603 | 597 | 323 | 177 | 146
yfaL | b2233 | JW2227 | non-essential | EC | FUNCTION-UNCERTAIN | NA | adhesin | YfaL is a potential adhesin. It was identified as a protein with similarity to antigen 43 (Ag43), a self-recognizing surface adhesin. Deletion of the yfaL gene has no significant effect on adhesion or biofilm formation, while increased expression of YfaL causes an increase in adhesion to solid surfaces and increased biofilm formation [ Roux05  ]. | - | -- | -- | -- | -- | Y | Y | 797 | 782 | 258 | 74 | 184 | Y | Y | 613 | 600 | 366 | 222 | 144
yfaV | b2246 | JW2240 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | C | -- | -- | -- | Y | 363 | 357 | 107 | 46 | 61 | -- | Y | 187 | 185 | 104 | 65 | 39
yfaW | b2247 | JW2241 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.enolase | predicted.enolase | MR | Y | K | -- | -- | -- | Y | 388 | 381 | 130 | 85 | 45 | -- | Y | 207 | 202 | 80 | 37 | 43
yfaZ | b2250 | JW5371 | non-essential | -- | FUNCTION-UNCERTAIN | NA | predicted.outer.membrane.porin.protein | Is a TOMP with unknown function. [NAME] (2009) predictions are p<0.1. EcoCyc: YfaZ localizes to the outer membrane in E. coli [ Marani06  ]. | - | Y | K | -- | -- | Y | Y | 797 | 783 | 178 | 50 | 128 | Y | Y | 579 | 569 | 337 | 219 | 118
yfbE | b2253 | JW5372 | non-essential | CY | CORE | LPS.AND.ECA | uridine.5.beta.1.threo.pentapyranosyl.4.ulose.diphosphate.aminotransferase.PLP.dependent | ybfE(arnB) part of the biosynthesis of undecaprenyl phosphate-alpha-L-Ara4N (UndPLAra4N) | M | -- | -- | -- | -- | Y | Y | 786 | 772 | 227 | 96 | 131 | Y | Y | 576 | 563 | 291 | 210 | 81
yfbF | b2254 | JW2248 | non-essential | IM | CORE | LPS.AND.ECA | undecaprenyl.phosphate.L.Ara4FN.transferase | ybfE(arnC) part of the biosynthesis of undecaprenyl phosphate-alpha-L-Ara4N (UndPLAra4N) | M | -- | -- | -- | -- | Y | Y | 797 | 784 | 305 | 209 | 96 | Y | Y | 533 | 524 | 279 | 190 | 89
yfbG | b2255 | JW2249 | non-essential | CY | CORE | LPS.AND.ECA | fused.UDP.L.Ara4N.formyltransferase.UDP.GlcA.C.4.decarboxylase | ybfG(arnA) part of the biosynthesis of undecaprenyl phosphate-alpha-L-Ara4N (UndPLAra4N) | JMG | -- | -- | Y | 8.168 | Y | Y | 518 | 509 | 225 | 121 | 104 | Y | Y | 351 | 343 | 172 | 111 | 61
yfbH | b2256 | JW2250 | non-essential | CY | CORE | LPS.AND.ECA | conserved.protein | ybfH(arnD) part of the biosynthesis of undecaprenyl phosphate-alpha-L-Ara4N (UndPLAra4N) | G | Y | M | -- | -- | Y | Y | 814 | 800 | 191 | 67 | 124 | Y | Y | 190 | 186 | 82 | 38 | 44
yfbJ | b2258 | [NAME] | non-essential | IM | CORE | LPS.AND.ECA | predicted.inner.membrane.protein | yfbJ (arnF) and yfbW (arnE) were characterized genetically and biochemically as the flipases of undecaprenyl phosphate-alpha-L-Ara4N across the IM [PMID:17928292] | GER | Y | M | -- | -- | Y | Y | 511 | 502 | 172 | 128 | 44 | Y | Y | 301 | 295 | 134 | 103 | 31
yfbS | b2292 | JW2289 | non-essential | IM | PREDICTED | ENTEROBACTIN.AND.METAL.ION.TRANSPORT | predicted.transporter | [NAME] (2009) predict YfbS in COG-P-Inorganic ion transport and metabolism - 0.6572 | P | Y | P | -- | -- | -- | Y | 393 | 387 | 170 | 125 | 45 | -- | Y | 192 | 191 | 100 | 71 | 29
yfbW | b4544 | JW2252 | non-essential | IM | CORE | LPS.AND.ECA | conserved.protein | yfbJ (arnF) and yfbW (arnE) were characterized genetically and biochemically as the flipases of undecaprenyl phosphate-alpha-L-Ara4N across the IM [PMID:17928292] | - | Y | M | -- | -- | Y | Y | 526 | 517 | 190 | 104 | 86 | Y | Y | 331 | 325 | 146 | 113 | 33
yfcC | b2298 | JW2295 | non-essential | IM | PREDICTED | NA | predicted.inner.membrane.protein | [NAME] (2009) predicted yeeF as COG-E-Amino acid transport and metabolism - 0.2981. EcoCyc annotate yfcC as predicted inner membrane protein; putative S-transferase but has no more information. | S | Y | E | -- | -- | -- | Y | 394 | 387 | 196 | 82 | 114 | -- | Y | 209 | 206 | 107 | 57 | 50
yfcJ | b2322 | JW2319 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | E | -- | -- | -- | Y | 393 | 385 | 207 | 107 | 100 | -- | Y | 199 | 195 | 105 | 71 | 34
[NAME] | b2338 | JW2335 | non-essential | OM | PREDICTED | NA | predicted.export.usher.protein | predicted.export.usher.protein | -- | Y | U N | -- | -- | -- | Y | 394 | 388 | 209 | 141 | 68 | -- | Y | 211 | 207 | 121 | 55 | 66
yfcX | b2341 | JW2338 | non-essential | CY | CORE | FAD | fused.enoyl.CoA.hydratase.and.epimerase.and.isomerase.3.hydroxyacyl.CoA.dehydrogenase | -- | I | -- | -- | Y | 2.199 | Y | Y | 799 | 784 | 243 | 73 | 170 | Y | Y | 516 | 503 | 260 | 133 | 127
yfcY | b2342 | JW2339 | non-essential | CY | CORE | FAD | beta.ketoacyl.CoA.thiolase.anaerobic.subunit | -- | I | -- | -- | -- | -- | Y | Y | 526 | 521 | 175 | 104 | 71 | Y | Y | 354 | 352 | 170 | 87 | 83
yfdG | b2350 | JW2346 | non-essential | IM | FUNCTION-UNCERTAIN | NA | CPS.53.KpLE1.prophage.bactoprenol.linked.glucose.translocase.flippase | CPS.53.KpLE1.prophage.bactoprenol.linked.glucose.translocase.flippase | S | -- | -- | -- | -- | -- | Y | 391 | 387 | 139 | 65 | 74 | -- | Y | 202 | 199 | 94 | 40 | 54
yfdH | b2351 | JW2347 | non-essential | IM | FUNCTION-UNCERTAIN | NA | CPS.53.KpLE1.prophage.bactoprenol.glucosyl.transferase | CPS.53.KpLE1.prophage.bactoprenol.glucosyl.transferase | M | -- | -- | -- | -- | -- | Y | 392 | 388 | 148 | 89 | 59 | -- | Y | 200 | 197 | 111 | 66 | 45
yfdI | b2352 | JW5382 | non-essential | IM | PREDICTED | NA | CPS.53.KpLE1.prophage.predicted.inner.membrane.protein | CPS.53.KpLE1.prophage.predicted.inner.membrane.protein | - | Y | M | -- | -- | -- | Y | 392 | 388 | 212 | 158 | 54 | -- | Y | 188 | 185 | 120 | 102 | 18
yfdV | b2372 | JW2369 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | R | Y | C | -- | -- | -- | Y | 390 | 389 | 198 | 140 | 58 | -- | Y | 191 | 191 | 88 | 62 | 26
yfeH | b2410 | JW5876 | non-essential | IM | PREDICTED | NA | predicted.inner.membrane.protein | [NAME] (2009) predicted yfeH as COG-F-Nucleotide transport and metabolism - 0.4676, Multifun-1.5-Building block biosynthesis - 0.9369, GO:0006164-Purine nucleotide biosynthetic process - 0.9247, GO:0008652-Amino acid biosynthetic process - 0.9775. Riley et al annotated yfeH as Putative uncharacterized transport protein. A yfeH mutant had strongly repressed swarming motility, but swimming was unchanged [ Inoue07  ]. Expression of yfeH was induced by autoinducer 2 quorum signaling [ DeLisa01  ] | R | Y | F | -- | -- | -- | Y | 396 | 391 | 223 | 159 | 64 | -- | Y | 209 | 208 | 113 | 65 | 48
yfeN | b2408 | JW2399 | non-essential | -- | PREDICTED | NA | conserved.outer.membrane.protein | conserved.outer.membrane.protein | - | Y | H | -- | -- | -- | Y | 394 | 389 | 125 | 67 | 58 | -- | Y | 218 | 217 | 126 | 59 | 67
yfeO | b2389 | JW2386 | non-essential | IM | PREDICTED | NA | [NAME] | [NAME] | P | Y | E | -- | -- | -- | Y | 364 | 360 | 292 | 238 | 54 | -- | Y | 195 | 194 | 143 | 129 | 14
yfeW | b2430 | [NAME] | non-essential | PE | CORE | CELL.WALL.BIOGENESIS | predicted.periplasmic.esterase | dacB catalyzes both D-alanyl-D-alanine carboxypeptidase and D-alanyl-D-alanine endopeptidase activities, whereas yfeB is a predicted penicillin-binding protein 4B with EPase and/or Cpase activities [PMID:16402224]. Check for SSL between dacB and yfeW | V | Y | C | -- | -- | Y | -- | 710 | 706 | 299 | 199 | 100 | Y | -- | 62 | 61 | 29 | 17 | 12
yfgA | b2516 | JW2500 | non-essential | -- | CORE | CELL.SHAPE,CELL.WALL.BIOGENESIS | conserved.protein | RodZ (yfgA) is responsible for maintaining the rod shape of the E. coli cell and is specifically involved in regulating the length of the long axis of the cell. The cytoplasmic domain allows the protein to form helical filaments along the periphery of the cell, while the periplasmic domain likely interacts with peptidoglycan biosynthesis machinery to regulate cell shape. Deletion of rodZ with surA, yciB, yciM, or yhcB results in a synthetic lethal phenotype [PMID:18180259] Hu et al (2009) predict YfgA (RodA) as 'COG:Posttranslational modification, protein turnover Chaperones P=0.94'. Whereas EcoCyc describes RodZ is responsible for maintaining the rod shape of the E. coli cell and is specifically involved in regulating the length of the long axis of the cell, and annotates RodZ is responsible for maintaining the rod shape of the E. coli cell and is specifically involved in regulating the length of the long axis of the cell. So is this a false positive hit for [NAME]? Or a dual (related??) function?. Check if we recapitulate the SSL's reported in [PMID:18180259] | S | Y | O | Y | 12.797 | Y | -- | 654 | 648 | 509 | 431 | 78 | Y | -- | 493 | 489 | 339 | 292 | 47
yfgH | b2505 | JW5400 | non-essential | -- | PREDICTED | NA | predicted.outer.membrane.lipoprotein | predicted.outer.membrane.lipoprotein | - | Y | K | -- | -- | -- | Y | 394 | 392 | 205 | 117 | 88 | -- | Y | 205 | 204 | 135 | 96 | 39
yfgL | b2512 | JW2496 | non-essential | -- | CORE | PROTEIN.SECRETION | protein.assembly.complex.lipoprotein.component | For a review of OM biogenesis see [PMID:19270402]. FkpA(chaperones, currently NOT_IN_EMAP) and yfgL(bamB) has a SSL interaction [PMID:15968066] | S | -- | -- | -- | -- | -- | Y | 396 | 393 | 181 | 75 | 106 | Y | Y | 211 | 211 | 96 | 29 | 67
yfhM | b2520 | JW2504 | non-essential | PE | PREDICTED | CELL.SHAPE,CELL.WALL.BIOGENESIS | conserved.protein | [NAME] (2009) predicted [NAME] as 'GO:0008360.Regulation of cell shape - 0.6509' and 'COG.M.Cell wall/membrane/envelope biogenesis - 0.5578'. [NAME] is an ?2-macroglobulin involved in colonization [ Budd04  , Doan08  ]. YfhM homologs in bacteria are always paired with a pbpC gene encoding a very efficient peptidoglycan glycosyltransferase [ Budd04  ] | R | Y | M | Y | 0.716 | Y | Y | 527 | 523 | 171 | 78 | 93 | Y | Y | 353 | 352 | 146 | 68 | 78
yfiB | b2605 | JW2586 | non-essential | OM | PREDICTED | NA | predicted.outer.membrane.lipoprotein | [NAME] (2009) predicted as 'COG:L.Replication, recombination and repair' (p=0.3). [NAME] is a TOMP with unknown function. | M | Y | L | -- | -- | -- | Y | 499 | 495 | 227 | 99 | 128 | Y | Y | 339 | 336 | 175 | 108 | 67
yfiH | b2593 | JW2575 | non-essential | CY | PREDICTED | CELL.WALL.BIOGENESIS | conserved.protein | [NAME] (2009) predicted yfiH as 'GO:0009252.Peptidoglycan biosynthetic process - 0.5739'. EcoCyc has no information | S | Y | M | -- | -- | Y | Y | 523 | 518 | 157 | 88 | 69 | Y | Y | 331 | 327 | 156 | 100 | 56
yfiO | b2595 | JW2577 | essential | PE | CORE | PROTEIN.SECRETION | predicted.lipoprotein | For a review of OM biogenesis see [PMID:19270402] -- | R | -- | -- | -- | -- | Y | Y | 789 | 783 | 263 | 120 | 143 | Y | Y | 596 | 593 | 318 | 127 | 191
ygaD | b2700 | JW2670 | non-essential | CY | FUNCTION-UNCERTAIN | NA | conserved.protein | Conserved protein of unknown function | R | Y | I | -- | -- | -- | Y | 389 | 385 | 136 | 72 | 64 | Y | Y | 200 | 197 | 85 | 44 | 41
ygbN | b2740 | JW2710 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predicted YgbN as both COG-E-Amino acid transport and metabolism - 0.9346 and [NAME] transport and metabolism - 0.8321. EcoCyc annotates YgbN is a transporter of unknown function belonging to the Gnt family of gluconate transporters [ Peekhaus97  ]. Based on sequence similarity, YgbN may function as a proton-driven metabolite uptake system. The cloned ygbN gene did not confer gluconate transport [ Peekhaus97  ]. | GE | Y | G E | -- | -- | -- | Y | 391 | 388 | 148 | 115 | 33 | -- | Y | 203 | 201 | 117 | 86 | 31
ygcS | b2771 | JW5845 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | H | -- | -- | -- | Y | 395 | 391 | 154 | 46 | 108 | -- | Y | 221 | 218 | 89 | 46 | 43
ygeD | b2835 | JW2803 | non-essential | IM | CORE | PHOSPHOLIPIDS | predicted.inner.membrane.protein | flippase for transbilayer movement of lysophospholipids LplT is a major facilitator superfamily (MFS) protein that acts as a flippase for transbilayer movement of lysophospholipids [PMID:15661733] | - | -- | -- | -- | -- | Y | Y | 813 | 808 | 239 | 140 | 99 | Y | Y | 628 | 623 | 399 | 163 | 236
ygeR | b2865 | JW2833 | non-essential | -- | FUNCTION-UNCERTAIN | NA | Tetratricopeptide.repeat.transcriptional.regulator | Tetratricopeptide.repeat.transcriptional.regulator | M | -- | -- | Y | 0.335 | -- | Y | 391 | 390 | 157 | 86 | 71 | -- | Y | 205 | 204 | 138 | 103 | 35
ygfQ | [NAME] | JW5467 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | -- | -- | -- | -- | -- | -- | Y | 392 | 390 | 155 | 97 | 58 | -- | Y | 193 | 193 | 120 | 86 | 34
ygfU | b2888 | JW5470 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | F | Y | F | Y | 1.503 | -- | Y | 388 | 386 | 144 | 94 | 50 | -- | Y | 205 | 205 | 100 | 75 | 25
yggU | b2953 | JW5479 | non-essential | -- | PREDICTED | CELL.WALL.BIOGENESIS | conserved.protein | [NAME] (2009) predicted YggU as 'COG.M.Cell wall/membrane/envelope biogenesis - 0.27'. Ecocyc no info, but the 3D structure was reprted by NRM [PMID:12975589] [NAME] (accession number 5596). This protein has ~100 aa residues. | S | Y | M | -- | -- | Y | Y | 505 | 502 | 158 | 80 | 78 | Y | Y | 334 | 331 | 179 | 86 | 93
ygiH | b3059 | JW3031 | non-essential | IM | FUNCTION-UNCERTAIN | PHOSPHOLIPIDS,FAS | conserved.inner.membrane.protein | Involvement of the YneS(B. subtilis)/YgiH(E. coli) and [NAME] proteins in phospholipid biosynthesis in both Bacillus subtilis and [NAME]]. We found that plsB is essential for E. coli growth, indicating that PlsB plays an important role in 1-acyl-G3P synthesis in E. coli. We also found, that the simultaneous inactivation of [NAME] and ygiH was impossible, revealing important roles for [NAME] and YgiH in E. coli growth, possibly by regulating the intracellular concentration of acyl-ACP [PMID:17645809]. In E. coli the first step in [NAME] biosynthesis is catalyzed by PlsB. A new two-step pathway catalyzed by [NAME] and PlsY proteins for the initiation of phospholipid formation in Streptococcus pneumoniae has been reported [PMID:17308305]. B. subtilis ortholog of S. pneumoniae PlsY, YneS, is required for [NAME] acyltransferase activity, together with PlsX. The B. subtilis genome lacks plsB, and we show in vivo that the [NAME]/Y pathway is indeed essential for the growth of bacteria lacking plsB [PMID:17645809]. In E. coli, PlsB plays a principal role in 1-acyl-G3P synthesis and is also essential for bacterial growth. [NAME] and [NAME] ortholog) also, however, play important roles in E. coli growth, possibly by regulating the intracellular concentration of acyl-ACP [PMID:17645809] but actual role was not determined. Check for SSL's between PlsB and (plsX or ygiH) | S | Y | L | -- | -- | Y | Y | 782 | 775 | 257 | 150 | 107 | Y | Y | 562 | 556 | 328 | 211 | 117
ygjI | b3078 | JW5512 | non-essential | IM | PREDICTED | NA | predicted.transporter | The YgjI protein is an uncharacterised member of the APC superfamily of amino acid transporters. Based on sequence similarity, YgjI may function as a proton-driven amino acid uptake system [ Riley06  ]. [NAME] (2009) has no significant predictions | - | Y | K | -- | -- | -- | Y | 388 | 385 | 116 | 62 | 54 | -- | Y | 216 | 213 | 75 | 30 | 45
ygjJ | b3079 | JW3050 | non-essential | -- | PREDICTED | NA | conserved.protein | conserved.protein | - | Y | K | -- | -- | -- | Y | 392 | 390 | 160 | 63 | 97 | -- | Y | 203 | 201 | 65 | 29 | 36
yhaO | b3110 | JW5519 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | E | Y | E | -- | -- | -- | Y | 385 | 384 | 116 | 58 | 58 | -- | Y | 204 | 204 | 80 | 28 | 52
yhbN | b3200 | JW3167 | essential | PE | CORE | LPS.AND.ECA | predicted.transporter.subunit.periplasmic.binding.component.of.ABC.superfamily | [NAME] (LptA) is part of the LptABC ABC transporter which is involved in the transfer of lipopolysaccharide from the outer leaflet of the inner membrane to the outer membrane [PMID:18768814,PMID:18534617]. Disruption of the pathway at any step after [NAME] leads to indistinguishable phenotypes: in all cases, LPS accumulates in the outer leaflet of the IM. Therefore, we cannot conduct epistasis analysis to determine exact pathway order. We can only rely on the information about the cellular location of these proteins to predict temporal order in the pathway as follows: MsbA followed by a complex of LptB, [NAME], [NAME] and LptG, followed by LptA and finally by a complex of LptD and LptE [PMID:19633680] | S | -- | -- | -- | -- | Y | Y | 505 | 489 | 229 | 141 | 88 | Y | Y | 314 | 303 | 217 | 153 | 64
yhbT | b3157 | JW3126 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.lipid.carrier.protein | predicted.lipid.carrier.protein | I | Y | H | -- | -- | -- | Y | 388 | 384 | 150 | 95 | 55 | -- | Y | 199 | 197 | 105 | 74 | 31
yhcB | b3233 | JW5539 | non-essential | -- | FUNCTION-UNCERTAIN | NA | conserved.protein | [NAME] (2009) predicted [NAME] as 'GO:0006508.Proteolysis - 0.936' because GC inferences with DegPQS. But check SSL's with [NAME], because in a study of membrane protein complexes, the [NAME] protein was found in together with CydA and CydB in the inner membrane; it was therefore suggested that it may be a new subunit of the cytochrome bd ubiquinol oxidase [ Stenberg05  ]. However, it was later shown that [NAME] is not associated with the [NAME] heterodimer and is not required for the assembly or function of cytochrome bd [ Mogi06  ]. If [NAME] doesn't interact with [NAME] perhaps does with DegPQS? | S | Y | K | -- | -- | Y | Y | 797 | 784 | 471 | 139 | 332 | Y | Y | 592 | 582 | 365 | 186 | 179
yhcD | b3216 | JW3183 | non-essential | OM | PREDICTED | NA | predicted.outer.membrane.protein | predicted.outer.membrane.protein | - | Y | K T | -- | -- | -- | Y | 373 | 362 | 166 | 79 | 87 | -- | Y | 211 | 203 | 103 | 54 | 49
yhfK | b3358 | [NAME] | non-essential | IM | PREDICTED | NA | conserved.inner.membrane.protein | conserved.inner.membrane.protein | S | Y | T | -- | -- | -- | Y | 364 | 354 | 155 | 75 | 80 | -- | Y | 183 | 180 | 91 | 65 | 26
yhfT | b3377 | JW3340 | non-essential | IM | PREDICTED | NA | predicted.inner.membrane.protein | predicted.inner.membrane.protein | - | Y | L | -- | -- | -- | Y | 365 | 362 | 147 | 109 | 38 | -- | Y | 204 | 202 | 116 | 70 | 46
yhgE | [NAME] | JW3365 | non-essential | IM | PREDICTED | NA | predicted.inner.membrane.protein | predicted.inner.membrane.protein | - | Y | C | -- | -- | -- | Y | 393 | 389 | 119 | 54 | 65 | -- | Y | 223 | 221 | 83 | 41 | 42
yhgN | b3434 | JW3397 | non-essential | IM | PREDICTED | RESPONSE.TO.ANTIBIOTIC | predicted.antibiotic.transporter | YhgN, [NAME] and MarC are paralogs. MarC was thought to be involved in multiple antibiotic resistance, but neither a marC single deletion mutant nor a triple marC ychE yhgN deletion mutant shows a difference in susceptibility to various antibiotics compared to wild type [ McDermott08  ]. | U | Y | L | -- | -- | -- | Y | 392 | 385 | 181 | 128 | 53 | -- | Y | 211 | 207 | 105 | 72 | 33
yhhH | b3483 | JW3449 | non-essential | -- | FUNCTION-UNCERTAIN | NA | predicted.protein | [NAME] (2009) predicted YhhH as 'COG.M.Cell wall/membrane/envelope biogenesis - 0.9956' but is NOT clear to me why since no PPI data and GC relate it with Rhs elements which causes repetitive sequences in the chromosome' | - | Y | M | -- | -- | -- | Y | 472 | 470 | 237 | 194 | 43 | Y | Y | 284 | 284 | 177 | 93 | 84
yhhS | b3473 | JW5945 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | E | -- | -- | -- | Y | 391 | 388 | 127 | 70 | 57 | -- | Y | 196 | 194 | 115 | 72 | 43
yhiI | b3487 | JW3454 | non-essential | IM | PREDICTED | PROTEIN.SECRETION | predicted.HlyD.family.secretion.protein | [NAME] (2009) predicted yhiI as   Multifun.5.6.Protection - 0.89. EcoCyc:  predicted HlyD family secretion protein (no more info) | M | Y | V | Y | 0.612 | -- | Y | 384 | 380 | 132 | 68 | 64 | -- | Y | 203 | 200 | 83 | 33 | 50
yhiM | b3491 | JW5944 | non-essential | IM | PREDICTED | NA | conserved.inner.membrane.protein | conserved.inner.membrane.protein | - | Y | K | -- | -- | -- | Y | 394 | 392 | 125 | 71 | 54 | -- | Y | 206 | 205 | 85 | 61 | 24
yhiP | b3496 | JW3463 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | E | Y | T | -- | -- | -- | Y | 394 | 392 | 177 | 66 | 111 | -- | Y | 208 | 207 | 82 | 33 | 49
yhjD | b3522 | JW3490 | non-essential | IM | FUNCTION-UNCERTAIN | LPS.AND.ECA | conserved.inner.membrane.protein | The yhjD mutant also suppresses the lethal waaA deletion mutant which is unable to attach [NAME] to lipid IVA [ Mamat08  ]. The yhjD mutation makes MsbA dispensable for transport of lipid IVA across the inner membrane [ Mamat08  ]. | S | Y | J | -- | -- | Y | -- | 706 | 695 | 444 | 329 | 115 | Y | -- | 90 | 89 | 61 | 45 | 16
[NAME] | b3523 | JW3491 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | C | -- | -- | -- | Y | 393 | 385 | 327 | 235 | 92 | -- | Y | 204 | 202 | 164 | 138 | 26
yhjR | b3535 | JW3503 | non-essential | -- | PREDICTED | CELL.WALL.BIOGENESIS | conserved.protein | [NAME] (2009) predicted YhjR as 'COG.M.Cell wall/membrane/envelope biogenesis - 0.994'. It is in chromosomal proximity to cellulose synthase components, although In the commensal cellulose-producing E. coli strain 1094, yhjR is not necessary for cellulose production [ Le09  ]. | - | Y | M | -- | -- | Y | Y | 804 | 790 | 254 | 91 | 163 | Y | Y | 244 | 242 | 111 | 34 | 77
yhjV | b3539 | JW3508 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | E | Y | E | -- | -- | -- | Y | 362 | 355 | 209 | 186 | 23 | -- | Y | 192 | 190 | 117 | 92 | 25
yhjX | b3547 | JW3516 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | H | -- | -- | -- | Y | 371 | 366 | 162 | 83 | 79 | -- | Y | 209 | 208 | 116 | 60 | 56
yhjY | b3548 | JW5659 | non-essential | EC | PREDICTED | NA | conserved.protein | conserved.protein | N | Y | K | -- | -- | -- | Y | 394 | 388 | 151 | 89 | 62 | -- | Y | 220 | 219 | 87 | 40 | 47
yiaF | b3554 | JW5655 | non-essential | -- | PREDICTED | NA | conserved.protein | [NAME] (2009) predicted yiaF as COG-G-Carbohydrate transport and metabolism - 0.9967. Added to CE-eMAP because shows PPI's with donors in the eMAP from low-throughput studies | - | Y | G | Y | 0.202 | Y | Y | 783 | 770 | 178 | 80 | 98 | Y | Y | 628 | 619 | 278 | 166 | 112
yiaT | b3584 | JW3556 | non-essential | OM | PREDICTED | NA | predicted.protein | predicted.protein | M | Y | T | -- | -- | -- | Y | 395 | 394 | 99 | 41 | 58 | -- | Y | 223 | 222 | 100 | 61 | 39
yiaV | b3586 | JW3558 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | membrane.fusion.protein.MFP.component.of.efflux.pump.signal.anchor | [NAME] (2009) predict yiaV in a GC-module with several drug efflux pumps including acr-, emr-, mdt-, etc.  A transposon insertion in the yiaW-aldB intergenic region has higher tolerance to kanamycin, while a mutant lacking that region is more sensitive to kanamycin than wild type. A yiaV deletion has no effect on kanamycin sensitivity [ Hu05  ]. | V | -- | -- | Y | 2.289 | Y | Y | 791 | 786 | 251 | 112 | 139 | Y | Y | 541 | 538 | 307 | 127 | 180
yibD | b3615 | JW3590 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.glycosyl.transferase | predicted.glycosyl.transferase | M | Y | M | -- | -- | -- | Y | 393 | 382 | 99 | 55 | 44 | -- | Y | 203 | 195 | 91 | 59 | 32
yibH | b3597 | JW3571 | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.protein | predicted.protein | V | Y | V | -- | -- | -- | Y | 367 | 361 | 262 | 216 | 46 | -- | Y | 194 | 189 | 145 | 117 | 28
yibJ | b3595 | JW5647 | essential | -- | FUNCTION-UNCERTAIN | NA | predicted.Rhs.family.protein | [NAME] (2009) predicted [NAME] as 'COG.M.Cell wall/membrane/envelope biogenesis - 0.7965'  but is NOT clear to me why since no PPI data and GC relate it with Rhs elements which causes repetitive sequences in the chromosome'. EcoCyc annotates as 'predicted Rhs-family protein' | -- | Y | M | -- | -- | Y | -- | 213 | 208 | 82 | 68 | 14 | Y | -- | 152 | 147 | 65 | 51 | 14
yicJ | b3657 | JW5939 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predict YicJ as [NAME] transport and metabolism - 0.5567, Multifun-1.1-Carbon compound utilization - 0.6605, GO:0008152-Metabolic process - 0.9115. The YicJ protein is an uncharacterised member of the GPH family of galactose-pentose-hexuronide transporters [ Poolman96  ]. Based on sequence similarity, it may function as a proton or other ion-driven sugar uptake system. | G | Y | G | -- | -- | -- | Y | 378 | 374 | 155 | 97 | 58 | -- | Y | 207 | 204 | 145 | 119 | 26
yicO | b3664 | JW5636 | non-essential | IM | PREDICTED | NA | predicted.xanthine.uracil.permase | predicted.xanthine.uracil.permase | R | Y | F | -- | -- | -- | Y | 389 | 388 | 108 | 45 | 63 | -- | Y | 215 | 215 | 82 | 48 | 34
yidB | b3698 | JW3675 | non-essential | -- | PREDICTED | FAS | conserved.protein | [NAME] (2009) predicted as 'GO:0008610.Lipid biosynthetic process - p=0.7346'. No info in EcoCyc | S | Y | M | -- | -- | Y | Y | 812 | 805 | 225 | 126 | 99 | Y | Y | 675 | 669 | 305 | 108 | 197
yidC | b3705 | JW3683 | essential | IM | CORE | PROTEIN.SECRETION | cytoplasmic.insertase.into.membrane.protein.Sec.system | For a review of protein translocation across the IM by the Sec-system see [PMID:18078384] -- | U | -- | -- | -- | -- | Y | Y | 520 | 518 | 219 | 87 | 132 | Y | Y | 311 | 310 | 201 | 133 | 68
yidE | b3685 | JW3662 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predicted YidE as COG-E-Amino acid transport and metabolism - 0.9996, Multifun-1.5-Building block biosynthesis - 0.9265, GO:0009073-Aromatic amino acid family biosynthetic process - 1.0. Sequence analysis has suggested YidE is a membrane associated transporter. A Tnp transposon mutant of yidE showed increased adherence of EHEC O157:H7 to HELA cells [ Torres03a  ]. | R | Y | C | -- | -- | -- | Y | 386 | 385 | 155 | 102 | 53 | -- | Y | 206 | 205 | 130 | 94 | 36
yidK | b3679 | JW3655 | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.transporter | [NAME] (2009) doesn't give a significant label prediction for YdiK, but several operon rearrangement interactions. YdiK is an inner membrane protein with eight predicted [NAME] (EcoCyc). GOA | R | Y | G | -- | -- | -- | Y | 391 | 390 | 153 | 75 | 78 | -- | Y | 204 | 203 | 102 | 54 | 48
yieG | b3714 | JW3692 | non-essential | IM | PREDICTED | NA | predicted.inner.membrane.protein | predicted.inner.membrane.protein | R | Y | F | -- | -- | -- | Y | 390 | 387 | 224 | 147 | 77 | -- | Y | 197 | 194 | 119 | 66 | 53
yifK | b3795 | JW5595 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predict YifK as COG-E-Amino acid transport and metabolism - 0.9965. YifK is an uncharacterized member of the APC superfamily of amino acid transporters [ Jack00  ]. Based on sequence similarity, YifK may serve as a proton-driven amino acid or metabolite uptake system (EcoCyc) | E | Y | E | -- | -- | -- | Y | 395 | 388 | 141 | 75 | 66 | -- | Y | 207 | 203 | 94 | 68 | 26
yifL | b4558 | JW3781 | non-essential | PE | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | N | Y | L | -- | -- | -- | Y | 391 | 381 | 91 | 44 | 47 | -- | Y | 204 | 199 | 58 | 33 | 25
yihA | b3865 | JW5930 | essential | CY | FUNCTION-UNCERTAIN | CELL.DIVISION | GTP.binding.protein | Depletion of YihA protein led to a severe reduction in growth rate and to extensive filamentation, with a block beyond the stage of nucleoid segregation. Filamentation was correlated with reduced FtsZ levels and could be specifically suppressed by overexpression of ftsQI, ftsA and ftsZ, and to some extent by ftsZ alone. We hypothesize that YihA, like the Era GTPase, may participate in a checkpoint mechanism that ensures a correct coordination of cell cycle events. [PMID:10572302] -- | R | -- | -- | -- | -- | Y | Y | 482 | 477 | 262 | 153 | 109 | Y | Y | 307 | 305 | 166 | 119 | 47
yihN | b3874 | JW3845 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | C | -- | -- | -- | Y | 327 | 327 | 171 | 129 | 42 | -- | Y | 154 | 154 | 82 | 47 | 35
yihP | b3877 | JW3848 | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.transporter | [NAME] (2009) predict YjhP as [NAME], recombination and repair - 0.8889. EcoCyc annotate as '[NAME] phage-like element; predicted methyltransferase' but has no supporting information | G | Y | G | -- | -- | -- | Y | 367 | 367 | 213 | 190 | 23 | -- | Y | 194 | 194 | 131 | 121 | 10
yiiD | b3888 | JW3859 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.acetyltransferase | predicted.acetyltransferase | - | Y | M | Y | 21.438 | -- | Y | 365 | 364 | 113 | 47 | 66 | -- | Y | 205 | 205 | 69 | 35 | 34
yiiU | b3928 | JW3899 | non-essential | CY | CORE | CELL.DIVISION | conserved.protein | ZapB protein is a cell division factor that is required for proper Z ring formation. Localization of ZapB to the divisome depended on FtsZ but not FtsA, ZipA or FtsI, and ZapB interacted with FtsZ in a bacterial two-hybrid analysis [PMID:18394147].  -- | S | Y | P | Y | 545.308 | Y | Y | 794 | 788 | 233 | 87 | 146 | Y | Y | 561 | 556 | 357 | 233 | 124
yijE | b3943 | JW5557 | non-essential | IM | PREDICTED | NA | predicted.permease | predicted.permease | - | Y | M | -- | -- | -- | Y | 392 | 388 | 82 | 29 | 53 | -- | Y | 217 | 213 | 78 | 25 | 53
yjaH | b4001 | JW3965 | non-essential | -- | PREDICTED | LPS.AND.ECA | conserved.protein | [NAME] (2009) predicted YjaH as 'GO:0009103.Lipopolysaccharide biosynthetic process - 0.9927'. Seems that this was based in one PPI with KdsB. A predictor of beta-barrels predicts YjaH may contain ?-barrel structure(s) [ Zhai02  ], but is small (231aa), and PRED-TMBB doesn't predict beta-sheets. MajorityConsensus=--. CELLO=PE. | - | Y | M | -- | -- | Y | Y | 794 | 786 | 224 | 94 | 130 | Y | Y | 258 | 254 | 100 | 52 | 48
yjbF | b4027 | JW5711 | non-essential | PE | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | - | Y | K | -- | -- | -- | Y | 390 | 385 | 238 | 206 | 32 | -- | Y | 191 | 190 | 130 | 109 | 21
yjcD | b4064 | JW4025 | non-essential | IM | PREDICTED | NA | predicted.permease | predicted.permease | R | Y | L | -- | -- | -- | Y | 395 | 389 | 284 | 170 | 114 | -- | Y | 201 | 199 | 121 | 88 | 33
yjcE | b4065 | JW4026 | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.cation.proton.antiporter | [NAME] (2009) predicted [NAME] as GO:0006364-RRNA processing - 0.9334. EcoCyc annotate [NAME] is predicted to be a CPA1 family sodium/proton exchanger based on sequence similarity to eukaryotic exchangers. However, a yjcE mutant had no discernable sodium transport-related phenotype, though a yjcE/ycgO double mutant grew more slowly than wild-type at low pH [ Verkhovska01  ]. | P | Y | L | -- | -- | -- | Y | 390 | 385 | 230 | 147 | 83 | -- | Y | 203 | 202 | 103 | 59 | 44
yjcH | b4068 | JW4029 | non-essential | IM | PREDICTED | NA | conserved.inner.membrane.protein.involved.in.acetate.transport | [NAME] (2009) found yjcH in gene fusion with actP. yjcH is cotranscribed with the acs and actP genes, which encode proteins involved in acetate dissimilation and transport [ Gimenez03  ]. | S | Y | I | -- | -- | Y | Y | 785 | 778 | 307 | 141 | 166 | Y | Y | 591 | 586 | 244 | 157 | 87
yjcP | b4080 | JW4041 | non-essential | OM | FUNCTION-UNCERTAIN | NA | predicted.outer.membrane.factor.of.efflux.pump | This proteins could form another class called 'Response.to.drugs' or 'Cell.proliferation', perhaps together with 'Biofilm.formation' | MU | -- | -- | -- | -- | Y | Y | 526 | 525 | 158 | 96 | 62 | Y | Y | 376 | 376 | 275 | 53 | 222
yjcR | b4082 | JW4043 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | predicted.membrane.fusion.protein.of.efflux.pump | [NAME] (2009) predict yjcR in a module of ~45 genes mainly with antibiotic resistance components. SdsR (yjcR) is predicted to be the membrane fusion protein component of the SdsRQP multidrug efflux pump [ Dinh94  , Shimada09  ]. An E.coli yjcR null mutant is more sensitive to sulfur drugs than wild type [ Shimada09  ]. | V | -- | -- | -- | -- | -- | Y | 396 | 395 | 206 | 105 | 101 | -- | Y | 193 | 192 | 98 | 67 | 31
yjdL | b4130 | JW4091 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | E | Y | E | -- | -- | -- | Y | 390 | 374 | 142 | 82 | 60 | -- | Y | 198 | 191 | 109 | 81 | 28
yjeI | b4144 | JW5736 | non-essential | PE | PREDICTED | CELL.DIVISION | conserved.protein | [NAME] (2009) predict YjeI as GO:0007049-Cell cycle - 0.8289 | - | Y | G | -- | -- | Y | -- | 664 | 650 | 417 | 323 | 94 | -- | -- | -- | -- | -- | -- | --
yjeM | b4156 | JW5739 | non-essential | IM | PREDICTED | NA | predicted.transporter | [NAME] (2009) predict YjeM as both COG-E-Amino acid transport and metabolism - 0.7211 and GO:0006508-Proteolysis - 0.936. YjeM is an uncharacterized member of the APC superfamily of amino acid transporters [ Jack00  ]. | - | Y | E | -- | -- | -- | Y | 354 | 337 | 290 | 214 | 76 | -- | Y | 171 | 164 | 118 | 106 | 12
yjeP | b4159 | JW4120 | non-essential | IM | PREDICTED | NA | predicted.mechanosensitive.channel | predicted.mechanosensitive.channel | M | Y | H | -- | -- | -- | Y | 367 | 349 | 285 | 202 | 83 | -- | Y | 157 | 147 | 118 | 86 | 32
yjfM | b4185 | JW4143 | non-essential | -- | PREDICTED | FAS | conserved.protein | [NAME] (2009) predicted YjfM as ' COG.I.Lipid transport and metabolism - 0.9821' primarily based on operon rearrangemets with FAS enzymes'. EcoCyc has no information. | S | Y | I | -- | -- | Y | Y | 520 | 514 | 198 | 146 | 52 | Y | Y | 354 | 351 | 158 | 107 | 51
yjgJ | b4251 | JW4208 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.transcriptional.regulator | predicted.transcriptional.regulator | - | Y | M U | -- | -- | -- | Y | 390 | 387 | 165 | 85 | 80 | -- | Y | 197 | 195 | 85 | 51 | 34
yjgK | b4252 | JW5756 | non-essential | CY | FUNCTION-UNCERTAIN | NA | conserved.protein | The toxin-antitoxin biofilm protein YjgK (TabA) may decrease biofilm dispersal in response to the combined activity of several toxin-antitoxin (TA) systems [EcoCyc]. So this proteins could form a separate class 'Biofilm.formation', but here I'm just wondering if they do have SSL's | G | Y | M | Y | 38.652 | Y | Y | 814 | 808 | 203 | 63 | 140 | Y | Y | 615 | 611 | 410 | 261 | 149
yjgP | b4261 | JW4218 | essential | IM | CORE | LPS.AND.ECA | conserved.inner.membrane.protein | [NAME] (LptF) has been genetically and biochemically characterized as part of an ABC transporter LptBFGC complex required for the outer membrane sorting of lipopolysaccharides has been reported [PMID:19500581,PMID:18375759]. Disruption of the pathway at any step after [NAME] leads to indistinguishable phenotypes: in all cases, LPS accumulates in the outer leaflet of the IM. Therefore, we cannot conduct epistasis analysis to determine exact pathway order. We can only rely on the information about the cellular location of these proteins to predict temporal order in the pathway as follows: MsbA followed by a complex of LptB, [NAME], [NAME] and LptG, followed by LptA and finally by a complex of LptD and LptE [PMID:19633680] | R | Y | M | -- | -- | Y | -- | 687 | 679 | 238 | 167 | 71 | Y | -- | 568 | 561 | 231 | 164 | 67
[NAME] | b4262 | JW5760 | essential | IM | CORE | LPS.AND.ECA | conserved.inner.membrane.protein | [NAME] (LptG) has been genetically and biochemically characterized as part of an ABC transporter LptBFGC complex required for the outer membrane sorting of lipopolysaccharides has been reported [PMID:19500581,PMID:18375759]. Disruption of the pathway at any step after [NAME] leads to indistinguishable phenotypes: in all cases, LPS accumulates in the outer leaflet of the IM. Therefore, we cannot conduct epistasis analysis to determine exact pathway order. We can only rely on the information about the cellular location of these proteins to predict temporal order in the pathway as follows: MsbA followed by a complex of LptB, [NAME], [NAME] and LptG, followed by LptA and finally by a complex of LptD and LptE [PMID:19633680] | R | Y | M | -- | -- | Y | Y | 509 | 502 | 225 | 155 | 70 | Y | Y | 329 | 328 | 212 | 139 | 73
yjhA | b4311 | JW5778 | non-essential | OM | PREDICTED | NA | [NAME] | [NAME] | - | -- | -- | -- | -- | -- | Y | 360 | 353 | 208 | 175 | 33 | -- | Y | 179 | 179 | 136 | 118 | 18
yjhB | b4279 | JW5768 | non-essential | IM | PREDICTED | NA | KpLE2.phage.like.element.predicted.transporter | KpLE2.phage.like.element.predicted.transporter | - | Y | G | -- | -- | -- | Y | 369 | 361 | 194 | 123 | 71 | -- | Y | 197 | 196 | 96 | 63 | 33
yjhF | b4296 | JW4258 | non-essential | IM | PREDICTED | NA | KpLE2.phage.like.element.predicted.transporter | [NAME] (2009) predicted yjhF as COG-E-Amino acid transport and metabolism - 0.8954 and [NAME] transport and metabolism - 0.9389.  YjhF is a transporter of unknown function belonging to the Gnt family of gluconate transporters [ Peekhaus97  ]. Based on sequence similarity, it may function as a proton-driven metabolite uptake system. The cloned yjhF gene did not confer gluconate transport [ Peekhaus97  ]. | GE | Y | E G | -- | -- | -- | Y | 394 | 387 | 157 | 79 | 78 | -- | Y | 226 | 226 | 89 | 40 | 49
yjhR | b4308 | JW4271 | non-essential | CY | FUNCTION-UNCERTAIN | NA | KpLE2.phage.like.element.predicted.frameshift.suppressor | -- | -- | Y | V | -- | -- | Y | -- | 659 | 650 | 494 | 424 | 70 | -- | -- | -- | -- | -- | -- | --
yjiJ | b4332 | JW4295 | non-essential | IM | PREDICTED | NA | predicted.inner.membrane.protein | predicted.inner.membrane.protein | - | Y | H | -- | -- | -- | Y | 369 | 366 | 231 | 152 | 79 | -- | Y | 181 | 179 | 105 | 58 | 47
yjiO | b4337 | JW4300 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | multidrug.efflux.system.protein | Overexpression of the cloned yjiO (mdtM) gene in a drug-sensitive background strain resulted in a four-fold increase in resistance to acriflavine and a two-fold increase in resistance to chloramphenicol, ethidium bromide and TPP [ Nishino01  ]. | - | -- | -- | -- | -- | -- | Y | 388 | 384 | 180 | 119 | 61 | -- | Y | 195 | 192 | 107 | 70 | 37
yjiY | b4354 | JW5791 | non-essential | IM | PREDICTED | PROTEIN.SECRETION | predicted.inner.membrane.protein | [NAME] (2009) predicted YjiY as GO:0006950-Response to stress - 0.9985. Added to CE-eMAP because shows PPI's with secA from low-throughput studies | T | Y | T | Y | 134.859 | Y | Y | 773 | 766 | 180 | 84 | 96 | Y | Y | 568 | 564 | 316 | 202 | 114
yjiZ | b4356 | [NAME] | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | -- | -- | -- | -- | -- | Y | 370 | 366 | 107 | 46 | 61 | -- | Y | 203 | 200 | 72 | 24 | 48
yjjA | b4360 | JW5795 | non-essential | -- | FUNCTION-UNCERTAIN | NA | conserved.protein | [NAME] (2009) predicted [NAME] as both 'COG.M.Cell wall/membrane/envelope biogenesis - 0.2878' and 'GO:0007049.Cell cycle - 0.4623'. Kind of makes sense with EcoCyc as yjjA is cotranscribed with dnaT and dnaC. An N-terminal signal peptide was predicted [ Masai88  ]. Also operon rearrangemets with yjjO 'Phosphoglycerol transferase I' involved in Phospholipids biosynthesis | - | Y | M | -- | -- | Y | Y | 815 | 810 | 236 | 101 | 135 | Y | Y | 116 | 114 | 70 | 46 | 24
ylbH | b0499 | JW0488 | non-essential | CY | FUNCTION-UNCERTAIN | NA | conserved.protein.rhs.like | conserved.protein.rhs.like | -- | Y | M | -- | -- | -- | Y | 394 | 391 | 172 | 83 | 89 | -- | Y | 205 | 204 | 90 | 40 | 50
yliI | b0837 | JW0821 | non-essential | PE | FUNCTION-UNCERTAIN | NA | predicted.dehydrogenase | Outer membrane localization for five proteins (YftM, YaiO, [NAME], CsgF, and YliI) has been confirmed experimentally [PMID:16522795], however EcoCyc mention this protein as periplasmic [ Southall06  ]. The function of this protein may need a closser look of predictions, and is described as an aldose sugar dehydrogenase that requires the cofactor pyrroloquinoline quinone (PQQ) for activity [ Southall06 ]. | G | -- | -- | -- | -- | Y | Y | 816 | 806 | 268 | 94 | 174 | Y | Y | 565 | 558 | 291 | 117 | 174
ymcA | b0984 | JW0967 | non-essential | OM | PREDICTED | NA | conserved.protein | conserved.protein | - | -- | -- | -- | -- | -- | Y | 395 | 390 | 159 | 72 | 87 | -- | Y | 205 | 204 | 75 | 37 | 38
ymgF | b4520 | JW1156 | non-essential | -- | FUNCTION-UNCERTAIN | CELL.DIVISION | predicted.protein | YmgF interacts with the cell division proteins FtsI, FtsN and FtsQ [PMID:15774864] as well as other components of the cell division machinery [PMID:18978050], and it localizes to the septum during cell division. [NAME] (2009) has no clear clues. -- | - | Y | K | -- | -- | Y | Y | 791 | 780 | 294 | 157 | 137 | Y | Y | 553 | 544 | 345 | 175 | 170
ynaI | b1330 | JW1323 | non-essential | IM | PREDICTED | FAS | conserved.inner.membrane.protein | [NAME] (2009) predicted YnaI as 'COG.M.Cell wall/membrane/envelope biogenesis - 0.9994' mainly based on operon rearrangements with FAS enzymes. Also has Translation hits. EcoCyc: YnaI is a putative member of the small mechanosensitive ion channel MscS family. It is a homolog of YggB, but its function has not been determined experimentally [EcoCyc]. | M | Y | M | -- | -- | Y | Y | 526 | 523 | 170 | 94 | 76 | Y | Y | 314 | 311 | 179 | 63 | 116
ynbB | b1409 | JW1406 | non-essential | IM | FUNCTION-UNCERTAIN | NA | predicted.CDP.diglyceride.synthase | EcoCyc annotates ynbB as predicted CDP-diglyceride synthase, but has no more information. | R | Y | M | -- | -- | Y | Y | 786 | 772 | 301 | 87 | 214 | Y | Y | 615 | 604 | 245 | 49 | 196
ynbE | b1382 | JW1377 | non-essential | CY | PREDICTED | NA | predicted.lipoprotein | predicted.lipoprotein | - | Y | T | -- | -- | -- | Y | 367 | 360 | 124 | 81 | 43 | -- | Y | 180 | 177 | 80 | 56 | 24
yncD | b1451 | JW1446 | non-essential | OM | PREDICTED | NA | predicted.iron.outer.membrane.transporter | predicted.iron.outer.membrane.transporter | P | Y | P | -- | -- | -- | Y | 394 | 393 | 162 | 114 | 48 | -- | Y | 211 | 211 | 75 | 26 | 49
ynfM | b1596 | JW1588 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | P | -- | -- | -- | Y | 393 | 392 | 134 | 52 | 82 | -- | Y | 211 | 211 | 76 | 23 | 53
yohG | b2138 | JW5838 | non-essential | OM | FUNCTION-UNCERTAIN | NA | predicted.outer.membrane.protein | [NAME] (2009) predict YohG 'COG-M-Cell wall/membrane/envelope biogenesis – 0.9994' but also 'COG-J-Translation, ribosomal structure and biogenesis – 0.9884' | -- | Y | J M | -- | -- | Y | Y | 808 | 801 | 238 | 89 | 149 | Y | Y | 620 | 614 | 360 | 238 | 122
yojI | b2211 | JW2199 | non-essential | IM | FUNCTION-UNCERTAIN | RESPONSE.TO.ANTIBIOTIC | fused.predicted.multidrug.transport.subunits.of.ABC.superfamily.membrane.component.ATP.binding.component | Mutation and complementation studies indicate that YojI forms an efflux pump that, when expressed from a multicopy vector and with the help of the outer membrane channel TolC, is able to export the peptide antibiotic microcin J25, making the cell resistant [ Delgado05  ]. | QP | -- | -- | -- | -- | -- | Y | 395 | 393 | 146 | 96 | 50 | -- | Y | 213 | 212 | 90 | 39 | 51
ypdA | b2380 | JW5388 | non-essential | IM | PREDICTED | CELL.WALL.BIOGENESIS | [NAME].YpdB | [NAME] (2009) predicted ypdA as Multifun.4.3.Primary Active Transporters - 0.9656 and Multifun.5.6.Protection - 0.9073, whereas GOA GO:0007047.cell.wall.organization. EcoCyc: predicted sensory kinase in two-component system with YpdB. A mutant containing a deletion of both ypdA and ypdB does not show a significant phenotype when measured by phenotype microarray [ [NAME]  ]. | T | Y | M | -- | -- | Y | Y | 480 | 477 | 156 | 91 | 65 | Y | Y | 293 | 290 | 140 | 73 | 67
ypdI | b2376 | JW2373 | non-essential | PE | FUNCTION-UNCERTAIN | M.ANTIGEN.AND.OSMOTIC.STRESS.RESPONSE | predicted.lipoprotein.involved.in.colanic.acid.biosynthesis | YpdI is a putative membrane lipoprotein which has been shown to play a role in colonic acid synthesis [EcoCyc]. [NAME] (2009) neither predictions nor interactions | - | -- | -- | -- | -- | Y | Y | 805 | 795 | 231 | 113 | 118 | Y | Y | 275 | 273 | 95 | 32 | 63
ypjA | b2647 | JW5422 | non-essential | EC | FUNCTION-UNCERTAIN | NA | adhesin.like.autotransporter | YpjA was identified as a protein with similarity to antigen 43 (Ag43), a self-recognizing surface adhesin. Deletion of the ypjA gene has no significant effect on adhesion, while increased expression of YpjA causes an increase in adhesion to solid surfaces. Neither deleting nor overexpressing ypjA appears to affect on biofilm formation [ Roux05  ]. | - | -- | -- | -- | -- | -- | Y | 390 | 389 | 234 | 179 | 55 | Y | Y | 195 | 194 | 129 | 120 | 9
yqcE | b2775 | JW2746 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | E | -- | -- | -- | Y | 389 | 387 | 127 | 84 | 43 | -- | Y | 191 | 190 | 110 | 86 | 24
yqeG | b2845 | JW2813 | non-essential | IM | PREDICTED | NA | predicted.transporter | predicted.transporter | - | Y | E | -- | -- | -- | Y | 392 | 391 | 110 | 53 | 57 | -- | Y | 215 | 214 | 120 | 40 | 80
yqhH | b3014 | JW2982 | non-essential | -- | PREDICTED | NA | predicted.outer.membrane.lipoprotein | predicted.outer.membrane.lipoprotein | M | Y | L | -- | -- | -- | Y | 392 | 389 | 127 | 77 | 50 | -- | Y | 208 | 207 | 85 | 45 | 40
yqiG | b3046 | JW5507 | non-essential | OM | PREDICTED | NA | predicted.outer.membrane.usher.protein | predicted.outer.membrane.usher.protein | -- | Y | L | -- | -- | -- | Y | 389 | 385 | 104 | 53 | 51 | -- | Y | 204 | 201 | 80 | 36 | 44
yraJ | b3144 | JW3113 | non-essential | OM | PREDICTED | NA | predicted.outer.membrane.protein | predicted.outer.membrane.protein | - | Y | H E | -- | -- | -- | Y | 387 | 385 | 130 | 69 | 61 | -- | Y | 205 | 204 | 86 | 42 | 44
yraP | b3150 | JW3119 | non-essential | PE | FUNCTION-UNCERTAIN | PROTEIN.SECRETION,CHAPERONES | predicted.protein | YraP is a lipoprotein Deletion of yraP resulted in sensitivity to SDS and slight induction of ?E activity. A yraP surA double mutant had a very small colony phenotype, suggesting that YraP is part of the DegP/Skp folding pathway (PMID:15968066). [NAME] (2009) predicted yraP as COG-M-Cell wall/membrane/envelope biogenesis - 0.2856 and  GO:0006260-DNA replication - 0.9902 | R | Y | M | -- | -- | Y | Y | 768 | 763 | 281 | 194 | 87 | Y | Y | 536 | 532 | 369 | 230 | 139
yrbB | b3191 | JW5535 | essential | -- | CORE | PHOSPHOLIPIDS | predicted.protein | Recently discovered ABC transport system '[NAME]' that maintains lipid asymmetry in the Gram-negative outer membrane. [NAME] (vacJ), mlaB (yrbB), [NAME] (yrbC), mlaD (yrbD), mlaE (yrbE), and mlaF (yrbF)  [[NAME] (2009) predicted [NAME] as both 'COG.M.Cell wall/membrane/envelope biogenesis - 0.9869' and 'GO:0007049.Cell cycle - 0.9859'. [NAME] (2009) found both PPI and GC hits with other memeber of MlaBCDEF transporter. EcoCyc annotates [NAME] as part of the c phospholipid ABC transporter  [ Saurin99  , Malinverni09  ]. Earlier versions (v12) plain text has only MlaEF. The fate of phospholipid is unknown but may be incorporated in to the inner membrane [ Malinverni09  ]. The [NAME] pathway prevents phospholipid accumulation in the outer leaflet of the outer membrane. | R | Y | M | Y | 23.886 | Y | Y | 802 | 786 | 296 | 137 | 159 | Y | Y | 600 | 588 | 338 | 228 | 110
yrbK | b3199 | JW3166 | essential | -- | CORE | LPS.AND.ECA | conserved.protein | YrbK (LptC) is part of the LptABC ABC transporter which is involved in the transfer of lipopolysaccharide from the outer leaflet of the inner membrane to the outer membrane. Disruption of the pathway at any step after [NAME] leads to indistinguishable phenotypes: in all cases, LPS accumulates in the outer leaflet of the IM. Therefore, we cannot conduct epistasis analysis to determine exact pathway order. We can only rely on the information about the cellular location of these proteins to predict temporal order in the pathway as follows: MsbA followed by a complex of LptB, [NAME], [NAME] and LptG, followed by LptA and finally by a complex of LptD and LptE [PMID:19633680] | S | -- | -- | -- | -- | -- | Y | 472 | 457 | 266 | 186 | 80 | -- | Y | 305 | 294 | 180 | 134 | 46
yrbL | b3207 | JW3174 | non-essential | CY | FUNCTION-UNCERTAIN | NA | predicted.protein | [NAME] (2009) predict YrbL as [NAME] transport and metabolism - 0.967, Multifun-1.7-Central intermediary metabolism - 0.8863, Multifun-1.6-Macromolecules (cellular constituent) biosynthesis - 0.9551, GO:0009103-Lipopolysaccharide biosynthetic process - 0.3187 | - | Y | G | -- | -- | Y | -- | 687 | 671 | 187 | 94 | 93 | -- | -- | -- | -- | -- | -- | --
ytfB | b4206 | JW5745 | non-essential | EC | PREDICTED | NA | predicted.cell.envelope.opacity.associated.protein | EcoCyc annotates yftB as 'predicted cell envelope opacity-associated protein' but has ni reference to this. Presumably may be by an INTERPRO:IPR013731 conserved domain similar to [NAME] protein whose expression is associated with a distinctive transparent colony phenotype. [NAME] (2009) predicted YtfB as 'COG.L.Replication' | M | Y | L | -- | -- | Y | Y | 776 | 767 | 201 | 66 | 135 | Y | Y | 608 | 601 | 175 | 60 | 115
ytfF | b4210 | JW4168 | non-essential | IM | PREDICTED | NA | predicted.inner.membrane.protein | predicted.inner.membrane.protein | - | Y | G M | -- | -- | -- | Y | 373 | 369 | 199 | 123 | 76 | -- | Y | 186 | 184 | 88 | 55 | 33
ytfM | b4220 | JW4179 | non-essential | OM | PREDICTED | RESPONSE.TO.ANTIBIOTIC | predicted.outer.membrane.protein.and.surface.antigen | [NAME] (2009) predicted YtfM in a module with several 'multidrug resistance proteins' . EcoCyc: YtfM, a homolog of YaeT and member of the Omp85 family [ Robert06  ], localizes to the outer membrane in E. coli [ Marani06  ] | M | Y | K | -- | -- | Y | Y | 808 | 801 | 240 | 66 | 174 | Y | Y | 733 | 726 | 439 | 261 | 178
ytfN | b4221 | JW4180 | non-essential | OM | PREDICTED | NA | conserved.protein | conserved.protein | S | Y | H | Y | 0.617 | -- | Y | 372 | 368 | 304 | 287 | 17 | -- | Y | 178 | 174 | 143 | 126 | 17
zapA | b2910 | JW2878 | non-essential | -- | CORE | CELL.DIVISION | protein.that.localizes.to.the.cytokinetic.ring | We demonstrate that the putative Escherichia coli ZapA orthologue, [NAME], exists in a dimer/tetramer equilibrium in solution, binds to FtsZ polymers, strongly promotes FtsZ polymer bundling and is a potent inhibitor of the FtsZ GTPase activity [PMID:17428494] -- | S | -- | -- | -- | -- | Y | Y | 529 | 525 | 140 | 76 | 64 | Y | Y | 341 | 339 | 120 | 72 | 48
zipA | b2412 | JW2404 | essential | IM | CORE | CELL.DIVISION,CELL.SHAPE | cell.division.protein.involved.in.Z.ring.assembly | FtsA and ZipA initially associate with FtsZ, followed by addition of FtsEX, FtsK, FtsQ, FtsL/FtsB, FtsW, FtsI, FtsN and AmiC, and EnvC apparently in this defined order guided by PPIs to form complexes for the divisome [PMID:17326815] -- | D | -- | -- | -- | -- | Y | Y | 802 | 794 | 400 | 84 | 316 | Y | Y | 686 | 681 | 524 | 356 | 168
a Target protein-coding genes linking to cell envelope related processes.
b b-number represents Blattner numbers.
c JW ID is the old systematic identification number to represent each E. coli gene.
d Gene representing whether it is an non-essential, essential or non-coding small RNAs.
e Localization is based on Díaz-Mejía et al (2009) (PMID: 19054114). OM, outer membrane; PE, periplasm; IM, inner membrane; CY, cytoplasm; EC, extracellular; No data, localization information is not clear
f In the E-MAP, each gene is grouped into one of the three categories: core, function uncertain and predicted.
g Each gene has been manually assigned to a specific pathway based on existing pathway annotations. In cases, where a gene is not assigned with a pathway annotation, we represented it as "NA". See main text for further details.
h The alphabet represent a specific functional group in COG (Cluster of orthologus genes). See [NAME] in Hu et al (2009) for details.
i Each orphan gene has been assigned with a predicited COG function using a stepPLR approach in the large scale proteomics approach ([NAME], 2009; PMID 19402753)
j Indicates whether the gene has been tested as an orphan gene in our previous study ([NAME], 2009). If there was a prediction made it is included under the subheading "predicted COG category for orphans". "Y" represents presence of an oprhan gene in our previous study ([NAME], 2009).
k Indicates the availability of yellow fluroscent protein expression data for each E. coli gene (reresented as "Y"). The abundances in individual live E. coli cells were measured using a single-molecule fluorescence microscopy (Tanuguchi et al., 2010; PMID: 20671182 )
l Indicates the number of protein expression molecules per cell for each E. coli gene. For  details see [NAME] et al., 2010 (PMID: 20671182 ).
m [NAME] mutations were constructed in E. coli Hfr Cavalli strain by insertion of the CmR (chloramphenicol) cassette into the desired locus using a PCR based in-vivo recombination approach ([NAME], 2000).
n The essential genes used in the recipient array were tagged at the C-terminal end with  a sequential peptide affinity (SPA)-tag (Butland et al., 2005), while the non-essential F- recipient E. coli deletion strains were from Keio collection.
o Number of times the gene pair has been tested in the E-MAP prior to removing 30 kbp region flanking the query gene.
p Number of times the gene pair has been tested in the E-MAP after removing 30 kbp region flanking the query gene.
q Number of times the gene pair has been tested in the E-MAP with an |E-score >2|. The E-score is a quantitative measure to identify the aggravating and alleviating genetic interactions. See main text for details.
r Number of times the gene pair has been tested in the E-MAP with an E-score <-2. See main text for details.
s Number of times the gene pair has been tested in the E-MAP with an E-score > 2. See main text for details.