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Home , AMP nucleosidase, Carnitine dehydratase, Creatinase, Exonuclease VII, Farnesyltransferase, Homoserine kinase

b0013 b0012 b0011 b0010 b0014 b0009 b0008 b0007 b0016 b0015 b0006 b0017 b0005 b0004 b0020 b0019 b0018 b0003 b0002 b0025 b0021 b0001 b0024 b0023 b0022

B number yaaI htgA b0011 yaaH dnaK mog talB yaaJ yi81_1 dnaJ yaaA yi82_1 b0005 thrC nhaR nhaA gef thrB thrA ribF insB_1 thrL b0024 rpsT insA_1

Gene name + + + + + + + + + + + + + + + ------Strand orientation 134 196 237 188 638 195 317 476 370 376 258 102 428 301 388 310 820 313 167 98 69 21 72 87 91 length 13283 20561 15039 13624 1296 4492 1047 1174 6781 3873 1344 7837 288 149 338 407 342 432 215 135 645 163 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P mRNA present 11 13 32 20 13 11 17 18 13 39 15 7 2 7 8 5 3 6 7 9 1 4 9 3 5 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 23 13 10 18 0 0 0 0 0 0 4 1 0 0 0 0 0 3 0 0 0 0 0 2 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 24 16 11 18 0 0 0 0 0 0 6 2 0 0 0 0 0 3 0 0 0 0 0 2 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 23 13 10 18 0 0 0 0 0 0 4 1 0 0 0 0 0 3 0 0 0 0 0 2 0 # of tryptic peptides detected (long list) P(m) P(m) detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein positive regulatorforsigma32heatshockpromoters putative orf, hypotheticalprotein required fortheefficientincorporationofmolybdateintomolybdoproteins inner membranetransportprotein chaperone withDnaK;heatshockprotein chaperone Hsp70;DNAbiosynthesis;autoregulatedheatshockproteins transaldolase B orf, hypotheticalprotein IS186 hypotheticalprotein orf, hypotheticalprotein Gef proteininterfereswithmembranefunctionwhen in excess IS186 andIS421hypotheticalprotein synthase homoserine Na+/H antiporter,pHdependent putative regulator transcriptional activatorofnhaA aspartokinase I,homoserinedehydrogenaseI thr operonleaderpeptide orf, hypothetical protein 30S ribosomalsubunitprotein S20 IS1 proteinInsA IS1 proteinInsB

Gene description Open readingframes Cell processes Miscellaneous Open readingframes ofsmallmolecules Miscellaneous Cell processes Cell processes Metabolism ofsmallmolecules Open readingframes Extrachromosomal Open readingframes Cell processes Extrachromosomal Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Metabolism of smallmolecules Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open reading frames Structural elements Extrachromosomal Extrachromosomal

Functional category 10 11 11 12 14 13 15 19 16 19 18 17 17 9 8 7 6 4 5 3 2 1 1 1 1 Operon ID b0030 b0029 b0028 b0027 b0026 b0034 b0033 b0032 b0031 b0035 b0036 b0037 b0038 b0039 b0040 b0041 b0042 b0043 b0045 b0044 b0046 b0047 b0049 b0048 b0050

B number yaaF lytB slpA lspA ileS caiF carB carA dapB caiE caiD caiC caiB caiA caiT fixA fixB fixC yaaU fixX yabF kefC apaH folA apaG

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 1073 304 316 149 164 938 166 382 273 203 297 522 405 380 504 268 313 428 443 176 620 280 159 125 95 Protein length 1331 2825 3643 4036 7656 9312 2348 1588 2140 685 813 190 476 285 291 308 148 105 365 135 215 133 356 543 703 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 16 46 48 14 16 14 25 19 18 14 19 29 11 5 6 8 9 7 5 6 7 7 6 7 5 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 13 17 2 1 0 0 8 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 14 19 2 2 0 0 8 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 13 17 2 1 0 0 8 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

Membrane protein assignment control ofstringentresponse;involvedinpenicillintolerance tRNAsynthetase rotamase) probable FKBX-type16KDpeptidyl-prolylcis-transisomerase(a prolipoprotein signalpeptidase(SPaseII) carbamoyl-phosphate synthaselargesubunit carbamoyl-phosphate synthetase,(small)subunit dihydrodipicolinate reductase orf, hypotheticalprotein transcriptional regulatorofcaioperon possible synthesisofcofactorforcarnitineracemaseanddehydratase carnitine racemase probable crotonobetaine/carnitine-CoAligase l-carnitine probable carnitineoperonoxidoreductase probable carnitinetransporter probable flavoproteinsubunit,carnitinemetabolism probable flavoproteinsubunit,carnitinemetabolism putative ferredoxin flavoprotein; electrontransport putative transportprotein putative NAD(P)Hoxidoreductase dihydrofolate reductasetype I;trimethoprimresistance K+ effluxantiporter,-regulated orf, hypothetical protein diadenosine tetraphosphatase

Gene description Global functions Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Open reading frames Metabolism of smallmolecules

Functional category 20 20 21 20 24 24 23 22 25 26 26 26 26 26 26 27 27 27 27 28 29 30 29 32 31 Operon ID b0055 b0054 b0053 b0052 b0051 b0056 b0058 b0057 b0060 b0059 b0061 b0062 b0063 b0064 b0065 b0066 b0067 b0068 b0069 b0070 b0072 b0071 b0073 b0074 b0075

B number yabH imp surA pdxA ksgA yabP yabO yabQ polB hepA araD araA araB araC yabI yabJ yabK tbpA yabN setA leuC leuD leuB leuA leuL

Gene name + + + + + + ------Strand orientation 271 784 428 329 273 216 219 783 968 231 500 566 292 254 232 536 327 551 392 466 201 364 523 52 28 Protein length 10437 10273 11143 2737 3825 1543 2240 1379 4770 1458 797 327 470 525 350 571 268 307 704 396 458 774 957 472 218 mRNA intensity A A P P P P P P P P P P P P P P P P P P P P P P P mRNA present 42 19 13 10 16 12 44 40 17 20 10 12 14 13 27 10 18 12 28 3 8 8 6 7 1 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 5 4 0 1 0 0 0 0 2 0 0 0 0 0 0 0 0 1 0 9 0 9 8 7 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 0 5 0 2 0 0 0 0 2 0 0 0 0 0 0 0 0 1 0 7 0 7 8 7 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 0 4 0 1 0 0 0 0 2 0 0 0 0 0 0 0 0 1 0 9 0 9 8 7 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt GenProt PHD Membrane protein assignment pyridoxine biosynthesis S-adenosylmethionine-6-N',N'-adenosyl (rRNA)dimethyltransferase organic solventtolerance outer membraneproteins(1stmodule) peptidyl-prolyl cis-transisomerase(PPIase),involvedinmaturationof putative DNAbindingprotein orf, hypotheticalprotein orf, hypotheticalprotein probable ATP-dependentRNAhelicase orf, hypotheticalprotein DNA polymeraseII L-ribulose-5-phosphate 4-epimerase L- L- transcriptional regulatorforaraoperon orf, hypotheticalprotein putative ATP-bindingcomponentofatransportsystem putative transportsystempermeaseprotein thiamin-binding periplasmicprotein putative transportprotein isopropylmalate isomerasesubunit Sugar effluxprotein 3-isopropylmalate isomerase (dehydratase)subunit 3-isopropylmalate dehydrogenase leu operonleader peptide 2-isopropylmalate synthase

Gene description Metabolism ofsmallmolecules Cell processes Cell processes Cell processes Miscellaneous Open readingframes Open readingframes Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Cell processes Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism of smallmolecules Metabolism of smallmolecules

Functional category 32 32 33 32 34 35 35 36 36 37 38 38 38 39 40 41 41 41 42 44 43 44 44 44 44 Operon ID b0100 b0099 b0098 b0097 b0096 b0095 b0091 b0076 b0094 b0093 b0092 b0080 b0079 b0078 b0077 b0087 b0086 b0085 b0084 b0083 b0082 b0081 b0088 b0090 b0089

B number b0100 mutT secA yacA lpxC ftsZ murC leuO ftsA ftsQ ddlB fruR fruL ilvH ilvI mraY murF murE ftsI ftsL yabC yabB murD murG ftsW

Gene name + + + + + + + + + + + + + + + + + + + + + + + + - Strand orientation 129 901 195 305 383 491 373 420 276 306 334 163 604 360 452 495 588 121 313 152 438 355 414 44 28 Protein length 1587 1819 4592 9268 4248 3716 2982 1330 2778 3201 1392 1162 2390 1921 4103 1052 1036 437 226 641 158 510 990 698 963 mRNA intensity A P P P P P P P P P P P P P P P P P P P P P P P P mRNA present 46 13 22 19 15 18 10 14 27 14 21 32 13 11 11 18 17 14 2 7 9 1 9 7 7 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 0 3 0 0 6 1 0 0 0 0 1 0 2 2 1 0 1 0 2 0 0 0 1 1 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 6 0 1 7 2 0 0 0 0 1 0 5 2 1 1 0 0 2 0 0 0 1 0 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 0 3 0 0 6 1 0 0 0 0 1 0 2 2 1 0 0 0 2 0 0 0 1 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt PHD Membrane protein assignment orf, hypothetical protein preprotein ;secretion protein orf, hypotheticalprotein UDP-3-O-acyl N-acetylglucosaminedeacetylase; Abiosynthesis transversions 7,8-dihydro-8-oxoguanine-, prefersdGTP,causesAT-GC and GTPase cell division;formscircumferentialring;-likeGTP-binding protein associated withjunctionsofinnerandoutermembranes ATP-binding celldivisionprotein,septationprocess, complexes withFtsZ, pyrophosphoryl-undecaprenol N-acetylglucosaminetransferase UDP-N-acetylglucosamine:N-acetylmuramyl- (pentapeptide) D--D-alanine ligaseB,affectscelldivision L-alanine addingenzyme,UDP-N-acetyl-muramate:alanineligase fruR leaderpeptide acetolactate synthaseIII,valinesensitive,smallsubunit acetolactate synthaseIII,valinesensitive,largesubunit probable transcriptionalactivatorforleuABCDoperon cell divisionprotein;ingrowthofwallatseptum meso-diaminopimelate-adding cell divisionprotein;ingrowthofwallatseptum putative apolipoprotein orf, hypotheticalprotein transcriptional repressoroffruoperonandothers D-alanine:D-alanine-adding enzyme septum formation;penicillin-bindingprotein3;peptidoglycansynthetase phospho-N-acetylmuramoyl-pentapeptide ? cell division;membraneproteininvolvedinshapedetermination UDP-N-acetylmuramoylalanine-D-glutamate

Gene description Open reading frames Cell processes Open readingframes Macromolecule metabolism Metabolism of smallmolecules Cell processes Cell processes Structural elements Cell processes Structural elements Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Structural elements Cell processes Miscellaneous Open readingframes Metabolism ofsmallmolecules Cell processes Cell processes Structural elements Cell processes Structural elements

Functional category 53 51 50 49 52 48 48 47 47 47 46 45 45 45 48 47 47 47 47 46 47 47 47 47 47 Operon ID b0117 b0108 b0107 b0103 b0102 b0101 b0121 b0120 b0119 b0118 b0109 b0106 b0105 b0104 b0122 b0110 b0124 b0123 b0111 b0125 b0113 b0112 b0114 b0116 b0115

B number yacH ppdD hofB yacE yacF yacG speE speD yacL acnB nadC hofC b0105 guaC yacC ampD gcd yacK ampE hpt pdhR aroP aceE lpdA aceF

Gene name + + + + + + + + + + + ------Strand orientation 617 146 461 206 247 288 264 136 865 297 400 347 156 183 796 516 284 182 254 457 887 474 630 65 35 Protein length 11091 15349 21822 1143 4581 1043 4087 3117 1945 2328 2238 8150 392 147 106 130 132 884 273 109 525 739 408 431 311 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 11 14 41 19 22 13 15 11 18 32 14 44 34 17 4 3 7 4 3 8 8 7 8 7 8 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 22 24 13 15 0 1 0 0 0 0 0 0 0 3 2 0 0 0 0 2 1 0 0 0 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 19 24 12 10 0 3 0 0 2 0 0 0 0 3 1 1 0 0 0 1 0 0 1 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 22 24 13 15 0 1 0 0 0 0 0 0 0 3 2 0 0 0 0 2 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 4 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

MP MP Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein and pyruvatecomplexes;L-proteinofglycinecleavagecomplex lipoamide dehydrogenase(NADH);componentof2-oxodehydrogenase protein transport,DNAuptake putative integralmembraneproteininvolvedinbiogenesisoffimbriae, protein transport,DNAuptake putative integralmembraneproteininvolvedinbiogenesisoffimbriae, S-adenosylmethionine decarboxylase orf, hypotheticalprotein aconitate hydraseB putative membraneprotein prelipin peptidasedependentprotein orf, hypotheticalprotein GMP reductase putative DNArepairprotein =putrescineaminopropyltransferase quinolinate phosphoribosyltransferase orf, hypotheticalprotein orf, hypotheticalprotein regulates ampC hypoxanthine phosphoribosyltransferase dehydrogenase regulates ampC aromatic aminoacidtransportprotein transcriptional regulatorforpyruvatedehydrogenasecomplex pyruvate dehydrogenase(dihydrolipoyltransacetylasecomponent) pyruvate dehydrogenase(decarboxylasecomponent)

Gene description Open readingframes Open readingframes Metabolism ofsmallmolecules Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Miscellaneous Miscellaneous Open readingframes Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Metabolism of smallmolecules Metabolism of smallmolecules Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 53 53 59 55 55 63 62 61 60 55 55 54 53 63 56 65 64 57 67 66 57 58 59 59 59 Operon ID b0126 b0127 b0128 b0129 b0130 b0132 b0131 b0135 b0134 b0133 b0137 b0136 b0138 b0139 b0140 b0141 b0142 b0144 b0143 b0147 b0146 b0145 b0148 b0149 b0150

B number yadF yadG yadH yadI yadE yadD panD yadC panB panC yadL yadK yadM htrE ecpD yadN folK yadB pcnB yadP sfsA dksA hrpB mrcB fhuA

Gene name + + + + + + + + ------Strand orientation 220 308 256 146 409 300 126 412 264 283 201 198 203 865 246 194 159 308 454 179 234 151 824 844 747 Protein length 17436 3337 5716 1978 3015 3051 5687 1105 952 337 180 213 176 430 409 639 542 491 62 64 84 96 71 16 69 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P P mRNA present 16 10 24 12 15 11 10 35 10 24 18 11 44 38 38 8 2 2 6 4 4 8 6 5 8 # of tryptic peptides predicted P P P P P P P Protein detected - total list 4 0 0 0 0 1 0 3 5 0 0 0 0 0 0 0 0 2 0 0 0 0 0 3 1 # of tryptic peptides detected (total list) P P Protein detected - short list 5 0 0 0 0 1 0 2 6 0 0 0 0 0 0 0 0 2 0 0 1 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 4 0 0 0 0 1 0 3 5 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 1 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt MP-GenProt

Membrane protein assignment T1, T5,andphi80 outer membrane proteinreceptorforferrichrome, colicinM,andphages putative carbonicanhdrase(EC4.2.1.1) putative ATP-bindingcomponentofatransportsystem orf, hypotheticalprotein putative PTSenzymeIIBcomponent aspartate 1-decarboxylase orf, hypotheticalprotein 3-methyl-2-oxobutanoate hydroxymethyltransferase pantothenate synthetase orf, hypotheticalprotein putative fimbrialprotein putative fimbrial-likeprotein putative fimbrialprotein putative fimbrial-likeprotein probable outermembraneporinproteininvolvedinfimbrialassembly probable pilinchaperonesimilartoPapD putative fimbrial-likeprotein poly(A) polymeraseI 7,8-dihydro-6-hydroxymethylpterin- pyrophosphokinase probable regulatorformaltosemetabolism dnaK suppressorprotein putative tRNAsynthetase orf, hypotheticalprotein , ATP-dependent peptidoglycan synthetase;penicillin-binding protein1B

Gene description Structural elements Miscellaneous Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Open readingframes Miscellaneous Structural elements Structural elements Miscellaneous Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Macromolecule metabolism Structural elements Macromolecule metabolism Structural elements

Functional category 84 68 69 69 70 72 71 74 74 73 75 75 75 75 76 76 77 78 78 80 80 79 81 82 83 Operon ID b0152 b0151 b0157 b0156 b0155 b0154 b0153 b0158 b0160 b0159 b0162 b0161 b0164 b0163 b0167 b0166 b0165 b0169 b0168 b0175 b0174 b0173 b0172 b0171 b0170

B number fhuD fhuC yadS yadR yadQ hemL fhuB yadT dgt pfs yaeG htrA yaeI yaeH glnD dapD b0165 rpsB map cdsA uppS dxr frr pyrH tsf

Gene name + + + + + + + + + + + + + + + ------Strand orientation 296 265 207 114 473 426 660 266 505 232 391 474 247 128 890 274 241 264 249 253 398 185 241 283 43 Protein length 22176 1066 1779 1274 1457 1016 1127 4162 3407 1208 3673 8142 9865 378 114 864 420 412 253 334 508 312 982 984 525 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 14 15 13 14 15 17 24 22 13 11 51 16 11 11 18 18 9 4 8 8 7 1 6 9 5 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 10 13 0 0 2 5 0 0 0 0 1 4 1 0 5 9 0 0 0 2 0 3 0 0 0 # of tryptic peptides detected (total list) P P P P P P Protein detected - short list 0 0 2 7 0 0 0 0 2 5 1 0 7 9 0 0 0 2 8 0 3 0 9 0 0 # of tryptic peptides detected (short list) P P P P P P P P P P P Protein detected - long list 10 13 0 0 2 5 0 0 0 0 1 4 1 0 5 9 0 0 0 2 0 3 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD MP-PHD PHD PHD PHD PHD Membrane protein assignment ATP-binding componentofhydroxymate-dependentirontransport orf, hypotheticalprotein glutamate-1-semialdehyde aminotransferase(aminomutase) hydroxamate-dependent ironuptake,cytoplasmicmembranecomponent putative channeltransporter hydroxamate-dependent ironuptake,cytoplasmicmembranecomponent orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein periplasmic serineproteaseDo;heatshockproteinHtrA deoxyguanosine triphosphatetriphosphohydrolase putative structuralprotein orf, hypotheticalprotein 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase orf, hypotheticalprotein orf, hypotheticalprotein aminopeptidase protein PII;uridylyltransferaseactsonregulatorofglnA Undecaprenyl pyrophosphatesynthetase ribosome releasingfactor uridylate kinase protein chainelongationfactorEF-Ts 30S ribosomalsubunitproteinS2 1-deoxy-D- 5-phosphate reductoisomerase CDP-diglyceride synthetase

Gene description Cell processes Open readingframes Metabolism ofsmallmolecules Cell processes Miscellaneous Cell processes Open readingframes Metabolism ofsmallmolecules Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Metabolism of smallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Macromolecule metabolism Structural elements Miscellaneous Metabolism of smallmolecules

Functional category 100 84 87 85 84 86 84 88 88 88 90 89 92 91 93 93 93 94 93 99 97 96 95 95 98 Operon ID b0200 b0199 b0198 b0197 b0196 b0195 b0194 b0193 b0192 b0191 b0190 b0189 b0188 b0187 b0186 b0185 b0184 b0183 b0182 b0181 b0179 b0178 b0177 b0180 b0176

B number yaeD abc yaeE yaeC rcsF yaeB proS yaeF cutF yaeJ yaeQ rof mesJ yaeR ldcC accA dnaE rnhB lpxB lpxA lpxD hlpA yaeT fabZ yaeL

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 1160 191 343 217 271 134 235 572 292 236 140 181 432 138 713 319 198 382 262 341 161 810 151 450 86 Protein length 16241 14314 1976 1966 3318 2746 1361 1170 1010 1073 1969 3020 1303 1814 4646 4380 7246 3689 510 780 951 666 720 952 33 mRNA intensity A P P P P P P P P P P P P P P P P P P P P P P P P mRNA present 13 13 29 12 11 10 19 24 18 58 11 21 40 19 9 6 6 8 6 2 6 7 6 7 6 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 11 12 0 3 1 7 2 0 0 0 0 1 0 0 0 0 6 0 0 0 1 0 1 0 2 # of tryptic peptides detected (total list) P P Protein detected - short list 12 1 2 0 0 0 0 0 0 0 1 0 1 0 0 5 0 0 0 1 0 1 1 0 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 11 0 0 0 0 0 0 0 0 0 1 0 0 0 0 6 0 0 0 1 0 1 1 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 12 0 3 1 7 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 detected (membrane sample) GenProt-PHD GenProt GenProt PHD MP Membrane protein assignment putative ATP-binding component ofatransporter putative transportsystem permease protein putative lipoprotein regulator incolanicacidsynthesis;interactswithRcsB orf, hypotheticalprotein tRNAsynthetase orf, hypotheticalprotein copper homeostasisprotein(lipoprotein) orf, hypotheticalprotein orf, hypotheticalprotein Modulator ofRho-dependenttranscriptiontermination. cell cycleprotein orf, hypotheticalprotein decarboxylase2,constitutive acetylCoA carboxylase,carboxytransferasecomponent,alphasubunit DNA polymeraseIII,alphasubunit RNAse HII,degradesRNAofDNA-RNAhybrids tetraacyldisaccharide-1-P; lipidAbiosynthesis,penultimatestep UDP-N-acetylglucosamine acetyltransferase;lipidAbiosynthesis histone-like protein,locatedinoutermembraneornucleoid orf, hypotheticalprotein (3R)-hydroxymyristol acylcarrierproteindehydratase orf, hypotheticalprotein of endotoxin(lipidA)synthesis UDP-3-O-(3-hydroxymyristoyl)-glucosamine N-acyltransferase;thirdstep

Gene description Miscellaneous Cell processes Cell processes Miscellaneous Structural elements Miscellaneous Macromolecule metabolism Open readingframes Cell processes Open readingframes Open readingframes Macromolecule metabolism Cell processes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Structural elements Macromolecule metabolism Open readingframes Metabolism ofsmallmolecules Open readingframes Structural elements

Functional category 112 111 111 111 110 110 109 109 108 108 108 107 106 105 105 104 103 103 103 103 101 100 102 100 101 Operon ID b0225 b0224 b0223 b0222 b0221 b0214 b0213 b0212 b0220 b0219 b0218 b0217 b0216 b0215 b0211 b0210 b0209 b0208 b0207 b0206 b0205 b0204 b0203 b0202 b0201

B number yafQ yafK yafJ gmhA yafH rnhA yafS gloB ykfE yafV yafU yafT aspV dnaQ dniR yafE yafD yafC yafB aspU rrfH rrlH alaV ileV rrsH

Gene name + + + + + + + + + + + + + + ------Strand orientation 246 255 192 826 155 246 251 157 256 112 261 243 452 207 266 304 267 92 Protein length 74978 69573 69593 2128 3000 1050 1083 3358 1504 2032 1638 3927 4171 225 819 216 491 551 104 756 128 361 304 564 84 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 10 15 10 39 12 19 14 18 13 15 10 5 9 8 8 2 9 9 # of tryptic peptides predicted P P P P P Protein detected - total list 0 0 0 4 1 0 0 1 1 0 0 0 0 0 0 1 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 4 0 0 0 1 1 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 0 0 0 4 0 0 0 1 1 0 0 0 0 0 0 1 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) PHD PHD Membrane protein assignment orf, hypothetical protein orf, hypothetical protein putative amidotransferase phosphoheptose isomerase putative acyl-CoAdehydrogenase(EC1.3.99.-) orf, hypotheticalprotein tRNA-Sec orf, hypotheticalprotein probable hydroxyacylglutathionehydrolase transcriptional regulatorfornitritereductase(cytochromec552) tRNA-Val 5S ribosomalRNA 23S ribosomalRNA alanine tRNA1B(duplicateofalaT,U) isoleucine tRNA1(duplicateofileT,U) 16S ribosomalRNA orf, hypotheticalprotein replication RNase HI,degradesRNAofDNA-RNAhybrids,participatesinDNA putative EC3.5.amidase-typeenzyme putative aminopeptidase DNA polymeraseIII,epsilonsubunit putative biotinsynthesisprotein orf, hypotheticalprotein putative transcriptionalregulatorLYSR-type 2,5-diketo-D-gluconate

Gene description Open reading frames Open reading frames Miscellaneous Structural elements Miscellaneous Open readingframes tRNA Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules tRNA Structural elements Structural elements tRNA tRNA Structural elements Open readingframes Macromolecule metabolism Open readingframes Miscellaneous Macromolecule metabolism Miscellaneous Open readingframes Miscellaneous Open readingframes

Functional category 129 128 127 126 125 124 118 117 116 122 119 123 121 120 115 115 114 113 Operon ID b0250 b0249 b0248 b0247 b0246 b0245 b0244 b0243 b0242 b0241 b0240 b0239 b0238 b0237 b0236 b0235 b0234 b0233 b0229 b0228 b0227 b0232 b0231 b0230 b0226

B number ykfB ykfF yafX ykfG yafW b0245 thrW proA proB phoE crl yafA gpt pepD prfH b0235 yafP yafO fhiA yafM yafL yafN dinP mbhA dinJ

Gene name + + + + + + + + + + + + + + + ------Strand orientation 155 152 158 105 113 417 367 351 133 414 152 485 166 150 132 579 165 249 351 261 79 88 97 86 Protein length 2446 7201 2952 1500 2143 539 275 822 248 103 794 126 560 268 144 162 155 194 152 140 229 57 32 54 99 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 20 22 18 27 19 11 22 16 15 3 3 2 5 8 3 8 5 8 3 5 3 8 9 6 # of tryptic peptides predicted P P P P P Protein detected - total list 0 0 0 0 4 0 0 1 0 3 2 0 8 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 0 0 5 0 0 3 0 3 2 1 7 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 0 0 0 4 0 0 1 0 3 2 0 8 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD MP-GenProt

Membrane protein assignment orf, hypothetical protein orf, hypothetical protein tRNA-Thr orf, hypotheticalprotein putative DNArepairprotein orf, hypotheticalprotein orf, hypotheticalprotein gamma-glutamylphosphate reductase gamma-glutamate kinase outer membraneporeproteinE(E,Ic,NmpAB) transcriptional regulatorofcrypticcsgAgeneforcurlisurfacefibers orf, hypotheticalprotein guanine-hypoxanthine phosphoribosyltransferase aminoacyl- dipeptidase(peptidaseD) probable peptidechainreleasefactor orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative lipoprotein damage-inducible proteinJ flagellar biosynthesis damage-inducible proteinP;putativetRNAsynthetase putative motilityprotein

Gene description Open reading frames Open reading frames tRNA Open readingframes Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Structural elements Structural elements Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism Macromolecule metabolism Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Structural elements Miscellaneous Miscellaneous

Functional category 146 145 144 144 143 143 142 142 141 140 139 138 137 136 136 135 135 135 131 130 129 132 134 133 Operon ID b0275 b0274 b0273 b0272 b0271 b0270 b0269 b0268 b0267 b0266 b0265 b0264 b0263 b0262 b0261 b0260 b0259 b0258 b0257 b0256 b0255 b0254 b0253 b0252 b0251

B number insA_3 insB_3 argF yagI yagH yagG yagF yagE yagA yagB insA_2 insB_2 b0263 afuC mmuM mmuP trs5_1 ykfC b0257 tra8_1 yi91a perR ykfA yafZ yafY

Gene name + + + + + + + + + + ------Strand orientation 167 334 252 536 460 655 309 384 125 167 120 352 310 475 338 376 141 383 134 297 288 278 285 91 91 Protein length 3188 641 414 337 352 275 228 628 190 424 499 253 421 847 174 243 221 93 54 mRNA intensity A A A A A A A A A A A P P P P P P P P mRNA present 13 22 16 25 11 10 21 14 19 14 12 13 13 19 15 5 9 7 5 9 7 9 6 6 5 # of tryptic peptides predicted

P Protein detected - total list 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 5 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 # of tryptic peptides detected (short list)

P Protein detected - long list 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD PHD PHD Membrane protein assignment IS1 proteinInsA IS1 proteinInsB ornithine carbamoyltransferase 2,chainF putative regulator putative beta-xylosidase(EC3.2.1.37) putative permease putative dehydratase putative /synthase orf, hypotheticalprotein orf, hypotheticalprotein IS1 proteinInsA IS1 proteinInsB putative transportsystempermeaseprotein putative ATP-bindingcomponentofatransportsystem S-methylmethionine:homocysteine methyltransferase S-methylmethionine permease IS5 orf, hypotheticalprotein putative transposase IS30 transposase IS911 hypotheticalprotein,variant(IS911A) putative transcriptionalregulatorLYSR-type putative GTP-bindingprotein orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Extrachromosomal Extrachromosomal Metabolism ofsmallmolecules Miscellaneous Miscellaneous Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Extrachromosomal Extrachromosomal Miscellaneous Cell processes Metabolism ofsmallmolecules Cell processes Extrachromosomal Open readingframes Miscellaneous Extrachromosomal Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes

Functional category 162 162 161 160 159 159 158 158 157 156 155 155 155 155 154 154 153 152 151 150 150 149 148 147 146 Operon ID b0297 b0296 b0295 b0294 b0293 b0292 b0291 b0290 b0289 b0288 b0287 b0286 b0285 b0284 b0283 b0282 b0300 b0299 b0298 b0281 b0280 b0279 b0278 b0277 b0276

B number eaeH ykgM ykgL ykgK yagZ yagY yagX yagW yagV ykgJ yagU yagT yagS yagR yagQ yagP ykgA tra5_5 b0298 intF yagN yagM yagL yagK yagJ

Gene name + + + + + + ------Strand orientation 295 196 195 222 841 547 251 109 204 229 318 732 318 136 239 288 102 466 146 284 232 208 243 87 75 Protein length 1257 2274 126 761 382 114 286 764 157 396 160 149 109 120 82 44 81 66 70 31 92 58 64 mRNA intensity A A A A A A A A A A A A A A A P P P P P P P P mRNA present 13 30 19 17 12 12 10 17 32 22 16 12 14 12 13 5 7 4 7 7 7 8 9 5 5 # of tryptic peptides predicted

P Protein detected - total list 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD

PHD Membrane protein assignment orf, hypotheticalprotein putative ARAC-type regulatoryprotein putative ribosomalprotein orf, hypotheticalprotein putative regulator orf, hypotheticalprotein orf, hypotheticalprotein putative enzyme putative receptor orf, hypotheticalprotein putative ferredoxin putative xanthinedehydrogenase(EC1.1.1.20) orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transcriptionalregulatorLYSR-type putative phageintegrase attaching andeffacingprotein, pathogenesisfactor IS3 putativetransposase putative factor orf, hypotheticalprotein orf, hypotheticalprotein DNA-binding protein orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes

Functional category 169 177 175 174 173 172 171 171 171 171 170 168 168 168 168 168 167 176 176 176 166 165 165 164 163 Operon ID b0325 b0324 b0323 b0322 b0321 b0320 b0319 b0318 b0317 b0316 b0315 b0314 b0313 b0312 b0311 b0310 b0309 b0308 b0307 b0306 b0305 b0304 b0303 b0302 b0301

B number yahK yahJ yahI yahH yahG yahF yahE yahD yahC yahB yahA betT betI betB betA ykgH b0309 ykgG ykgF ykgE ykgD ykgC ykgI b0302 ykgB

Gene name + + + + + + + + + + + + + + + ------Strand orientation 349 460 316 106 472 515 287 201 165 310 362 677 195 490 556 222 282 475 239 284 450 200 70 83 89 Protein length 2065 1334 2077 2262 1062 180 360 266 132 212 943 510 495 285 591 132 200 136 171 44 46 70 72 32 38 mRNA intensity A A A A A A A A A A A A A P P P P P P P P P P P P mRNA present 16 22 17 19 14 18 11 16 16 13 17 21 10 16 21 13 14 19 2 0 9 2 5 3 5 # of tryptic peptides predicted P P Protein detected - total list 5 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 7 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 5 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt PHD PHD PHD PHD Membrane protein assignment putative oxidoreductase putative deaminase putative kinase(EC2.7.2.2). orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative oxidoreductasesubunit orf, hypotheticalprotein putative transcriptionfactor putative transcriptionalregulatorLYSR-type orf, hypotheticalprotein high-affinity cholinetransport probably transcriptionalrepressorofbetgenes NAD+-dependent betainealdehydedehydrogenase orf, hypotheticalprotein choline dehydrogenase,aflavoprotein orf, hypotheticalprotein putative transporter orf, hypotheticalprotein putative dehydrogenasesubunit putative ARAC-typeregulatoryprotein putative oxidoreductase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Open readingframes Cell processes Cell processes Cell processes Open readingframes Cell processes Open readingframes Miscellaneous Open readingframes Miscellaneous Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes

Functional category 193 192 192 191 190 191 191 191 191 189 188 187 186 186 185 186 184 183 183 183 182 181 180 179 178 Operon ID b0350 b0349 b0348 b0347 b0341 b0340 b0339 b0338 b0346 b0345 b0343 b0342 b0337 b0336 b0335 b0334 b0333 b0332 b0331 b0330 b0344 b0329 b0328 b0327 b0326

B number mhpD mhpC mhpB mhpA cynX cynS cynT cynR mhpR lacI lacY lacA codA codB prpE prpD prpC b0332 prpB prpR lacZ yahO yahN yahM yahL

Gene name + + + + + + + + + + + + + + + + ------Strand orientation 1024 271 309 314 554 384 156 219 299 315 360 417 203 427 419 628 483 389 148 296 528 223 271 91 91 Protein length 1278 6804 8160 7860 195 232 234 178 190 272 324 333 166 111 183 282 124 232 221 109 37 55 92 62 31 mRNA intensity A A A A A A A A A A A A A A P P P P P P P P P P P mRNA present 11 17 19 22 16 12 16 47 30 22 20 13 10 23 16 8 9 9 5 4 4 9 5 3 6 # of tryptic peptides predicted P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 5 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 0 0 0 0 0 5 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment 2-keto-4-pentenoate hydratase 2-hydroxy-6-ketonona-2,4-dienedioic acid 2,3-dihydroxyphenylpropionate 1,2-dioxygenase 3-(3-hydroxyphenyl)propionate hydroxylase transcriptional regulatorformhpoperon cyanate ,cyanase cyn operonpositiveregulator cytosine deaminase cyanate transport cytosine permease/transport putative citratesynthase;propionatemetabolism? transcriptional repressorofthelacoperon beta-D-galactosidase thiogalactoside acetyltransferase putative propionyl-CoAsynthetase orf, hypotheticalprotein orf, hypotheticalprotein putative phosphonomutase2 regulator forprpoperon orf, hypotheticalprotein galactoside permease(Mprotein) putative cytochromesubunitofdehydrogenase orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Metabolism of smallmolecules Metabolism of smallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Cell processes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Open readingframes Miscellaneous Miscellaneous Open readingframes Cell processes Miscellaneous Open readingframes Open readingframes

Functional category 208 208 208 208 207 204 204 203 202 204 202 201 206 205 205 201 201 200 199 198 197 205 196 195 194 Operon ID b0375 b0374 b0373 b0372 b0371 b0370 b0369 b0368 b0367 b0366 b0365 b0364 b0363 b0362 b0361 b0360 b0359 b0358 b0356 b0355 b0357 b0354 b0353 b0352 b0351

B number yaiV yaiU b0373 tra5_1 yaiT b0370 hemB tauD tauC tauB tauA yaiS yaiP b0362 yi22_1 yi21_1 b0359 yaiO adhC yaiM yaiN yaiL mhpT mhpF mhpE

Gene name + + + + + + + + + + + + + ------Strand orientation 222 467 102 288 486 335 283 275 255 339 136 398 128 301 136 147 257 369 277 218 418 337 316 89 98 Protein length 2117 1673 1322 963 166 318 389 257 185 156 255 359 151 10 87 84 15 40 67 54 97 mRNA intensity A A A A A A A A A A A A A A P P P P P P P mRNA present 11 13 16 14 17 12 16 13 10 13 14 11 13 9 5 5 4 8 7 8 8 3 7 7 8 # of tryptic peptides predicted P P P P Protein detected - total list 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 3 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt PHD PHD Membrane protein assignment taurine transportsystemperiplasmicprotein polysaccharide metabolism orf, hypothetical protein putative flagellin structuralprotein putative factor IS3 putativetransposase orf, hypotheticalprotein orf, hypotheticalprotein 5-aminolevulinate dehydratase=porphobilinogensynthase taurine dioxygenase,2-oxoglutarate-dependent taurine transportsystempermeaseprotein taurine ATP-bindingcomponentofatransportsystem orf, hypotheticalprotein orf, hypotheticalprotein IS2 hypotheticalprotein IS2 hypotheticalprotein putative transferase orf, hypotheticalprotein putative alphahelixchain putative (EC3.1.1.1) nucleoprotein/polynucleotide-associated enzyme glutathione-dependent alcohol dehydrogenaseclassIII;formaldehydedehydrogenase, putative transportprotein 4-hydroxy-2-ketovalerate aldolase dehydrogenase

Gene description Cell processes Miscellaneous Open reading frames Miscellaneous Open readingframes Miscellaneous Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Cell processes Open readingframes Open readingframes Extrachromosomal Extrachromosomal Miscellaneous Open readingframes Miscellaneous Miscellaneous Miscellaneous Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 216 214 221 221 220 220 219 218 217 216 216 216 215 214 213 213 212 212 211 210 209 211 209 208 208 Operon ID b0400 b0399 b0398 b0397 b0396 b0395 b0394 b0393 b0392 b0391 b0390 b0389 b0388 b0387 b0386 b0385 b0384 b0383 b0377 b0376 b0382 b0381 b0380 b0379 b0378

B number phoR phoB sbcD sbcC araJ b0395 yajF yaiD b0392 yaiE aroM yaiA aroL yaiI proC yaiC psiF phoA sbmA yaiH yaiB ddlA b0380 b0379 yaiW

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 1048 431 229 400 394 348 303 225 174 192 269 371 112 494 406 385 364 114 102 364 80 93 94 63 86 Protein length 1155 1835 3068 1337 1974 1126 1506 3353 399 822 247 598 181 648 537 145 269 293 396 465 373 124 318 38 90 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 23 16 41 17 15 11 14 16 26 12 15 15 9 5 2 3 2 5 4 8 8 7 3 6 2 # of tryptic peptides predicted P P P P Protein detected - total list 0 0 0 0 0 0 2 3 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 3 3 0 1 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 0 0 0 0 0 0 2 3 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD Membrane protein assignment positive andnegative sensorproteinfor phoregulon positive response regulatorforphoregulon, sensorisPhoR(orCreC) ATP-dependent dsDNAexonuclease ATP-dependent dsDNAexonuclease involved ineithertransportorprocessingofarabinose polymers orf, hypotheticalprotein possible NAGC-liketranscriptionalregulator orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein protein ofarooperon,regulatedbyaroR orf, hypotheticalprotein shikimate kinaseII orf, hypotheticalprotein pyrroline-5-carboxylate reductase orf, hypotheticalprotein induced byphosphatestarvation orf, hypotheticalprotein putative enzyme orf, hypotheticalprotein sensitivity tomicrocinB17,possiblyenvelopprotein D-alanine-D-alanine ligaseA orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Global functions Global functions Macromolecule metabolism Macromolecule metabolism Cell processes Open readingframes Miscellaneous Macromolecule metabolism Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Cell processes Structural elements Open readingframes Open readingframes

Functional category 240 240 239 239 238 237 237 236 235 234 233 233 233 232 231 230 229 228 227 222 225 223 226 224 223 Operon ID b0425 b0424 b0423 b0422 b0421 b0414 b0420 b0413 b0412 b0411 b0419 b0418 b0410 b0417 b0409 b0416 b0408 b0407 b0415 b0406 b0405 b0404 b0403 b0402 b0401

B number apbA thiJ yajK xseB ispA ribD dxs ybaD yajI tsx yajO pgpA yajD thiL secF nusB secD yajC ribH tgt queA yajB malZ proY brnQ

Gene name + + + + + + + + + + + + + + + + ------Strand orientation 303 198 482 299 367 620 149 199 294 348 172 115 325 323 139 615 110 156 375 356 193 605 457 439 80 Protein length 1169 1001 4985 2792 1589 1012 1953 2270 1747 1429 1033 1004 3916 1976 7898 3781 5025 512 146 519 797 416 320 373 410 mRNA intensity A P P P P P P P P P P P P P P P P P P P P P P P P mRNA present 12 25 12 20 24 10 19 13 30 19 11 10 30 7 5 8 9 4 1 9 8 3 5 8 8 # of tryptic peptides predicted P P P P P P P P P P P P Protein detected - total list 0 1 2 3 0 2 1 0 1 2 0 0 0 0 0 1 8 2 2 2 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 1 0 2 0 3 3 0 0 2 0 0 0 1 0 2 1 2 3 3 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P P P Protein detected - long list 0 1 2 3 0 2 1 0 0 2 0 0 0 0 0 1 0 2 2 2 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 8 2 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt Membrane protein assignment involved inthiamin biosynthesis,alternative pyrimidinebiosynthesis 4-methyl-5(beta-hydroxyethyl)-thiazole monophosphate synthesis putative oxidoreductase VII,smallsubunit (farnesyldiphosphatesynthase) 1-deoxyxylulose-5-phosphate synthase;flavoprotein orf, hypotheticalprotein nucleoside channel;receptorofphageT6andcolicinK putative NAD(P)H-dependentxylosereductase orf, hypotheticalprotein orf, hypotheticalprotein phosphatidylglycerophosphatase thiamin-monophosphate kinase protein secretion,membrane transcription termination;Lfactor protein secretion;membraneprotein,partofthechannel orf, hypotheticalprotein ,betachain tRNA-guanine transglycosylase synthesis bifunctional pyrimidinedeaminase/reductaseinpathwayofriboflavin ribosyltransferase-isomerase synthesis ofqueuineintRNA;probablyS-adenosylmethionine:tRNA putative glycoprotein maltodextrin glucosidase proline permeasetransportprotein branched chainaminoacidtransportsystemIIcarrierprotein

Gene description Metabolism of smallmolecules Metabolism of smallmolecules Miscellaneous Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Cell processes Open readingframes Open readingframes Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Cell processes Macromolecule metabolism Cell processes Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Macromolecule metabolism Miscellaneous Metabolism ofsmallmolecules Cell processes Cell processes

Functional category 255 255 254 253 253 252 249 247 251 248 246 250 250 245 249 245 245 249 245 249 245 244 243 242 241 Operon ID b0450 b0449 b0448 b0447 b0446 b0445 b0444 b0443 b0442 b0437 b0441 b0436 b0440 b0435 b0427 b0439 b0438 b0434 b0433 b0432 b0431 b0430 b0429 b0428 b0426

B number glnK mdlB mdlA ybaO cof ybaE ybaX ybaW ybaV clpP ybaU tig hupB bolA yajR lon clpX yajG ampG cyoA cyoB cyoC cyoD cyoE yajQ

Gene name + + + + + + + + + + + + + + + ------Strand orientation 112 593 590 181 276 566 231 132 123 207 623 432 116 456 784 424 226 491 315 663 204 109 296 169 90 Protein length 22781 19085 13478 12084 4300 1170 7545 7520 2088 3719 2012 3525 1985 3822 295 236 346 704 269 645 453 282 411 267 98 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 26 23 10 31 10 17 33 24 37 22 10 10 18 10 13 7 7 4 6 4 5 7 4 1 1 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 17 0 2 0 0 0 0 0 0 0 0 7 3 1 8 8 4 1 0 3 0 6 0 0 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 12 11 1 2 0 0 0 0 0 0 0 0 1 3 2 8 0 0 0 5 0 1 1 0 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 17 0 2 0 0 0 0 0 0 0 0 1 3 1 8 8 0 0 0 3 0 1 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 4 1 0 0 0 6 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

Membrane protein assignment regulatory proteinP-II2 putative ATP-binding componentofatransport system ATP-binding componentof atransportsystem putative LRP-liketranscriptional regulator orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative proteasematurationprotein trigger factor;amolecularchaperoneinvolvedincelldivision DNA-binding proteinHU-beta,NS1(HU-1) possible regulatorofmureingenes DNA-binding, ATP-dependentproteaseLa;heatshockK-protein putative /proteinase orf, hypotheticalprotein chaperone ATP-dependent specificitycomponentofclpPserineprotease, shock proteinF21.5 ATP-dependent proteolyticsubunitofclpA-clpPserineprotease,heat protoheme IXfarnesyltransferase(haemeObiosynthesis) putative transportprotein regulates beta-lactamasesynthesis cytochrome oubiquinoloxidasesubunitII cytochrome oubiquinoloxidasesubunitI cytochrome oubiquinoloxidasesubunitIII cytochrome oubiquinoloxidasesubunitIV

Gene description Metabolism of smallmolecules Cell processes Cell processes Miscellaneous Miscellaneous Cell processes Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Macromolecule metabolism Structural elements Global functions Miscellaneous Open readingframes Macromolecule metabolism Macromolecule metabolism Metabolism ofsmallmolecules Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 272 271 271 271 270 269 268 267 266 265 261 264 260 263 259 256 262 262 258 257 259 258 258 258 258 Operon ID b0474 b0473 b0472 b0471 b0470 b0469 b0468 b0467 b0466 b0465 b0464 b0463 b0462 b0461 b0460 b0459 b0475 b0458 b0457 b0456 b0455 b0454 b0453 b0452 b0451

B number htpG recR ybaB dnaX apt ybaN priC ybaM kefA acrR acrA acrB ybaJ hha ylaD hemH ylaC ylaB ybaA ffs ybaZ ybaY tesB amtB

Gene name + + + + + + + + + + + + + + ------Strand orientation 1120 1049 214 624 201 109 643 183 125 175 215 397 124 183 320 169 518 117 129 190 286 428 53 72 Protein length 7814 2319 3698 1250 3354 5723 1618 2421 1197 1154 2975 970 960 861 662 494 260 960 461 192 274 351 896 364 51 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 13 37 36 48 21 37 13 18 12 13 8 6 8 5 9 2 4 5 8 7 5 7 5 4 # of tryptic peptides predicted P P P P P P Protein detected - total list 14 4 0 0 0 4 0 0 0 0 5 5 0 0 0 0 0 0 0 0 3 0 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 16 4 0 0 1 2 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 14 4 0 0 0 4 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 5 5 0 0 0 0 0 0 0 0 3 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt PHD PHD PHD Membrane protein assignment chaperone Hsp90,heatshock proteinC62.5 recombination andrepair orf, hypotheticalprotein DNA polymeraseIII,tauandgammasubunits;elongation factorIII phosphoribosyltransferase putative gene58 primosomal replicationproteinN'' orf, hypotheticalprotein Component oftheMscSmechanosensitivechannel acridine effluxpump acridine effluxpump acrAB operonrepressor orf, hypotheticalprotein haemolysin expressionmodulatingprotein putative transferase orf, hypotheticalprotein 4.5S RNA(componentofribonucleoproteinparticle) acyltransferase activity adenylate kinaseactivity;pleiotropic effectsonglycerol-3-phosphate orf, hypotheticalprotein ferrochelatase: finalenzymeofhemebiosynthesis orf, hypotheticalprotein orf, hypotheticalprotein glycoprotein/polysaccharide metabolism acyl-CoA thioesteraseII probable ammoniumtransporter

Gene description Cell processes Macromolecule metabolism Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Macromolecule metabolism Open readingframes Cell processes Cell processes Cell processes Cell processes Open readingframes Cell processes Miscellaneous Open readingframes Structural elements Metabolism of smallmolecules Open readingframes Metabolism of smallmolecules Open readingframes Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 288 287 287 287 286 285 284 284 283 281 281 282 280 280 279 278 289 277 290 276 275 274 273 272 Operon ID b0500 b0499 b0498 b0497 b0496 b0495 b0494 b0493 b0491 b0490 b0489 b0488 b0492 b0487 b0486 b0485 b0484 b0483 b0482 b0481 b0479 b0478 b0477 b0476 b0480

B number ybbD b0499 ybbC rhsD ybbP ybbA tesA ybbO ybbM ybbL ybbK ybbJ ybbN ybbI ybaT ybaS copA ybaQ ybaP ybaK fsr ybaL gsk ybaC ushA

Gene name + + + + + + + + + + + + + + ------Strand orientation 1426 236 122 804 228 208 269 268 225 305 151 296 135 430 310 834 131 264 159 406 558 434 319 550 86 Protein length 1200 2692 1358 1284 1930 207 119 485 533 879 202 442 935 671 488 608 658 232 443 207 755 370 66 63 81 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P P P P mRNA present 12 77 10 28 12 14 12 14 12 29 19 22 14 21 2 4 2 7 5 5 7 7 8 8 7 # of tryptic peptides predicted P P P P P P Protein detected - total list 0 0 0 0 0 0 1 0 0 1 0 4 0 0 0 0 4 0 0 0 0 1 0 4 0 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 0 0 0 0 2 0 0 0 0 6 0 0 0 0 1 0 0 0 0 1 0 5 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 0 0 0 0 0 1 0 0 0 0 4 0 0 0 0 2 0 0 0 0 1 0 4 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD Membrane protein assignment orf, hypothetical protein orf, hypothetical protein orf, hypotheticalprotein rhsD proteininrhselement putative oxidoreductase putative ATP-bindingcomponentofatransportsystem acyl-CoA thioesteraseI;alsofunctionsasprotease I orf, hypotheticalprotein putative oxidoreductase putative thioredoxin-likeprotein putative ATP-bindingcomponentofatransportsystem putative protease putative transcriptionalregulator putative metalresistanceprotein putative aminoacid/aminetransportprotein putative Cu(I)-translocating P-typeATPase orf, hypotheticalprotein putative ligase orf, hypotheticalprotein UDP-sugar hydrolase(5'-) putative transportprotein inosine-guanosine kinase putative (EC3.1.1.-) fosmidomycin resistanceprotein

Gene description Open reading frames Open reading frames Open readingframes Extrachromosomal Miscellaneous Cell processes Metabolism ofsmallmolecules Open readingframes Miscellaneous Miscellaneous Cell processes Open readingframes Miscellaneous Cell processes Cell processes Open readingframes Cell processes Open readingframes Miscellaneous Open readingframes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Miscellaneous Cell processes

Functional category 306 306 306 306 305 305 304 302 304 304 303 302 301 303 300 300 299 298 297 296 295 293 292 291 294 Operon ID b0508 b0507 b0525 b0518 b0517 b0516 b0515 b0514 b0513 b0512 b0511 b0506 b0505 b0504 b0503 b0502 b0524 b0523 b0522 b0521 b0520 b0519 b0510 b0509 b0501

B number gcl ppiB fdrA ylbC ylbB ylbA ybbZ ybbY ybbX ybbW ybbU ybbT ybbS ybbB b0502 ybbF purE purK arcC ylbF ylbE ybbV ybbQ b0501 gip

Gene name + + + + + + + + + + + + + + + ------Strand orientation 593 164 555 349 411 261 381 435 453 437 271 160 308 364 135 240 169 355 297 271 333 292 258 92 63 Protein length 8209 1071 1129 3543 1507 180 210 546 264 197 173 316 206 432 265 211 108 142 121 134 78 92 90 72 18 mRNA intensity A A A A A A A A A A A A A A A P P P P P P P P P P mRNA present 18 11 15 25 20 10 16 10 12 18 14 15 15 13 10 12 16 7 8 7 8 5 6 7 0 # of tryptic peptides predicted P P P Protein detected - total list 0 1 1 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 3 1 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 1 1 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt PHD PHD PHD Membrane protein assignment peptidyl-prolyl cis-transisomeraseB(rotamase B) glyoxylate carboligase putative regulator putative transport orf, hypothetical protein putative malatedehydrogenase(EC1.1.1.37) putative hydantoinutilizationprotein orf, hypotheticalprotein orf, hypotheticalprotein putative hydrolase putative transportprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transcriptionalregulatorLYSR-type putative capsuleanchoringprotein orf, hypotheticalprotein orf, hypotheticalprotein subunit phosphoribosylaminoimidazole carboxylase=AIRcarboxylase,catalytic fixing subunit phosphoribosylaminoimidazole carboxylase=AIRcarboxylase,CO(2)- orf, hypotheticalprotein ftsH mutants involved inproteintransport;multicopysuppressorof dominantnegative putative carbamatekinase(EC2.7.2.2) putative carboxylase putative oxidoreductase Hydroxpyruvate isomerase

Gene description Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Miscellaneous Open reading frames Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Structural elements Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Cell processes Open readingframes Open readingframes Miscellaneous Miscellaneous

Functional category 320 312 311 315 320 316 316 316 315 314 313 313 310 309 308 307 306 319 319 318 317 318 318 313 312 Operon ID b0550 b0549 b0548 b0547 b0546 b0545 b0544 b0543 b0542 b0541 b0540 b0529 b0539 b0538 b0537 b0536 b0535 b0534 b0533 b0532 b0531 b0530 b0528 b0527 b0526

B number rus ybcO ninE ybcN ybcM ybcL ybcK emrE b0542 tra5_2 b0540 folD b0539 b0538 intD argU fimZ sfmF sfmH sfmD sfmC sfmA ybcJ ybcI cysS

Gene name + + + + + + + + + + + + + + + + + + + ------Strand orientation 120 151 265 183 508 110 288 102 288 186 387 210 171 325 867 230 191 173 461 96 56 45 87 77 Protein length 2638 262 155 112 159 313 629 345 152 233 165 745 83 18 93 24 54 96 71 85 79 14 mRNA intensity A A A A A A A A A A A A A A A P P P P P P P mRNA present 10 27 16 11 31 14 19 16 8 4 3 9 3 1 6 9 5 6 6 4 7 2 8 8 # of tryptic peptides predicted P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 3 0 0 0 2 0 0 0 0 0 0 4 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 0 0 0 0 0 3 0 0 0 2 0 0 0 0 0 0 4 0 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 0 0 0 0 0 3 0 0 0 2 0 0 0 0 0 0 4 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD MP-GenProt

Membrane protein assignment RUS(Holliday junction resolvase) orf, hypothetical protein similar tophage82andlambda proteins orf, hypotheticalprotein putative ARAC-typeregulatoryprotein orf, hypotheticalprotein orf, hypotheticalprotein methylviologen resistance orf, hypotheticalprotein IS3 putativetransposase orf, hypotheticalprotein putative exonuclease(EC3.1.11.3)similartolambda tRNA-Arg orf, hypotheticalprotein tetrahydrofolate cyclohydrolase 5,10-methylene-tetrahydrofolate dehydrogenase;5,10-methylene- putative sensorytransductionregulator prophage DLP12integrase fimbrial Zprotein;probablesignaltransducer putative fimbrial-likeprotein involved infimbrialasembly putative outermembraneprotein,exportfunction putative chaperone putative fimbrial-likeprotein orf, hypotheticalprotein tRNAsynthetase

Gene description Macromolecule metabolism Open reading frames Extrachromosomal Open readingframes Miscellaneous Open readingframes Open readingframes Cell processes Open readingframes Miscellaneous Open readingframes Miscellaneous tRNA Open readingframes Metabolism ofsmallmolecules Miscellaneous Extrachromosomal Structural elements Miscellaneous Miscellaneous Miscellaneous Miscellaneous Miscellaneous Open readingframes Macromolecule metabolism

Functional category 335 335 335 335 334 334 333 332 331 330 330 329 323 323 328 327 326 325 325 325 325 324 322 321 Operon ID b0575 b0574 b0568 b0567 b0566 b0565 b0573 b0572 b0571 b0570 b0569 b0564 b0563 b0562 b0561 b0560 b0559 b0558 b0557 b0556 b0555 b0554 b0553 b0552 b0551

B number ybdE ylcD nfrA ybcH envY ompT ylcC ylcB ylcA ybcZ nfrB appY ylcE ybcY ybcX nohB ybcW ybcV ybcU ybcT ybcS ybcR nmpC trs5_2 ybcQ

Gene name + + + + + + + + + + + + + ------Strand orientation 1047 407 990 296 253 317 110 457 227 480 745 249 143 247 181 150 153 165 375 338 127 61 68 97 71 Protein length 47106 20919 1797 2087 468 121 112 766 989 386 211 127 232 124 67 49 98 40 15 28 47 99 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P mRNA present 43 18 14 17 60 18 15 19 10 23 29 10 14 14 3 1 3 9 5 8 4 8 6 1 7 # of tryptic peptides predicted P P P P P Protein detected - total list 1 0 0 6 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 1 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # of tryptic peptides detected (short list)

P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 1 0 0 6 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 1 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt MP-GenProt GenProt

MP Membrane protein assignment putative inner membranecomponentfor irontransport putative resistance protein orf, hypotheticalprotein orf, hypotheticalprotein envelope protein;thermoregulationofporinbiosynthesis outer membraneprotein3b(a),proteaseVII regulatory proteinaffectingappAandothergenes bacteriophage N4receptor,outermembraneprotein bacteriophage N4receptor,outermembraneprotein putative resistanceprotein putative 2-componenttranscriptionalregulator putative 2-componentsensorprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein bacteriophage DNApackagingprotein orf, hypotheticalprotein putative anenvelopprotein bacteriophage lambdaBorproteinhomolog bacteriophage lambdaendopeptidasehomolog bacteriophage lambdalysozymehomolog orf, hypotheticalprotein outer membraneporinprotein;locusofqsrprophage IS5 transposase orf, hypotheticalprotein

Gene description Cell processes Cell processes Open readingframes Open readingframes Structural elements Structural elements Metabolism ofsmallmolecules Extrachromosomal Extrachromosomal Open readingframes Miscellaneous Miscellaneous Open readingframes Extrachromosomal Extrachromosomal Extrachromosomal Extrachromosomal Miscellaneous Extrachromosomal Extrachromosomal Extrachromosomal Extrachromosomal Extrachromosomal Extrachromosomal Open readingframes

Functional category 351 351 351 347 346 346 345 348 348 350 349 349 344 343 342 342 341 340 339 338 338 338 337 337 336 Operon ID b0583 b0582 b0581 b0600 b0599 b0598 b0597 b0587 b0586 b0585 b0584 b0580 b0579 b0576 b0596 b0589 b0588 b0578 b0577 b0595 b0594 b0590 b0593 b0592 b0591

B number entD yi81_2 ybdK ybdL ybdH cstA ybdB fepE entF fes fepA ybdJ ybdF pheP entA fepG fepC nfnB ybdG entB entE fepD entC fepB ybdA

Gene name + + + + + + + + + + + + + ------Strand orientation 1293 209 370 372 386 362 701 137 377 374 746 122 458 248 330 271 217 415 285 536 334 391 318 416 82 Protein length 13067 2638 1279 1247 189 134 574 154 371 937 858 124 327 911 576 192 371 277 261 288 719 158 212 499 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 17 14 51 10 12 11 12 19 27 20 11 11 11 17 13 10 11 19 17 11 10 0 5 7 4 # of tryptic peptides predicted P P P P P P Protein detected - total list 0 0 1 0 0 0 0 2 0 0 2 0 0 4 0 0 0 3 0 0 1 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 1 0 0 1 0 0 0 0 0 0 0 4 0 1 0 3 0 0 1 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 0 0 1 0 0 0 0 0 0 0 0 0 0 4 0 0 0 3 0 0 1 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt GenProt PHD PHD PHD Membrane protein assignment IS186 hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein biosynthesis 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase, enterochelin synthase ascomponentF) ATP-dependent serineactivatingenzyme(maybepartofenterobactin colicins BandD outer membranereceptorforferricenterobactin(enterochelin)and enterochelin synthetase,componentD putative aminotransferase putative oxidoreductase carbon starvationprotein orf, hypotheticalprotein enterochelin esterase orf, hypotheticalprotein oxygen-insensitive NAD(P)Hnitroreductase ferric enterobactin(enterochelin)transport putative transport -specific transportsystem 2,3-dihydro-2,3-dihydroxybenzoate synthetase,isochroismatase ATP-binding componentofferricenterobactintransport ferric enterobactintransportprotein 2,3-dihydroxybenzoate-AMP ligase isochorismate hydroxymutase2,enterochelinbiosynthesis ferric enterobactin(enterochelin)transport ferric enterobactin(enterochelin)bindingprotein;periplasmic component putative transport

Gene description Extrachromosomal Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Miscellaneous Miscellaneous Global functions Open readingframes Cell processes Open readingframes Cell processes Cell processes Miscellaneous Cell processes Metabolism ofsmallmolecules Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Cell processes Cell processes

Functional category 358 357 356 364 360 359 359 368 367 366 365 360 355 354 360 353 352 364 361 361 364 364 361 363 362 Operon ID b0625 b0624 b0621 b0620 b0619 b0618 b0623 b0622 b0617 b0616 b0615 b0614 b0613 b0612 b0611 b0610 b0609 b0608 b0607 b0606 b0605 b0604 b0603 b0602 b0601

B number ybeH crcB dcuC citB citA citC cspE crcA citD citE citF ybdU citG citT rna rnk b0609 ybdR ybdQ ahpF ahpC dsbG ybdO ybdN ybdM

Gene name + + + + + + + + + ------Strand orientation 127 461 226 552 381 186 307 510 183 292 487 268 136 153 412 142 531 187 268 300 406 209 75 69 98 Protein length 38698 6086 1709 3105 656 247 161 320 143 161 156 577 948 185 275 679 161 180 17 81 35 70 29 85 34 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 10 26 21 10 15 11 14 13 20 20 24 17 15 19 12 3 3 5 7 4 8 5 9 6 9 # of tryptic peptides predicted P P P P P Protein detected - total list 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 1 6 9 1 0 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 0 0 0 2 0 0 0 0 0 0 0 1 0 0 0 0 1 6 6 1 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 1 6 9 1 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment orf, hypothetical protein orf, hypothetical protein cold shockprotein sequence similaritytoShigellaregulator putative sensor-typeprotein citrate lyasesynthetase(citrate(pro-3S)-lyaseligase citrate lyaseacylcarrierprotein(gammachain) transport ofdicarboxylates orf, hypotheticalprotein citrate lyasebetachain(acylsubunit) citrate lyasealphachain orf, hypotheticalprotein orf, hypotheticalprotein Citrate Carrier RNase I,cleavesphosphodiesterbondbetweenanytwonucleotides regulator ofnucleosidediphosphatekinase orf, hypotheticalprotein putative oxidoreductase orf, hypotheticalprotein hydroperoxides alkyl hydroperoxidereductase,F52asubunit;detoxificationof hydroperoxides alkyl hydroperoxidereductase,C22subunit;detoxificationof putative transcriptionalregulatorLYSR-type thiol:disulfide interchangeprotein orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Open reading frames Cell processes Miscellaneous Miscellaneous Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Cell processes Cell processes Miscellaneous Metabolism ofsmallmolecules Open readingframes Open readingframes

Functional category 385 384 383 380 380 379 379 381 382 379 379 379 379 378 377 376 375 374 373 372 372 370 371 369 369 Operon ID b0650 b0649 b0648 b0647 b0646 b0645 b0644 b0643 b0642 b0641 b0640 b0639 b0638 b0637 b0632 b0636 b0635 b0634 b0633 b0631 b0630 b0629 b0628 b0627 b0626

B number ybeW ybeV ybeU ybeT ybeS ybeR ybeQ ybeL leuS rlpB holA ybeN phpB ybeB dacA ybeA mrdA mrdB rlpA ybeD lipB ybeF lipA tatE ybeM

Gene name + + + + + + + ------Strand orientation 556 483 235 184 475 235 327 160 860 193 343 213 203 403 155 633 370 362 191 266 321 187 69 87 67 Protein length 2254 3675 3178 1049 1131 2373 2227 1611 1246 1907 1068 183 151 121 111 212 990 393 285 902 314 67 25 78 88 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P P mRNA present 25 25 12 16 27 11 10 41 10 14 22 10 11 12 16 10 31 7 4 5 2 3 9 9 5 # of tryptic peptides predicted P P P P P P P Protein detected - total list 11 0 0 0 0 0 0 0 3 0 0 0 0 0 5 1 0 1 3 0 0 0 2 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 13 0 0 0 0 0 0 0 3 0 0 0 0 0 2 1 0 0 0 0 0 0 3 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 11 0 0 0 0 0 0 0 3 0 0 0 0 0 2 1 0 0 0 0 0 0 2 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 1 3 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt GenProt GenProt GenProt PHD PHD PHD Membrane protein assignment orf, hypothetical protein putative enzymeofpolynucleotidemodification putative dnaK protein putative tRNAligase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative alphahelicalprotein tRNAsynthetase a minorlipoprotein DNA polymeraseIII,deltasubunit orf, hypotheticalprotein homolog ofSalmonellacobC,aphosphohistidineprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein protein 2 cell elongation,ephase;peptidoglycansynthetase;penicillin-binding drugs rod shape-determiningmembraneprotein;sensitivitytoradiationand a minorlipoprotein 5 D-alanyl-D-alanine carboxypeptidase,fractionA;penicillin-bindingprotein putative transcriptionalregulatorLYSR-type Component ofSec-independenttranslocase(seethetatoperon) protein oflipoatebiosynthesis lipoate synthesis,sulfurinsertion? putative amidase

Gene description Open reading frames Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Cell processes Cell processes Macromolecule metabolism Cell processes Miscellaneous Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes

Functional category 396 394 397 396 395 394 393 392 391 391 391 391 391 390 390 388 390 390 390 389 387 386 387 387 385 Operon ID b0661 b0660 b0675 b0674 b0673 b0672 b0671 b0670 b0659 b0655 b0654 b0653 b0652 b0669 b0668 b0667 b0666 b0665 b0664 b0663 b0662 b0658 b0657 b0656 b0651

B number miaB ybeZ nagD asnB metT leuW b0671 glnU ybeY gltI gltJ gltK gltL b0669 glnW b0667 metU glnV glnX b0663 yleB ybeX lnt trs5_3 ybeK

Gene name + + + + + ------Strand orientation 474 359 250 554 155 302 246 224 241 111 391 292 512 338 311 50 39 45 Protein length 1450 3091 1569 3855 5983 5999 2321 5452 5868 4108 1638 1627 2721 1038 736 182 584 678 958 891 432 67 17 19 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 27 18 10 14 30 16 14 19 14 1 4 3 8 9 7 7 3 3 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 3 5 2 0 5 5 0 0 0 0 0 2 2 0 0 0 1 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 5 6 3 0 4 7 0 0 0 0 0 2 2 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 3 5 2 0 5 5 0 0 0 0 0 2 2 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD

Membrane protein assignment putative ATP-bindingproteininphoregulon N-acetylglucosamine metabolism tRNA-Met tRNA-Leu glutamine tRNA1(duplicateofglnW) orf, hypotheticalprotein synthetase B putative RNA putative RNA tRNA-Gln tRNA-Met tRNA-Gln tRNA-Gln putative transportprotein glutamate/aspartate transportsystempermease glutamate/aspartate transportsystempermease ATP-binding proteinofglutamate/aspartatetransportsystem putative tRNAsynthetase (2nd module) involved inmethylthiolationofisopentenylatedA37derivativestRNA membrane apolipoprotein N-acyltransferase,copperhomeostasisprotein,inner protein glutamate/aspartate transportsystemperiplasmicbinding putative RNA putative RNA orf, hypotheticalprotein IS5 transposase

Gene description Cell processes Metabolism of smallmolecules tRNA tRNA tRNA Open readingframes Metabolism of smallmolecules Miscellaneous Miscellaneous tRNA tRNA tRNA tRNA Open readingframes Cell processes Cell processes Cell processes Open readingframes Macromolecule metabolism Cell processes Cell processes Miscellaneous Miscellaneous Open readingframes Extrachromosomal

Functional category 403 408 403 407 406 406 402 399 399 399 398 404 402 400 406 406 405 401 Operon ID b0700 b0698 b0697 b0696 b0695 b0694 b0693 b0692 b0691 b0690 b0689 b0699 b0688 b0687 b0686 b0685 b0684 b0683 b0682 b0681 b0680 b0679 b0678 b0677 b0676

B number rhsC kdpA kdpB kdpC kdpD kdpE speF potE ybfH ybfG ybfP ybfA pgm seqA ybfF ybfE fldA fur ybfN ybfM glnS nagE nagB nagA nagC

Gene name + + + + + + + + + ------Strand orientation 1397 557 682 190 894 225 732 439 105 120 164 546 181 254 120 176 148 108 468 554 648 266 382 406 68 Protein length 1043 4865 6895 4618 1254 1185 1204 575 200 749 652 643 177 386 381 892 799 36 41 48 17 19 10 95 39 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 80 24 36 15 32 24 10 13 18 31 17 12 16 24 4 3 6 6 3 6 5 5 7 8 7 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 0 0 0 0 0 1 0 0 0 0 0 0 6 3 1 0 2 4 0 0 6 5 2 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 1 0 0 1 0 0 0 0 0 0 7 3 0 0 1 3 0 0 7 0 3 0 1 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 0 0 0 0 0 1 0 0 0 0 0 0 6 3 1 0 2 4 0 0 6 0 2 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt Membrane protein assignment rhsC proteinin rhselement orf, hypothetical protein ATPase ofhigh-affinitypotassium transportsystem,Bchain high-affinity potassiumtransportsystem sensor forhigh-affinitypotassiumtransportsystem regulator ofkdpoperon(transcriptionaleffector) ornithine decarboxylaseisozyme,inducible putrescine transportprotein orf, hypotheticalprotein orf, hypotheticalprotein putative pectinase phosphoglucomutase ATPase ofhigh-affinitypotassium transportsystem,Achain negative modulatorofinitiationreplication orf, hypotheticalprotein orf, hypotheticalprotein flavodoxin 1 negative regulator orf, hypotheticalprotein orf, hypotheticalprotein glutamine tRNAsynthetase PTS system,N-acetylglucosamine-specificenzymeIIABC glucosamine-6-phosphate deaminase N-acetylglucosamine-6-phosphate deacetylase transcriptional repressorofnag(N-acetylglucosamine)operon

Gene description Extrachromosomal Open reading frames Cell processes Cell processes Global functions Global functions Metabolism ofsmallmolecules Cell processes Open readingframes Open readingframes Miscellaneous Metabolism ofsmallmolecules Cell processes Macromolecule metabolism Open readingframes Open readingframes Metabolism ofsmallmolecules Global functions Open readingframes Open readingframes Macromolecule metabolism Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 424 423 423 422 422 421 420 419 418 417 416 423 416 415 414 413 412 411 411 410 409 408 408 408 Operon ID b0725 b0724 b0723 b0722 b0721 b0720 b0719 b0718 b0717 b0716 b0715 b0714 b0713 b0712 b0711 b0709 b0708 b0707 b0706 b0705 b0704 b0703 b0702 b0710 b0701

B number b0725 sdhB sdhA sdhD sdhC gltA ybgD ybgQ ybgP ybgO abrB nei ybgL ybgK ybgJ ybgH phrB ybgA ybfD ybfL ybfC b0703 ybfB ybgI b0701

Gene name + + + + + + + + + + + + + + + + + + ------Strand orientation 238 588 115 129 427 188 818 242 362 363 263 244 310 218 493 472 169 253 285 189 477 108 247 86 73 Protein length 13343 18927 16326 12121 11527 5467 1289 1335 3721 215 950 230 738 685 33 40 87 50 90 53 14 7 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P mRNA present 15 29 17 26 13 18 12 10 13 29 11 11 16 11 22 4 3 5 6 5 6 4 9 5 5 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 11 12 12 0 1 3 0 0 0 0 0 0 0 3 1 0 0 0 0 0 0 0 4 0 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 12 0 5 0 0 8 0 0 0 0 0 0 0 3 1 0 0 0 0 0 0 0 4 0 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 12 12 0 3 0 0 0 0 0 0 0 0 0 3 1 0 0 0 0 0 0 0 4 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 11 11 0 1 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt PHD PHD Membrane protein assignment orf, hypothetical protein succinate dehydrogenase, ironsulfurprotein citrate synthase succinate dehydrogenase, flavoproteinsubunit succinate dehydrogenase, hydrophobicsubunit succinate dehydrogenase,cytochromeb556 putative fimbrial-likeprotein putative outermembraneprotein putative chaperone orf, hypotheticalprotein putative transportprotein VIIIandDNAN-glycosylasewithanAPlyaseactivity putative lactamutilizationprotein putative carboxylase putative carboxylase orf, hypotheticalprotein orf, hypotheticalprotein deoxyribodipyrimidine (photoreactivation) orf, hypotheticalprotein putative DNAligase putative receptorprotein orf, hypotheticalprotein orf, hypotheticalprotein protein inrhselement putative transportprotein

Gene description Open reading frames Metabolism of smallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Miscellaneous Miscellaneous Open readingframes Miscellaneous Macromolecule metabolism Miscellaneous Miscellaneous Miscellaneous Open readingframes Open readingframes Macromolecule metabolism Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Extrachromosomal Cell processes

Functional category 438 437 436 437 437 437 435 434 434 434 433 432 432 432 432 426 432 430 430 429 428 427 427 425 431 Operon ID b0737 b0750 b0749 b0748 b0747 b0746 b0745 b0744 b0743 b0736 b0731 b0730 b0742 b0741 b0740 b0739 b0738 b0735 b0734 b0733 b0732 b0729 b0728 b0727 b0726

B number tolQ nadA lysQ lysZ lysY valZ lysW valT lysT ybgC hrsA farR ybgF pal tolB tolA tolR ybgE cydB cydA ybgG sucD sucC sucB sucA

Gene name + + + + + + + + + + + + + + + + + + + + + + + + - Strand orientation 230 347 134 658 240 263 173 430 421 142 379 523 877 289 388 405 933 97 Protein length 21953 23350 21360 20546 23115 23626 21994 13638 40902 20532 11040 1325 2364 1627 6035 6246 1400 1031 3951 3720 7268 940 105 345 47 mRNA intensity A A P P P P P P P P P P P P P P P P P P P P P P P mRNA present 10 15 14 15 19 15 43 24 15 39 9 9 7 3 8 5 3 7 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 21 12 1 0 0 0 0 3 5 0 0 0 4 0 5 5 0 5 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 19 13 0 0 0 0 0 4 6 0 0 0 0 0 9 1 0 3 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 21 12 0 0 0 0 0 3 5 0 0 0 0 0 5 1 0 5 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 1 0 0 0 0 0 0 0 0 0 4 0 0 5 0 3 0 1 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt MP-GenProt GenProt PHD Membrane protein assignment quinolinate synthetase, Aprotein tRNA-Lys tRNA-Lys tRNA-Lys tRNA-Val tRNA-Lys tRNA-Val tRNA-Lys orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein transcriptional regulatorofsuccinylCoAsynthetaseoperon succinyl-CoA synthetase,alphasubunit colicins periplasmic proteininvolvedinthetonb-independentuptakeofgroupA membrane spanningprotein,requiredforouterintegrity of groupAcolicins putative innermembraneprotein,involvedinthetonB-independentuptake envelope; tolerancetogroupAcolicins inner membraneprotein,membrane-spanning,maintainsintegrityofcell cytochrome dterminaloxidasepolypeptidesubunitII cytochrome dterminaloxidase,polypeptidesubunitI protein modificationenzyme,inductionofompC component) 2-oxoglutarate dehydrogenase(dihydrolipoyltranssuccinaseE2 peptidoglycan-associated lipoprotein putative sugarhydrolase succinyl-CoA synthetase,betasubunit 2-oxoglutarate dehydrogenase(decarboxylasecomponent)

Gene description Metabolism of smallmolecules tRNA tRNA tRNA tRNA tRNA tRNA tRNA Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Extrachromosomal Extrachromosomal Miscellaneous Extrachromosomal Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Macromolecule metabolism Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 447 444 443 446 440 439 445 445 445 445 442 442 441 439 446 441 439 439 Operon ID b0775 b0774 b0773 b0772 b0771 b0770 b0769 b0768 b0767 b0766 b0765 b0764 b0763 b0762 b0761 b0760 b0759 b0758 b0757 b0756 b0755 b0754 b0752 b0751 b0753

B number bioB bioA ybhB ybhC ybhJ ybhI ybhH ybhD ybhE ybhA modC modB modA b0762 modE modF galE galT galK galM gpmA aroG ybgR pnuC b0753

Gene name + + + + + + + + + + + ------Strand orientation 346 429 158 427 761 477 350 338 331 272 352 229 257 262 490 338 348 382 346 250 350 313 239 126 49 Protein length 3252 1461 1645 2605 3144 1143 1742 1657 3273 4960 5169 5196 1028 244 872 267 567 999 380 501 198 983 42 52 91 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 16 18 12 26 10 11 16 11 18 10 17 10 21 15 16 12 13 13 17 5 7 0 2 1 4 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 13 0 0 0 4 0 0 0 0 3 0 0 0 0 0 0 2 2 1 5 6 5 0 1 0 # of tryptic peptides detected (total list) P P P P P P Protein detected - short list 1 1 0 1 0 0 0 0 4 0 0 0 2 0 0 4 5 1 3 7 9 5 0 1 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 13 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 2 1 5 6 5 0 1 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

PHD Membrane protein assignment biotin synthesis, sulfurinsertion? 7,8-diaminopelargonic acidsynthetase orf, hypotheticalprotein putative putative membranepumpprotein putative transcriptionalregulatorLYSR-type putative enzyme orf, hypotheticalprotein putative isomerase putative phosphatase ATP-binding componentofmolybdatetransport molybdate transportpermeaseprotein molybdate-binding periplasmicprotein;permease orf, hypotheticalprotein molybdate uptakeregulatoryprotein ATP-binding componentofmolybdatetransportsystem UDP-galactose-4-epimerase galactose-1-phosphate uridylyltransferase galactose-1-epimerase (mutarotase) phosphoglyceromutase 1 synthetase, phenylalaninerepressible) 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase(DAHP putative homeoboxprotein required forNMNtransport putative transportsystempermeaseprotein

Gene description Metabolism of smallmolecules Metabolism of smallmolecules Open readingframes Miscellaneous Cell processes Miscellaneous Miscellaneous Open readingframes Miscellaneous Open readingframes Cell processes Cell processes Cell processes Open readingframes Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Cell processes Cell processes

Functional category 467 466 465 464 462 460 463 461 459 458 457 457 457 456 455 454 453 453 453 453 452 451 450 448 449 Operon ID b0800 b0799 b0798 b0797 b0796 b0795 b0794 b0793 b0792 b0791 b0790 b0789 b0788 b0787 b0786 b0785 b0784 b0783 b0782 b0781 b0780 b0779 b0778 b0777 b0776

B number ybiB dinG ybiA rhlE ybiH b0795 ybhF ybhS ybhR ybhQ ybhP ybhO ybhN ybhM ybhL moaE moaD moaC moaB moaA ybhK uvrB bioD bioC bioF

Gene name + + + + + + + + + + + + + + + ------Strand orientation 320 716 160 454 227 332 583 377 368 136 253 413 318 237 234 150 161 170 329 302 673 225 251 384 81 Protein length 1077 2474 1129 3175 3563 3559 1554 1308 1274 952 229 109 309 280 380 460 223 563 848 407 141 429 684 927 92 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 16 17 39 10 24 12 13 20 10 25 20 15 30 16 6 8 3 6 7 8 4 8 9 7 8 # of tryptic peptides predicted P P P P P P Protein detected - total list 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 2 0 1 4 0 1 0 2 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 3 0 1 1 2 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 4 0 1 0 2 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt

PHD PHD PHD Membrane protein assignment putative membraneprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative enzyme probably ATP-dependent helicase orf, hypotheticalprotein putative ATP-dependentRNA helicase putative transcriptionalregulator putative ATP-bindingcomponentofatransportsystem orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein Cardiolipin synthaseactivity molybdopterin convertingfactor,subunit2 molybdopterin biosynthesis molybdopterin biosynthesis,proteinC molybdopterin biosynthesis,proteinB molybdopterin biosynthesis,proteinA putative structuralprotein DNA repair;excisionnucleasesubunitB dethiobiotin synthetase biotin biosynthesis;reactionpriortopimeloylCoA 8-amino-7-oxononanoate synthase

Gene description Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Macromolecule metabolism Open readingframes Miscellaneous Miscellaneous Cell processes Cell processes Cell processes Open readingframes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 475 474 473 472 471 478 478 477 476 475 475 475 475 473 473 470 470 470 470 470 469 468 467 467 467 Operon ID b0825 b0824 b0823 b0822 b0821 b0820 b0819 b0818 b0817 b0816 b0815 b0814 b0813 b0812 b0811 b0810 b0809 b0808 b0807 b0806 b0805 b0804 b0803 b0802 b0801

B number mipB ybiY ybiW b0822 ybiU ybiT ybiS ybiR b0817 b0816 ybiP ompX ybiF dps glnH glnP glnQ ybiO ybiN ybiM b0805 ybiX ybiI ybiJ ybiC

Gene name + + + + + + + + ------Strand orientation 244 308 810 271 421 530 306 372 155 527 171 295 167 248 219 240 786 335 134 760 237 361 89 88 86 Protein length 22609 16120 2262 6175 4090 3281 2836 344 313 680 359 836 394 890 127 338 263 577 706 366 415 369 501 55 62 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P P P P mRNA present 15 37 12 20 23 12 12 14 19 12 28 29 12 13 13 9 6 7 4 3 9 6 5 4 3 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 0 0 0 0 0 1 1 2 0 0 0 6 5 0 0 1 2 0 0 0 0 0 0 0 3 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 0 0 0 0 2 3 0 0 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 4 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 0 0 0 0 1 1 0 0 0 0 6 5 0 0 0 0 0 0 0 0 0 0 0 3 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt MP-GenProt MP-PHD PHD PHD PHD Membrane protein assignment putative transaldolase putative pyruvate formate-lyase2activating enzyme putative formateacetyltransferase orf, hypotheticalprotein orf, hypotheticalprotein putative ATP-bindingcomponentofatransportsystem orf, hypotheticalprotein outer membraneproteinX orf, hypotheticalprotein putative toxin orf, hypotheticalprotein putative enzyme putative transmembranesubunit global regulator,starvationconditions periplasmic glutamine-bindingprotein;permease glutamine high-affinitytransportsystem;membranecomponent ATP-binding componentofglutaminehigh-affinitytransportsystem putative transportprotein orf, hypotheticalprotein orf, hypotheticalprotein putative outermembranereceptorforirontransport putative enzyme orf, hypotheticalprotein orf, hypotheticalprotein putative dehydrogenase

Gene description Miscellaneous Metabolism of smallmolecules Miscellaneous Open readingframes Open readingframes Cell processes Open readingframes Structural elements Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Global functions Cell processes Cell processes Cell processes Miscellaneous Open readingframes Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes

Functional category 498 497 497 496 495 494 493 489 492 492 491 490 488 487 486 486 486 485 484 483 482 482 481 480 479 Operon ID b0849 b0848 b0847 b0846 b0845 b0844 b0843 b0842 b0841 b0840 b0839 b0838 b0837 b0836 b0835 b0834 b0833 b0832 b0831 b0830 b0829 b0850 b0828 b0827 b0826

B number grxA ybjM b0847 b0846 b0845 b0844 ybjH cmr ybjG deoR dacC yliJ yliI b0836 yliG b0834 b0833 b0832 b0831 b0830 b0829 ybjC ybiK moeA moeB

Gene name + + + + + + + + + + + + + + ------Strand orientation 125 561 178 402 262 410 198 252 400 210 371 127 441 442 782 303 306 512 612 321 411 249 85 94 95 Protein length 2227 1738 1655 1062 1054 1782 2228 1231 536 158 363 329 429 482 223 390 509 185 464 248 180 443 792 772 193 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 14 12 21 11 15 18 39 20 21 32 14 15 3 5 6 4 1 4 4 9 6 8 3 1 9 # of tryptic peptides predicted P P P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 0 3 0 0 1 4 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 0 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 0 0 4 0 0 1 6 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 3 0 0 1 4 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD PHD PHD PHD PHD PHD Membrane protein assignment putative transportprotein putative DEOR-typetranscriptionalregulator orf, hypotheticalprotein putative DEOR-typetranscriptionalregulator orf, hypotheticalprotein orf, hypotheticalprotein proton motiveforceeffluxpump orf, hypotheticalprotein transcriptional repressorfordeooperon,tsx,nupG D-alanyl-D-alanine carboxypeptidase;penicillin-bindingprotein6 putative transferase putative dehydrogenase orf, hypotheticalprotein orf, hypotheticalprotein putative receptor orf, hypotheticalprotein putative transportsystempermeaseprotein putative transportsystempermeaseprotein putative transportprotein putative ATP-bindingcomponentofatransportsystem orf, hypothetical protein L- reductase glutaredoxin1 redoxcoenzyme forglutathione-dependentribonucleotide molybdopterin biosynthesis molybdopterin biosynthesis

Gene description Miscellaneous Miscellaneous Open readingframes Miscellaneous Open readingframes Open readingframes Cell processes Open readingframes Metabolism ofsmallmolecules Cell processes Miscellaneous Miscellaneous Open readingframes Open readingframes Miscellaneous Open readingframes Cell processes Cell processes Cell processes Cell processes Open reading frames Metabolism ofsmallmolecules Metabolism of smallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 513 511 514 512 511 510 509 508 507 506 505 504 501 501 503 502 500 500 500 500 516 500 515 499 499 Operon ID b0875 b0874 b0873 b0872 b0871 b0870 b0869 b0868 b0867 b0866 b0865 b0864 b0863 b0862 b0861 b0860 b0859 b0858 b0857 b0856 b0855 b0854 b0853 b0852 b0851

B number aqpZ ybjE hcp hcr poxB itaA ybjT b0868 b0867 b0866 ybjP artP artI artQ artM artJ ybjF ybjO potI potH potG potF ybjN rimK mdaA

Gene name + + + + + + + + + + + ------Strand orientation 231 315 552 322 572 333 486 349 276 107 171 242 243 238 222 243 375 162 281 317 404 370 158 300 240 Protein length 3121 1509 2012 2647 4200 4421 1447 1059 4456 2781 2900 129 184 191 761 444 758 171 374 490 401 531 641 399 40 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 26 14 23 17 23 16 13 12 12 10 17 11 14 16 12 1 5 2 7 5 5 7 6 5 3 # of tryptic peptides predicted P P P P P P P Protein detected - total list 0 0 0 0 4 1 0 0 0 1 4 0 2 0 0 6 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 0 0 0 4 1 0 0 0 1 0 0 4 0 0 7 0 0 0 0 0 0 0 0 3 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 0 0 0 0 4 1 0 0 0 1 0 0 2 0 0 6 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD Membrane protein assignment transmembrane waterchannel;aquaporin Z putative surface protein Hybrid clusterprotein(HCP) NADH oxidoreductaseforthe HCP pyruvate oxidase L-allo-threonine aldolase,PLP-dependent putative dTDP-glucoseenzyme putative nucleotidedi-P-sugarepimeraseordehydratase putative regulator orf, hypotheticalprotein putative enzyme ATP-binding componentof3rdargininetransportsystem 3rdtransportsystemperiplasmicbindingprotein arginine 3rdtransportsystempermeaseprotein arginine 3rdtransportsystempermeaseprotein arginine 3rdtransportsystemperiplasmicbindingprotein orf, hypotheticalprotein putative enzyme putrescine transportprotein;permease putrescine transportprotein;permease ATP-binding componentofputrescinetransportsystem periplasmic putrescine-bindingprotein;permeaseprotein putative sensorytransductionregulator ribosomal proteinS6modification modulator ofdrugactivityA

Gene description Cell processes Miscellaneous Miscellaneous Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Miscellaneous Open readingframes Open readingframes Miscellaneous Cell processes Cell processes Cell processes Cell processes Cell processes Open readingframes Miscellaneous Cell processes Cell processes Cell processes Cell processes Miscellaneous Structural elements Metabolism ofsmallmolecules

Functional category 528 527 526 526 525 525 525 524 523 523 522 521 521 521 521 521 520 520 519 519 519 519 518 517 516 Operon ID b0889 b0888 b0887 b0886 b0885 b0884 b0883 b0882 b0881 b0880 b0879 b0878 b0894 b0893 b0892 b0891 b0890 b0877 b0876 b0900 b0899 b0898 b0896 b0895 b0897

B number lrp trxB cydD cydC aat infA serW clpA yljA cspD ybjZ b0878 dmsA serS ycaJ lolA ftsK ybjX ybjD ycaN b0899 ycaD dmsC dmsB ycaC

Gene name + + + + + + + + + + + + + + + ------Strand orientation 1329 164 321 588 573 234 758 106 648 380 785 430 447 204 330 552 302 540 382 287 205 208 72 74 Protein length 17935 3450 1462 5273 2470 2333 5279 2667 1717 5834 1752 380 665 372 496 514 175 643 561 328 186 371 132 144 38 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 12 23 20 15 40 27 21 12 41 19 22 25 30 38 13 10 17 9 3 7 2 7 8 6 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 3 4 1 0 0 2 5 0 1 0 0 3 0 0 9 0 0 0 0 0 0 0 1 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 4 5 0 0 0 1 8 0 1 0 0 5 0 0 9 0 0 0 0 0 0 0 1 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 3 4 0 0 0 2 5 0 1 0 0 3 0 0 9 0 0 0 0 0 0 0 1 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt GenProt GenProt Membrane protein assignment thioredoxin reductase ATP-binding componentofcytochrome-relatedtransport,Znsensitive ATP-binding componentofcytochrome-relatedtransport leucyl, phenylalanyl-tRNA-proteintransferase protein chaininitiationfactorIF-1 tRNA-Ser ATP-binding componentofserineprotease orf, hypotheticalprotein cold shockprotein putative ATP-bindingcomponentofatransportsystem putative membraneprotein putative enzyme membrane toouter periplasmic proteineffectstranslocationoflipoproteinsfrominner cell divisionprotein amino acidtransportsystem regulator forleucine(orlrp)regulonandhigh-affinitybranched-chain tRNAsynthetase;alsochargesselenocystein tRNAwithserine putative polynucleotideenzyme orf, hypotheticalprotein anaerobic dimethylsulfoxidereductasesubunitA putative transcriptional regulatorLYSR-type putative transport putative transport orf, hypotheticalprotein anaerobic dimethylsulfoxidereductasesubunitB anaerobic dimethylsulfoxidereductasesubunitC

Gene description Metabolism ofsmallmolecules Cell processes Cell processes Macromolecule metabolism Macromolecule metabolism tRNA Macromolecule metabolism Open readingframes Miscellaneous Cell processes Miscellaneous Miscellaneous Cell processes Cell processes Metabolism ofsmallmolecules Macromolecule metabolism Miscellaneous Open readingframes Metabolism ofsmallmolecules Miscellaneous Cell processes Miscellaneous Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 537 536 536 535 534 533 533 532 531 531 530 540 539 538 541 540 529 542 545 544 544 543 542 542 Operon ID b0925 b0924 b0923 b0922 b0921 b0920 b0919 b0918 b0917 b0916 b0915 b0914 b0913 b0912 b0911 b0910 b0909 b0908 b0907 b0906 b0905 b0904 b0903 b0902 b0901

B number ycbB mukB mukE mukF smtA ycbC b0919 kdsB ycaR ycaQ ycaH msbA ycaI himD rpsA cmk ycaL aroA serC ycaP ycaO focA pflB pflA ycaK

Gene name + + + + + + + + + + + + + + + + + + + + - - - - - Strand orientation 1486 615 225 440 261 259 297 248 410 328 582 780 557 227 262 427 362 230 589 285 760 246 196 60 94 Protein length 10452 29325 2884 2195 2010 3950 2547 3622 5838 3882 5044 897 954 994 313 197 171 567 751 206 950 272 875 129 99 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 24 75 30 11 12 15 15 15 26 16 26 23 10 10 19 17 11 16 38 14 9 5 4 3 8 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 20 10 15 0 6 0 0 0 0 0 2 2 0 3 0 0 0 3 0 3 0 0 1 0 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 14 14 0 6 1 0 0 0 0 4 3 0 0 0 0 0 1 0 3 9 0 0 3 0 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 20 10 15 0 6 0 0 0 0 0 2 2 0 0 0 0 0 3 0 3 0 0 1 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 3 0 0 0 3 0 0 0 0 0 0 0 1 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt PHD PHD PHD Membrane protein assignment putative amidase -like cell divisionproteininvolved inchromosomepartitioning putative killingproteinsuppressor mukF protein(killingfactor KICB) S-adenosylmethionine-dependent methyltransferase orf, hypotheticalprotein orf, hypotheticalprotein CTP:CMP-3-deoxy-D-manno-octulosonate transferase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative EC1.2enzyme ATP-binding transportprotein;multicopysuppressorofhtrB integration hostfactor(IHF),betasubunit;site-specificrecombination 30S ribosomalsubunitproteinS1 putative heatshockprotein 5-enolpyruvylshikimate-3-phosphate synthetase 3-phosphoserine aminotransferase orf, hypotheticalprotein probable formatetransporter(formatechannel1) orf, hypotheticalprotein formate acetyltransferase1 pyruvate formatelyaseactivatingenzyme1 orf, hypotheticalprotein

Gene description Miscellaneous Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Open readingframes Open readingframes Structural elements Open readingframes Open readingframes Open readingframes Macromolecule metabolism Cell processes Macromolecule metabolism Structural elements Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Cell processes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes

Functional category 561 560 560 560 560 559 558 557 557 556 556 556 556 555 554 553 552 551 551 550 548 549 547 547 546 Operon ID b0950 b0949 b0948 b0947 b0946 b0940 b0939 b0938 b0937 b0936 b0935 b0934 b0933 b0945 b0944 b0943 b0942 b0941 b0932 b0931 b0930 b0929 b0928 b0927 b0926

B number pqiA uup ycbY b0947 ycbW ycbS ycbR ycbQ ssuE ssuA ssuD ssuC ssuB pyrD ycbF b0943 b0942 b0941 pepN pncB asnS ompF aspC ycbL ycbK

Gene name + + + + + + + + + + + + + + + ------Strand orientation 417 635 702 369 192 866 233 182 191 333 381 278 255 336 245 187 180 356 870 400 466 362 396 215 182 Protein length 32813 1179 1955 1962 1464 8281 1614 7075 369 849 794 429 136 261 137 162 216 284 308 185 220 670 55 94 81 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 13 29 36 20 15 20 31 11 13 10 11 37 14 12 22 23 16 23 12 8 6 8 8 1 8 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 13 12 16 0 1 1 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 5 6 1 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 15 10 16 0 2 1 1 0 0 0 2 0 0 0 0 0 0 0 0 0 0 5 2 2 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 13 12 16 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 5 2 1 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 6 0 0 0 detected (membrane sample) MP-GenProt MP-GenProt PHD PHD PHD Membrane protein assignment paraquat-inducible proteinA putative ATP-binding componentofatransport system putative oxidoreductase orf, hypotheticalprotein orf, hypotheticalprotein dihydro-orotate dehydrogenase putative chaperone putative fimbrial-likeprotein Reducing enzymeforSsuD Probable componentofABCtransporter Alkanesulfonate monooxygenase Probable componentofABCtransporter Probable componentofABCtransporter aminopeptidase N homolog ofSalmonellaFimHprotein putative outermembraneprotein putative chaperone putative fimbrial-likeprotein putative fimbrial-likeprotein nicotinate phosphoribosyltransferase asparagine tRNAsynthetase outer membraneprotein1a(Ia;b;F) aspartate aminotransferase orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Miscellaneous Cell processes Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Miscellaneous Miscellaneous Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Cell processes Macromolecule metabolism Miscellaneous Miscellaneous Miscellaneous Miscellaneous Miscellaneous Metabolism ofsmallmolecules Macromolecule metabolism Structural elements Metabolism ofsmallmolecules Open readingframes Open readingframes

Functional category 575 574 574 573 572 571 570 569 568 568 568 568 568 567 570 570 570 570 570 566 565 564 563 562 562 Operon ID b0971 b0972 b0970 b0969 b0973 b0968 b0967 b0975 b0974 b0966 b0965 b0964 b0963 b0962 b0961 b0960 b0959 b0958 b0957 b0956 b0954 b0955 b0953 b0952 b0951

B number serT hyaA yccA yccK hyaB b0968 b0967 hyaD hyaC yccV b0965 b0964 mgsA helD yccF b0960 b0959 sulA ompA ycbG fabA b0955 rmf ymbA pqiB

Gene name + + + + + + + + + + + + ------Strand orientation 372 219 128 597 367 195 235 122 164 220 155 684 148 720 209 169 346 150 172 586 182 546 92 55 Protein length 36891 42181 8585 1126 2010 3808 1053 1038 2570 1181 197 508 282 981 117 284 730 285 759 780 255 308 364 960 16 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 12 16 31 11 41 23 12 16 23 26 3 5 6 3 9 8 6 6 4 8 7 7 3 7 # of tryptic peptides predicted P P P P P Protein detected - total list 19 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 1 0 0 0 2 0 0 0 0 0 0 0 0 7 1 2 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 0 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 5 1 2 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD MP-GenProt GenProt GenProt PHD PHD PHD Membrane protein assignment tRNA-Ser putative carrier/transportprotein putative sulfitereductase(EC1.8.-.-) orf, hypotheticalprotein hydrogenase-1 smallsubunit putative oxidoreductase orf, hypotheticalprotein hydrogenase-1 largesubunit processing of HyaAandHyaBproteins probable Ni/Fe-hydrogenase 1b-typecytochrome subunit orf, hypotheticalprotein orf, hypotheticalprotein methylglyoxal synthase orf, hypotheticalprotein orf, hypotheticalprotein DNA helicaseIV orf, hypotheticalprotein suppressor oflon;inhibitscelldivisionandftsZringformation outer membraneprotein3a(II*;G;d) putative dehydrogenase putative ATP-dependentprotease ribosome modulationfactor isomerase beta-hydroxydecanoyl thioesterdehydrase,trans-2-decenoyl-ACP orf, hypotheticalprotein paraquat-inducible proteinB

Gene description tRNA Miscellaneous Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism of smallmolecules Metabolism of smallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Miscellaneous Macromolecule metabolism Open readingframes Cell processes Structural elements Miscellaneous Miscellaneous Structural elements Metabolism ofsmallmolecules Open readingframes Miscellaneous

Functional category 590 590 589 591 588 588 591 591 591 587 586 585 583 583 584 582 581 580 579 578 576 577 575 575 Operon ID b0993 b0992 b1000 b0999 b0998 b0997 b0996 b0995 b0994 b0991 b0990 b0989 b0988 b0987 b0986 b0985 b0984 b0983 b0982 b0981 b0980 b0979 b0978 b0977 b0976

B number torS yccM cbpA yccD torD torA torC torR torT sfa cspG cspH insB_4 ymcD ymcC ymcB ymcA yccZ yccY yccC appA appB appC hyaF hyaE

Gene name + + + + + + + + + + + + ------Strand orientation 904 357 306 101 199 848 390 230 342 167 107 214 248 698 379 152 726 432 378 514 285 132 76 70 70 Protein length 2616 176 133 446 599 222 444 311 391 222 102 368 272 244 289 193 315 146 80 77 79 78 95 62 mRNA intensity A A A A A A A A A A A A A A P P P P P P P P P P mRNA present 10 38 41 10 18 20 30 16 35 13 18 9 2 2 7 5 4 9 0 3 8 8 8 9 8 # of tryptic peptides predicted P P Protein detected - total list 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt PHD Membrane protein assignment orf, hypotheticalprotein curved DNA-binding protein;functionsclosely relatedtoDnaJ suppresses fabAandtsgrowthmutation sensor proteintorS(regulatorTorR) orf, hypothetical protein part oftrimethylamine-N-oxide oxidoreductase trimethylamine N-oxidereductase subunit trimethylamine N-oxidereductase,cytochromec-type subunit response transcriptionalregulatorfortorA(sensorTorS) part ofregulationtoroperon,periplasmic homolog ofSalmonellacoldshockprotein cold shock-likeprotein IS1 proteinInsB orf, hypotheticalprotein putative regulator orf, hypotheticalprotein orf, hypotheticalprotein putative functioninexopolysaccharideproduction putative phosphatase orf, hypotheticalprotein phosphoanhydride ;pH2.5acidphosphatase;periplasmic probable thirdcytochromeoxidase,subunitII probable thirdcytochromeoxidase,subunitI nickel incorporationintohydrogenase-1proteins processing ofHyaAandHyaBproteins

Gene description Open readingframes Cell processes Miscellaneous Metabolism ofsmallmolecules Open reading frames Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Miscellaneous Extrachromosomal Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 599 604 598 600 604 603 603 603 602 601 597 596 595 594 593 593 593 593 593 593 592 592 592 591 591 Operon ID b1020 b1019 b1018 b1017 b1004 b1016 b1015 b1006 b1003 b1022 b1021 b1014 b1013 b1012 b1011 b1010 b1009 b1008 b1007 b1005 b1002 b1001 b1025 b1024 b1023

B number phoH ycdB ycdO b1017 wrbA b1016 putP ycdG yccJ ycdQ ycdP putA ycdC b1012 b1011 b1010 b1009 b1008 b1007 ycdF agp yccE ycdT ycdS ycdR

Gene name + + + + + + + + + + + ------Strand orientation 1320 354 423 375 243 198 502 464 441 137 212 382 244 128 266 196 152 413 418 452 807 672 39 75 76 Protein length 1237 6589 1133 2597 1606 2197 365 379 469 548 358 112 121 357 128 166 148 108 246 80 90 61 78 67 65 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 17 17 21 12 57 11 15 13 18 46 15 11 17 16 30 9 2 5 5 4 3 4 4 2 8 # of tryptic peptides predicted P P P P Protein detected - total list 0 0 0 7 0 0 0 2 2 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 0 5 0 0 0 3 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 0 0 0 7 0 0 0 2 2 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt GenProt PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein putative cytochrome orf, hypotheticalprotein orf, hypotheticalprotein major sodium/prolinesymporter proline dehydrogenase,P5Cdehydrogenase orf, hypotheticalprotein periplasmic glucose-1-phosphatase orf, hypotheticalprotein induced byPstarvation PhoB-dependent, ATP-bindingphoreguloncomponent; maybehelicase; putative transportprotein operator trp repressorbindingprotein;affectsassociationofand putative tetoperonregulator orf, hypotheticalprotein putative synthetase orf, hypotheticalprotein putative acetyltransferase putative enzyme orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein putative outer membraneprotein orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open readingframes Miscellaneous Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes Open reading frames Miscellaneous Open readingframes Open readingframes

Functional category 614 614 613 613 607 612 611 608 606 616 615 609 607 610 609 609 609 609 609 609 605 617 616 616 616 Operon ID b1049 b1041 b1040 b1039 b1038 b1037 b1036 b1048 b1047 b1046 b1045 b1044 b1043 b1042 b1035 b1034 b1050 b1033 b1032 b1031 b1030 b1029 b1028 b1027 b1026

B number mdoH csgB csgD csgE csgF csgG ycdZ mdoG mdoC ymdC b1045 b1044 csgC csgA ycdY ycdX yceK ycdW serX ycdV b1030 ycdU b1028 b1027 tra5_3

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 847 151 216 129 138 277 179 511 385 493 177 103 110 151 184 245 325 137 328 107 102 288 75 83 Protein length 3791 1307 1904 2446 976 120 469 217 516 190 494 202 193 612 177 321 175 131 111 51 22 32 28 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P mRNA present 32 15 14 25 11 29 11 11 17 10 16 4 5 4 4 8 3 5 2 2 6 4 4 5 # of tryptic peptides predicted P P P P P P Protein detected - total list 2 0 0 0 0 0 7 0 5 0 0 2 0 0 0 2 0 4 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 1 0 0 0 0 0 9 0 4 0 0 2 0 0 0 2 0 4 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 1 0 0 0 0 0 7 0 5 0 0 2 0 0 0 2 0 4 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt GenProt GenProt PHD PHD Membrane protein assignment orf, hypotheticalprotein periplasmic glucansbiosynthesis protein putative 2-componenttranscriptionalregulatorfor2ndcurlioperon curli productionassembly/transportcomponent,2ndoperon curli productionassembly/transportcomponent,2ndoperon curli productionassembly/transportcomponent,2ndoperon putative oxidoreductasecomponent minor curlinsubunitprecursor,similarroCsgA Essential forsuccinylation of osmoregulatedperiplasmicglucans putative synthase putative polyprotein orf, hypotheticalprotein putative curliproductionprotein curlin majorsubunit,coiledsurfacestructures;cryptic putative DNApolymerasesubunit orf, hypothetical protein putative dehydrogenase serine tRNA5(duplicateofserW) oligosaccharide (MDO) membrane glycosyltransferase; synthesisofmembrane-derived orf, hypotheticalprotein putative ribosomalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein IS3 putativetransposase

Gene description Open readingframes Cell processes Miscellaneous Structural elements Structural elements Structural elements Miscellaneous Structural elements Cell processes Miscellaneous Open readingframes Open readingframes Miscellaneous Structural elements Macromolecule metabolism Open reading frames Miscellaneous tRNA Cell processes Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous

Functional category 623 630 624 624 624 624 622 625 629 628 628 627 626 625 622 631 621 630 619 620 620 619 618 618 Operon ID b1075 b1074 b1073 b1072 b1071 b1070 b1069 b1068 b1067 b1065 b1066 b1064 b1063 b1062 b1061 b1060 b1059 b1058 b1057 b1056 b1053 b1052 b1051 b1055 b1054

B number flgD flgC flgB flgA flgM flgN mviN mviM yceH yceL rimJ grxB yceB pyrC dinI yceP solA yceO b1057 yceI yceE b1052 msyB yceA htrB

Gene name + + + + + + + + ------Strand orientation 231 134 138 219 138 511 307 215 412 194 215 186 348 372 188 191 408 125 350 306 97 81 84 46 32 Protein length 19634 1589 3115 8708 4514 1229 2261 1562 216 101 239 261 271 327 412 136 758 938 770 566 126 608 85 35 5 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P P P P mRNA present 17 12 11 11 12 16 19 11 18 11 2 6 8 5 7 5 9 7 4 4 2 3 1 3 9 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 0 0 0 0 0 0 0 0 2 1 0 7 1 5 0 0 6 0 0 1 0 2 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 0 0 0 0 0 0 0 3 1 0 4 0 4 0 0 8 0 0 1 0 2 1 0 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 0 0 0 0 0 0 0 0 2 1 0 7 0 5 0 0 6 0 0 1 0 2 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment flagellar biosynthesis, initiationofhook assembly flagellar biosynthesis, cell-proximalportion ofbasal-bodyrod flagellar biosynthesis,cell-proximal portionofbasal-bodyrod flagellar biosynthesis;assembly ofbasal-bodyperiplasmicPring anti-FliA (anti-sigma)factor;alsoknownasRflBprotein putative virulencefactor protein offlagellarbiosynthesis putative virulencefactor orf, hypotheticalprotein acetylation ofN-terminalalanine30SribosomalsubunitproteinS5 glutaredoxin 2 orf, hypotheticalprotein orf, hypotheticalprotein dihydro-orotase damage-inducible proteinI orf, hypotheticalprotein N-methyltryptophan oxidase,FADbinding(1stmodule) orf, hypotheticalprotein putative cytochrome orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein acidic proteinsuppressesmutantslackingfunctionofexport putative transportprotein heat shockprotein

Gene description Structural elements Structural elements Structural elements Structural elements Structural elements Miscellaneous Structural elements Open readingframes Open readingframes Structural elements Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Cell processes Cell processes Macromolecule metabolism

Functional category 646 646 646 645 645 644 645 643 643 643 641 642 640 639 638 637 636 636 635 635 634 632 632 632 633 Operon ID b1100 b1099 b1098 b1097 b1096 b1095 b1094 b1093 b1092 b1091 b1090 b1089 b1088 b1087 b1086 b1085 b1084 b1083 b1082 b1081 b1080 b1079 b1078 b1077 b1076

B number ycfH holB tmk yceG pabC fabF acpP fabG fabD fabH plsX rpmF yceD yceF yceC b1085 rne flgL flgK flgJ flgI flgH flgG flgF flgE

Gene name + + + + + + + + + + + + + + + + + + + + + + + - - Strand orientation 1061 265 334 213 340 269 413 244 309 317 346 173 207 319 124 317 547 313 365 232 260 251 402 78 57 Protein length 42769 24478 15309 23085 1239 8101 5633 4599 1642 598 399 277 429 645 963 387 107 189 179 253 175 68 13 75 63 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 15 17 13 16 14 14 10 11 13 12 18 43 17 15 20 15 3 3 6 7 6 9 9 9 8 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 0 0 0 0 0 3 3 4 2 4 0 0 2 3 0 0 5 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 10 0 0 0 0 1 2 3 5 3 3 0 0 2 3 1 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 0 0 0 0 0 3 3 4 2 4 0 0 2 3 0 0 5 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt PHD MP Membrane protein assignment orf, hypothetical protein DNA polymerase III,deltaprimesubunit putative thymidylatekinase (EC2.7.4.9) 4-amino-4-deoxychorismate lyase 3-oxoacyl-[acyl-carrier-protein] synthaseII acyl carrierprotein 3-oxoacyl-[acyl-carrier-protein] reductase malonyl-CoA-[acyl-carrier-protein] transacylase 3-oxoacyl-[acyl-carrier-protein] synthaseIII;acetylCoAACPtransacylase glycerolphosphate auxotrophyinplsBbackground 50S ribosomalsubunitproteinL32 orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein RNase E,membraneattachment,mRNAturnover,maturation5SRNA layer) ringprotein flagellar biosynthesis,basal-bodyouter-membraneL(lipopolysaccharide flagellar biosynthesis;hook-filamentjunctionprotein flagellar biosynthesis,hook-filamentjunctionprotein1 flagellar biosynthesis homolog ofSalmonellaP-ringflagellabasalbody flagellar biosynthesis,cell-distalportionofbasal-bodyrod flagellar biosynthesis,cell-proximalportionofbasal-bodyrod flagellar biosynthesis,hookprotein

Gene description Open reading frames Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Structural elements Open readingframes Open readingframes Macromolecule metabolism Open readingframes Macromolecule metabolism Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements

Functional category 657 657 657 657 657 656 656 655 655 655 654 653 652 651 650 649 648 646 647 646 646 646 646 646 646 Operon ID b1120 b1119 b1118 b1117 b1116 b1115 b1114 b1113 b1110 b1109 b1112 b1111 b1108 b1107 b1106 b1105 b1125 b1124 b1104 b1123 b1122 b1121 b1103 b1102 b1101

B number cobB ycfX ycfW ycfV ycfU ycfT mfd ycfS ycfJ ndh ycfR ycfQ ycfP ycfO ycfN ycfM potB potC ycfL potD ymfA b1121 ycfF fhuE ptsG

Gene name + + + + + + + + + + + + + + + ------Strand orientation 1148 279 303 414 228 399 357 320 179 434 236 199 341 274 213 275 264 125 348 156 262 119 729 477 85 Protein length 1640 1158 1102 1003 4100 3089 2095 2592 3389 2467 5107 2777 1611 879 846 592 239 111 362 606 698 190 220 29 44 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 12 10 12 13 63 19 24 11 10 14 13 14 15 33 8 9 2 7 7 2 5 7 5 8 6 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 1 0 0 1 1 0 4 0 1 0 0 3 0 1 0 2 0 0 0 2 5 3 0 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 2 0 0 1 0 0 4 0 0 0 0 3 0 1 0 0 0 0 0 5 3 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 1 0 0 0 0 0 4 0 0 0 0 3 0 1 0 0 0 0 0 2 5 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt GenProt PHD PHD PHD Membrane protein assignment putative NAGC-liketranscriptionalregulator orf, hypotheticalprotein putative kinase putative ATP-bindingcomponentofatransportsystem orf, hypotheticalprotein transcription-repair couplingfactor;mutationfrequencydecline orf, hypotheticalprotein orf, hypotheticalprotein respiratory NADHdehydrogenase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative beta-glucosidase(EC3.2.1.21) orf, hypotheticalprotein orf, hypotheticalprotein spermidine/putrescine transportsystem permease spermidine/putrescine transportsystem permease spermidine/putrescine periplasmic transportprotein orf, hypotheticalprotein homolog ofvirulencefactor phosphoribosyltransferase putative nicotinicacidmononucleotide:5,6-dimethylbenzimidazole (DMB) PTS system,glucose-specificIIBCcomponent orf, hypotheticalprotein outer membranereceptorforferricironuptake

Gene description Open readingframes Open readingframes Cell processes Cell processes Cell processes Macromolecule metabolism Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Cell processes Cell processes Cell processes Open readingframes Miscellaneous Open readingframes Cell processes Open readingframes Cell processes

Functional category 668 667 668 668 668 666 665 664 661 660 662 663 660 660 660 660 670 670 670 660 669 668 658 669 659 Operon ID b1150 b1149 b1148 b1147 b1146 b1145 b1144 b1143 b1142 b1141 b1140 b1139 b1138 b1137 b1136 b1135 b1134 b1133 b1132 b1131 b1130 b1129 b1128 b1127 b1126

B number ymfR ymfN ymfM ymfL b1146 b1145 ymfJ ymfI ymfH b1141 intE lit ymfE ymfD icdA ymfC b1134 ycfB ycfC purB phoP phoQ ycfD pepT potA

Gene name + + + + + + + + + ------Strand orientation 455 112 189 167 224 128 103 375 297 234 221 416 207 153 383 213 456 223 486 376 408 378 60 94 81 Protein length 42636 2340 3150 2271 6704 1143 1171 101 163 100 298 129 292 110 208 592 567 854 575 91 62 70 69 95 87 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 10 21 21 13 21 10 10 14 10 22 11 22 12 19 19 1 9 9 9 7 6 2 6 7 5 # of tryptic peptides predicted P P P P P P Protein detected - total list 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 7 8 0 1 3 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 6 8 0 1 3 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 7 8 0 1 3 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt PHD PHD PHD PHD Membrane protein assignment orf, hypothetical protein orf, hypothetical protein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative phagerepressor orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein phage T4lategeneexpression;atlocusofe14element orf, hypotheticalprotein prophage e14integrase orf, hypotheticalprotein isocitrate dehydrogenase,specificforNADP+ orf, hypotheticalprotein putative phosphohydrolase orf, hypotheticalprotein orf, hypotheticalprotein adenylosuccinate lyase transcriptional regulatoryprotein sensor proteinPhoQ orf, hypotheticalprotein putative peptidaseT ATP-binding componentofspermidine/putrescinetransport

Gene description Open reading frames Open reading frames Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Extrachromosomal Open readingframes Extrachromosomal Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Global functions Global functions Open readingframes Miscellaneous Cell processes

Functional category 683 683 683 683 683 682 681 679 680 679 678 677 679 677 676 675 675 675 675 674 673 673 672 671 670 Operon ID b1174 b1173 b1172 b1171 b1170 b1169 b1168 b1167 b1166 b1165 b1175 b1164 b1163 b1162 b1161 b1160 b1159 b1158 b1157 b1156 b1155 b1154 b1153 b1152 b1151

B number minE b1173 b1172 b1171 b1170 b1169 b1168 ymgC ymgB ymgA minD ycgZ b1163 ycgE ycgX ycgW mcrA pin b1157 ycfA b1155 ycfK b1153 b1152 ymfO

Gene name + + + + + + + + + + + + + + + ------Strand orientation 111 338 506 521 270 403 243 134 107 277 184 179 200 137 209 194 263 157 88 70 94 82 88 90 78 Protein length 2930 5617 975 534 272 107 803 731 182 718 181 149 103 149 252 226 81 31 27 38 23 45 93 12 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P mRNA present 14 16 24 14 19 13 14 6 3 4 6 5 4 5 4 9 7 9 6 5 9 9 5 8 6 # of tryptic peptides predicted P P P P Protein detected - total list 2 0 0 0 0 0 0 0 0 0 0 5 0 1 0 0 0 0 0 0 1 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 1 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 1 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 2 0 0 0 0 0 0 0 0 0 0 5 0 1 0 0 0 0 0 0 1 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt

Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative partofATP-bindingcomponenta transportsystem putative ATP-bindingcomponentofatransportsystem putative proteases orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein cell divisioninhibitor, amembraneATPase, activatesminC ring formation cell divisiontopologicalspecificity factor,reversesMinCinhibitionofftsZ orf, hypotheticalprotein putative transcriptionalregulator orf, hypotheticalprotein orf, hypotheticalprotein restriction ofDNAat5-methylcytosineresidues;locuse14element inversion ofadjacentDNA;atlocuse14element putative tailfiberprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Cell processes Open readingframes Miscellaneous Open readingframes Open readingframes Extrachromosomal Extrachromosomal Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes

Functional category 697 696 696 695 694 693 692 691 691 691 698 698 690 689 688 687 686 685 684 684 683 683 683 683 683 Operon ID b1183 b1182 b1181 b1200 b1180 b1199 b1198 b1179 b1197 b1196 b1191 b1190 b1178 b1177 b1195 b1194 b1193 b1192 b1189 b1188 b1187 b1186 b1185 b1184 b1176

B number umuD hlyE ycgN dhaK1 b1180 dhaK2 ycgC ycgL treA ycgY b1191 dadX ycgK ycgJ ymgE ycgR mltE ldcA dadA ycgB fadR nhaB dsbB umuC minC

Gene name + + + + + + + + + + + + ------Strand orientation 139 305 158 366 219 210 473 108 565 146 536 356 133 122 244 241 304 432 510 239 513 176 422 231 84 Protein length 3466 1080 3006 1511 1352 1361 1139 1825 6644 213 557 618 180 212 499 867 365 647 581 373 300 243 73 54 81 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P P P P mRNA present 16 15 10 21 27 14 13 13 20 11 12 13 20 14 13 21 2 7 9 8 7 7 2 1 5 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 0 0 0 5 1 2 0 7 3 1 0 1 0 0 0 0 2 0 0 0 0 0 0 0 1 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 0 0 6 1 2 1 6 6 1 0 1 0 0 0 0 2 0 0 1 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 0 0 0 5 1 2 0 7 3 1 0 1 0 0 0 0 2 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt PHD PHD Membrane protein assignment hemolysin E putative dihydroxyacetone kinase(EC2.7.1.2) orf, hypotheticalprotein putative isomerase putative dihydroxyacetone kinase(EC2.7.1.2) orf, hypotheticalprotein putative PTSsystemenzyme I , periplasmic orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein alanine racemase2,catabolic D-amino aciddehydrogenasesubunit orf, hypotheticalprotein cell divisioninhibitor,inhibitsftsZringformation murein transglycosylaseE orf, hypotheticalprotein flagella. reoxidizes DsbAproteinfollowingformationofdisulfidebondinP-ring complex withUmuC SOS mutagenesis;error-pronerepair;processedtoUmuD';forms orf, hypotheticalprotein L,D-carboxypeptidase putative sporulationprotein negative regulatorforfadregulon,andpositiveactivatoroffabA Na+/H+ antiporter,pHindependent SOS mutagenesisandrepair

Gene description Cell processes Metabolism of smallmolecules Open readingframes Miscellaneous Metabolism of smallmolecules Open readingframes Miscellaneous Cell processes Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Cell processes Structural elements Cell processes Structural elements Macromolecule metabolism Open readingframes Open readingframes Miscellaneous Metabolism ofsmallmolecules Cell processes Macromolecule metabolism

Functional category 704 718 703 702 718 701 718 717 700 716 715 710 710 699 698 713 711 706 705 714 712 709 708 707 705 Operon ID b1208 b1207 b1206 b1221 b1220 b1219 b1218 b1205 b1217 b1216 b1204 b1223 b1222 b1215 b1214 b1213 b1212 b1211 b1210 b1209 b1203 b1202 b1201 b1225 b1224

B number ychB prsA ychM narL ychP ychN chaC ychH chaB chaA pth narK narX kdsA ychA b1213 hemK prfA hemA hemM ychF b1202 b1201 narH narG

Gene name + + + + + + + + + + + + + + ------Strand orientation 1247 283 315 550 216 417 117 238 366 194 463 598 284 269 130 277 360 418 207 363 955 642 512 92 76 Protein length 6082 2638 2563 1088 1008 1402 1617 2855 3419 1146 337 799 590 693 105 151 946 395 328 626 897 145 295 33 53 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 13 12 11 17 13 32 15 16 19 12 12 20 17 22 28 64 11 25 9 2 5 9 3 6 7 # of tryptic peptides predicted P P P P P P Protein detected - total list 0 4 0 2 0 0 0 0 0 1 0 0 4 2 6 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 6 0 2 0 0 0 0 1 3 0 0 4 0 6 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 4 0 2 0 0 0 0 0 1 0 0 4 0 6 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt GenProt GenProt PHD PHD Membrane protein assignment phosphoribosylpyrophosphate synthetase orf, hypotheticalprotein orf, hypotheticalprotein putative factor orf, hypotheticalprotein cation transportregulator cation transportregulator peptidyl-tRNA hydrolase sodium-calcium/proton antiporter 2-dehydro-3-deoxyphosphooctulonate aldolase putative GTP-bindingprotein nitrate/nitrate sensor,histidine proteinkinaseactsonNarLregulator nar, frd,dmsandtorgenes pleiotrophic regulationofanaerobicrespiration:response regulatorfor orf, hypotheticalprotein glutamyl-tRNA dehydrogenase an enzymeinmainpathwayofsynthesis5-aminolevulinate,possibly deoxyxylulose pathwayforbiosynthesisofterpenoids Phosphorylates 4-diphosphocytidyl-2-C-methylerythritolinthe orf, hypotheticalprotein possible protoporphyrinogenoxidase peptide chainreleasefactorRF-1 enzyme inalternatepathofsynthesis5-aminolevulinate putative adhesionandpenetrationprotein putative sensor-typeregulator nitrate reductase 1,alphasubunit nitrite extrusionprotein nitrate reductase 1,betasubunit

Gene description Metabolism ofsmallmolecules Cell processes Open readingframes Miscellaneous Open readingframes Cell processes Cell processes Macromolecule metabolism Cell processes Structural elements Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Open readingframes Miscellaneous Metabolism of smallmolecules Cell processes Metabolism of smallmolecules

Functional category 725 724 723 731 730 729 729 722 728 727 721 732 732 727 726 726 727 727 727 727 720 719 734 733 734 Operon ID b1241 b1240 b1239 b1238 b1237 b1249 b1246 b1245 b1244 b1236 b1235 b1250 b1248 b1247 b1243 b1242 b1234 b1230 b1227 b1226 b1233 b1231 b1229 b1228 b1232

B number adhE b1240 ychG tdk hns cls oppD oppC oppB galU hnr kch b1248 oppF oppA ychE ychK tyrV narI narJ ychJ tyrT tpr b1228 purU

Gene name + + + + + + + + + + + + + ------Strand orientation 891 196 205 137 486 337 302 306 302 337 417 135 334 543 215 314 225 236 152 280 76 33 91 Protein length 34541 10687 11229 4865 1533 2301 3242 1036 1366 7098 1126 1292 3490 419 122 424 880 577 692 816 176 157 244 69 48 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 41 10 20 12 13 19 13 26 14 14 17 13 11 5 7 5 9 3 7 6 1 6 3 # of tryptic peptides predicted P P P P P P P Protein detected - total list 24 18 0 0 4 0 0 1 0 4 1 0 0 0 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (total list) P P P P Protein detected - short list 22 16 0 1 4 0 0 0 0 4 0 0 0 0 0 1 0 0 0 0 0 0 1 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 24 18 0 0 4 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein DNA-binding proteinHLP-II(HU,BH2,HD,NS);pleiotropicregulator glucose-1-phosphate uridylyltransferase homolog ofSalmonellaoligopeptidetransportpermease protein oligopeptide transportpermeaseprotein orf, hypotheticalprotein oligopeptide transport;periplasmicbindingprotein Hnr protein orf, hypotheticalprotein sensitivity cardiolipin synthase,amajor membranephospholipid;novobiocin system homolog ofSalmonellaATP-binding proteinofoligopeptideABCtransport system homolog ofSalmonellaATP-bindingproteinoligopeptide ABCtransport putative channelprotein dehydrogenase; pyruvate-formate-lyasedeactivase CoA-linked acetaldehydedehydrogenaseandiron-dependentalcohol putative potassium channelprotein orf, hypotheticalprotein tRNA-Tyr a protaminelikeprotein nitrate reductase1,deltasubunit,assemblyfunction nitrate reductase1,cytochromeb(NR),gammasubunit formyltetrahydrofolate deformylase;forpurT-dependentFGARsynthesis tRNA-Tyr orf, hypotheticalprotein

Gene description Open readingframes Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Cell processes Cell processes Open readingframes Cell processes Macromolecule metabolism Open readingframes Macromolecule metabolism Cell processes Cell processes Open readingframes Metabolism ofsmallmolecules Miscellaneous Open readingframes tRNA Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules tRNA Open readingframes

Functional category 743 743 742 741 740 746 746 748 746 739 738 748 747 746 745 744 749 737 736 734 734 737 735 Operon ID b1275 b1274 b1273 b1272 b1262 b1271 b1270 b1261 b1269 b1268 b1260 b1267 b1259 b1258 b1257 b1256 b1266 b1255 b1265 b1254 b1252 b1264 b1263 b1253 b1251

B number cysB topA yciN sohB trpC yciK btuR trpB yciL yciQ trpA yciO yciG yciF yciE yciD yciV yciC trpL yciB tonB trpE trpD yciA yciI

Gene name + + + + + + + + + ------Strand orientation 324 865 349 453 252 196 397 291 631 268 218 166 168 212 293 247 179 239 520 531 132 130 83 78 14 Protein length 1147 3784 1026 7588 1281 1889 2495 1675 2849 1463 2589 1601 1713 2693 3403 1254 2853 566 570 520 520 943 292 341 69 mRNA intensity A P P P P P P P P P P P P P P P P P P P P P P P P mRNA present 16 44 18 23 15 18 10 15 14 19 11 12 19 15 5 8 5 8 8 7 0 7 9 5 2 # of tryptic peptides predicted P P P P P P P P P P P P P P P Protein detected - total list 1 5 0 1 4 1 4 0 3 9 0 3 0 1 1 0 0 1 0 0 0 6 2 0 1 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 10 1 7 0 1 5 1 6 0 3 0 2 0 2 1 0 0 0 0 0 0 8 3 0 1 # of tryptic peptides detected (short list) P P P P P P P P P P P P P P Protein detected - long list 1 5 0 1 4 1 4 0 3 9 0 3 0 1 1 0 0 0 0 0 0 6 2 0 1 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD MP-GenProt PHD PHD PHD PHD Membrane protein assignment positive transcriptional regulatorforcysteine regulon DNA topoisomerase typeI,omegaprotein orf, hypotheticalprotein putative protease putative oxidoreductase synthase,betaprotein cob(I)alamin adenolsyltransferase orf, hypotheticalprotein ,alphaprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative putative structuralproteins orf, hypotheticalprotein putative outermembraneprotein orf, hypotheticalprotein trp operonleaderpeptide orf, hypotheticalprotein anthranilate synthasecomponentI orf, hypotheticalprotein orf, hypotheticalprotein phosphoribosylanthranilate transferase anthranilate synthasecomponentII,glutamineamidotransferaseand glycerolphosphate synthetase N-(5-phosphoribosyl)anthranilate isomeraseandindole-3- colicins energy transducer;uptakeofiron,cyanocobalimin;sensitivitytophages,

Gene description Metabolism of smallmolecules Macromolecule metabolism Open readingframes Miscellaneous Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes

Functional category 764 763 762 761 760 757 760 759 757 758 758 756 758 755 755 754 753 757 753 757 752 750 757 757 751 Operon ID b1296 b1293 b1292 b1291 b1290 b1289 b1300 b1299 b1298 b1297 b1295 b1294 b1288 b1287 b1286 b1285 b1284 b1283 b1278 b1282 b1281 b1280 b1277 b1279 b1276

B number ycjJ sapB sapC sapD sapF ycjD aldH ycjC ycjL b1297 ymjA sapA fabI yciW rnb yciR b1284 osmB pgpB yciH pyrF yciM ribA yciS acnA

Gene name + + + + + + + + + ------Strand orientation 479 321 296 330 268 117 495 185 258 498 547 262 401 644 661 249 254 109 245 389 196 102 891 81 72 Protein length 5468 2388 3833 2263 1712 1240 1319 1671 201 509 141 427 569 516 289 522 482 763 185 248 672 982 314 66 75 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 19 15 11 20 14 25 23 32 31 15 11 10 10 19 34 5 4 5 8 8 7 7 1 5 2 # of tryptic peptides predicted P P P P P P P Protein detected - total list 10 0 0 0 0 0 0 0 5 0 0 0 0 1 0 9 0 0 0 0 1 0 2 2 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 13 0 0 0 0 0 0 1 4 0 0 0 0 0 0 9 0 0 0 0 0 0 2 0 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 10 0 0 0 0 0 0 0 5 0 0 0 0 1 0 9 0 0 0 0 1 0 2 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

PHD Membrane protein assignment orf, hypotheticalprotein homolog ofSalmonellapeptidetransportpermeaseprotein putative ATP-bindingproteinofpeptidetransportsystem putative ATP-bindingproteinofpeptidetransportsystem orf, hypotheticalprotein enoyl-[acyl-carrier-protein] reductase(NADH) putative aminoacid/aminetransportprotein homolog ofSalmonellapeptidetransportpermeaseprotein aldehyde dehydrogenase, prefersNADP overNAD orf, hypothetical protein probable amidotransferase subunit putative glutaminesynthetase (EC6.3.1.2) homolog ofSalmonellapeptidetransportperiplasmic protein putative oxidoreductase RNase II,mRNAdegradation orf, hypotheticalprotein putative DEOR-typetranscriptionalregulator osmotically induciblelipoprotein orf, hypotheticalprotein GTP cyclohydrolaseII orotidine-5'-phosphate decarboxylase putative heatshockprotein orf, hypotheticalprotein aconitate hydrase1 bound non-essential phosphatidylglycerophosphatephosphatase,membrane

Gene description Open readingframes Cell processes Cell processes Cell processes Open readingframes Metabolism ofsmallmolecules Cell processes Cell processes Metabolism of smallmolecules Open reading frames Miscellaneous Miscellaneous Cell processes Miscellaneous Macromolecule metabolism Open readingframes Miscellaneous Cell processes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism

Functional category 778 777 777 777 776 775 779 777 782 781 781 780 777 774 773 772 771 770 769 766 769 768 768 765 767 Operon ID b1311 b1310 b1309 b1308 b1312 b1307 b1306 b1325 b1323 b1322 b1321 b1320 b1319 b1318 b1317 b1316 b1315 b1314 b1313 b1305 b1324 b1304 b1303 b1302 b1301

B number ycjO b1310 ycjM pspE ycjP pspD pspC ycjG tyrR ycjF ycjX ycjW ompG ycjV ycjU ycjT ycjS b1314 ycjQ pspB tpx pspA pspF goaG ordL

Gene name + + + + + + + + + + + + + + + + + + + + + + - - - Strand orientation 293 430 568 104 280 119 335 513 353 465 332 301 322 219 755 351 265 350 168 222 330 421 426 73 74 Protein length 1959 7051 1054 116 162 663 570 117 525 499 662 280 570 276 117 200 310 207 320 48 83 68 11 96 88 mRNA intensity A A A A A A A A A A A A A P P P P P P P P P P P P mRNA present 18 20 10 27 19 12 15 29 14 17 12 14 13 12 15 15 21 5 4 9 5 4 3 7 7 # of tryptic peptides predicted P P P P Protein detected - total list 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 9 1 0 0 3 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 3 0 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 9 0 0 0 3 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD MP-GenProt PHD MP Membrane protein assignment putative transportperiplasmicprotein putative polysaccharidehydrolase phage shockprotein phage shockprotein putative binding-proteindependenttransportprotein phage shockprotein:activatesshock-proteinexpression phage shockprotein putative transportsystempermeaseprotein putative muconate cycloisomeraseI(EC 5.5.-.-) thiol peroxidase orf, hypotheticalprotein putative EC2.1enzymes putative LACI-typetranscriptionalregulator outer membraneprotein putative ATP-bindingcomponentofatransportsystem putative beta-phosphoglucomutase orf, hypotheticalprotein putative dehydrogenase putative transientreceptorpotentiallocus putative oxidoreductase phage shockprotein,innermembraneprotein transport transcriptional regulationof aroF,aroG,tyrAandaromaticaminoacid psp operontranscriptionalactivator 4-aminobutyrate aminotransferase probable oxidoreductase

Gene description Cell processes Miscellaneous Extrachromosomal Extrachromosomal Cell processes Extrachromosomal Extrachromosomal Cell processes Open reading frames Cell processes Open readingframes Miscellaneous Miscellaneous Structural elements Cell processes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Extrachromosomal Cell processes Extrachromosomal Metabolism ofsmallmolecules Miscellaneous

Functional category 786 786 784 785 786 784 784 786 792 791 789 789 788 787 786 786 786 786 786 786 784 790 783 782 782 Operon ID b1350 b1349 b1348 b1347 b1346 b1345 b1344 b1343 b1342 b1341 b1340 b1339 b1338 b1337 b1336 b1335 b1334 b1333 b1332 b1331 b1330 b1329 b1328 b1327 b1326

B number recE recT lar ydaC ydaQ b1345 ydaO dbpA b1342 b1341 ydaL ydaK ydaJ b1337 ydaH ogt fnr ydaA ynaJ trs5_4 b1330 mppA ycjZ b1327 ycjI

Gene name + + + + + + + + ------Strand orientation 866 269 411 311 457 327 430 187 302 441 481 510 171 250 316 338 343 544 299 310 262 64 69 79 85 Protein length 114 153 133 309 258 156 253 107 557 457 201 257 551 14 58 48 25 26 59 18 93 76 38 85 mRNA intensity A A A A A A A A A A A A A A A A A A P P P P P P mRNA present 33 11 19 21 15 17 15 16 14 27 18 12 22 17 16 4 2 4 9 8 9 1 9 9 4 # of tryptic peptides predicted

P P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD

PHD PHD PHD PHD Membrane protein assignment exonuclease VIII, dsDNAexonuclease, 5'-->3'specific recombinase, DNArenaturation restriction alleviationandmodification enhancement orf, hypotheticalprotein orf, hypotheticalprotein balance transcriptional regulationofaerobic,anaerobicrespiration,osmotic orf, hypotheticalprotein orf, hypotheticalprotein multiple antibioticresistance periplasmic mureintripeptidetransportprotein,alsonegativeregulatorof orf, hypotheticalprotein orf, hypotheticalprotein putative transposase orf, hypotheticalprotein ATP-dependent RNAhelicase orf, hypotheticalprotein putative transcriptionalregulatorLYSR-type putative aminohydrolase(EC3.5.1.14) orf, hypotheticalprotein putative pumpprotein(transport) O-6-alkylguanine-DNA/cysteine-protein methyltransferase orf, hypotheticalprotein IS5 transposase putative transcriptionalregulatorLYSR-type orf, hypotheticalprotein putative carboxypeptidase

Gene description Macromolecule metabolism Macromolecule metabolism Extrachromosomal Open readingframes Open readingframes Global functions Open readingframes Open readingframes Cell processes Open readingframes Open readingframes Miscellaneous Open readingframes Macromolecule metabolism Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Cell processes Macromolecule metabolism Open readingframes Extrachromosomal Miscellaneous Open readingframes Miscellaneous

Functional category 810 810 810 806 805 801 799 797 796 810 809 809 808 807 804 803 802 802 802 802 800 798 795 794 793 Operon ID b1375 b1374 b1373 b1372 b1371 b1370 b1369 b1368 b1367 b1366 b1365 b1364 b1363 b1362 b1361 b1360 b1359 b1358 b1357 b1356 b1355 b1354 b1353 b1352 b1351

B number ynaE b1374 ynaC b1372 b1371 trs5_5 b1369 b1368 b1367 ydaY b1365 b1364 trkG b1362 ydaW b1360 ydaU ydaT ydaS ydaR b1355 b1354 sieB ydaD racC

Gene name + + + + + + + + + + + + + + + + + + ------Strand orientation 1122 196 191 153 326 342 119 485 101 203 248 285 140 158 203 88 51 77 87 93 98 59 58 77 91 Protein length 171 335 130 277 194 244 332 214 118 881 47 56 11 95 97 39 87 58 55 64 43 17 mRNA intensity A A A A A A A A A A A A A A A A P P P P P P mRNA present 11 49 13 19 11 13 12 10 7 2 3 3 3 5 6 2 5 9 5 6 2 2 3 4 8 # of tryptic peptides predicted

Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD PHD PHD MP Membrane protein assignment orf, hypothetical protein putative membraneprotein putative transposon resolvase orf, hypotheticalprotein orf, hypotheticalprotein IS5 transposase orf, hypotheticalprotein putative alphahelixprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein trk systempotassiumuptake;partofRacprophage phage superinfectionexclusionprotein putative Racprophageendopeptidase orf, hypotheticalprotein putative DNAreplicationfactor orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein defective prophagerac;containsrecEandoriJ

Gene description Open reading frames Miscellaneous Miscellaneous Open readingframes Open readingframes Extrachromosomal Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Extrachromosomal Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Extrachromosomal Open readingframes Open readingframes Open readingframes Extrachromosomal Extrachromosomal

Functional category 823 821 822 821 820 819 818 818 817 816 816 816 816 812 815 815 815 815 815 815 814 813 812 811 811 Operon ID b1400 b1399 b1398 b1397 b1396 b1395 b1394 b1393 b1392 b1391 b1390 b1389 b1388 b1387 b1386 b1385 b1384 b1383 b1382 b1381 b1380 b1379 b1378 b1377 b1376

B number b1400 b1399 b1398 b1397 b1396 ydbU b1394 ydbS b1392 b1391 ydbP ynbF ydbO maoC tynA feaB feaR ydbL ynbE ydbH ldhA hslJ nifJ b1377 ynaF

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 1174 196 316 437 401 140 475 262 255 356 167 248 309 681 757 500 301 110 879 329 140 377 168 95 61 Protein length 1170 5755 488 393 350 806 114 155 143 198 143 123 128 266 223 423 353 208 368 648 81 79 97 74 78 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 13 16 18 13 15 13 12 22 12 24 33 19 41 12 48 12 7 9 3 7 6 4 3 8 7 # of tryptic peptides predicted P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 3 0 2 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 4 0 2 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 3 0 2 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 detected (membrane sample) MP-GenProt

Membrane protein assignment putative transferase orf, hypothetical protein orf, hypotheticalprotein putative acyltransferase orf, hypotheticalprotein putative enzyme putative enzyme putative enzyme putative oxidoreductase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative aldehydedehydrogenase copper amineoxidase(tyramineoxidase) phenylacetaldehyde dehydrogenase regulatory proteinfor2-phenylethylaminecatabolism orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein fermentative D-lactatedehydrogenase,NAD-dependent heat shockproteinhslJ putative pyruvate-flavodoxinoxidoreductase,Fe-Ssubunit(2ndmodule) putative outermembraneprotein putative filamentprotein

Gene description Miscellaneous Metabolism of smallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Cell processes Open readingframes

Functional category 835 835 834 834 834 834 834 834 834 834 834 834 834 833 832 831 830 829 829 829 828 827 826 825 824 Operon ID b1421 b1425 b1424 b1423 b1422 b1420 b1419 b1418 b1417 b1416 b1415 b1414 b1413 b1412 b1411 b1410 b1409 b1408 b1407 b1406 b1405 b1404 b1403 b1402 b1401

B number trg b1425 ydcG b1423 b1422 b1420 ydcA cybB gapC_1 gapC_2 aldA ydcF hrpA acpD ynbD b1410 b1409 b1408 ydbD ydbC ydbA_2 tra8_2 yi21_2 yi22_2 ydbA_1

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 1281 1107 546 551 447 354 188 134 479 266 201 430 585 298 203 770 286 383 136 301 852 67 55 57 83 Protein length 2607 1734 8892 361 780 282 231 563 332 795 679 996 470 220 159 194 486 233 114 88 39 53 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P mRNA present 33 29 20 18 23 75 10 12 13 27 36 33 19 16 20 1 3 3 5 4 2 9 6 4 8 # of tryptic peptides predicted P P P P P Protein detected - total list 19 0 0 0 3 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 13 0 0 0 3 0 0 0 0 0 0 1 3 2 0 0 1 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 19 0 0 0 3 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD PHD PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein methyl-accepting chemotaxisproteinIII,ribosesensor receptor orf, hypothetical protein putative glycoprotein orf, hypotheticalprotein putative transcriptionalregulator LYSR-type orf, hypotheticalprotein cytochrome b(561) glyceraldehyde 3-phosphatedehydrogenaseC,interrupted glyceraldehyde-3-phosphate dehydrogenase(secondfragment) aldehyde dehydrogenase,NAD-linked orf, hypotheticalprotein helicase, ATP-dependent putative phosphatidatecytidiltransferase probable enzyme acyl carrierproteinphosphodiesterase putative enzymes orf, hypotheticalprotein orf, hypotheticalprotein putative dehydrogenase split orf IS30 transposase IS2 hypotheticalprotein IS2 hypotheticalprotein split orf

Gene description Open readingframes Cell processes Open reading frames Miscellaneous Open readingframes Miscellaneous Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Extrachromosomal Extrachromosomal Extrachromosomal Open readingframes

Functional category 850 851 855 854 853 852 849 848 847 847 846 845 844 842 842 843 842 842 841 840 839 838 837 837 836 Operon ID b1450 b1449 b1448 b1447 b1446 b1439 b1438 b1437 b1427 b1445 b1444 b1443 b1442 b1441 b1440 b1436 b1435 b1434 b1433 b1432 b1431 b1430 b1429 b1428 b1426

B number b1450 yncB b1448 b1447 b1446 b1439 b1438 b1437 rimL b1445 b1444 b1443 b1442 b1441 b1440 b1436 ydcP ydcN b1433 b1432 b1431 tehB tehA b1428 ydcH

Gene name + + + + + + + + + + + + + + + + + + + ------Strand orientation 240 376 172 149 468 145 179 474 264 313 337 381 667 178 478 402 222 197 330 326 77 65 82 76 55 Protein length 1394 1047 1015 220 884 102 285 539 221 349 456 746 383 676 598 366 205 106 326 692 648 297 313 76 84 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P P mRNA present 17 12 18 20 17 22 32 19 12 12 4 3 3 4 3 8 3 2 6 6 7 6 5 8 9 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 2 1 0 0 1 0 0 1 1 0 0 0 0 3 0 0 5 0 0 0 1 4 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 4 1 0 0 0 0 0 1 1 0 0 0 0 4 0 0 6 0 0 0 0 3 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 2 1 0 0 1 0 0 1 1 0 0 0 0 3 0 0 5 0 0 0 0 4 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment orf, hypothetical protein putative oxidoreductase putative resistanceprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transportsystempermeaseprotein component ofatransportsystem multi modular;putativetranscriptionalregulator;alsoATP-binding acetyl transferase acetylation ofN-terminalserine30SribosomalsubunitproteinL7; putative aldehydedehydrogenase putative transportsystempermeaseprotein putative ATP-bindingcomponentofatransportsystem putative transportprotein putative collagenase orf, hypotheticalprotein putative membranetransportprotein putative virulenceprotein orf, hypotheticalprotein tellurite resistance tellurite resistance orf, hypotheticalprotein

Gene description Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Miscellaneous Structural elements Miscellaneous Cell processes Cell processes Cell processes Open readingframes Open readingframes Miscellaneous Miscellaneous Open readingframes Cell processes Cell processes Open readingframes

Functional category 873 872 871 871 870 869 866 865 864 856 868 867 857 868 868 868 868 863 863 862 861 860 859 859 858 Operon ID b1475 b1465 b1464 b1463 b1462 b1474 b1473 b1472 b1471 b1470 b1469 b1468 b1467 b1466 b1461 b1460 b1459 b1458 b1457 b1456 b1455 b1454 b1453 b1451 b1452

B number fdnH narV yddE b1463 b1462 fdnG yddG b1472 b1471 b1470 narU narZ narY narW ydcE ydcC b1459 b1458 ydcD rhsE b1455 b1454 ansP b1451 b1452

Gene name + + + + + + + + + + + + ------Strand orientation 1015 1246 294 226 297 281 205 293 318 111 462 514 231 378 248 160 682 205 516 700 353 96 77 66 70 Protein length 1586 2465 395 127 203 199 421 269 263 287 332 273 299 115 11 13 70 43 74 93 12 61 14 5 mRNA intensity A A A A A A A A A A A A A A A P P P P P P P P P mRNA present 11 15 11 15 55 63 11 10 31 14 20 12 36 12 15 31 7 4 1 3 6 4 6 4 3 # of tryptic peptides predicted

P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 # of tryptic peptides detected (short list)

P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt MP-GenProt GenProt GenProt PHD PHD Membrane protein assignment formate dehydrogenase-N, nitrate-inducible, alphasubunit orf, hypotheticalprotein putative N-hydroxyarylamineO-acetyltransferase orf, hypotheticalprotein orf, hypotheticalprotein formate dehydrogenase-N, nitrate-inducible, iron-sulfurbetasubunit orf, hypotheticalprotein cryptic nitratereductase2,alphasubunit cryptic nitratereductase2,gammasubunit orf, hypotheticalprotein putative outermembraneporin protein putative glycoportein orf, hypotheticalprotein nitrite extrusionprotein2 cryptic nitratereductase2,betasubunit cryptic nitratereductase2,deltasubunit,assemblyfunction putative receptor orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein rhsE proteininrhselement putative transferase L-asparagine permease putative receptor putative outermembranereceptorforirontransport

Gene description Metabolism of smallmolecules Open readingframes Miscellaneous Open readingframes Open readingframes Metabolism of smallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Miscellaneous Open readingframes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Open readingframes Extrachromosomal Miscellaneous Cell processes Miscellaneous Miscellaneous

Functional category 890 885 884 883 882 890 889 886 886 878 888 888 888 887 886 886 881 880 880 879 879 877 876 875 874 Operon ID b1500 b1499 b1498 b1497 b1496 b1495 b1494 b1485 b1484 b1483 b1493 b1492 b1491 b1490 b1489 b1488 b1487 b1486 b1482 b1481 b1480 b1479 b1478 b1477 b1476

B number b1500 b1499 b1498 b1497 yddA yddB pqqL ddpC ddpD ddpE gadB xasA b1491 b1490 b1489 ddpX ddpA ddpB osmC b1481 rpsV sfcA adhP yddM fdnI

Gene name + + ------Strand orientation 253 571 390 561 790 931 298 328 308 466 511 439 460 807 193 516 340 143 574 346 120 217 65 92 45 Protein length 32277 3972 1659 5905 1196 1814 2389 654 120 216 212 248 258 346 731 296 198 421 155 16 33 45 98 67 86 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 13 22 19 26 48 12 36 20 11 13 25 28 32 22 26 14 1 4 6 7 7 3 2 6 3 # of tryptic peptides predicted P P P P P P Protein detected - total list 0 0 0 0 0 0 0 0 6 1 0 0 6 0 0 0 0 0 2 0 1 9 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 0 0 0 0 0 0 0 7 0 0 0 6 0 0 0 0 0 3 0 1 9 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 0 0 0 0 0 0 0 6 0 0 0 6 0 0 0 0 0 2 0 1 9 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

PHD Membrane protein assignment orf, hypothetical protein putative ARAC-type regulatoryprotein putative putative enzyme putative ATP-bindingcomponentofatransportsystem orf, hypotheticalprotein putative peptidase glutamate decarboxylaseisozyme ATP-binding componentofdipeptidetransportsystem ATP-binding componentofdipeptidetransportsystem osmotically inducibleprotein acid sensitivityprotein,putativetransporter dipeptide transport,permeaseprotein orf, hypotheticalprotein orf, hypotheticalprotein putative enzyme D-ala-D-ala dipeptidase dipeptide transport,periplasmicbindingprotein dipeptide transport,permeaseprotein orf, hypotheticalprotein 30S ribosomalsubunitproteinS22 NAD-linked malatedehydrogenase(malicenzyme) alcohol dehydrogenase gamma subunit formate dehydrogenase-N,nitrate-inducible,cytochromeB556(Fdn) orf, hypotheticalprotein

Gene description Open reading frames Miscellaneous Open readingframes Open readingframes Cell processes Open readingframes Miscellaneous Metabolism ofsmallmolecules Cell processes Miscellaneous Cell processes Cell processes Cell processes Open readingframes Open readingframes Miscellaneous Open readingframes Cell processes Cell processes Open readingframes Structural elements Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes

Functional category 905 904 903 903 902 902 902 901 897 897 896 900 897 899 898 898 897 897 897 895 894 893 892 890 891 Operon ID b1525 b1524 b1523 b1522 b1521 b1520 b1514 b1513 b1512 b1511 b1509 b1519 b1515 b1510 b1508 b1507 b1506 b1505 b1504 b1503 b1502 b1501 b1518 b1517 b1516

B number b1525 yneH b1523 b1522 uxaB b1520 ydeY b1513 ydeW ydeV b1509 tam ydeZ ydeK hipB hipA b1506 b1505 b1504 b1503 b1502 b1501 b1518 yneB b1516

Gene name + + + + + + + ------Strand orientation 1325 470 308 119 315 483 321 342 511 317 530 466 252 330 440 382 176 167 304 759 291 340 88 59 96 Protein length 1103 773 482 210 139 104 295 106 495 195 412 413 688 219 111 373 117 341 481 89 24 73 95 24 72 mRNA intensity A A A A A A A A A A A A A P P P P P P P P P P P P mRNA present 19 17 10 15 23 39 15 21 14 25 25 13 13 32 11 18 7 5 8 7 7 1 8 4 8 # of tryptic peptides predicted P P P Protein detected - total list 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 3 0 # of tryptic peptides detected (total list)

Protein detected - short list 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 3 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD MP-GenProt PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein putative aldehyde dehydrogenase putative glutaminase orf, hypotheticalprotein altronate oxidoreductase orf, hypotheticalprotein trans-aconitate methyltransferase putative ATP-bindingcomponentofatransportsystem putative transcriptionalregulator,sorCfamily putative kinase orf, hypotheticalprotein persistence toinhibitionofmureinorDNAbiosynthesis;regulatoryprotein putative transportsystempermeaseprotein protein putative ATP-bindingcomponentofatransportsystemandadhesin regulator persistence toinhibitionofmureinorDNAbiosynthesis,DNA-binding putative adhesin;similartoFimHprotein orf, hypotheticalprotein orf, hypotheticalprotein putative outermembraneprotein putative fimbrial-likeprotein putative fimbrial-likeprotein putative oxidoreductase,majorsubunit putative transportsystempermeaseprotein orf, hypotheticalprotein putative LACI-typetranscriptionalregulator

Gene description Miscellaneous Miscellaneous Open reading frames Open readingframes Metabolism ofsmallmolecules Open readingframes Miscellaneous Miscellaneous Open readingframes Miscellaneous Open readingframes Structural elements Cell processes Open readingframes Structural elements Miscellaneous Open readingframes Open readingframes Miscellaneous Miscellaneous Miscellaneous Miscellaneous Miscellaneous Open readingframes Cell processes

Functional category 918 920 919 919 917 916 915 914 913 912 911 910 914 911 910 907 914 909 908 908 908 906 914 914 914 Operon ID b1550 b1549 b1548 b1547 b1546 b1545 b1544 b1543 b1542 b1541 b1540 b1539 b1538 b1537 b1536 b1535 b1534 b1533 b1532 b1531 b1530 b1529 b1528 b1527 b1526

B number b1550 ydfO nohA b1547 ydfM b1545 ydfK b1543 ydfI b1541 ydfH ydfG dcp ydeJ ydeI ydeH ydeF ydeD marB marA marR ydeB ydeA b1527 yneJ

Gene name + + + + + + + + + + + + + + ------Strand orientation 141 189 320 191 196 427 486 228 248 681 172 130 296 395 266 129 125 221 396 371 293 58 88 67 72 Protein length 3383 1113 1163 215 104 251 359 456 262 345 176 438 810 171 553 307 260 39 21 84 35 mRNA intensity A A A A A A P P P P P P P P P P P P P P P mRNA present 10 11 11 23 10 10 25 17 18 14 4 9 2 6 6 5 9 6 6 3 1 8 5 5 8 # of tryptic peptides predicted P P P Protein detected - total list 1 0 0 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 2 0 0 0 0 0 0 0 0 0 0 2 6 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 1 0 0 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment orf, hypothetical protein orf, hypothetical protein homolog ofQinprophagepackaging proteinNU1 orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transportprotein putative oxidoreductase orf, hypotheticalprotein orf, hypotheticalprotein putative oxidoreductase dipeptidyl carboxypeptidaseII orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transportprotein multiple antibioticresistanceprotein multiple antibioticresistance;transcriptionalactivatorofdefensesystems orf, hypotheticalprotein multiple antibioticresistanceprotein;repressorofmaroperon L-arabinose andisopropyl-b-D-thiogalactopyranosideexporterprotein orf, hypotheticalprotein putative transcriptionalregulatorLYSR-type

Gene description Open reading frames Open reading frames Extrachromosomal Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Miscellaneous Open readingframes Miscellaneous Miscellaneous Macromolecule metabolism Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Cell processes Cell processes Open readingframes Cell processes Cell processes Open readingframes Miscellaneous

Functional category 941 940 939 939 939 938 937 936 935 934 933 932 931 926 930 929 928 927 925 925 924 925 923 922 921 Operon ID b1575 b1574 b1573 b1572 b1571 b1570 b1569 b1568 b1567 b1566 b1565 b1564 b1563 b1562 b1561 b1560 b1559 b1558 b1557 b1556 b1555 b1554 b1553 b1552 b1551

B number dicB dicF ydfC ydfB ydfA dicA dicC b1568 b1567 flxA b1565 relB relE relF rem b1560 b1559 cspF cspB b1556 b1555 b1554 b1553 cspI b1551

Gene name + + + + + + + + ------Strand orientation 135 110 101 362 260 103 177 165 62 72 56 51 76 96 49 79 95 51 83 70 71 96 70 63 Protein length 1308 1625 248 158 116 194 114 100 161 769 206 144 131 19 87 43 93 56 36 30 67 62 41 40 12 mRNA intensity A A A A A A A A A A A A A A A A A A A A P P P P P mRNA present 21 12 11 1 3 3 0 6 7 4 2 7 7 3 6 2 6 4 5 2 7 6 5 5 # of tryptic peptides predicted

Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample)

Membrane protein assignment Qin prophage; DicFantisenseRNAinhibits ftsZtranslation inhibition ofcell division orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein regulator ofdicB regulator ofdicB orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein negative regulatoroftranslation orf, hypotheticalprotein polypeptide destructivetomembranepotential orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein cold shockprotein cold shockprotein;mayaffecttranscription orf, hypotheticalprotein orf, hypotheticalprotein putative orf, hypotheticalprotein cold shock-likeprotein orf, hypotheticalprotein

Gene description Extrachromosomal Cell processes Open readingframes Open readingframes Open readingframes Cell processes Cell processes Open readingframes Open readingframes Open readingframes Open readingframes Global functions Open readingframes Cell processes Open readingframes Open readingframes Open readingframes Miscellaneous Cell processes Open readingframes Open readingframes Miscellaneous Open readingframes Miscellaneous Open readingframes

Functional category 956 955 955 955 954 953 953 953 952 951 950 950 949 948 947 947 946 945 944 944 944 944 943 942 Operon ID b1600 b1599 b1598 b1597 b1596 b1595 b1594 b1593 b1592 b1591 b1590 b1589 b1588 b1587 b1586 b1585 b1584 b1583 b1582 b1581 b1580 b1579 b1578 b1577 b1576

B number b1600 b1599 b1598 asr ynfM ynfL mlc b1593 b1592 b1591 b1590 b1589 b1588 b1587 b1586 ynfC speG b1583 b1582 rspA rspB b1579 b1578 ydfE ydfD

Gene name + + + + + + + + + + + + + + + + ------Strand orientation 121 109 273 111 417 297 406 235 438 207 284 205 808 808 115 248 186 113 108 404 339 398 218 306 63 Protein length 11538 1348 1225 3633 307 140 512 227 432 288 155 179 402 302 125 146 334 632 240 81 81 80 83 19 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P mRNA present 15 19 40 10 38 10 12 12 16 10 16 21 3 7 2 2 8 9 5 9 7 3 6 3 4 # of tryptic peptides predicted P P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 3 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 2 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 3 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD PHD PHD PHD PHD Membrane protein assignment possible chaperone possible chaperone orf, hypotheticalprotein acid shockprotein putative DMSOreductaseanchorsubunit putative transportprotein putative transcriptionalregulatorLYSR-type putative NAGC-liketranscriptionalregulator orf, hypotheticalprotein putative chloridechannel putative oxidoreductasecomponent putative oxidoreductase,Fe-Ssubunit putative oxidoreductase,majorsubunit putative oxidoreductase,majorsubunit orf, hypotheticalprotein orf, hypotheticalprotein spermidine N1-acetyltransferase orf, hypotheticalprotein orf, hypotheticalprotein starvation sensingprotein starvation sensingprotein putative transposase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Cell processes Open reading frames Open readingframes Miscellaneous Metabolism ofsmallmolecules Cell processes Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Miscellaneous Miscellaneous Miscellaneous Miscellaneous Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Global functions Global functions Miscellaneous Open readingframes Open readingframes Open readingframes

Functional category 972 972 971 970 964 969 968 967 966 965 964 964 964 963 962 961 960 959 960 958 958 957 957 957 956 Operon ID b1619 b1618 b1617 b1616 b1615 b1614 b1613 b1612 b1611 b1610 b1609 b1605 b1625 b1624 b1623 b1622 b1621 b1620 b1608 b1607 b1606 b1604 b1603 b1602 b1601

B number hdhA uidR uidA uidB uidC ydgA manA fumA fumC tus rstB b1605 b1625 b1624 add malY malX malI rstA ydgC ydgB b1604 pntA pntB b1601

Gene name + + + + + + + + + + + + + ------Strand orientation 255 196 603 457 417 502 391 548 467 309 433 460 359 333 390 530 342 242 111 240 314 510 462 344 71 Protein length 18004 2814 3778 1536 4018 1968 1185 3267 474 205 619 684 340 834 313 906 867 231 323 199 581 418 57 66 44 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 12 11 22 21 26 18 31 15 17 18 13 19 13 16 11 16 13 17 21 8 5 8 3 9 7 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 12 10 1 0 0 0 0 4 6 0 3 0 1 2 0 6 0 0 0 0 0 0 0 5 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 13 2 0 0 0 0 4 7 0 3 0 0 1 0 9 0 1 0 0 0 0 0 0 5 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 12 10 1 0 0 0 0 3 6 0 3 0 0 2 0 0 0 0 0 0 0 0 0 5 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 4 1 0 0 0 0 1 0 0 0 6 0 0 0 0 0 0 0 5 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt

PHD PHD PHD Membrane protein assignment repressor foruidoperon beta-D-glucuronidase glucuronide permease membrane-associated protein orf, hypotheticalprotein -6-phosphate isomerase A=fumaratehydrataseClassI;aerobicisozyme orf, hypothetical protein fumarase C=fumaratehydrataseClassII;isozyme DNA-binding protein;inhibitionofreplicationatTersites sensor histidineproteinkinase(RstAregulator) response transcriptionalregulatoryprotein(RstBsensor) orf, hypotheticalprotein inducer, probablyaminotrasferase enzyme thatmaydegrade or blockbiosynthesisofendogenousmal PTS system,maltoseandglucose-specificIIABC of bileacids NAD-dependent 7alpha-hydroxysteroiddehydrogenase, dehydroxylation orf, hypotheticalprotein putative arginine/ornithineantiporter pyridine nucleotidetranshydrogenase,betasubunit putative transportprotein orf, hypothetical protein repressor ofmalXandYgenes putative oxidoreductase pyridine nucleotidetranshydrogenase,alphasubunit

Gene description Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Structural elements Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open reading frames Metabolism ofsmallmolecules Macromolecule metabolism Global functions Miscellaneous Open readingframes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Open readingframes Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open reading frames Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules

Functional category 986 985 985 984 983 982 981 992 980 979 978 978 975 989 989 987 977 976 974 973 991 990 988 976 974 Operon ID b1640 b1639 b1644 b1641 b1638 b1645 b1643 b1642 b1637 b1636 b1648 b1647 b1646 b1635 b1634 b1633 b1632 b1631 b1630 b1629 b1628 b1627 b1626 b1649 b1650

B number b1640 ydhA b1644 slyB pdxH b1645 b1643 slyA tyrS pdxY b1648 b1647 sodC gst ydgR nth ydgQ b1631 ydgO b1629 b1628 b1627 b1626 b1649 nemA

Gene name + + + + + + + + + + + + + + + + ------Strand orientation 369 299 155 218 670 146 424 287 125 298 173 201 500 211 231 206 352 740 192 193 154 199 365 82 78 Protein length 15928 1682 3141 2372 1511 1595 2223 174 442 146 114 549 199 211 145 978 467 539 806 836 378 325 253 429 97 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P P P P mRNA present 13 12 13 17 12 13 10 26 11 12 33 11 18 6 2 4 7 6 9 4 8 6 4 3 8 # of tryptic peptides predicted P P P P P P P Protein detected - total list 0 0 1 0 0 2 1 7 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 3 0 0 0 1 8 0 4 1 0 3 0 0 0 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 0 0 1 0 0 0 1 7 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD MP-GenProt MP-GenProt MP-GenProt PHD PHD PHD PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein pyridoxinephosphate oxidase orf, hypotheticalprotein putative membraneprotein transcriptional regulatorforcryptichemolysin putative outermembraneprotein tRNAsynthetase orf, hypotheticalprotein superoxide dismutaseprecursor(Cu-Zn) orf, hypotheticalprotein pyridoxal kinase2/pyridoxine glutathionine S-transferase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transportprotein endonuclease III;specificforapurinicand/orapyrimidinicsites orf, hypotheticalprotein putative membraneprotein orf, hypotheticalprotein orf, hypothetical protein N-ethylmaleimide reductase

Gene description Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Miscellaneous Cell processes Open readingframes Macromolecule metabolism Open readingframes Cell processes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Macromolecule metabolism Open readingframes Miscellaneous Metabolism ofsmallmolecules Miscellaneous Metabolism of smallmolecules

Functional category 1000 1001 1004 1004 1003 1002 1006 1005 1004 1006 1007 1007 999 998 997 996 994 994 994 993 995 994 994 994 994 Operon ID b1652 b1651 b1653 b1655 b1654 b1656 b1657 b1659 b1658 b1660 b1662 b1661 b1663 b1664 b1668 b1667 b1666 b1665 b1669 b1670 b1671 b1672 b1673 b1674 b1675

B number rnt gloA lhr ydhO ydhD sodB b1657 ydhB purR ydhC ribE cfa ydhE b1664 b1668 b1667 valW valV b1669 ydhU b1671 b1672 b1673 b1674 b1675

Gene name + + + + + + + + + + + + + ------Strand orientation 1538 215 135 271 115 193 389 310 341 403 213 382 457 418 534 101 270 261 239 215 700 208 69 Protein length 12459 2992 6502 1323 2979 4312 849 452 189 416 163 628 390 201 448 925 429 152 164 145 385 142 42 82 47 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 71 10 18 13 21 11 14 20 13 15 10 34 7 9 5 8 6 3 8 5 4 3 9 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 0 0 0 3 0 2 2 0 0 0 4 3 1 4 1 1 0 0 0 0 0 1 0 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 0 3 0 3 3 0 0 0 4 3 0 4 1 1 0 0 0 0 0 1 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 0 0 0 3 0 2 2 0 0 0 4 3 0 4 1 1 0 0 0 0 0 1 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

Membrane protein assignment lactoylglutathione lyase RNase T,degradestRNA orf, hypotheticalprotein member ofATP-dependenthelicasesuperfamilyII putative lipoprotein superoxide dismutase,iron transcriptional repressorforpurregulon,glyA,glnB,prsA,speA putative transportprotein putative transcriptionalregulatorLYSR-type cyclopropane fattyacylphospholipidsynthase putative transportprotein riboflavin synthase,alphachain putative transportprotein orf, hypotheticalprotein tRNA-Val tRNA-Val possible enzyme orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative oxidoreductase,Fe-Ssubunit orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein putative oxidoreductase, Fe-Ssubunit

Gene description Metabolism ofsmallmolecules Macromolecule metabolism Open readingframes Macromolecule metabolism Open readingframes Cell processes Metabolism ofsmallmolecules Cell processes Miscellaneous Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Cell processes Open readingframes tRNA tRNA Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Open reading frames Miscellaneous

Functional category 1008 1009 1010 1009 1011 1012 1014 1013 1015 1017 1016 1018 1019 1021 1020 1022 1023 1023 1023 1023 1023 1024 1023 Operon ID b1679 b1678 b1677 b1676 b1686 b1685 b1684 b1683 b1682 b1681 b1680 b1689 b1688 b1687 b1690 b1691 b1692 b1693 b1694 b1695 b1696 b1697 b1698 b1699 b1700

B number ynhA ynhG lpp pykF b1686 b1685 ydiC ynhE ynhD sufD sufS b1689 b1688 ydiJ b1690 b1691 ydiB aroD ydiF b1695 b1696 ydiQ ydiR ydiS ydiT

Gene name + + + + + + + + + + + + + + ------Strand orientation 1018 138 334 470 136 122 508 248 423 406 127 370 404 423 288 252 531 401 303 254 312 429 78 89 97 Protein length 55069 1063 3969 1375 3318 2057 1745 1913 1044 1795 625 975 438 142 909 117 165 108 197 305 135 220 70 70 37 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 27 26 14 18 14 47 12 15 21 14 15 12 20 3 6 6 6 6 5 8 6 7 6 7 5 # of tryptic peptides predicted P P P P P P Protein detected - total list 13 3 1 0 0 0 2 0 0 0 0 5 0 0 0 0 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 14 1 2 0 0 0 2 1 0 1 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 13 1 1 0 0 0 2 0 0 0 0 2 0 0 0 0 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt PHD Membrane protein assignment orf, hypotheticalprotein murein lipoprotein pyruvate kinaseI(formerlyF),fructosestimulated orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative ATP-bindingcomponentofatransportsystem Required forstabilityofthe[2Fe-2S]FhuFprotein. Selenocysteine lyase.InvolvedinformationofFhuF[2Fe-2S]cluster. orf, hypotheticalprotein putative oxidase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transportsystempermeaseprotein putative aminoacid/aminetransportprotein putative oxidoreductase 3-dehydroquinate dehydratase putative enzyme putative oxidoreductase putative ARAC-typeregulatoryprotein putative transportprotein putative flavoprotein orf, hypothetical protein flavoprotein; probably electrontransport

Gene description Open readingframes Structural elements Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous Cell processes Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open readingframes Miscellaneous Miscellaneous Open readingframes Open reading frames Miscellaneous

Functional category 1027 1026 1025 1029 1028 1028 1028 1028 1028 1028 1029 1029 1030 1031 1032 1033 1033 1033 1034 1034 1035 1036 1036 1037 1037 Operon ID b1707 b1706 b1705 b1701 b1708 b1704 b1703 b1702 b1711 b1710 b1709 b1713 b1712 b1715 b1714 b1718 b1717 b1716 b1720 b1719 b1721 b1722 b1725 b1724 b1723

B number b1707 b1706 ydiE ydiD nlpC aroH ydiA ppsA btuC btuE btuD pheT himA pheM pheS infC rpmI rplT b1720 thrS b1721 b1722 b1725 b1724 pfkB

Gene name + + + + + + + + + ------Strand orientation 237 478 566 154 348 277 792 326 183 249 795 327 180 118 157 642 471 252 286 309 63 99 14 65 96 Protein length 10398 19377 34009 1407 1279 2862 2419 1013 4469 4088 4824 8201 3765 4224 130 153 179 820 635 334 115 956 75 19 48 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P P P P mRNA present 21 11 26 12 36 15 10 35 18 35 18 16 11 4 9 9 6 6 1 2 5 8 5 4 8 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 14 12 0 0 0 0 0 0 2 6 0 2 0 8 0 0 3 3 7 0 0 0 3 0 1 # of tryptic peptides detected (total list) P P P P P P P Protein detected - short list 16 17 0 0 0 0 0 0 2 5 0 2 0 8 0 0 3 5 7 0 0 0 4 0 1 # of tryptic peptides detected (short list) P P P P P P P P P P P Protein detected - long list 14 12 0 0 0 0 0 0 2 6 0 2 0 8 0 0 3 3 7 0 0 0 3 0 1 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein synthetase, tryptophanrepressible) 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase(DAHP orf, hypotheticalprotein orf, hypotheticalprotein phosphoenolpyruvate synthase putative ligase/synthetase vitamin B12transport ATP-binding componentofvitaminB12transportsystem lipoprotein integration hostfactor(IHF),alphasubunit;sitespecificrecombination vitamin B12transportpermeaseprotein phenylalanine tRNAsynthetase,alpha-subunit phenylalanine tRNAsynthetase,beta-subunit 50S ribosomalsubunitproteinA 50S ribosomalsubunitproteinL20,andregulator phenylalanyl-tRNA synthetase(pheST)operonleaderpeptide threonine tRNAsynthetase protein chaininitiationfactorIF-3 orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein 6- II;suppressor ofpfkA orf, hypotheticalprotein orf, hypothetical protein

Gene description Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Miscellaneous Cell processes Cell processes Macromolecule metabolism Macromolecule metabolism Cell processes Macromolecule metabolism Macromolecule metabolism Structural elements Structural elements Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Open readingframes Miscellaneous Open reading frames Metabolism ofsmallmolecules Open readingframes Open reading frames

Functional category 1042 1041 1040 1043 1039 1038 1037 1045 1045 1044 1046 1045 1047 1047 1048 1048 1047 1048 1048 1049 1049 1052 1051 1050 1053 Operon ID b1741 b1740 b1739 b1738 b1737 b1728 b1727 b1726 b1742 b1730 b1729 b1743 b1733 b1732 b1731 b1744 b1734 b1745 b1735 b1746 b1736 b1747 b1748 b1750 b1749

B number b1741 nadE osmE celA celB b1728 yniC b1726 b1742 b1730 b1729 spy ydjC katE b1731 astE celF astB celD astD celC astA astC ydjX xthA

Gene name + + + + + + + + ------Strand orientation 295 275 112 106 452 200 222 178 212 271 463 161 249 753 322 450 447 280 492 116 344 406 252 268 87 Protein length 2929 2821 1079 2700 2791 1584 215 820 121 133 525 104 140 666 215 307 240 238 249 388 427 137 31 65 97 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 15 13 13 12 11 12 30 11 16 20 15 19 12 13 22 16 4 5 3 6 6 6 8 7 6 # of tryptic peptides predicted P P P P P P Protein detected - total list 8 2 1 0 0 0 0 3 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 2 0 # of tryptic peptides detected (total list) P P Protein detected - short list 11 1 1 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 2 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 8 1 1 0 0 0 0 1 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 2 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 2 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD PHD PHD PHD PHD Membrane protein assignment NAD synthetase,prefersNH3overglutamine activator ofntrLgene putative phosphatase and salicin PEP-dependent phosphotransferaseenzymeIVforcellobiose,arbutin, and salicin PEP-dependent phosphotransferaseenzymeIIforcellobiose,arbutin, and salicin PEP-dependent phosphotransferaseenzymeIIIforcellobiose,arbutin, orf, hypotheticalprotein putative excinucleasesubunit part ofakinase orf, hypotheticalprotein orf, hypotheticalprotein catalase; hydroperoxidaseHPII(III) orf, hypotheticalprotein orf, hypotheticalprotein periplasmic proteinrelatedtospheroblastformation orf, hypotheticalprotein succinylglutamate desuccinylase phospho-beta-glucosidase; cryptic succinylarginine dihydrolase negative transcriptionalregulatorofceloperon succinylglutamic semialdehydedehydrogenase arginine succinyltransferase exonuclease III succinylornithine aminotransferase orf, hypothetical protein

Gene description Metabolism ofsmallmolecules Global functions Open readingframes Cell processes Cell processes Cell processes Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes Cell processes Cell processes Open readingframes Miscellaneous Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Open reading frames

Functional category 1064 1063 1055 1062 1062 1062 1054 1065 1057 1056 1066 1060 1059 1058 1067 1061 1068 1062 1068 1062 1068 1068 1069 1068 1070 Operon ID b1751 b1752 b1753 b1754 b1755 b1756 b1757 b1759 b1758 b1763 b1762 b1761 b1760 b1766 b1765 b1764 b1768 b1767 b1769 b1770 b1771 b1772 b1773 b1774 b1775

B number ydjY ydjZ ynjA b1754 b1755 b1756 b1757 b1759 b1758 topB b1762 gdhA b1760 sppA ydjA selD ydjB ansA ydjE b1770 b1771 b1772 b1773 ydjJ b1775

Gene name + + + + + + + + + + + + ------Strand orientation 279 235 182 389 496 217 440 135 208 653 387 447 618 183 347 219 338 452 252 326 322 278 347 459 90 Protein length 2794 2812 2441 1743 101 151 309 376 118 161 612 106 310 197 448 667 998 133 143 150 214 178 103 44 58 mRNA intensity A A A A A A A A A A A A A P P P P P P P P P P P P mRNA present 17 11 19 20 23 19 15 35 26 14 16 18 14 18 10 7 6 7 4 4 2 9 9 8 9 # of tryptic peptides predicted P P P P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 8 0 0 1 4 0 1 2 1 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 0 0 0 0 0 7 1 0 2 3 0 0 2 1 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 0 0 0 0 0 0 0 0 8 0 0 1 4 0 0 2 1 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transportsystempermeaseprotein putative ATP-bindingcomponentofatransportsystem putative thiosulfatesulfurtransferase putative cytochromeoxidase NADP-specific glutamatedehydrogenase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein selenophosphate synthase,H(2)Seaddedtoacrylyl-tRNA DNA topoisomeraseIII cytoplasmic L-asparaginaseI protease IV,asignalpeptidepeptidase orf, hypotheticalprotein putative transportprotein putative DEOR-typetranscriptionalregulator orf, hypotheticalprotein putative kinase putative aldolase putative oxidoreductase putative transport protein

Gene description Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Cell processes Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Open readingframes Macromolecule metabolism Macromolecule metabolism Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Cell processes Miscellaneous Open readingframes Miscellaneous Miscellaneous Miscellaneous Miscellaneous

Functional category 1070 1070 1070 1070 1070 1070 1071 1072 1075 1074 1073 1076 1078 1077 1076 1080 1079 1081 1082 1083 1084 1084 1084 1084 1084 Operon ID b1776 b1778 b1777 b1779 b1781 b1780 b1784 b1783 b1782 b1788 b1787 b1786 b1785 b1789 b1790 b1791 b1792 b1794 b1793 b1796 b1795 b1797 b1798 b1799 b1800

B number b1776 yeaA b1777 gapA b1781 yeaD yeaH yeaG mipA b1788 yeaK yeaJ yeaI yeaL yeaM yeaN yeaO yeaP yoaF yoaG yeaQ yeaR yeaS yeaT yeaU

Gene name + + + + + + + + + + + + ------Strand orientation 358 137 105 331 284 301 427 644 248 167 556 491 148 273 393 122 384 119 212 314 361 50 84 60 82 Protein length 11724 41263 5143 1358 3833 9156 1106 1997 125 273 362 259 166 205 218 820 906 297 328 107 467 106 10 47 88 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P P mRNA present 19 20 11 36 10 18 28 18 18 19 19 7 8 6 8 1 4 9 6 2 8 2 2 5 8 # of tryptic peptides predicted P P P P P P Protein detected - total list 13 0 0 2 5 0 9 3 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 10 0 0 3 4 0 9 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 13 0 0 2 5 0 9 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 2 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt PHD PHD PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein putative oxidoreductase orf, hypotheticalprotein orf, hypotheticalprotein glyceraldehyde-3-phosphate dehydrogenaseA orf, hypotheticalprotein putative analdehydereductase Scaffolding proteinformurein-synthesisingholoenzyme. orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative ARAC-typeregulatoryprotein putative aminoacid/aminetransportprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transcriptional regulatorLYSR-type putative tartrate dehydrogenase

Gene description Open readingframes Miscellaneous Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Structural elements Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous

Functional category 1085 1084 1085 1087 1086 1090 1088 1089 1092 1091 1092 1092 1093 1094 1095 1096 1097 1096 1099 1098 1100 1100 1101 1102 1103 Operon ID b1801 b1802 b1803 b1804 b1805 b1806 b1808 b1807 b1812 b1811 b1810 b1809 b1813 b1814 b1815 b1816 b1819 b1818 b1817 b1821 b1820 b1822 b1825 b1824 b1823

B number yeaV yeaW yeaX rnd fadD b1806 b1808 yeaZ pabB b1811 b1810 b1809 yeaB sdaA b1815 yoaE manZ manY manX b1821 b1820 rrmA b1825 b1824 cspC

Gene name + + + + + + + + + + + + + + ------Strand orientation 481 374 321 375 561 193 636 231 453 119 130 192 454 542 518 286 266 323 206 152 269 59 95 47 69 Protein length 27601 30711 1064 1211 4419 6265 5528 105 190 193 414 523 346 966 245 475 477 180 148 216 912 134 158 468 91 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P P P P mRNA present 14 14 18 20 10 35 18 10 19 15 13 12 13 9 8 2 6 4 9 3 4 7 3 3 5 # of tryptic peptides predicted P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 4 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 2 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 4 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 1 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt PHD PHD PHD Membrane protein assignment putative transportprotein orf, hypotheticalprotein putative diogenasebetasubunit RNase D,processestRNAprecursor acyl-CoA synthetase,long-chain-fatty-acid--CoAligase orf, hypotheticalprotein putative outermembraneprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative enzyme p-aminobenzoate synthetase,componentI orf, hypotheticalprotein L-serine deaminase orf, hypotheticalprotein PTS enzymeIIAB,mannose-specific putative transportprotein PTS enzymeIIC,mannose-specific PTS enzymeIID,mannose-specific orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein orf, hypothetical protein cold shockprotein 23S rRNAm1G745methyltransferase

Gene description Cell processes Miscellaneous Miscellaneous Macromolecule metabolism Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Cell processes Open readingframes Cell processes Cell processes Open readingframes Open readingframes Open reading frames Open reading frames Miscellaneous Miscellaneous

Functional category 1104 1104 1105 1106 1107 1108 1108 1112 1111 1110 1109 1113 1113 1114 1115 1117 1116 1117 1117 1118 1119 1122 1121 1121 1120 Operon ID b1843 b1842 b1841 b1840 b1839 b1827 b1826 b1844 b1828 b1845 b1834 b1833 b1832 b1831 b1830 b1829 b1846 b1835 b1850 b1849 b1848 b1847 b1838 b1837 b1836

B number b1843 holE b1841 b1840 b1839 b1827 b1826 exoX b1828 ptrB b1834 b1833 b1832 proQ prc htpX yebE yebU eda purT yebG yebF pphA b1837 b1836

Gene name + + + + + + + + + + ------Strand orientation 218 124 290 113 263 220 494 686 879 427 183 682 293 219 481 213 392 122 219 76 47 39 96 91 83 Protein length 1254 2259 1318 1248 2202 4057 3318 1360 3019 1831 1843 2297 4122 2973 293 571 874 141 258 238 218 762 583 214 109 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 11 18 10 35 10 26 38 12 10 17 16 10 5 1 6 3 0 7 2 8 2 9 5 7 3 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 0 0 0 1 0 0 2 0 2 0 6 1 0 0 1 0 1 0 2 4 0 3 0 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 0 1 0 0 1 0 2 0 6 0 0 0 0 0 0 0 3 4 0 2 0 0 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 0 0 0 1 0 0 2 0 2 0 6 0 0 0 0 0 0 0 2 4 0 3 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment DNA polymeraseIII,thetasubunit orf, hypotheticalprotein putative resistanceprotein orf, hypotheticalprotein orf, hypotheticalprotein hydroxyglutarate aldolase 2-keto-3-deoxygluconate 6-phosphatealdolase and2-keto-4- misfolding protein phosphatase1modulatesphosphoproteins,signals orf, hypotheticalprotein putative regulator Exonuclease X orf, hypotheticalprotein Activation ofsolutetransporterProP carboxy-terminal proteaseforpenicillin-bindingprotein3 heat shockprotein,integralmembraneprotein orf, hypotheticalprotein putative transportprotein protease II orf, hypotheticalprotein phosphoribosylglycinamide formyltransferase 2 orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative nucleolarproteins

Gene description Macromolecule metabolism Open readingframes Cell processes Open readingframes Open readingframes Metabolism of smallmolecules Miscellaneous Open readingframes Miscellaneous Open readingframes Open readingframes Miscellaneous Macromolecule metabolism Cell processes Open readingframes Cell processes Macromolecule metabolism Open readingframes Metabolism of smallmolecules Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous

Functional category 1134 1133 1133 1133 1123 1141 1132 1135 1124 1135 1128 1127 1127 1126 1129 1125 1136 1129 1140 1139 1138 1137 1131 1131 1130 Operon ID b1855 b1854 b1853 b1852 b1851 b1856 b1858 b1857 b1859 b1860 b1862 b1861 b1867 b1866 b1865 b1864 b1863 b1868 b1870 b1869 b1871 b1872 b1873 b1874 b1875

B number msbB pykA yebK zwf edd yebA yebM yebL yebI ruvB yebB ruvA yecD aspS ntpA yebC ruvC yecE yecO yecN yecP bisZ yecK cutC yecM

Gene name + + + + + + + + + + ------Strand orientation 323 480 289 491 603 419 251 328 261 336 233 203 199 590 150 246 173 272 247 141 323 815 366 146 190 Protein length 1782 1193 2415 4856 1559 1347 3503 3255 3190 1138 1934 1119 762 494 245 414 632 955 299 997 359 150 185 75 97 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 22 13 28 22 12 20 14 13 15 33 15 15 19 40 18 10 3 4 8 8 6 7 8 4 7 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 12 15 13 0 0 0 0 2 0 0 1 0 0 0 3 0 0 0 0 2 0 0 0 0 2 # of tryptic peptides detected (total list) P P P Protein detected - short list 13 14 11 0 0 0 0 3 0 0 1 0 0 0 3 0 1 0 0 2 0 0 0 0 1 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 12 15 13 0 0 0 0 2 0 0 1 0 0 0 3 0 0 0 0 2 0 0 0 0 2 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt PHD PHD Membrane protein assignment pyruvate kinaseII,glucosestimulated orf, hypotheticalprotein glucose-6-phosphate dehydrogenase 6-phosphogluconate dehydratase suppressor ofhtrB,heatshockprotein putative adhesin orf, hypotheticalprotein putative ATP-bindingcomponentofatransportsystem orf, hypotheticalprotein Holliday junctionhelicasesubunitB;branchmigration;repair Holliday junctionhelicasesubunitA;branchmigration;repair aspartate tRNAsynthetase dATP pyrophosphohydrolase orf, hypotheticalprotein Holliday junctionnuclease;resolutionofstructures;repair orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative enzyme biotin sulfoxidereductase 2 putative cytochromeC-type protein orf, hypothetical protein copper homeostasis protein

Gene description Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Miscellaneous Open readingframes Cell processes Cell processes Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Metabolism ofsmallmolecules Open readingframes Macromolecule metabolism Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open reading frames Cell processes

Functional category 1144 1143 1142 1141 1145 1147 1146 1148 1148 1149 1149 1152 1151 1151 1151 1150 1153 1153 1153 1153 1153 1154 1154 1156 1155 Operon ID b1893 b1892 b1889 b1883 b1882 b1876 b1895 b1894 b1890 b1884 b1877 b1899 b1896 b1891 b1885 b1878 b1900 b1898 b1897 b1886 b1879 b1887 b1880 b1888 b1881

B number insB_5 flhD motB cheB cheY argS yecG insA_5 motA cheR yecT araH_1 otsA flhC tap flhE araG araH_2 otsB tar flhA cheW flhB cheA cheZ

Gene name + + + ------Strand orientation 167 119 308 349 129 577 142 295 286 169 234 474 192 533 130 504 266 553 692 167 382 654 214 91 86 Protein length 4018 810 202 231 689 161 109 109 183 201 759 231 177 163 196 213 155 148 157 83 29 79 40 mRNA intensity A A A A A A A A A A A A A P P P P P P P P P P mRNA present 19 21 29 14 21 14 16 23 23 27 10 29 10 9 7 5 5 7 8 8 2 6 6 5 8 # of tryptic peptides predicted P P P Protein detected - total list 0 0 0 0 5 0 0 0 0 0 0 0 7 0 0 0 2 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 0 0 7 0 0 0 0 0 0 0 7 0 0 0 2 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 5 0 0 0 0 0 0 0 7 0 0 0 2 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt Membrane protein assignment transcriptional initiationfactor regulator offlagellarbiosynthesis,actingonclass2operons; initiation factor regulator offlagellarbiosynthesisactingonclass2operons;transcription and CheY sensory transducerkinasebetweenchemo-signalreceptorsandCheB components chemotaxis regulatortransmitschemoreceptorsignalstoflagelllarmotor switch regulator chemotactic response;CheYproteinphophatase;antagonistofas IS1 proteinInsA IS1 proteinInsB enables flagellarmotorrotation,linkingtorquemachinerytocellwall response regulatorforchemotaxis(cheAsensor);proteinmethylesterase arginine tRNAsynthetase putative regulator proton conductorcomponentofmotor;noeffectonswitching response regulatorforchemotaxis;proteinglutamatemethyltransferase orf, hypotheticalprotein high-affinity L-arabinosetransport system;membraneprotein,fragment2 high-affinity L-arabinose transportsystem; membraneprotein,fragment 1 trehalose-6-phosphate phophatase, biosynthetic trehalose-6-phosphate synthase flagellar protein methyl-accepting chemotaxisproteinIV,peptidesensorreceptor ATP-binding component ofhigh-affinity L-arabinose transportsystem flagellar biosynthesis;possibleexportofproteins methyl-accepting chemotaxisproteinII,aspartatesensorreceptor positive regulatorofCheAproteinactivity putative partofexportapparatusforflagellarproteins

Gene description Structural elements Structural elements Cell processes Cell processes Cell processes Extrachromosomal Extrachromosomal Cell processes Cell processes Macromolecule metabolism Open readingframes Cell processes Cell processes Open readingframes Cell processes Cell processes Cell processes Cell processes Structural elements Cell processes Cell processes Structural elements Cell processes Cell processes Miscellaneous

Functional category 1162 1162 1161 1160 1160 1163 1163 1161 1160 1157 1164 1161 1160 1158 1166 1166 1165 1165 1159 1160 1166 1159 1160 1161 1159 Operon ID b1924 b1923 b1913 b1901 b1925 b1916 b1915 b1914 b1902 b1917 b1903 b1921 b1920 b1919 b1918 b1904 b1922 b1906 b1905 b1907 b1908 b1909 b1912 b1911 b1910

B number fliD fliC uvrC araF fliS sdiA yecF uvrY yecI yecC b1903 fliZ fliY yedO yecS b1904 fliA yecH ftn tyrP yecA leuZ pgsA glyW cysT

Gene name + + + + + + + + ------Strand orientation 468 498 588 329 136 240 218 167 250 112 195 266 360 222 107 239 165 403 221 182 74 79 Protein length 2055 5516 1906 1087 2858 4256 1512 103 392 340 708 235 153 241 845 912 126 161 671 325 627 99 82 94 77 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P P mRNA present 22 26 19 19 12 10 12 18 13 10 15 3 8 8 5 9 3 7 2 3 7 5 # of tryptic peptides predicted P P P P P P Protein detected - total list 0 1 0 0 0 0 0 0 0 2 0 6 3 0 0 0 2 0 0 0 0 2 # of tryptic peptides detected (total list)

P P Protein detected - short list 0 1 0 0 0 2 0 0 0 0 0 9 4 0 0 0 2 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 0 1 0 0 0 0 0 0 0 0 0 6 3 0 0 0 2 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD

Membrane protein assignment activity) flagellar biosynthesis; repressorofclass 3aand3boperons(RflA operons flagellar biosynthesis;alternative sigmafactor28;regulationofflagellar phosphate phosphatidyltransferase phosphatidylglycerophosphate synthetase=CDP-1,2-diacyl-sn-glycero-3- flagellar biosynthesis; filamentcappingprotein; enablesfilamentassembly flagellar biosynthesis;flagellin, filamentstructuralprotein orf, hypotheticalprotein putative 2-componenttranscriptionalregulator excinuclease ABC,subunitC;repairofUVdamagetoDNA L-arabinose-binding periplasmicprotein transcriptional regulatorofftsQAZgenecluster ferritin-like protein putative periplasmicbindingtransportprotein putative 1-aminocyclopropane-1-carboxylatedeaminase putative ATP-bindingcomponentofatransportsystem orf, hypotheticalprotein putative transportsystempermeaseprotein(former yecC) orf, hypotheticalprotein cytoplasmic ferritin(anironstorageprotein) orf, hypotheticalprotein orf, hypotheticalprotein tyrosine-specific transportsystem orf, hypotheticalprotein tRNA-Gly tRNA-Cys tRNA-Leu

Gene description Structural elements Structural elements Macromolecule metabolism Structural elements Structural elements Open readingframes Miscellaneous Macromolecule metabolism Cell processes Cell processes Cell processes Cell processes Miscellaneous Cell processes Open readingframes Cell processes Miscellaneous Cell processes Open readingframes Open readingframes Cell processes Open readingframes tRNA tRNA tRNA

Functional category 1179a 1180 1179 1173 1180 1176 1175 1174 1166 1177 1167 1179 1178 1178 1167 1178 1179 1169 1168 1170 1171 1172 Operon ID b1947 b1946 b1940 b1939 b1938 b1931 b1930 b1929 b1928 b1927 b1926 b1950 b1949 b1948 b1941 b1932 b1942 b1933 b1943 b1934 b1944 b1935 b1945 b1936 b1937

B number fliO fliN fliH fliG fliF yedK yedF yedE yedD amyA fliT fliR fliQ fliP fliI yedL fliJ b1933 fliK yedN fliL yedM fliM b1936 fliE

Gene name + + + + + + + + + + + + + + + + + + + + - - - - - Strand orientation 101 137 235 331 552 217 401 137 495 121 261 245 457 159 147 375 106 154 116 334 104 77 89 63 92 Protein length 2739 3659 2060 1363 129 122 113 213 299 320 239 217 222 221 66 52 71 57 71 11 88 18 71 12 85 mRNA intensity A A A A A A A A A A A A A A A A A P P P P P P P P mRNA present 13 18 31 13 12 15 25 10 11 17 4 9 5 3 2 4 2 7 7 4 7 9 8 7 6 # of tryptic peptides predicted P P P Protein detected - total list 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD PHD PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein putative transportsystempermeaseprotein orf, hypotheticalprotein cytoplasmic alpha- enabling rotationanddeterminingitsdirection flagellar biosynthesis,componentofmotorswitchand energizing, enabling rotationanddeterminingitsdirection flagellar biosynthesis,componentofmotorswitchand energizing, enabling rotationanddeterminingitsdirection flagellar biosynthesis,componentofmotorswitchingandenergizing, ring andcollarprotein flagellar biosynthesis;basal-bodyMS(membraneandsupramembrane)- junction flagellar biosynthesis;basal-bodycomponent,possiblyat(MS-ring)-rod activity) flagellar biosynthesis;repressorofclass3aand3boperons(RflA flagellar biosynthesis flagellar biosynthesis flagellar biosynthesis;exportofproteins? orf, hypotheticalprotein flagellar biosynthesis flagellar biosynthesis flagellum-specific ATPsynthase orf, hypotheticalprotein flagellar fliJprotein orf, hypotheticalprotein flagellar hook-lengthcontrolprotein orf, hypotheticalprotein flagellar biosynthesis orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Open readingframes Miscellaneous Open readingframes Macromolecule metabolism Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Open readingframes Structural elements Structural elements Structural elements Open readingframes Structural elements Open readingframes Structural elements Open readingframes Structural elements Open readingframes Open readingframes

Functional category 1183 1183 1182 1181 1191 1191 1190 1190 1189 1180 1191 1191 1190 1184 1191 1191 1190 1185 1190 1186 1190 1186 1191 1187 1188 Operon ID b1956 b1955 b1954 b1953 b1952 b1951 b1959 b1958 b1957 b1960 b1961 b1962 b1964 b1963 b1965 b1966 b1969 b1968 b1967 b1970 b1971 b1973 b1972 b1974 b1975

B number b1956 b1955 dsrA b1953 dsrB rcsA yedA yedI b1957 vsr dcm yedJ b1964 b1963 b1965 b1966 yedW yedV yedU b1970 b1971 b1973 b1972 yodB serU

Gene name + + + + + + + + + + + + + ------Strand orientation 569 271 207 306 305 156 472 231 171 127 134 239 452 283 137 334 216 211 186 80 62 60 69 Protein length 1001 1048 3393 579 548 817 166 111 205 411 489 145 250 154 565 252 408 143 208 529 66 86 89 81 89 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 13 25 27 15 10 14 24 17 5 0 4 8 9 5 9 4 6 1 5 4 8 3 5 # of tryptic peptides predicted P P P Protein detected - total list 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 3 0 0 0 0 3 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 4 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 3 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt MP-GenProt MP-PHD GenProt PHD PHD PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein factor positive regulatorforctrcapsulebiosynthesis,transcription orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transmembranesubunit DNA mismatchendonuclease,patchrepairprotein DNA cytosinemethylase orf, hypotheticalprotein orf, hypotheticalprotein putative outermembraneprotein orf, hypotheticalprotein orf, hypotheticalprotein putative outermembraneprotein putative 2-componentsensorprotein putative 2-componenttranscriptionalregulator orf, hypotheticalprotein putative reductase orf, hypotheticalprotein orf, hypotheticalprotein putative cytochrome tRNA-Ser

Gene description Open readingframes Open readingframes Miscellaneous Structural elements Structural elements Open readingframes Open readingframes Open readingframes Open readingframes Macromolecule metabolism Macromolecule metabolism Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Miscellaneous Miscellaneous Miscellaneous Miscellaneous Miscellaneous Open readingframes Open readingframes Miscellaneous tRNA

Functional category 1195 1194 1193 1192 1198 1197 1196 1199 1200 1200 1201 1201 1202 1202 1204 1203 1205 1205 1206 1207 1207 1208 1209 Operon ID b1988 b1979 b1978 b1977 b1976 b1990 b1989 b1980 b1993 b1992 b1991 b1981 b1994 b1983 b1982 b1995 b1985 b1984 b1996 b1987 b1986 b1997 b1999 b1998 b2000

B number nac b1979 b1978 asnT b1976 erfK asnV b1980 cobU cobS cobT shiA trs5_6 b1983 amn b1995 yeeO asnW yi22_3 cbl asnU yi21_3 yeeP b1998 flu

Gene name + + + + + + + + + + + + ------Strand orientation 2383 1091 305 108 278 310 234 181 247 359 438 338 238 484 139 547 301 316 136 236 86 Protein length 4039 1919 4020 1294 1273 4533 4205 148 300 420 722 426 633 145 110 501 275 565 131 11 55 8 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P mRNA present 76 10 15 14 11 18 12 16 19 39 13 7 4 8 4 5 9 6 9 5 8 # of tryptic peptides predicted P P P P P Protein detected - total list 0 2 0 0 0 0 0 0 0 0 4 0 2 0 0 0 1 0 0 3 0 # of tryptic peptides detected (total list) P P Protein detected - short list 0 1 0 0 1 0 0 0 0 0 4 0 1 0 0 0 1 0 0 5 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 2 0 0 0 0 0 0 0 0 4 0 2 0 0 0 1 0 0 3 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 detected (membrane sample) GenProt-PHD GenProt PHD PHD MP Membrane protein assignment putative factor tRNA-Asn orf, hypotheticalprotein affecting cysM transcriptional regulatorcysregulon;accessoryregulatorycircuit tRNA-Asn nitrogen assimilationcontrolprotein orf, hypotheticalprotein cobalamin 5'-phosphatesynthase orf, hypotheticalprotein orf, hypotheticalprotein nicotinate- dimethylbenzimidazole-Pphophoribosyltransferase cobinamide kinase/cobinamidephosphateguanylyltransferase AMP nucleosidase putative transportprotein,shikimate IS5 transposase tRNA-Asn orf, hypotheticalprotein orf, hypotheticalprotein tRNA-Asn orf, hypotheticalprotein IS2 hypotheticalprotein orf, hypotheticalprotein IS2 hypotheticalprotein outer membrane fluffingprotein,similar to adhesin putative histone

Gene description Miscellaneous tRNA Open readingframes Metabolism ofsmallmolecules tRNA Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Extrachromosomal tRNA Open readingframes Open readingframes tRNA Miscellaneous Extrachromosomal Open readingframes Extrachromosomal Structural elements Open reading frames

Functional category 1211 1210 1217 1218 1212 1220 1219 1212 1220 1220 1214 1213 1221 1215 1222 1216 1223 1224 1223 1225 1224 Operon ID b2025 b2024 b2023 b2001 b2002 b2003 b2004 b2005 b2010 b2009 b2008 b2007 b2006 b2011 b2014 b2013 b2012 b2015 b2016 b2022 b2021 b2020 b2019 b2018 b2017

B number hisF hisA hisH b2001 yeeS yeeT yeeU yeeV dacD sbmC yeeA yeeX yeeW sbcB yeeF yeeE yeeD yeeY b2016 hisB hisC hisD hisG hisL yefM

Gene name + + + + + + + + + + + + + + + ------Strand orientation 258 246 196 512 148 122 124 390 157 352 131 475 454 352 316 274 356 356 434 299 73 64 75 16 92 Protein length 3366 4310 2569 1086 1085 8922 1531 3091 2631 3584 5358 4684 2664 129 112 174 232 645 525 879 199 727 41 38 23 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 15 13 23 10 19 20 11 13 16 18 12 14 9 6 5 6 6 3 4 2 1 7 8 1 5 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 2 1 1 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 3 3 5 2 0 0 # of tryptic peptides detected (total list)

P P P P Protein detected - short list 2 1 3 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 4 4 6 5 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 2 1 1 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 3 3 5 2 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD PHD PHD PHD Membrane protein assignment imidazole glycerol phsphatesynthaseholoenzyme imidazole glycerol phosphatesynthase subunit inheterodimerwith HisH= imidazolecarboxamide isomerase N-(5'-phospho-L-ribosyl-formimino)-5-amino-1-(5'- phosphoribosyl)-4- glycerol phosphatesynthase holoenzyme glutamine amidotransferase subunitofheterodimerwithHisF=imidazole phosphatase imidazoleglycerolphosphate dehydrataseandhistidinol-phosphate orf, hypotheticalprotein putative DNArepairprotein,RADCfamily orf, hypotheticalprotein putative structuralprotein SbmC protein orf, hypotheticalprotein putative alphahelixprotein orf, hypotheticalprotein orf, hypotheticalprotein penicillin bindingprotein6b orf, hypotheticalprotein exonuclease I,3'-->5'specific;deoxyribophosphodiesterase putative transportsystempermeaseprotein putative aminoacid/aminetransportprotein putative transcriptionalregulatorLYSR-type histidinol-phosphate aminotransferase L-histidinal:NAD+ oxidoreductase;L-histidinol:NAD+ oxidoreductase ATP phosphoribosyltransferase his operonleaderpeptide orf, hypotheticalprotein putative enzymeofsugarmetabolism

Gene description Metabolism of smallmolecules Metabolism of smallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Miscellaneous Macromolecule metabolism Open readingframes Miscellaneous Open readingframes Open readingframes Structural elements Open readingframes Macromolecule metabolism Miscellaneous Cell processes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous

Functional category 1240 1240 1240 1240 1226 1226 1227 1228 1232 1231 1230 1229 1229 1233 1235 1234 1235 1236 1237 1240 1240 1240 1239 1238 1237 Operon ID b2043 b2028 b2027 b2026 b2044 b2030 b2029 b2045 b2037 b2036 b2035 b2034 b2033 b2032 b2031 b2047 b2046 b2038 b2048 b2042 b2041 b2040 b2039 b2049 b2050

B number wcaM ugd wzzB hisI wcaL trs5_7 gnd wcaK rfbX glf wbbH wbbI wbbJ wbbK yefJ wcaJ wzxC rfbC cpsG galF rfbB rfbD rfbA cpsB wcaI

Gene name + ------Strand orientation 464 388 338 203 406 338 468 426 415 367 388 330 196 372 157 464 492 185 456 297 361 299 293 478 407 Protein length 1679 1384 4998 1393 1058 1578 2265 1838 5460 2839 2723 3609 202 257 352 126 690 530 155 956 572 146 189 75 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 14 22 24 22 14 20 20 16 24 12 10 13 19 15 13 19 11 17 23 24 20 4 9 7 9 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 19 1 1 0 0 0 0 7 5 1 0 0 0 0 0 0 1 0 3 9 2 7 0 0 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 19 10 1 2 0 0 0 0 7 0 0 1 0 0 0 0 0 2 0 3 4 8 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 19 1 1 0 0 0 0 7 0 0 0 0 0 0 0 0 1 0 3 9 2 7 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 1 0 0 0 0 0 0 0 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD PHD PHD PHD PHD PHD PHD Membrane protein assignment regulator oflengthO-antigencomponentlipopolysaccharidechains UDP-gal transferase homolog ofSalmonellaUTP--glucose-1-Puridyltransferase, probablya phosphoribosyl-amp cyclohydrolase;phosphoribosyl-ATP orf, hypotheticalprotein gluconate-6-phosphate dehydrogenase,decarboxylating UDP-glucose 6-dehydrogenase putative colanicacidbiosynthesisglycosyltransferase UDP-galactopyranose mutase putative Galftransferase putative O-acetyltransferase putative glucosetransferase putative creatinase(EC3.5.-) IS5 transposase O-antigen polymerase probable exportprotein putative galactokinase(EC2.7.1.6). putative O-antigentransporter putative colanicacidbiosynthsis UDP-glucoselipidcarriertransferase dTDP-glucose 4,6dehydratase dTDP-6-deoxy-L-mannose-dehydrogenase glucose-1-phosphate thymidylyltransferase dTDP-6-deoxy-D-glucose-3,5 epimerase phosphomannomutase mannose-1-phosphate guanyltransferase putative colanic biosynthesisglycosyltransferase

Gene description Structural elements Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Miscellaneous Extrachromosomal Macromolecule metabolism Cell processes Miscellaneous Structural elements Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism of smallmolecules Open reading frames

Functional category 1241 1246 1240 1247 1243 1242 1247 1244 1244 1244 1244 1244 1244 1244 1248 1247 1245 1248 1245 1245 1245 1245 1249 1249 1250 Operon ID b2051 b2052 b2053 b2054 b2055 b2057 b2056 b2059 b2058 b2061 b2060 b2062 b2064 b2063 b2066 b2065 b2068 b2067 b2069 b2071 b2070 b2072 b2073 b2075 b2074

B number wcaH wcaG gmd wcaF wcaE wcaC wcaD wcaA wcaB wzb b2060 wza asmA yegH udk dcd alkA yegE yegD b2071 b2070 b2072 b2073 yegN b2074

Gene name + + + + + + ------Strand orientation 1105 1040 160 321 373 182 248 405 405 279 162 147 732 379 617 549 231 193 282 471 153 648 253 219 464 Protein length 1052 146 140 281 114 611 633 176 654 241 239 161 293 112 338 12 40 20 64 87 57 58 46 6 5 mRNA intensity A A A A A A A A A A A A A A A A A P P P P P P P P mRNA present 11 18 12 20 12 36 15 28 20 13 34 17 20 24 27 19 8 8 9 7 8 8 7 6 8 # of tryptic peptides predicted P P P P Protein detected - total list 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 detected (membrane sample) MP-GenProt-PHD GenProt-PHD PHD PHD PHD PHD PHD PHD Membrane protein assignment GDP-mannose mannosylhydrolase putative nucleotidedi-P-sugarepimeraseordehydratase GDP-D-mannose dehydratase putative transferase putative colanicacidbiosynthesisglycosyltransferase putative colanicacidpolymerase putative glycosyltransferase putative transferase putative regulator orf, hypotheticalprotein probable protein-tyrosine-phosphatase putative polysaccharideexportprotein putative transportprotein 2'-deoxycytidine 5'-triphosphatedeaminase suppressor ofompFassemblymutants putative sensor-typeprotein uridine/cytidine kinase 3-methyl-adenine DNAglycosylaseII,inducible putative heatshockprotein putative chaperonin orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative membrane protein orf, hypothetical protein

Gene description Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open readingframes Extrachromosomal Miscellaneous Miscellaneous Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes Metabolism ofsmallmolecules Structural elements Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous Cell processes

Functional category 1250 1250 1250 1250 1250 1250 1250 1250 1250 1251 1251 1251 1252 1254 1253 1255 1254 1256 1257 1258 1259 1260 1260 1261 1261 Operon ID b2077 b2076 b2078 b2079 b2081 b2080 b2083 b2082 b2084 b2085 b2086 b2087 b2088 b2089 b2092 b2091 b2090 b2094 b2093 b2095 b2096 b2097 b2098 b2099 b2100

B number yegB yegO baeS baeR yegQ b2080 b2083 ogrK b2084 b2085 b2086 gatR_1 b2088 tra5_4 gatC gatD gatR_2 gatA gatB gatZ gatY b2097 yegT b2099 b2100

Gene name + + + + + + + + + + + + ------Strand orientation 1025 471 467 240 453 123 125 299 148 102 288 451 346 112 150 420 286 374 425 334 321 48 72 88 94 Protein length 43258 31493 51189 56901 47588 10583 3604 8850 3175 185 143 465 868 708 574 380 152 205 270 25 87 95 84 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P P mRNA present 34 25 15 21 13 16 12 17 13 16 14 14 8 8 4 3 5 8 7 5 5 4 9 8 7 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 0 0 0 0 2 0 2 0 0 0 0 0 0 0 5 0 4 5 4 5 7 8 0 0 0 # of tryptic peptides detected (total list) P P P P P P Protein detected - short list 0 0 0 0 1 0 4 0 0 0 0 0 0 0 5 0 1 1 5 4 7 6 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 0 0 0 0 2 0 2 0 0 0 0 0 0 0 5 0 4 1 4 5 7 8 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 0 1 1 2 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

Membrane protein assignment orf, hypotheticalprotein putative transportprotein sensor protein(forBaeR) orf, hypotheticalprotein transcriptional responseregulatoryprotein(sensorBaeS) prophage P2ogrprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein split galactitolutilizationoperonrepressor,interrupted orf, hypotheticalprotein galactitol-1-phosphate dehydrogenase split galactitolutilizationoperonrepressor,fragment2 IS3 putativetransposase galactitol-specific enzymeIIBofphosphotransferase system PTS systemgalactitol-specificenzymeIIC galactitol-specific enzymeIIAofphosphotransferase system tagatose 6-phosphatealdolase2,subunitwithGatY tagatose-bisphosphate aldolase1 orf, hypotheticalprotein putative nucleosidepermease protein orf, hypothetical protein putative kinase

Gene description Cell processes Cell processes Global functions Open readingframes Global functions Extrachromosomal Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Open reading frames Miscellaneous

Functional category 1261 1261 1262 1263 1262 1265 1264 1266 1266 1266 1267 1267 1267 1268 1268 1267 1268 1268 1268 1268 1268 1269 1270 1270 1270 Operon ID b2101 b2102 b2103 b2107 b2106 b2105 b2104 b2108 b2109 b2110 b2111 b2115 b2114 b2113 b2112 b2116 b2117 b2119 b2118 b2120 b2121 b2122 b2123 b2124 b2125

B number yegW yegX thiD b2107 yohM yohL thiM yehA yehB yehC yehD molR_1 metG mrp yehE molR_2 molR_3 yehL yehI yehM yehP yehQ yehR yehS yehT

Gene name + + + + + + + + + + + + ------Strand orientation 1210 248 275 266 172 274 262 344 826 239 180 274 677 379 645 333 384 759 378 622 157 156 244 90 93 Protein length 2873 1194 2110 454 249 484 949 451 883 112 125 105 186 210 436 66 67 71 28 31 21 60 36 66 18 mRNA intensity A A A A A A A A A A A A A A A P P P P P P P P P P mRNA present 13 10 13 10 11 36 12 34 13 10 27 47 10 18 26 16 27 10 13 6 7 4 2 6 9 # of tryptic peptides predicted P P P P P Protein detected - total list 11 0 0 0 2 2 2 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 13 0 0 0 3 2 2 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 11 0 0 0 2 2 2 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt

PHD Membrane protein assignment putative transcriptionalregulator orf, hypotheticalprotein orf, hypotheticalprotein hydoxyethylthiazole kinase phosphomethylpyrimidine kinase orf, hypotheticalprotein orf, hypotheticalprotein putative type-1fimbrialprotein putative outermembraneprotein putative chaperone methionine tRNAsynthetase putative ATPase orf, hypotheticalprotein putative fimbrial-likeprotein molybdate metabolismregulator,firstfragment molybdate metabolismregulator,secondfragment2 putative regulator molybdate metabolismregulator,thirdfragment orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein orf, hypothetical protein

Gene description Miscellaneous Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Miscellaneous Miscellaneous Macromolecule metabolism Miscellaneous Open readingframes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open reading frames Miscellaneous

Functional category 1271 1272 1274 1273 1273 1275 1275 1276 1276 1276 1279 1278 1277 1276 1280 1280 1280 1280 1281 1281 1281 1281 1282 1283 1283 Operon ID b2150 b2132 b2127 b2126 b2134 b2133 b2128 b2137 b2136 b2135 b2129 b2138 b2131 b2130 b2139 b2140 b2142 b2141 b2143 b2144 b2146 b2145 b2147 b2148 b2149

B number mglB bglX yehV yehU pbpG dld yehW yohF yohD yohC yehX yohG yehZ yehY yohH yohI yohK yohJ cdd sanA b2146 b2145 yeiA mglC mglA

Gene name + + + + + + + + + + ------Strand orientation 332 765 243 561 313 571 243 253 204 203 308 398 305 385 315 231 132 294 239 412 413 336 506 96 79 Protein length 7569 1830 1068 1844 728 439 913 543 224 246 358 300 571 124 974 266 281 264 201 376 228 543 19 54 81 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 20 37 12 19 35 20 13 15 22 20 13 11 21 19 33 2 9 6 4 8 5 3 2 2 6 # of tryptic peptides predicted P P P P P Protein detected - total list 12 0 0 0 4 0 0 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 1 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 11 0 0 0 5 0 0 0 0 0 0 0 4 0 0 0 0 0 3 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 12 0 0 0 4 0 0 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD PHD PHD PHD Membrane protein assignment galactose-binding transportprotein;receptor forgalactosetaxis taxis ATP-binding componentof methyl-galactosidetransportandgalactose betaine cholinetransportforosmoprotection) putative ABCsuperfamily(peri_bind)transportprotein(possiblyglycine putative 2-componentsensorprotein D-lactate dehydrogenase,FADprotein,NADHindependent beta-D-glucoside glucohydrolase,periplasmic putative transcriptionalregulator penicillin-binding protein7 orf, hypotheticalprotein orf, hypotheticalprotein putative transportsystempermeaseprotein putative oxidoreductase putative ATP-bindingcomponentofatransportsystem putative transportsystempermeaseprotein putative channel/filamentproteins orf, hypotheticalprotein putative regulatorprotein orf, hypotheticalprotein putative seritonintransporter cytidine/deoxycytidine deaminase vancomycin sensitivity orf, hypotheticalprotein putative oxidoreductase putative oxidoreductase methyl-galactoside transport andgalactosetaxis

Gene description Cell processes Cell processes Cell processes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Structural elements Open readingframes Miscellaneous Miscellaneous Miscellaneous Cell processes Cell processes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Metabolism ofsmallmolecules Cell processes Open readingframes Miscellaneous Miscellaneous Cell processes

Functional category 1298 1298 1285 1283 1287 1286 1284 1288 1290 1289 1285 1291 1285 1285 1292 1292 1293 1294 1294 1295 1296 1296 1297 1297 1298 Operon ID b2157 b2156 b2151 b2158 b2155 b2154 b2153 b2152 b2160 b2159 b2161 b2162 b2163 b2164 b2165 b2166 b2167 b2168 b2169 b2170 b2172 b2171 b2173 b2175 b2174

B number yeiE lysP galS yeiH cirA yeiG folE yeiB yeiI nfo yeiJ yeiK yeiL yeiM yeiN yeiC fruA fruK fruB setB yeiQ yeiP yeiR spr b2174

Gene name + + + + + + + + + + + ------Strand orientation 293 489 346 349 663 278 222 385 362 285 416 313 219 416 312 313 563 312 376 393 488 275 328 188 249 Protein length 10328 1132 1209 2088 6048 1044 1445 397 313 202 308 244 164 300 546 719 878 231 364 336 223 63 85 28 85 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 12 19 30 13 10 12 14 12 11 11 14 12 14 13 14 14 21 17 7 6 5 5 9 8 9 # of tryptic peptides predicted P P P P P P P Protein detected - total list 0 0 0 5 3 2 0 1 0 0 0 0 0 0 0 0 1 0 0 0 2 0 0 2 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 5 2 0 1 0 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 0 0 0 0 3 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt GenProt PHD PHD PHD Membrane protein assignment lysine-specific permease requires tonBgeneproduct outer membranereceptorforiron-regulatedcolicinIreceptor;porin; putative transcriptionalregulatorLYSR-type putative esterase(EC3.1.1.-). GTP cyclohydrolaseI mgl repressor,galactoseoperoninducer orf, hypotheticalprotein endonuclease IV orf, hypotheticalprotein putative kinase putative transportsystempermeaseprotein orf, hypotheticalprotein putative transcriptionalregulator putative transportsystempermeaseprotein orf, hypotheticalprotein putative kinase PTS system,-specifictransportprotein fructose-1-phosphate kinase PTS system,fructose-specificIIA/fprcomponent putative elongationfactor Sugar effluxprotein putative oxidoreductase orf, hypotheticalprotein orf, hypothetical protein putative lipoprotein

Gene description Cell processes Structural elements Miscellaneous Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Macromolecule metabolism Open readingframes Miscellaneous Cell processes Open readingframes Miscellaneous Cell processes Open readingframes Miscellaneous Cell processes Metabolism ofsmallmolecules Cell processes Miscellaneous Cell processes Miscellaneous Open readingframes Open reading frames Miscellaneous

Functional category 1303 1302 1304 1301 1300 1299 1300 1306 1305 1307 1308 1309 1310 1311 1312 1312 1313 1313 1313 1315 1314 1316 1317 1317 1318 Operon ID b2176 b2177 b2178 b2179 b2180 b2181 b2182 b2184 b2183 b2189 b2188 b2187 b2186 b2185 b2190 b2192 b2191 b2193 b2194 b2195 b2196 b2197 b2199 b2198 b2200

B number rtn yejA yejB yejE yejF yejG bcr yejH rsuA proL yejM yejL yejK rplY yejO trs5_8 b2191 narP ccmH dsbE ccmF ccmE ccmC ccmD ccmB

Gene name + + + + + + + + + + + + ------Strand orientation 518 606 364 341 529 114 396 586 231 586 335 836 338 215 350 185 647 159 245 220 75 94 40 69 Protein length 29249 1276 2114 1059 461 276 296 165 438 688 215 260 477 292 222 878 287 211 136 188 225 133 227 22 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 22 30 11 10 28 34 16 20 30 14 18 18 6 9 4 6 4 1 9 6 1 9 6 2 # of tryptic peptides predicted P P P P Protein detected - total list 0 0 0 0 0 0 1 0 3 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 1 0 0 0 0 2 0 3 0 1 5 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 0 0 0 0 0 0 1 0 3 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt GenProt PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein putative transportsystempermeaseprotein putative transportsystempermeaseprotein putative ATP-bindingcomponentofatransportsystem orf, hypotheticalprotein 16S pseudouridylate516synthase bicyclomycin resistanceprotein;transmembraneprotein orf, hypotheticalprotein Present inspermidinenucleoids 50S ribosomalsubunitproteinL25 putative ATP-dependenthelicase putative sulfatase tRNA-Pro orf, hypotheticalprotein putative ATP-bindingcomponentofatransportsystem IS5 transposase nitrate/nitrite responseregulator(sensorNarQ) possible subunitofhemelyase disulfide oxidoreductase(inbiogenesisofcytochrome c? cytochrome c-typebiogenesisprotein heme exporterproteinC cytochrome cbiogenesis, possible subunitofahemelyase heme exporter proteinC heme exporter proteinB,cytochromec-type biogenesisprotein

Gene description Open readingframes Cell processes Cell processes Cell processes Cell processes Open readingframes Macromolecule metabolism Cell processes Open readingframes Macromolecule metabolism Structural elements Miscellaneous Miscellaneous tRNA Open readingframes Open readingframes Extrachromosomal Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Cell processes Cell processes

Functional category 1319 1320 1320 1320 1320 1321 1322 1322 1326 1325 1324 1323 1326 1328 1327 1329 1330 1331 1331 1331 1331 1331 1331 1331 Operon ID b2221 b2219 b2218 b2214 b2201 b2222 b2220 b2215 b2202 b2223 b2217 b2216 b2203 b2224 b2204 b2225 b2205 b2206 b2208 b2207 b2209 b2210 b2211 b2212 b2213

B number atoD atoS rcsC yojL ccmA atoA atoC ompC napC atoE rcsB yojN napB atoB napH b2225 napG napA napF napD eco yojH yojI alkB ada

Gene name + + + + + + + + + ------Strand orientation 220 608 933 351 205 216 461 367 200 440 216 890 156 394 287 258 231 828 164 162 548 547 216 354 87 Protein length 39955 3714 4923 208 494 304 309 162 388 372 138 143 163 206 286 248 227 746 238 414 185 418 50 88 92 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 10 24 46 18 25 18 10 32 15 16 40 25 18 11 22 8 6 9 4 4 7 7 2 5 8 # of tryptic peptides predicted P P P Protein detected - total list 0 0 0 0 0 0 5 0 0 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt GenProt PHD PHD Membrane protein assignment ATOS) response regulatorofato,ornithinedecarboxylaseantizyme (sensor RcsB sensor forctrcapsulebiosynthesis,probablehistidine kinaseactingon RcsC) positive responseregulatorforcolaniccapsulebiosynthesis, (sensor, activator/repressor O6-methylguanine-DNA methyltransferase;transcription acetyl-CoA:acetoacetyl-CoA transferasealphasubunit sensor proteinAtoSforresponseregulatorAtoC orf, hypotheticalprotein ATP bindingproteinofhemeexporterA acetyl-CoA:acetoacetyl-CoA transferasebetasubunit putative 2-componentsensorprotein outer membraneprotein1b(Ib;c) cytochrome c-typeprotein short chainfattyacidtransporter cytochrome c-typeprotein acetyl-CoA acetyltransferase ferredoxin-type protein:electrontransfer orf, hypothetical protein ferredoxin-type protein:electrontransfer orf, hypotheticalprotein probable nitratereductase3 ferredoxin-type protein:electrontransfer ecotin, aserineproteaseinhibitor orf, hypotheticalprotein Malate:quinone oxidoreductase DNA repairsystemspecificforalkylated

Gene description Metabolism ofsmallmolecules Structural elements Structural elements Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Open readingframes Cell processes Metabolism ofsmallmolecules Miscellaneous Structural elements Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism of smallmolecules Metabolism ofsmallmolecules Open reading frames Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Open readingframes Cell processes Macromolecule metabolism

Functional category 1341 1340 1339 1335 1342 1341 1336 1331 1342 1338 1337 1331 1343 1331 1342 1331 1344 1331 1331 1331 1331 1332 1333 1334 1335 Operon ID b2244 b2243 b2237 b2236 b2235 b2234 b2233 b2226 b2245 b2238 b2227 b2246 b2240 b2239 b2229 b2228 b2247 b2242 b2241 b2230 b2248 b2232 b2231 b2249 b2250

B number yfaD glpC inaA yfaE nrdB nrdA yfaL b2226 b2245 yfaH b2227 b2246 glpT glpQ b2229 b2228 b2247 glpB glpA yfaA b2248 ubiG gyrA b2249 b2250

Gene name + + + + + + + + + ------Strand orientation 1250 1337 299 396 216 376 761 549 267 161 442 452 358 216 405 419 542 578 260 240 875 400 187 84 68 Protein length 12296 1441 1563 2428 5247 3240 1921 2290 1303 340 365 296 607 181 172 128 226 117 155 19 76 73 26 99 94 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 16 27 19 35 16 10 30 18 61 15 14 27 13 27 12 40 10 14 2 5 3 8 9 8 5 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 10 11 0 0 0 2 9 1 0 0 0 0 0 0 4 0 0 1 6 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 12 12 0 0 0 3 0 0 0 0 0 0 9 0 0 0 0 2 7 0 0 1 0 0 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 10 11 0 0 0 2 9 0 0 0 0 0 0 0 0 0 0 1 6 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 1 0 0 0 0 0 1 0 4 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD MP-GenProt GenProt GenProt GenProt GenProt

MP Membrane protein assignment orf, hypotheticalprotein ribonucleoside-diphosphate reductase1,betasubunit,B2 ribonucleoside diphosphatereductase1,alphasubunit,B1 putative ATP-bindingcomponentofatransportsystem sn-glycerol-3-phosphate dehydrogenase(anaerobic), K-smallsubunit subunit sn-glycerol-3-phosphate dehydrogenase(anaerobic), membraneanchor phenol methylase 3-demethylubiquinone-9 3-methyltransferaseand2-octaprenyl-6-hydroxy orf, hypotheticalprotein pH-inducible proteininvolvedinstressresponse orf, hypotheticalprotein orf, hypotheticalprotein glycerophosphodiester ,periplasmic orf, hypotheticalprotein putative membraneprotein orf, hypotheticalprotein sn-glycerol-3-phosphate permease orf, hypotheticalprotein putative transportprotein sn-glycerol-3-phosphate dehydrogenase(anaerobic),largesubunit putative racemase DNA gyrase,subunitA,typeIItopoisomerase orf, hypotheticalprotein putative regulator orf, hypothetical protein orf, hypothetical protein

Gene description Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Cell processes Open readingframes Miscellaneous Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Cell processes Open readingframes Miscellaneous Metabolism ofsmallmolecules Miscellaneous Macromolecule metabolism Open readingframes Miscellaneous Open reading frames Open reading frames

Functional category 1349 1348 1348 1347 1353 1353 1346 1354 1350 1344 1355 1352 1351 1344 1344 1352 1344 1355 1353 1355 1345 1344 1355 1356 1357 Operon ID b2263 b2262 b2251 b2264 b2252 b2265 b2253 b2266 b2255 b2254 b2268 b2267 b2256 b2269 b2260 b2259 b2258 b2257 b2270 b2261 b2271 b2272 b2273 b2274 b2275

B number yfbB menB yfaO menD ais menF b2253 elaB b2255 b2254 elaC elaA b2256 elaD menE pmrD b2258 b2257 yfbK menC yfbL yfbM yfbN b2274 b2275

Gene name + + + + + + + + + + + + + ------Strand orientation 252 285 141 556 200 356 390 101 660 322 311 153 296 403 451 222 550 575 320 325 167 238 158 283 98 Protein length 10163 1392 1228 1665 1561 331 249 344 537 420 675 308 468 172 328 265 54 63 28 96 81 69 54 60 40 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 10 23 18 14 34 12 15 14 18 17 20 13 30 12 11 10 7 4 9 4 6 4 8 4 2 # of tryptic peptides predicted P P Protein detected - total list 0 0 0 0 0 0 0 2 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 2 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 0 0 0 0 0 0 2 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) PHD PHD PHD Membrane protein assignment dihydroxynaphtoic acidsynthetase succinylbenzoyl-CoA o-succinylbenzoyl-CoA synthase;conversionofchorismateto2-o- putative enzyme orf, hypotheticalprotein 2-oxoglutarate decarboxylase;SHCHCsynthase protein inducedbyaluminum isochorismate hydroxymutase2,menaquinonebiosynthesis putative enzyme putative sugartransferase orf, hypotheticalprotein orf, hypotheticalprotein putative transformylase orf, hypotheticalprotein polymyxin resistanceproteinB orf, hypotheticalprotein putative transport/receptorprotein orf, hypotheticalprotein putative sulfatase/phosphatase o-succinylbenzoate-CoA ligase orf, hypotheticalprotein putative aminopeptidase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein orf, hypothetical protein

Gene description Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Open readingframes Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Cell processes Open readingframes Miscellaneous Open readingframes Miscellaneous Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Open readingframes Open reading frames Open reading frames

Functional category 1362 1362 1362 1358 1362 1359 1362 1360 1360 1364 1363 1360 1365 1361 1360 1360 1360 1366 1362 1367 1368 1369 1370 1371 1372 Operon ID b2285 b2284 b2283 b2282 b2281 b2280 b2279 b2278 b2277 b2276 b2286 b2288 b2287 b2289 b2290 b2291 b2292 b2298 b2297 b2296 b2295 b2294 b2293 b2299 b2300

B number nuoE nuoF nuoG nuoH nuoI nuoJ nuoK nuoL nuoM nuoN nuoC nuoA nuoB lrhA b2290 b2291 yfbS yfcC pta ackA b2295 b2294 yfbT b2299 yfcE

Gene name + + + + + ------Strand orientation 166 445 910 325 180 184 100 613 509 425 600 147 220 312 405 199 610 513 714 400 151 170 222 180 184 Protein length 15463 11188 10132 8616 8178 7672 6191 4869 5100 5120 2636 3640 9713 1290 5299 8848 1242 2986 919 448 341 133 201 535 639 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 21 40 11 11 33 10 18 10 31 15 10 17 10 9 2 2 4 7 7 4 9 9 5 7 5 # of tryptic peptides predicted P P P P P P P P P P P P P P P Protein detected - total list 10 5 8 0 2 0 0 2 1 1 1 2 1 0 3 1 9 3 3 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P P P P Protein detected - short list 11 9 8 0 2 0 0 0 0 0 1 8 2 1 0 2 1 5 4 0 0 0 0 0 1 # of tryptic peptides detected (short list) P P P P P P P P P P P P Protein detected - long list 5 8 0 2 0 0 0 0 0 1 6 2 1 0 3 1 9 3 3 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 10 3 5 0 1 0 0 2 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD Membrane protein assignment NADH dehydrogenaseIchainF NADH dehydrogenaseIchainG NADH dehydrogenaseIchain NADH dehydrogenaseIchainH NADH dehydrogenaseIchainJ NADH dehydrogenaseIchainK NADH dehydrogenaseIchainL NADH dehydrogenaseIchainM NADH dehydrogenaseIchainN NADH dehydrogenaseIchainE NADH dehydrogenaseIchainB NADH dehydrogenaseIchainC,D NADH dehydrogenaseIchainA LysR homologuewhichmodulatesSprE(RssB)activity putative aminotransferase putative alphahelixprotein phosphotransacetylase orf, hypotheticalprotein putative phosphatase putative transportprotein orf, hypotheticalprotein putative S-transferase orf, hypothetical protein putative regulator

Gene description Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Open readingframes Miscellaneous Open reading frames Open reading frames

Functional category 1373 1373 1373 1373 1373 1373 1373 1373 1373 1373 1373 1373 1373 1374 1375 1376 1381 1380 1378 1378 1377 1379 1382 1384 1383 Operon ID b2311 b2310 b2301 b2314 b2313 b2312 b2302 b2320 b2319 b2318 b2317 b2316 b2315 b2304 b2303 b2321 b2305 b2322 b2306 b2324 b2323 b2309 b2308 b2307 b2325

B number ubiX argT yfcF dedD cvpA purF yfcG pdxB usg truA dedA accD folC b2304 folX div yfcI b2322 hisP b2324 fabB hisJ hisQ hisM b2325

Gene name + + + + + ------Strand orientation 189 260 214 211 162 505 215 378 337 270 219 304 422 297 120 331 296 392 257 688 406 260 228 238 92 Protein length 3551 4417 1384 1262 1740 1292 2828 1861 2525 7891 6475 1082 1121 145 436 876 703 792 860 231 365 156 974 652 271 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 15 10 20 12 18 16 19 21 12 18 19 13 12 25 7 9 8 8 4 8 9 8 6 9 4 # of tryptic peptides predicted P P P P P P P P P P P P Protein detected - total list 10 0 0 6 0 0 0 2 0 0 3 2 2 5 1 0 0 1 6 0 4 0 0 1 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 10 0 0 8 0 0 1 3 0 0 3 3 2 5 2 0 0 0 6 0 6 0 0 1 0 # of tryptic peptides detected (short list) P P P P P P P P P P P Protein detected - long list 10 0 0 6 0 0 0 2 0 0 3 2 2 5 1 0 0 0 6 0 4 0 0 1 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD GenProt-PHD

PHD PHD Membrane protein assignment lysine-, arginine-,ornithine-bindingperiplasmicprotein system histidine-binding periplasmicproteinofhigh-affinityhistidinetransport membrane proteinrequiredforcolicinVproduction amidophosphoribosyltransferase =PRPPamidotransferase 3-octaprenyl-4-hydroxybenzoate carboxy-lyase orf, hypotheticalprotein putative PTSsystemenzymeIIAcomponent pseudouridylate synthaseI orf, hypotheticalprotein acetylCoA carboxylase,carboxytransferasecomponent,betasubunit dihydrofolate:folylpolyglutamate synthetase;dihydrofolatesynthetase putative lipoprotein D-erythro-7,8-dihydroneopterin triPepimerase putative S-transferase erythronate-4-phosphate dehyrogenase putative sugarnucleotideepimerase cell divisionprotein orf, hypotheticalprotein 3-oxoacyl-[acyl-carrier-protein] synthaseI histidine transport,membraneproteinM ATP-binding componentofhistidinetransport putative transportprotein histidine transportsystempermeaseprotein orf, hypothetical protein putative peptidase

Gene description Cell processes Cell processes Extrachromosomal Metabolism ofsmallmolecules Miscellaneous Open readingframes Miscellaneous Macromolecule metabolism Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Miscellaneous Cell processes Open readingframes Metabolism ofsmallmolecules Cell processes Cell processes Cell processes Cell processes Open reading frames Miscellaneous

Functional category 1391 1390 1392 1392 1392 1385 1396 1396 1395 1394 1393 1393 1387 1386 1397 1387 1398 1388 1400 1389 1389 1399 1389 1402 1401 Operon ID b2326 b2328 b2327 b2331 b2330 b2329 b2332 b2333 b2334 b2335 b2336 b2337 b2338 b2339 b2341 b2340 b2342 b2343 b2344 b2345 b2348 b2347 b2346 b2349 b2350

B number b2326 mepA yfcA b2331 yfcB aroC b2332 b2333 b2334 b2335 yfcS b2337 yfcU b2339 b2341 b2340 b2342 b2343 fadL b2345 argW yfdC vacJ intC b2350

Gene name + + + + + + + ------Strand orientation 182 274 269 183 421 361 278 179 162 170 250 298 578 187 714 161 436 102 448 352 310 251 385 120 Protein length 1024 3474 2496 1072 1358 818 951 713 416 153 227 174 902 844 530 652 305 207 499 96 70 82 48 54 10 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 10 15 13 12 15 26 35 22 13 19 12 16 5 8 8 5 5 6 8 6 4 4 4 2 # of tryptic peptides predicted P P P P Protein detected - total list 0 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 detected (membrane sample) MP-GenProt MP-GenProt GenProt GenProt PHD PHD PHD Membrane protein assignment putative structuralprotein putative transportingATPase putative adenine-specificmethylase chorismate synthase murein DD-endopeptidase,penicillin-insensitive orf, hypotheticalprotein orf, hypotheticalprotein putative fimbrial-likeprotein orf, hypotheticalprotein putative fimbrialprotein putative chaperone putative outermembraneprotein putative outermembraneprotein orf, hypotheticalprotein putative fimbrial-likeprotein putative enzyme putative acyltransferase orf, hypotheticalprotein transport oflong-chainfattyacids;sensitivitytophage T2 orf, hypotheticalprotein putative transport lipoprotein precursor tRNA-Arg putative prophage Sf6-likeintegrase orf, hypothetical protein

Gene description Miscellaneous Miscellaneous Open readingframes Metabolism ofsmallmolecules Structural elements Open readingframes Open readingframes Miscellaneous Miscellaneous Miscellaneous Miscellaneous Miscellaneous Miscellaneous Global functions Miscellaneous Open readingframes Miscellaneous Open readingframes Cell processes Open readingframes Miscellaneous Macromolecule metabolism tRNA Miscellaneous Open reading frames

Functional category 1402 1402 1402 1402 1402 1403 1404 1404 1404 1404 1404 1404 1404 1406 1405 1407 1407 1408 1409 1410 1412 1411 1413 1414 Operon ID b2352 b2351 b2353 b2354 b2355 b2356 b2357 b2358 b2359 b2360 b2361 b2362 b2363 b2364 b2365 b2366 b2367 b2368 b2371 b2370 b2369 b2373 b2372 b2374 b2375

B number b2352 b2351 b2353 b2354 yfdL yfdM yfdN yfdO b2359 b2360 b2361 b2362 b2363 dsdC dsdX dsdA emrY emrK yfdE evgS evgA b2373 b2372 b2374 b2375

Gene name + + + + + + + + + + + + ------Strand orientation 1197 443 306 114 146 172 102 164 122 148 274 187 120 101 311 445 442 512 387 394 204 564 314 416 211 Protein length 1497 1039 101 163 212 180 125 159 102 154 22 98 14 81 79 18 94 82 96 53 51 19 20 75 59 mRNA intensity A A A A A A A A A A A A A A A A A A A A A P P P P mRNA present 10 20 10 14 12 18 23 47 11 19 25 12 18 4 2 5 5 9 6 5 4 7 9 7 9 # of tryptic peptides predicted

Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD Membrane protein assignment putative glycanbiosynthesisenzyme putative ligase orf, hypotheticalprotein orf, hypotheticalprotein putative RNApolymerasebeta orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein D-(deaminase)transcriptionalactivator transport systempermease(serine?) D-serine dehydratase(deaminase) multidrug resistanceproteinY putative positivetranscriptionregulator(sensorEvgS) multidrug resistanceproteinK putative sensorforregulatorEvgA putative enzyme putative receptorprotein putative enzyme putative enzyme orf, hypothetical protein

Gene description Open readingframes Miscellaneous Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Cell processes Miscellaneous Cell processes Miscellaneous Open readingframes Miscellaneous Miscellaneous Open reading frames Open reading frames

Functional category 1414 1414 1415 1416 1416 1416 1416 1416 1417 1418 1419 1419 1419 1420 1421 1421 1422 1423 1422 1423 1424 1424 1425 1426 1427 Operon ID b2378 b2376 b2381 b2380 b2379 b2377 b2382 b2383 b2384 b2385 b2386 b2387 b2390 b2389 b2388 b2391 b2392 b2398 b2397 b2396 b2395 b2394 b2393 b2399 b2400

B number ddg b2376 b2381 b2380 b2379 b2377 b2382 b2383 b2384 b2385 b2386 b2387 b2390 b2389 glk b2391 b2392 yfeC alaW alaX yfeA yi81_3 nupC yfeD gltX

Gene name + + + + + + + + + + + + ------Strand orientation 328 244 565 412 285 831 345 361 415 108 108 418 321 114 412 119 768 372 400 130 471 91 80 Protein length 1003 1515 4157 4853 1255 1430 126 786 560 426 213 147 105 164 188 101 268 432 269 295 26 58 53 49 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P mRNA present 22 16 20 13 16 33 19 17 11 13 14 32 16 23 1 4 4 3 7 7 8 7 4 # of tryptic peptides predicted P P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 7 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 1 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 8 # of tryptic peptides detected (short list) P P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 7 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD PHD PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein putative aminotransferase orf, hypotheticalprotein putative sensorprotein putative heatshockprotein putative 2-componenttranscriptionalregulator putative ARAC-typeregulatoryprotein putative PTSsystemenzymeIIAcomponent,I orf, hypotheticalprotein putative peptidase putative transportprotein putative PTSsystemenzymeIIBcomponent orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein tRNA-Ala tRNA-Ala putative transportsystempermease orf, hypotheticalprotein IS186 hypotheticalprotein permease oftransportsystemfor3nucleosides orf, hypotheticalprotein glutamate tRNA synthetase,catalyticsubunit orf, hypothetical protein

Gene description Open readingframes Miscellaneous Open readingframes Miscellaneous Miscellaneous Miscellaneous Miscellaneous Miscellaneous Open readingframes Miscellaneous Cell processes Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Open readingframes tRNA tRNA Miscellaneous Open readingframes Miscellaneous Cell processes Open readingframes Macromolecule metabolism Open reading frames

Functional category 1429 1431 1428 1432 1430 1432 1432 1433 1433 1433 1433 1434 1433 1435 1436 1436 1437 1440 1439 1438 1441 1442 1441 Operon ID b2425 b2424 b2423 b2405 b2404 b2403 b2402 b2401 b2406 b2407 b2408 b2409 b2411 b2410 b2412 b2413 b2414 b2416 b2415 b2418 b2417 b2419 b2422 b2421 b2420

B number cysP cysU cysW xapR lysV valY valX valU xapB xapA yfeN yfeR lig yfeH zipA cysZ cysK ptsI ptsH pdxK crr yfeK cysA cysM b2420

Gene name + + + + + + + + + + + ------Strand orientation 338 277 149 294 418 277 254 308 671 332 328 253 323 575 283 169 124 365 303 244 85 Protein length 23747 25758 21559 21158 13305 26197 20122 3266 1361 1423 8031 2069 1725 161 360 107 920 645 967 460 672 308 92 71 94 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 21 14 12 14 32 13 28 10 19 16 12 7 6 6 8 7 6 5 3 6 7 # of tryptic peptides predicted P P P P P P P Protein detected - total list 12 15 0 0 0 0 0 0 0 0 0 1 0 0 8 5 0 0 1 2 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 10 10 9 0 0 0 0 0 0 0 0 0 1 0 0 4 0 0 1 1 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 12 15 0 0 0 0 0 0 0 0 0 0 0 0 8 5 0 0 0 2 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 1 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment thiosulfate binding protein lysine tRNA(duplicateoflysT,W) tRNA-Val tRNA-Val tRNA1(duplicateofvalT,X,Y) sulfate, thiosulfate transportsystempermease Tprotein sulfate transportsystempermease Wprotein resistance ATP-binding componentof sulfatepermeaseAprotein;chromate regulator forxapA xanthosine permease xanthosine phosphorylase putative sugarhydrolase putative transcriptionalregulatorLYSR-type putative cytochromeoxidase DNA ligase cell divisionproteininvolvedinFtsZring required forsulfatetransport PTS systemproteinHPr cysteine synthaseA,O-acetylserinesulfhydrolaseA PTS system,glucose-specificIIAcomponent PEP-protein phosphotransferasesystemenzymeI pyridoxal/pyridoxine/pyridoxamine kinase cysteine synthaseB,O-acetylserinesulfhydrolaseB orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Cell processes tRNA tRNA tRNA tRNA Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Miscellaneous Miscellaneous Miscellaneous Macromolecule metabolism Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes

Functional category 1455 1455 1455 1455 1443 1443 1443 1444 1445 1446 1447 1448 1449 1451 1450 1452 1452 1453 1455 1454 1454 Operon ID b2426 b2427 b2428 b2430 b2429 b2431 b2432 b2436 b2435 b2434 b2433 b2437 b2438 b2439 b2440 b2441 b2442 b2443 b2444 b2445 b2446 b2447 b2448 b2449 b2450

B number ucpA yfeT yfeU b2430 b2429 b2431 b2432 hemF amiA b2434 b2433 yfeG b2438 b2439 eutC eutB b2442 b2443 b2444 b2445 b2446 b2447 b2448 b2449 b2450

Gene name + + + + + + + + + + + + + + ------Strand orientation 285 285 298 463 474 308 191 299 289 178 151 350 168 219 295 467 431 213 127 138 197 130 130 279 81 Protein length 1065 1098 1995 857 258 812 356 258 720 795 303 536 220 549 465 739 968 331 260 119 336 192 115 838 42 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 17 16 15 21 15 14 10 13 10 16 21 25 11 16 9 8 4 8 6 5 5 7 9 7 3 # of tryptic peptides predicted P P P P Protein detected - total list 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 # of tryptic peptides detected (total list)

Protein detected - short list 2 1 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 # of tryptic peptides detected (short list) P P P P Protein detected - long list 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) PHD PHD Membrane protein assignment putative oxidoreductase orf, hypotheticalprotein putative regulator putative PTSenzymeII putative beta-lactamase orf, hypotheticalprotein N-acetylmuramoyl-l-alanine amidaseI orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein coproporphyrinogen IIIoxidase putative ARAC-typeregulatoryprotein orf, hypotheticalprotein orf, hypotheticalprotein ethanolamine ammonia-lyase,lightchain ethanolamine ammonia-lyase,heavychain putative prophageintegrase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein orf, hypothetical protein

Gene description Miscellaneous Open readingframes Miscellaneous Cell processes Miscellaneous Open readingframes Structural elements Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open reading frames Open reading frames

Functional category 1456 1457 1458 1458 1458 1459 1462 1461 1460 1461 1462 1463 1463 1463 1463 1463 1464 1465 1466 1466 1467 1467 1468 1469 1468 Operon ID b2472 b2471 b2470 b2459 b2454 b2451 b2473 b2460 b2455 b2452 b2474 b2461 b2457 b2456 b2453 b2475 b2462 b2458 b2466 b2465 b2464 b2463 b2467 b2468 b2469

B number dapE yffB acrD b2459 eutJ b2451 ypfH b2460 eutE eutH ypfI b2461 cchA cchB eutG b2475 b2462 eutI b2466 tktB talA maeB yffH yffG narQ

Gene name + + + + + + ------Strand orientation 1037 375 118 267 278 467 240 233 467 408 671 159 111 404 287 135 338 347 667 316 759 191 659 566 95 Protein length 1042 2244 7999 4835 163 399 167 145 112 283 137 151 371 298 162 331 129 868 251 137 202 47 84 73 77 mRNA intensity A A A A A A A A A A A A A A A A P P P P P P P P P mRNA present 38 17 11 10 16 15 10 25 11 24 21 34 16 20 27 29 4 6 3 8 6 6 9 7 6 # of tryptic peptides predicted P P P P P P Protein detected - total list 12 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 6 8 0 0 0 1 0 # of tryptic peptides detected (total list)

P P P Protein detected - short list 12 10 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 1 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 12 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 8 0 0 0 1 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD

PHD Membrane protein assignment orf, hypotheticalprotein Aminoglycoside effluxpump NarP andnarL) sensor fornitratereductasesystem,proteinhistidine kinase(actson transferase ethanolamine utilization;homologofSalmonellaacetyl/butyrylP containing alcoholdehydrogenase ethanolamine utilization;homologofSalmonellaenzyme,similartoiron- N-succinyl-diaminopimelate deacylase orf, hypotheticalprotein ethanolamine utilization;homologofSalmonellagene orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein detox protein ethanolamine utilization;similartoacetaldehydedehydrogenase ethanolamine utilization;homologofSalmonellaputativetransportprotein orf, hypothetical protein orf, hypotheticalprotein detox protein orf, hypothetical protein transketolase 2isozyme transaldolase A multimodular MaeB:putativemalicoxidoreductase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative oxidoreductase,Fe-Ssubunit

Gene description Open readingframes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open reading frames Open readingframes Miscellaneous Open reading frames Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Miscellaneous

Functional category 1479 1478 1477 1471 1470 1479 1471 1470 1470 1480 1471 1470 1470 1470 1480 1471 1471 1480 1473 1473 1472 1471 1474 1475 1476 Operon ID b2481 b2480 b2479 b2478 b2477 b2476 b2487 b2486 b2485 b2484 b2483 b2482 b2488 b2489 b2490 b2491 b2492 b2493 b2495 b2494 b2496 b2500 b2499 b2498 b2497

B number hyfA bcp gcvR dapA nlpB purC hyfG hyfF hyfE hyfD hyfC hyfB hyfH hyfI b2490 hyfR focB perM b2495 b2494 b2496 purN purM upp uraA

Gene name + + + + + + + + + + + + + + + + + + ------Strand orientation 218 156 212 292 345 237 555 526 216 479 322 672 181 252 158 663 282 353 119 487 248 212 345 217 429 Protein length 5167 3742 8978 3434 6714 1327 3201 3990 6828 1852 260 230 191 118 173 216 752 546 93 34 86 90 58 65 17 mRNA intensity A A A A A A A A A A A A P P P P P P P P P P P P P mRNA present 10 11 17 13 10 27 11 11 18 10 30 17 10 11 11 10 7 7 6 9 4 1 7 9 7 # of tryptic peptides predicted P P P P P P P Protein detected - total list 5 1 2 4 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 5 1 5 0 8 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 5 5 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 5 1 2 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt Membrane protein assignment thiol peroxidase,thioredoxindependent transcriptional regulationofgcvoperon dihydrodipicolinate synthase lipoprotein-34 SAICAR synthetase phosphoribosylaminoimidazole-succinocarboxamide synthetase= hydrogenase 4Fe-Ssubunit hydrogenase 4membranesubunit hydrogenase 4membranesubunit hydrogenase 4membranesubunit hydrogenase 4membranesubunit hydrogenase 4membranesubunit hydrogenase 4subunit hydrogenase 4Fe-Ssubunit hydrogenase 4Fe-Ssubunit putative proteinprocessingelement putative 2-componentregulator,interactionwithsigma54 probable formatetransporter(formatechannel2) orf, hypotheticalprotein putative permease putative oxidoreductase phosphoribosylglycinamide formyltransferase 1 phosphoribosylaminoimidazole synthetase =AIRsynthetase uracil phosphoribosyltransferase putative DNAreplicationfactor uracil transport

Gene description Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Miscellaneous Cell processes Open readingframes Miscellaneous Miscellaneous Metabolism of smallmolecules Metabolism of smallmolecules Metabolism ofsmallmolecules Open readingframes Cell processes

Functional category 1483 1483 1482 1482 1481 1484 1484 1484 1484 1484 1484 1484 1484 1484 1484 1485 1485 1487 1486 1487 1490 1490 1489 1488 1488 Operon ID b2502 b2501 b2505 b2504 b2503 b2506 b2509 b2508 b2507 b2511 b2510 b2518 b2517 b2516 b2515 b2514 b2513 b2512 b2519 b2522 b2521 b2520 b2525 b2524 b2523

B number ppx ppk b2505 b2504 b2503 b2506 xseA guaB guaA b2511 b2510 ndk yfgB yfgA gcpE hisS b2513 yfgL pbpC sseB sseA b2520 fdx yfhJ pepB

Gene name + + + + + + + ------Strand orientation 1653 513 688 172 747 179 456 488 525 503 143 384 337 372 424 206 392 770 261 334 111 456 63 83 66 Protein length 19329 1102 5523 2859 1211 3428 1419 3338 2958 1897 2053 2771 3157 3045 549 586 100 122 141 339 553 534 599 875 50 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 41 27 24 17 27 27 26 19 22 23 10 15 79 41 13 25 4 5 6 3 9 6 6 6 3 # of tryptic peptides predicted P P P P P P P P P P P P P P P P Protein detected - total list 11 10 16 1 1 1 0 0 0 5 0 0 2 2 3 6 9 1 5 0 0 6 0 2 0 # of tryptic peptides detected (total list) P P P P P P P Protein detected - short list 10 12 17 0 0 1 0 0 0 7 0 1 3 3 2 7 1 0 5 0 0 6 0 2 1 # of tryptic peptides detected (short list) P P P P P P P P P P P P Protein detected - long list 11 10 16 1 0 1 0 0 0 5 0 0 2 2 0 6 9 0 0 0 0 6 0 2 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 1 0 0 0 0 0 0 0 0 0 0 3 0 0 1 5 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt MP-GenProt MP-PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein putative cytochromeC-typebiogenesisprotein putative outermembranelipoprotein IMP dehydrogenase GMP synthetase(glutamine-hydrolyzing) putative membraneprotein orf, hypotheticalprotein exonuclease VII,largesubunit orf, hypotheticalprotein putative membraneprotein orf, hypotheticalprotein histidine tRNAsynthetase orf, hypotheticalprotein putative serine/threonineproteinkinase putative GTP-bindingfactor nucleoside diphosphatekinase putative thiosulfatesulfurtransferase orf, hypotheticalprotein Penicillin bindingprotein1C(PBP1C) [2FE-2S] ferredoxin, electroncarrerprotein orf, hypothetical protein aminopeptidase B,acyteinylglycinase (2ndmodule) enhanced serinesensitivity

Gene description Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Open readingframes Macromolecule metabolism Open readingframes Miscellaneous Open readingframes Macromolecule metabolism Open readingframes Macromolecule metabolism Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open readingframes Miscellaneous Metabolism of smallmolecules Open reading frames Macromolecule metabolism Miscellaneous

Functional category 1491 1494 1492 1493 1495 1496 1496 1495 1498 1497 1501 1500 1500 1499 1499 1499 1498 1502 1504 1503 1503 1507 1507 1506 1505 Operon ID b2534 b2533 b2532 b2531 b2530 b2529 b2528 b2527 b2526 b2535 b2536 b2537 b2538 b2539 b2540 b2541 b2542 b2544 b2543 b2545 b2546 b2547 b2548 b2550 b2549

B number b2534 suhB b2532 b2531 iscS iscU iscA yfhE hscA csiE hcaT hcaR hcaA1 hcaA2 hcaC hcaB hcaD yphB yphA yphC yphD yphE yphF yphH yphG

Gene name + + + + + + + + + + ------Strand orientation 1124 293 267 246 162 412 128 107 171 616 433 379 296 453 172 106 270 400 290 164 364 332 503 327 399 Protein length 1221 4841 5845 6702 5460 1758 2192 112 479 485 232 747 308 145 269 258 255 238 738 165 174 149 236 172 149 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 22 26 11 16 14 10 22 11 10 14 17 24 17 52 17 8 9 7 6 9 8 2 4 7 6 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 2 3 9 5 3 1 3 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 2 2 9 5 1 1 3 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 2 3 9 5 3 1 3 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD

PHD Membrane protein assignment putative ATPsynthasebetasubunit orf, hypotheticalprotein putative FeSassemblyprotein orf, hypotheticalprotein heat shockprotein,chaperone,memberofHsp70proteinfamily modulate RNAseIIIlethalaction enhances synthesisofsigma32inmutant;extragenicsuppressor,may module) cysteine desulfurase(tRNAsulfurtransferase)PLP-dependent(1st repair putative regulatorbelievedtobeinvolvedinFe-Sproteinformationor putative enzyme(3.4.-) orf, hypotheticalprotein MFS (majorfacilitatorsuperfamily)transporter transcriptional activatorofhcacluster large terminalsubunitofphenylpropionatedioxygenase small terminalsubunitofphenylpropionatedioxygenase ferredoxin subunitofphenylpropionatedioxygenase 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase ferredoxin reductasesubunitofphenylpropionatedioxygenase orf, hypotheticalprotein orf, hypotheticalprotein putative oxidoreductase putative transportsystempermeaseprotein putative ATP-bindingcomponent ofatransportsystem orf, hypothetical protein putative LACI-typetranscriptional regulator putative NAGC-like transcriptionalregulator

Gene description Open readingframes Open readingframes Miscellaneous Cell processes Cell processes Global functions Macromolecule metabolism Cell processes Open readingframes Miscellaneous Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Cell processes Miscellaneous Open reading frames Cell processes Open reading frames

Functional category 1510 1509 1508 1507 1507 1511 1508 1508 1512 1513 1514 1515 1516 1516 1516 1516 1516 1516 1517 1517 1517 1517 1518 1517 1519 Operon ID b2551 b2552 b2553 b2559 b2558 b2557 b2556 b2555 b2554 b2560 b2561 b2563 b2562 b2565 b2564 b2566 b2568 b2567 b2570 b2569 b2574 b2573 b2572 b2571 b2575

B number glyA hmpA glnB yfhC yfhD purL yfhK yfhG yfhA yfhB yfhH acpS yfhL recO pdxJ era lepB rnc rseC lepA nadB rpoE rseA rseB yfiC

Gene name + + + + + ------Strand orientation 1295 417 396 112 178 472 496 237 444 190 306 126 242 243 301 324 226 159 599 540 191 216 318 285 86 Protein length 10756 1010 1241 1255 1689 1797 1535 3926 7387 1302 488 882 479 879 675 319 310 891 526 537 994 587 504 377 89 mRNA intensity P P P P P P P P P P P P P P P P P P P P P P P P P mRNA present 19 18 25 56 11 18 21 14 13 13 10 25 11 26 7 8 9 4 7 9 8 5 9 7 9 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 14 19 0 1 0 0 0 0 0 1 0 0 0 1 0 0 3 0 5 0 0 0 1 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 22 8 0 1 0 0 0 0 0 0 0 0 0 1 0 0 3 0 7 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 14 19 0 1 0 0 0 0 0 0 0 0 0 1 0 0 3 0 5 0 0 0 1 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD MP Membrane protein assignment serine hydroxymethyltransferase dihydropteridine reductase,ferrisiderophorereductaseactivity putative periplasmicbindingtransportprotein phosphoribosylformyl-glycineamide synthetase=FGAM putative alphahelixprotein putative 2-componenttranscriptionalregulator regulatory proteinP-IIforglutaminesynthetase putative 2-componentsensorprotein putative deaminase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein pyridoxine biosynthesis CoA:apo-[acyl-carrier-protein] pantetheinephosphotransferase protein interactswithRecRandpossiblyRecFproteins RNase III,dsRNA GTP-binding protein GTP-binding elongationfactor,maybeinnermembrane protein leader peptidase(signalI) RNA polymerase,sigma-E factor;heatshockandoxidativestress sigma-E factor,negativeregulatory protein regulates activityofsigma-Efactor sigma-E factor,negativeregulatoryprotein quinolinate synthetase, Bprotein putative enzyme

Gene description Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Miscellaneous Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Macromolecule metabolism Global functions Macromolecule metabolism Cell processes Global functions Global functions Global functions Global functions Metabolism of smallmolecules Miscellaneous

Functional category 1520 1521 1526 1525 1523 1523 1522 1524 1527 1527 1529 1528 1530 1530 1531 1531 1531 1533 1532 1535 1535 1534 1534 1536 1537 Operon ID b2576 b2577 b2579 b2578 b2581 b2580 b2582 b2583 b2588 b2587 b2586 b2585 b2584 b2589 b2590 b2591 b2593 b2592 b2596 b2595 b2594 b2597 b2600 b2599 b2598

B number srmB yfiE yfiD yfiK yfiF ung trxC yfiP rrfG kgtP yfiM pssA yfiQ rrlG gltW rrsG yfiH clpB b2596 b2595 sfhB yfiA tyrA pheA pheL

Gene name + + + + + + + + + + + + + ------Strand orientation 444 308 127 195 345 229 139 240 432 452 886 243 857 245 326 113 373 386 90 68 15 Protein length 89102 75748 40559 84250 11790 1023 6153 1700 1474 1606 3791 1954 1162 850 297 394 235 892 641 114 169 371 171 641 37 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 23 17 13 14 26 34 46 12 16 14 15 21 9 2 8 8 7 5 4 1 6 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 14 2 0 4 0 1 2 1 0 0 0 1 0 0 2 0 0 0 2 2 3 # of tryptic peptides detected (total list) P P Protein detected - short list 16 1 0 5 0 0 2 2 0 0 0 1 0 0 0 1 0 0 1 1 3 # of tryptic peptides detected (short list) P P P P P P P P P P Protein detected - long list 14 2 0 4 0 1 2 1 0 0 0 1 0 0 0 0 0 0 2 2 3 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt PHD Membrane protein assignment ATP-dependent RNAhelicase putative transcriptionalregulatorLYSR-type orf, hypotheticalprotein uracil-DNA-glycosylase putative formateacetyltransferase orf, hypotheticalprotein putative thioredoxin-likeprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein alpha-ketoglutarate permease phosphatidylserine synthase;phospholipidsynthesis 5S ribosomalRNA 23S ribosomalRNA tRNA-Sec heat shockprotein 16S ribosomalRNA orf, hypotheticalprotein suppressor offtsHmutation orf, hypotheticalprotein orf, hypotheticalprotein chorismate mutase-P andprephenatedehydratase leader peptideofchorismate mutase-P-prephenatedehydratase putative yhbHsigma54modulator chorismate mutase-T andprephenatedehydrogenase

Gene description Macromolecule metabolism Miscellaneous Miscellaneous Macromolecule metabolism Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Cell processes Macromolecule metabolism Structural elements Structural elements tRNA Macromolecule metabolism Structural elements Macromolecule metabolism Miscellaneous Open readingframes Open readingframes Metabolism of smallmolecules Metabolism ofsmallmolecules Miscellaneous Metabolism of smallmolecules

Functional category 1538 1539 1540 1542 1541 1543 1544 1546 1544 1544 1547 1545 1548 1550 1549 1549 1550 1551 1551 1550 1552 Operon ID b2622 b2615 b2602 b2601 b2623 b2616 b2603 b2624 b2618 b2617 b2605 b2604 b2625 b2619 b2607 b2606 b2621 b2620 b2608 b2613 b2612 b2611 b2610 b2609 b2614

B number intA yfjB yfiL aroF yfjH recN b2603 alpA b2618 smpA yfiB yfiN yfjI b2619 trmD rplS ssrA smpB rimM yfjD ypjE b2611 ffh rpsP grpE

Gene name + + + + + + + + + + + + + + + ------Strand orientation 413 292 134 356 318 553 172 102 160 408 469 158 255 115 160 185 227 196 288 453 197 70 50 82 Protein length 81113 18470 19104 37205 1894 1068 3359 1595 1726 2920 281 575 241 104 303 250 467 649 375 697 334 424 385 16 28 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 17 23 10 13 23 13 27 10 21 4 6 1 3 7 7 7 7 7 3 9 6 5 6 9 # of tryptic peptides predicted P P P P P P P Protein detected - total list 2 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 1 5 1 3 0 0 2 0 # of tryptic peptides detected (total list) P P Protein detected - short list 2 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 1 3 4 4 0 0 3 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 2 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 1 5 1 3 0 0 2 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 detected (membrane sample) MP-GenProt MP-GenProt PHD PHD PHD Membrane protein assignment incomplete polypeptides 10Sa RNA,non-ribosomalmediatestaggingand proteolysisof protein repair phage lambdareplication;hostDNAsynthesis;heatshockprotein; synthetase, tyrosinerepressible) 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase(DAHP prophage CP4-57integrase orf, hypotheticalprotein orf, hypotheticalprotein putative histone protein usedinrecombinationandDNArepair orf, hypotheticalprotein small membraneproteinA orf, hypotheticalprotein prophage CP4-57 regulatoryproteinalpA orf, hypotheticalprotein 50S ribosomalsubunitproteinL19 putative outermembraneprotein orf, hypothetical protein small proteinB orf, hypotheticalprotein tRNA methyltransferase;(guanine-7-)-methyltransferase GTP-binding exportfactorbindstosignalsequence,GTPandRNA 30S ribosomalsubunitproteinS16 16S rRNAprocessingprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transportprotein

Gene description Structural elements Extrachromosomal Metabolism ofsmallmolecules Extrachromosomal Open readingframes Open readingframes Miscellaneous Macromolecule metabolism Open readingframes Open readingframes Open readingframes Extrachromosomal Open readingframes Structural elements Miscellaneous Open reading frames Open readingframes Open readingframes Macromolecule metabolism Cell processes Structural elements Macromolecule metabolism Open readingframes Open readingframes Open readingframes

Functional category 1560 1552 1566 1561 1553 1567 1562 1554 1563 1554 1568 1564 1555 1554 1569 1565 1564 1556 1558 1557 1557 1559 1559 1559 Operon ID b2626 b2627 b2628 b2629 b2631 b2630 b2632 b2633 b2634 b2635 b2636 b2637 b2638 b2641 b2640 b2639 b2642 b2643 b2644 b2645 b2646 b2648 b2647 b2649 b2650

B number yfjJ yfjK yfjL yfjM yfjO yfjN yfjP yfjQ yfjR b2635 b2636 yfjT b2638 b2641 b2640 b2639 yfjW yfjX yfjY yfjZ ypjF b2648 ypjA b2649 b2650

Gene name + + + + + + + + + + + + + + ------Strand orientation 1569 208 729 538 106 357 289 273 233 130 230 155 104 172 567 152 160 105 109 263 160 87 38 66 47 Protein length 1785 172 414 205 146 107 259 276 154 120 30 88 47 21 61 12 41 43 54 83 59 72 28 44 38 mRNA intensity A A A A A A A A A A A A A A A A A A A P P P P P P mRNA present 37 29 12 16 12 10 12 18 43 10 8 6 6 5 6 7 2 0 8 3 7 4 3 2 8 # of tryptic peptides predicted

Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample)

PHD PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative celldivisionprotein orf, hypotheticalprotein orf, hypotheticalprotein putative GTP-bindingprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative pumpprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative DNArepairprotein orf, hypotheticalprotein putative ATP-bindingcomponent ofatransportsystem orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein orf, hypothetical protein

Gene description Open readingframes Open readingframes Open readingframes Cell processes Open readingframes Open readingframes Miscellaneous Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open reading frames Open reading frames

Functional category 1570 1571 1571 1573 1572 1573 1574 1575 1576 1576 1576 1576 1577 1578 1577 1578 1579 1580 1580 1581 1582 1581 1583 1584 1585 Operon ID b2651 b2652 b2653 b2654 b2655 b2657 b2656 b2658 b2663 b2662 b2661 b2660 b2659 b2671 b2670 b2669 b2668 b2667 b2666 b2665 b2664 b2675 b2674 b2673 b2672

B number b2651 ileY b2653 b2654 b2655 b2657 b2656 b2658 gabP gabT gabD ygaF b2659 ygaC b2670 stpA ygaP b2667 b2666 ygaU ygaE nrdE nrdI nrdH ygaM

Gene name + + + + + + + + + + + + + + + + + + + ------Strand orientation 110 164 210 466 426 482 444 360 114 149 134 174 149 226 714 136 113 43 57 62 90 99 52 81 Protein length 1841 2332 3553 1281 4742 1323 3443 1277 1904 3547 4994 265 269 396 215 183 552 15 31 54 47 22 49 5 5 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 21 22 21 18 12 12 16 32 1 2 6 4 8 6 6 9 5 1 8 3 8 7 5 4 # of tryptic peptides predicted P P P P P Protein detected - total list 0 0 0 0 0 0 0 5 6 0 0 0 4 0 0 3 0 0 0 0 0 0 1 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 0 0 0 0 0 0 7 8 0 3 0 4 0 0 1 0 0 0 0 0 0 1 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 0 0 0 0 0 0 0 5 6 0 0 0 4 0 0 1 0 0 0 0 0 0 1 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD PHD PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein tRNA-Ile orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative enzyme 4-aminobutyrate aminotransferaseactivity succinate-semialdehyde dehydrogenase,NADP-dependentactivity orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein DNA-binding protein;H-NS-likechaperoneactivity; RNAsplicing? orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transcriptionalregulator transport permeaseproteinofgamma-aminobutyrate orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein glutaredoxin-like protein;hydrogen donor orf, hypotheticalprotein orf, hypotheticalprotein ribonucleoside-diphosphate reductase2, alphasubunit

Gene description Open readingframes tRNA Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Macromolecule metabolism Open readingframes Open readingframes Open readingframes Miscellaneous Cell processes Open readingframes Open readingframes Metabolism of smallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism of smallmolecules

Functional category 1586 1587 1588 1588 1588 1589 1591 1591 1591 1591 1590 1595 1594 1593 1592 1591 1591 1596 1594 1599 1599 1598 1597 1599 Operon ID b2685 b2684 b2683 b2682 b2681 b2700 b2698 b2697 b2686 b2680 b2679 b2678 b2676 b2699 b2690 b2689 b2688 b2687 b2677 b2696 b2695 b2694 b2693 b2692 b2691

B number emrA emrR ygaH b2682 b2681 ygaD oraA alaS emrB b2680 proX proW nrdF recA yqaB b2689 gshA ygaG proV csrA serV argV argY argZ argQ

Gene name + + + + + + + + + + + ------Strand orientation 390 176 111 245 305 165 166 876 512 330 354 319 353 188 142 518 171 400 88 61 Protein length 4437 1979 1077 1185 6894 6568 5333 3341 1162 4821 3559 4860 7783 3333 1023 1106 1154 1041 337 171 119 158 472 418 75 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 24 49 11 12 15 21 13 8 4 4 4 1 7 3 8 3 7 5 9 2 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 13 1 0 0 0 0 0 2 7 2 0 6 0 0 4 3 0 4 0 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 15 2 0 0 0 0 0 2 8 0 0 6 0 0 5 1 0 1 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 13 1 0 0 0 0 0 2 7 1 0 6 0 0 4 3 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 4 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD PHD PHD Membrane protein assignment regulator ofplasmidmcrBoperon(microcinB17synthesis) orf, hypotheticalprotein orf, hypotheticalprotein putative transportprotein orf, hypotheticalprotein orf, hypothetical protein alanyl-tRNA synthetase multidrug resistancesecretionprotein high-affinity transportsystemforglycinebetaineandproline and ATP-dependent coprotease DNA strandexchangeand renaturation,DNA-dependentATPase,DNA- cell sizeandsurfaceproperties carbon storageregulator;controlsglycogensynthesis, gluconeogenesis, high-affinity transportsystemforglycinebetaineandproline proline ATP-binding componentoftransportsystemforglycine,betaineand regulator, OraAprotein orf, hypotheticalprotein gamma-glutamate-cysteine ligase orf, hypotheticalprotein multidrug resistance;probablymembranetranslocase ribonucleoside-diphosphate reductase2,betachain,frag tRNA-Ser tRNA-Arg arginine tRNA2(duplicateofargV,Q,Z) tRNA-Arg tRNA-Arg putative phosphatase

Gene description Extrachromosomal Open readingframes Open readingframes Open readingframes Open readingframes Open reading frames Macromolecule metabolism Cell processes Cell processes Macromolecule metabolism Global functions Cell processes Cell processes Miscellaneous Open readingframes Metabolism ofsmallmolecules Miscellaneous Cell processes Metabolism ofsmallmolecules tRNA tRNA tRNA tRNA tRNA Open readingframes

Functional category 1603 1602 1602 1601 1601 1612 1609 1604 1600 1611 1608 1600 1600 1610 1607 1606 1605 1604 1599 1607 Operon ID b2725 b2719 b2718 b2716 b2704 b2701 b2720 b2717 b2705 b2703 b2702 b2721 b2706 b2722 b2707 b2723 b2708 b2724 b2709 b2710 b2711 b2712 b2713 b2714 b2715

B number hycA hycG hycH ascB srlB mltB hycF hycI srlD srlE srlA hycE gutM hycD srlR hycC gutQ hycB ygaA b2710 ygbD hypF hydN ascG ascF

Gene name + + + + + + + + + + + ------Strand orientation 153 255 136 474 123 361 180 156 259 319 187 569 119 307 257 608 308 203 529 479 377 750 175 337 485 Protein length 259 326 170 272 972 365 376 302 111 602 138 233 560 187 354 148 153 229 183 443 249 40 40 96 84 mRNA intensity A A A A A A A A A A A A A A A A A P P P P P P P P mRNA present 12 23 12 12 29 12 13 14 21 22 16 23 15 14 9 6 9 2 5 5 9 5 6 9 9 # of tryptic peptides predicted

Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD MP-GenProt MP-GenProt GenProt GenProt GenProt PHD PHD Membrane protein assignment formate hydrogenlyase (FHL)complex) probable smallsubunitofhydrogenase-3, iron-sulfurprotein(partof complex) processing oflargesubunit(HycE)hydrogenase3 (partoftheFHL hydrogenase 3 protease involvedinprocessingC-terminalendofthe largesubunitof glucosides PTS systemenzymeIIABC(asc),cryptic,transportsspecificbeta- IIC components PTS system,glucitol/sorbitol-specificIIBcomponentandsecondoftwo transcriptional repressionofhycandhyp operons 6-phospho-beta-glucosidase; cryptic PTS system,glucitol/sorbitol-specificenzymeIIAcomponent membrane-bound lyticmureintransglycosylaseB hydrogenase activity PTS system,glucitol/sorbitol-specificIICcomponent,oneoftwo glucitol (sorbitol)-6-phosphatedehydrogenase probable iron-sulfurproteinofhydrogenase3(part FHLcomplex) glucitol operonactivator large subunitofhydrogenase3(partFHLcomplex) membrane-spanning protein ofhydrogenase3(partFHLcomplex) regulator forgut(srl),glucitoloperon membrane-spanning protein ofhydrogenase3(partFHLcomplex) orf, hypotheticalprotein putative 2-componenttranscriptionalregulator putative flavodoxin putative oxidoreductase transcriptional regulatoryprotein involved inelectrontransportfromformatetohydrogen,Fe-Scenters ascBF operonrepressor

Gene description Metabolism of smallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Cell processes Cell processes Metabolism of smallmolecules Metabolism ofsmallmolecules Cell processes Structural elements Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Miscellaneous Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 1622 1622 1621 1620 1614 1622 1620 1614 1613 1622 1614 1614 1622 1614 1622 1622 1614 1622 1614 1615 1616 1616 1617 1618 1619 Operon ID b2742 b2732 b2729 b2728 b2726 b2744 b2743 b2733 b2730 b2727 b2750 b2749 b2748 b2747 b2746 b2745 b2734 b2731 b2735 b2736 b2737 b2738 b2739 b2740 b2741

B number nlpD ygbA hypD hypC hypA surE pcm mutS hypE hypB cysC ygbE b2748 ispD ispF ygbO pphB fhlA ygbI b2736 b2737 ygbL ygbM b2740 rpoS

Gene name + + + + + + + + + + + + + ------Strand orientation 379 117 373 116 253 208 853 322 290 201 107 103 236 159 349 218 692 265 302 388 212 258 454 330 90 Protein length 41875 11146 1892 1667 2105 1562 1528 2505 247 157 674 362 974 379 447 298 332 300 470 179 252 145 87 93 85 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 10 15 10 39 13 10 14 20 35 11 14 16 17 6 6 6 8 8 6 7 1 9 6 9 9 # of tryptic peptides predicted

P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 1 0 0 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

P P P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt PHD Membrane protein assignment pleiotrophic effectson3hydrogenaseisozymes phase relatedproteins RNA polymerase,sigmaS(sigma38)factor;synthesisofmanygrowth operons formate hydrogen-lyasetranscriptionalactivatorforfdhF,hycandhyp subunit ofhydrogenase3 guanine-nucleotide bindingprotein,functionsasnickeldonorforlarge L-isoaspartate proteincarboxylmethyltransferasetype II lipoprotein orf, hypotheticalprotein pleiotrophic effectson3hydrogenaseisozymes pleiotrophic effectson3hydrogenaseisozymes adenosine 5'-phosphosulfate kinase orf, hypotheticalprotein Catalyses productionof4-diphosphocytidyl-2-C-methylerythritol Catalyses productionof2C-methyl-d-erythritol2,4-cyclodiphosphate putative hydrogenasesubunit survival protein methyl-directed mismatchrepair plays structuralroleinmaturationofall3hydrogenases putative cytochrome oxidasesubunit protein phosphatase2 putative DEOR-typetranscriptionalregulator putative dehydrogenase orf, hypotheticalprotein putative epimerase/aldolase orf, hypotheticalprotein putative transportprotein

Gene description Metabolism ofsmallmolecules Global functions Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Macromolecule metabolism Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism of smallmolecules Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Miscellaneous Miscellaneous Miscellaneous Macromolecule metabolism Open readingframes Open readingframes Cell processes

Functional category 1623 1632 1624 1623 1633 1632 1625 1623 1623 1636 1634 1634 1634 1634 1633 1626 1623 1635 1627 1628 1629 1629 1630 1630 1631 Operon ID b2753 b2752 b2751 b2754 b2755 b2756 b2757 b2758 b2759 b2760 b2761 b2765 b2764 b2763 b2762 b2766 b2768 b2767 b2769 b2770 b2771 b2772 b2773 b2774 b2775

B number iap cysD cysN ygbF b2755 b2756 b2757 b2758 ygcK b2760 ygcB ygcM cysJ cysI cysH ygcN ygcP ygcO ygcQ ygcR ygcS b2772 ygcU ygcW yqcE

Gene name + + + + + + ------Strand orientation 345 302 475 116 305 199 226 363 160 502 888 121 599 570 244 433 191 297 261 469 264 218 286 425 98 Protein length 9053 5046 6797 5071 4375 148 240 269 213 141 128 355 151 170 269 104 143 264 134 52 54 61 63 90 69 mRNA intensity A A A A A A A A A A A A A A A P P P P P P P P P P mRNA present 12 21 15 10 11 14 12 22 32 24 31 12 20 11 11 14 10 13 12 12 4 8 9 6 7 # of tryptic peptides predicted P P P P P Protein detected - total list 15 4 9 0 0 0 0 0 0 0 0 0 9 8 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 10 15 10 4 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 15 4 9 0 0 0 0 0 0 0 0 0 9 8 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD

Membrane protein assignment ATP:sulfurylase (ATP:sulfateadenylyltransferase),subunit2 GTPase ATP-sulfurylase (ATP:sulfateadenylyltransferase),subunit1,probablya alkaline phosphataseisozymeconversion,aminopeptidase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein sulfite reductase(NADPH),flavoproteinbetasubunit sulfite reductase,alphasubunit 3'-phosphoadenosine 5'-phosphosulfatereductase orf, hypotheticalprotein putative 6-pyruvoyltetrahydrobiopterinsynthase orf, hypotheticalprotein orf, hypotheticalprotein putative anti-terminatorregulatoryprotein putative flavoprotein putative transportprotein putative transportprotein orf, hypotheticalprotein putative oxidoreductasesubunit putative oxidoreductase putative transport protein

Gene description Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Cell processes Open readingframes Miscellaneous Miscellaneous Open reading frames

Functional category 1637 1636 1638 1639 1639 1639 1639 1639 1639 1639 1641 1641 1641 1640 1642 1642 1642 1642 1643 1643 1643 1643 1643 1644 1645 Operon ID b2785 b2776 b2786 b2777 b2787 b2779 b2778 b2788 b2781 b2780 b2789 b2782 b2790 b2784 b2783 b2791 b2792 b2793 b2794 b2796 b2795 b2798 b2797 b2799 b2800

B number ygcA ygcE barA ygcF ygcX eno ygcG ygcY mazG pyrG b2789 chpA b2790 relA chpR yqcB b2792 syd yqcD sdaC ygdH exo sdaB fucO fucA

Gene name + + + + + + + + ------Strand orientation 433 492 918 223 446 432 313 446 263 545 450 111 149 744 260 109 181 282 429 454 281 455 383 215 82 Protein length 11093 7990 1325 1053 975 105 329 433 202 207 892 116 680 936 815 348 939 618 555 875 232 247 190 402 51 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 19 18 47 11 10 19 19 27 13 19 11 37 13 15 22 12 14 15 6 4 5 6 5 8 8 # of tryptic peptides predicted P P P P P P Protein detected - total list 15 0 0 0 0 0 0 7 0 0 0 0 0 0 1 0 0 0 1 2 0 0 0 1 0 # of tryptic peptides detected (total list) P P Protein detected - short list 13 1 0 0 0 0 0 7 0 0 0 0 0 1 2 0 0 0 1 2 0 0 0 1 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 15 0 0 0 0 0 0 7 0 0 0 0 0 0 1 0 0 0 1 2 0 0 0 1 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt PHD PHD PHD Membrane protein assignment synthesis; stringentfactor (p)ppGpp synthetaseI(GTPpyrophosphokinase);regulationofRNA putative enzyme putative kinase sensor-regulator, activatesOmpRbyphophorylation orf, hypotheticalprotein orf, hypotheticalprotein putative glucaratedehydratase CTP synthetase putative glucaratedehydratase orf, hypotheticalprotein suppressor ofinhibitoryfunctionChpA,PemI-like,autoregulated probable growthinhibitor,PemK-like,autoregulated putative transportprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein interacts withsecY orf, hypotheticalprotein orf, hypotheticalprotein probable serinetransporter L-serine dehydratase(deaminase), L-SD2 5'-3' exonuclease L-1,2-propanediol oxidoreductase L-fuculose-1-phosphate aldolase

Gene description Global functions Miscellaneous Miscellaneous Global functions Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Open readingframes Miscellaneous Miscellaneous Miscellaneous Open readingframes Miscellaneous Open readingframes Cell processes Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Macromolecule metabolism Metabolism of smallmolecules Metabolism of smallmolecules

Functional category 1652 1652 1645 1653 1647 1646 1654 1649 1648 1654 1650 1651 1651 1654 1655 1655 1655 1656 1658 1657 1659 1660 1660 1661 1661 Operon ID b2823 b2821 b2820 b2801 b2824 b2822 b2802 b2825 b2803 b2804 b2806 b2805 b2808 b2807 b2810 b2809 b2811 b2813 b2812 b2817 b2816 b2815 b2814 b2819 b2818

B number ppdC ptr recB fucP ygdB recC fucI ppdB fucK fucU ygdE fucR gcvA ygdD b2810 b2809 ygdK mltA ygdL b2817 metV metW metZ recD argA

Gene name + + + + + + + + + + + ------Strand orientation 1180 1122 107 962 438 121 591 187 482 140 366 243 305 131 401 147 365 268 447 608 443 76 Protein length 11484 1316 9221 9920 1524 588 377 441 868 240 206 302 439 979 420 678 413 684 429 318 476 407 501 243 45 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 58 46 40 23 22 10 18 14 14 10 14 10 24 18 32 6 5 6 9 5 2 2 # of tryptic peptides predicted P P P Protein detected - total list 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD MP-GenProt PHD PHD Membrane protein assignment ssDNA endonuclease DNA helicase,ATP-dependent dsDNA/ssDNAexonucleaseVsubunit, ssDNA endonuclease DNA helicase,ATP-dependentdsDNA/ssDNAexonuclease Vsubunit, ssDNA endonuclease DNA helicase,ATP-dependentdsDNA/ssDNAexonuclease Vsubunit, prepilin peptidasedependent proteinC protease III fucose permease orf, hypothetical protein L-fucose isomerase prepilin peptidase dependentproteinB L-fuculokinase positive regulatorofthefucoperon protein offucoseoperon orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein positive regulatorofgcvoperon orf, hypotheticalprotein orf, hypotheticalprotein putative enzyme tRNA-Met tRNA-Met tRNA-Met membrane-bound lyticmureintransglycosylaseA N-acetylglutamate synthase;aminoacidacetyltransferase putative amidase

Gene description Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Structural elements Macromolecule metabolism Cell processes Open reading frames Metabolism ofsmallmolecules Structural elements Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous tRNA tRNA tRNA Structural elements Metabolism ofsmallmolecules Structural elements

Functional category 1672 1671 1671 1672 1671 1662 1672 1662 1672 1662 1662 1662 1663 1663 1665 1664 1666 1666 1667 1668 1670 1669 Operon ID b2837 b2831 b2830 b2829 b2826 b2838 b2832 b2828 b2827 b2839 b2836 b2835 b2834 b2833 b2840 b2841 b2842 b2843 b2844 b2845 b2846 b2847 b2848 b2849 b2850

B number galR mutH ygdP ptsP ppdA lysA b2832 lgt thyA lysR aas ygeD b2834 b2833 ygeA araE kduD kduI yqeF b2845 yqeH yqeI yqeJ yqeK ygeF

Gene name + + + + + + + + + + + ------Strand orientation 343 229 176 748 156 420 237 291 264 311 719 397 346 230 472 253 278 394 409 230 269 164 145 148 72 Protein length 3095 1003 1193 2657 1361 382 143 683 615 124 119 719 537 228 282 289 638 74 72 38 66 49 43 23 9 mRNA intensity A A A A A A A A A A A A P P P P P P P P P P P P P mRNA present 34 16 11 12 11 12 40 12 13 14 13 17 10 11 11 7 9 6 2 8 8 8 9 6 8 # of tryptic peptides predicted P P P P Protein detected - total list 0 2 0 0 0 0 3 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 4 0 0 0 0 3 2 0 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 0 2 0 0 0 0 3 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment putative invasionprotein protein synthetase 2-acyl-glycerophospho-ethanolamine acyltransferase;acyl-acyl-carrier proteins) PTS system,enzymeI,transcriptionalregulator(withNPRandNTR membrane phospholipid phosphatidylglycerol-prolipoprotein diacylglyceryltransferase;amajor repressor ofgalETKoperon methyl-directed mismatchrepair thymidylate synthetase prepilin peptidasedependentproteinA diaminopimelate decarboxylase orf, hypotheticalprotein orf, hypotheticalprotein putative transportprotein putative resistanceproteins positive regulatorforlys putative resistanceproteins low-affinity L-arabinosetransportsystemprotonsymportprotein 2-deoxy-D-gluconate 3-dehydrogenase homolog ofpectindegradingenzyme5-keto4-deoxyuronate isomerase putative acyltransferase putative transporterprotein orf, hypotheticalprotein putative sensorytransducer orf, hypotheticalprotein orf, hypothetical protein orf, hypothetical protein

Gene description Miscellaneous Metabolism ofsmallmolecules Cell processes Macromolecule metabolism Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Structural elements Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Cell processes Metabolism ofsmallmolecules Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Cell processes Open readingframes Miscellaneous Open readingframes Open reading frames Open reading frames

Functional category 1675 1680 1674 1673 1681 1676 1673 1672 1682 1679 1678 1677 1680 1683 1684 1685 1686 1686 1687 1688 1689 1690 1690 1691 1692 Operon ID b2851 b2853 b2852 b2854 b2855 b2856 b2857 b2858 b2859 b2860 b2861 b2862 b2863 b2864 b2865 b2866 b2867 b2868 b2869 b2870 b2871 b2872 b2873 b2874 b2875

B number ygeG b2853 ygeH b2854 ygeK b2856 b2857 b2858 b2859 yi22_4 yi21_4 b2862 b2863 glyU b2865 b2866 ygeT b2868 ygeV ygeW ygeX ygeY b2873 yqeA b2875

Gene name + + + + + + + + + + + + ------Strand orientation 163 458 138 148 143 141 301 121 278 259 752 292 159 592 363 398 403 465 310 541 72 51 73 99 Protein length 169 403 202 140 182 250 112 318 35 23 33 27 46 33 57 23 13 25 12 80 9 9 8 mRNA intensity A A A A A A A A A A A A A A A A A A P P P P P mRNA present 11 23 16 13 16 30 17 25 18 15 18 23 23 0 8 8 1 7 4 4 7 5 6 9 # of tryptic peptides predicted

P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 detected (membrane sample) GenProt PHD Membrane protein assignment orf, hypotheticalprotein putative invasionprotein orf, hypotheticalprotein orf, hypotheticalprotein putative 2-componenttranscriptionalregulator orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein IS2 hypotheticalprotein IS2 hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein tRNA-Gly putative lipoprotein orf, hypotheticalprotein putative dehydrogenase putative dehydrogenase putative transcriptionalregulator putative carbamoyltransferase putative dehydratase putative deacetylase orf, hypotheticalprotein putative kinase putative synthases

Gene description Open readingframes Miscellaneous Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Extrachromosomal Extrachromosomal Open readingframes Open readingframes tRNA Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Miscellaneous Miscellaneous Open readingframes Open reading frames Open reading frames

Functional category 1693 1694 1695 1696 1697 1697 1698 1698 1698 1698 1698 1699 1699 1700 1701 1701 1701 1702 1703 1704 1705 1705 1705 1706 Operon ID b2892 b2891 b2876 b2895 b2894 b2893 b2877 b2896 b2879 b2878 b2900 b2899 b2898 b2897 b2880 b2881 b2883 b2882 b2886 b2885 b2884 b2887 b2888 b2889 b2890

B number recJ prfB b2876 fldB xerD dsbC ygfJ b2896 ssnA b2878 yqfB b2899 ygfZ ygfY b2880 b2881 ygfP ygfO ygfS ygfR ygfQ ygfT ygfU idi lysS

Gene name + + + + + + + + + + + + + ------Strand orientation 1032 577 365 235 173 298 236 192 135 464 103 219 326 259 956 439 485 163 276 189 644 505 182 505 88 Protein length 8676 1998 1808 2239 1971 2513 1501 389 157 634 118 169 769 324 107 104 156 209 125 347 76 38 38 92 57 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 17 26 16 10 10 57 22 16 10 34 24 28 27 4 6 4 6 2 4 9 6 6 3 9 7 # of tryptic peptides predicted P P P P P Protein detected - total list 14 4 0 0 1 0 0 0 0 0 0 1 6 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 12 4 0 0 0 0 0 0 0 0 0 1 7 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 14 4 0 0 1 0 0 0 0 0 0 1 6 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD PHD PHD PHD PHD Membrane protein assignment peptide chainreleasefactorRF-2 primer RNA lysine tRNAsynthetase,constitutive;suppressorofColE1mutationin site-specific recombinase protein disulfideisomeraseII ssDNA exonuclease,5'-->3'specific orf, hypotheticalprotein flavodoxin 2 putative oxidoreductase,Fe-Ssubunit orf, hypotheticalprotein orf, hypothetical protein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein Functions inregulatingcellviabilityuponentryintostationaryphase putative oxidoreductase orf, hypotheticalprotein putative dehydrogenase putative transportprotein orf, hypotheticalprotein putative oxidoreductase orf, hypotheticalprotein putative oxidoreductase,Fe-Ssubunit putative oxidoreductase,Fe-Ssubunit putative permease Isopentenyl diphosphateisomerase

Gene description Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Structural elements Macromolecule metabolism Open readingframes Metabolism ofsmallmolecules Miscellaneous Open readingframes Open reading frames Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes Cell processes Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Cell processes Open readingframes

Functional category 1714 1715 1715 1715 1706 1716 1708 1707 1720 1718 1717 1717 1708 1719 1709 1709 1710 1710 1710 1710 1711 1711 1712 1713 Operon ID b2912 b2911 b2910 b2909 b2908 b2906 b2905 b2902 b2901 b2915 b2914 b2913 b2907 b2903 b2916 b2904 b2917 b2918 b2919 b2920 b2921 b2923 b2922 b2925 b2924

B number ygfA ssrS ygfE ygfB pepP visC gcvT ygfF bglA yqfE rpiA serA ubiH gcvP iciA gcvH sbm argK ygfG ygfH ygfI yggA yggE fba yggB

Gene name + + + + + + + + + ------Strand orientation 182 109 194 441 400 364 247 479 219 410 392 957 297 129 714 331 275 492 303 211 246 359 286 76 Protein length 12469 1585 6563 2528 2003 1912 2279 8054 6996 3307 5147 4032 194 531 807 536 302 185 138 137 304 31 81 99 90 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P P mRNA present 17 13 24 18 13 18 37 12 32 18 10 24 17 12 11 6 3 9 7 7 4 3 9 3 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 12 14 1 1 2 0 6 0 0 3 0 0 0 6 0 2 0 0 0 0 1 0 4 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 10 0 1 4 2 9 0 0 3 0 0 0 6 0 2 0 0 0 0 0 0 9 0 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 12 14 1 1 2 0 6 0 0 3 0 0 0 6 0 2 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 4 0 detected (membrane sample) GenProt PHD PHD Membrane protein assignment 6S RNA orf, hypotheticalprotein orf, hypotheticalprotein proline aminopeptidasePII 6-phospho-beta-glucosidase A;cryptic benzoquinone 2-octaprenyl-6-methoxyphenol--> 2-octaprenyl-6-methoxy-1,4- cleavage system aminomethyltransferase (Tprotein;tetrahydrofolate-dependent)ofglycine bound lipoylcofactor in glycinecleavagecomplex,carrierofaminomethylmoietyviacovalently ribosephosphate isomerase,constitutive D-3-phosphoglycerate dehydrogenase putative ligase orf, hypotheticalprotein putative oxidoreductase orf, hypotheticalprotein decarboxylase,Pproteinofcleavagesystem replication initiationinhibitor,bindsto13-mersatoriC methylmalonyl-CoA mutase(MCM) Arginine transportATPase putative enzyme putative coenzymeAtransferase putative actin putative transcriptionalregulatorLYSR-type fructose-bisphosphate aldolase,classII Component of theMscSmechanosensitive channel orf, hypotheticalprotein

Gene description Structural elements Open readingframes Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Open readingframes Miscellaneous Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Open readingframes Miscellaneous Miscellaneous Miscellaneous Metabolism of smallmolecules Miscellaneous Open readingframes

Functional category 1725 1724 1724 1721 1724 1723 1723 1728 1727 1726 1724 1722 1729 1723 1730 1731 1731 1731 1731 1733 1732 1736 1735 1734 Operon ID b2943 b2926 b2944 b2928 b2927 b2945 b2929 b2949 b2948 b2947 b2946 b2930 b2950 b2931 b2932 b2933 b2934 b2936 b2935 b2940 b2939 b2938 b2937 b2942 b2941

B number galP pgk sprT yggC epd endA yggD yqgF yqgE gshB yggJ yggF yggR b2931 yggP cmtA cmtB yggG tktA yqgC yqgB speA speB metK yqgD

Gene name + + + + + + + + + + ------Strand orientation 464 387 165 237 339 235 169 138 211 316 252 321 341 329 118 462 147 294 663 658 306 384 71 48 83 Protein length 16984 1647 1164 1431 1910 1912 1710 1472 1774 2768 293 158 317 786 710 205 140 127 124 641 82 53 61 86 36 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 18 18 12 10 15 13 19 17 12 20 13 22 20 6 8 6 5 7 8 5 5 2 8 3 4 # of tryptic peptides predicted P P P P P P P Protein detected - total list 19 0 0 0 0 0 0 0 3 0 1 0 0 0 0 0 0 9 1 0 2 0 0 8 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 15 10 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 8 0 0 4 2 0 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 19 0 0 0 0 0 0 0 3 0 1 0 0 0 0 0 0 9 0 0 2 0 0 8 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD PHD PHD Membrane protein assignment propylamine donor,corepressorofmetgenes methionine adenosyltransferase1(AdoMetsynthetase); methyland galactose-proton symportoftransportsystem D-erythrose 4-phosphatedehydrogenase orf, hypotheticalprotein putative kinase orf, hypotheticalprotein orf, hypotheticalprotein DNA-specific endonucleaseI putative transcriptionalregulator orf, hypothetical protein orf, hypotheticalprotein putative protein transport putative oxidoreductase orf, hypotheticalprotein PTS system,mannitol-specificenzymeIIcomponent,cryptic transketolase 1isozyme PTS system,mannitol-specificenzymeIIcomponent,cryptic orf, hypotheticalprotein biosynthetic argininedecarboxylase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein

Gene description Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Macromolecule metabolism Miscellaneous Open reading frames Open readingframes Miscellaneous Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Cell processes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes

Functional category 1745 1746 1736 1736 1747 1737 1749 1749 1749 1748 1737 1749 1737 1750 1737 1737 1737 1738 1737 1742 1741 1740 1739 1743 1744 Operon ID b2955 b2954 b2953 b2952 b2951 b2956 b2957 b2964 b2963 b2962 b2961 b2960 b2959 b2958 b2965 b2968 b2967 b2966 b2969 b2970 b2971 b2973 b2972 b2974 b2975

B number yggW yggV yggU yggT yggS yggM ansB nupG mltC yggX mutY yggH yggL yggN speC yghD pheV yqgA yghE b2970 b2971 b2973 b2972 b2974 yghK

Gene name + + + + + + + + + + + ------Strand orientation 378 197 100 188 234 335 348 434 360 350 239 118 239 731 178 235 286 288 136 848 310 675 560 91 Protein length 1186 2772 2251 2563 1199 2770 1226 2363 4990 1229 380 113 164 192 611 379 162 167 169 271 352 328 489 15 83 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 12 12 15 14 13 12 15 28 10 19 19 34 24 10 8 5 7 8 8 6 7 4 7 8 # of tryptic peptides predicted P P P P Protein detected - total list 1 0 0 1 0 0 0 3 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 3 1 0 1 0 0 0 3 0 0 3 1 0 0 1 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 1 0 0 1 0 0 0 3 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD MP-GenProt PHD PHD PHD Membrane protein assignment putative ribosomalprotein orf, hypotheticalprotein putative resistanceprotein orf, hypotheticalprotein putative oxidase putative alphahelixchain orf, hypotheticalprotein adenine glycosylase;G.C-->T.Atransversions orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein periplasmic L-asparaginaseII membrane-bound lyticmureintransglycosylaseC transport ofnucleosides,permeaseprotein tRNA-Phe ornithine decarboxylaseisozyme putative transportprotein putative secretionpathwayprotein putative generalsecretionpathwayforproteinexport (GSP) putative generalsecretionpathwayforproteinexport (GSP) orf, hypotheticalprotein putative peptidase orf, hypotheticalprotein putative endoglucanase putative permease

Gene description Miscellaneous Open readingframes Cell processes Open readingframes Miscellaneous Miscellaneous Open readingframes Macromolecule metabolism Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Structural elements Cell processes tRNA Metabolism ofsmallmolecules Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Miscellaneous Cell processes

Functional category 1751 1751 1751 1751 1751 1752 1756 1756 1755 1755 1754 1753 1757 1758 1759 1760 1761 1761 1762 1763 1764 1765 1765 1766 Operon ID b2991 b2979 b2978 b2977 b2976 b2992 b2981 b2980 b2993 b2982 b2994 b2984 b2983 b2995 b2985 b2996 b2986 b2997 b2987 b2998 b2988 b2999 b2990 b2989 b3000

B number hybF glcD glcF glcG glcB hybE b2981 glcC hybD trs5_9 hybC yghR yghQ hybB yghS hybA yghT b2997 pitB b2998 gsp b2999 hybG b2989 b3000

Gene name + + + + ------Strand orientation 113 499 761 134 723 162 390 254 164 338 567 252 325 392 237 328 230 372 499 619 136 304 141 95 82 Protein length 1129 5137 1082 1150 2488 176 543 240 209 227 211 175 132 227 255 268 314 241 480 99 53 63 84 61 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P mRNA present 32 30 23 13 10 14 14 14 25 15 20 12 31 15 4 4 4 9 6 9 8 8 1 6 7 # of tryptic peptides predicted P P P Protein detected - total list 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt GenProt GenProt PHD Membrane protein assignment glycolate oxidaseiron-sulfursubunit orf, hypotheticalprotein malate synthaseG hydrogenase-2 hydrogenase-2 operonprotein:mayeffectmaturationoflargesubunit may modulatelevelsofhydrogenease-2 transcriptional activatorforglcoperon glycolate oxidasesubunitD member ofhyboperon orf, hypotheticalprotein probable processingelementforhydrogenase-2 IS5 transposase orf, hypotheticalprotein orf, hypotheticalprotein probable largesubunit,hydrogenase-2 orf, hypotheticalprotein probable cytochromeNi/Fecomponentofhydrogenase-2 hydrogenase-2 smallsubunit orf, hypotheticalprotein putative hydrogenasesubunit low-affinity phosphatetransport orf, hypotheticalprotein orf, hypotheticalprotein glutathionylspermidine synthetase/amidase orf, hypothetical protein orf, hypothetical protein

Gene description Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Extrachromosomal Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Cell processes Open readingframes Miscellaneous Metabolism ofsmallmolecules Open reading frames Open reading frames

Functional category 1767 1767 1767 1777 1777 1768 1767 1777 1769 1777 1770 1771 1772 1777 1772 1777 1777 1773 1778 1774 1779 1776 1775 1780 1780 Operon ID b3001 b3004 b3003 b3002 b3010 b3009 b3008 b3007 b3006 b3005 b3013 b3012 b3011 b3015 b3014 b3017 b3016 b3018 b3019 b3020 b3021 b3023 b3022 b3025 b3024

B number b3001 b3004 yghA yqhA yqhC yghB metC b3007 exbB exbD yqhG yqhE yqhD b3015 yqhH sufI ygiR plsC parC b3020 b3021 b3023 b3022 ygiX ygiW

Gene name + + + + + + + + + + ------Strand orientation 346 294 164 375 219 395 244 141 309 236 387 413 470 325 245 752 535 131 160 219 130 81 51 85 98 Protein length 1332 1992 4857 2636 1421 1184 1497 2675 617 863 464 476 150 199 269 255 888 848 440 475 212 439 282 57 83 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 19 16 18 14 14 17 24 17 20 10 34 22 12 7 4 1 8 6 4 9 4 4 8 8 6 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 1 1 0 0 5 0 1 1 0 0 4 2 0 0 0 0 1 0 0 0 0 0 0 3 0 # of tryptic peptides detected (total list) P P Protein detected - short list 1 1 0 0 5 0 0 0 0 0 4 2 0 0 0 0 1 0 1 0 0 0 0 3 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 1 1 0 0 5 0 0 0 0 0 4 2 0 0 0 0 1 0 0 0 0 0 0 3 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt PHD PHD Membrane protein assignment putative oxidoreductase putative reductase orf, hypotheticalprotein cystathionine beta-lyase(beta-cystathionase) orf, hypotheticalprotein uptake ofenterochelin;tonB-dependentBcolicins orf, hypotheticalprotein orf, hypotheticalprotein uptake ofenterochelin;tonB-dependentBcolicins 2,5-diketo-D-gluconate reductaseA putative oxidoreductase putative ARAC-typeregulatoryprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein suppressor offtsI 1-acyl-sn-glycerol-3-phosphate acyltransferase DNA topoisomeraseIVsubunitA putative transportperiplasmicprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein orf, hypotheticalprotein putative 2-component transcriptionalregulator

Gene description Miscellaneous Cell processes Open readingframes Metabolism ofsmallmolecules Open readingframes Cell processes Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Macromolecule metabolism Macromolecule metabolism Cell processes Open readingframes Open readingframes Open reading frames Open readingframes Miscellaneous

Functional category 1783 1781 1782 1787 1786 1785 1784 1788 1785 1791 1790 1789 1792 1793 1794 1794 1795 1796 1797 1798 1799 1799 1801 1800 1802 Operon ID b3039 b3038 b3037 b3036 b3026 b3043 b3042 b3041 b3040 b3030 b3029 b3028 b3027 b3044 b3031 b3045 b3035 b3034 b3033 b3032 b3046 b3047 b3048 b3050 b3049

B number ygiD ygiC ygiB ygiA ygiY ygiL b3042 ribB ygiE parE ygiN mdaB b3027 yi21_5 yqiA yi22_5 tolC yqiE yqiB icc yqiG yqiH yqiI b3050 glgS

Gene name + + + + + + + + + + + + + + + + ------Strand orientation 271 386 234 449 183 116 217 257 630 104 193 110 121 193 301 495 209 140 275 821 252 354 209 86 66 Protein length 2040 6518 4471 1210 5845 1846 3776 1113 1438 1403 2011 434 126 159 100 460 412 915 12 82 79 54 93 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P mRNA present 17 10 11 21 29 22 11 16 41 10 2 9 9 7 4 1 3 5 7 2 9 7 9 4 3 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 10 0 2 1 1 2 0 1 1 0 0 2 0 0 0 0 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 1 1 1 3 0 1 1 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 0 2 1 1 2 0 1 1 0 0 2 0 0 0 0 0 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt MP-GenProt MP-GenProt PHD PHD PHD PHD Membrane protein assignment putative synthetase/amidase orf, hypotheticalprotein orf, hypotheticalprotein daughter chromosomes outer membranechannel;specifictolerancetocolicinE1;segregationof orf, hypotheticalprotein 3,4 dihydroxy-2-butanone-4-phosphatesynthase orf, hypotheticalprotein orf, hypotheticalprotein modulator ofdrugactivityB putative 2-componentsensorprotein orf, hypotheticalprotein orf, hypotheticalprotein putative fimbrial-likeprotein DNA topoisomeraseIVsubunitB IS2 hypotheticalprotein orf, hypotheticalprotein putative enzyme regulator oflacZ orf, hypotheticalprotein IS2 hypotheticalprotein putative membraneprotein putative membraneprotein glycogen biosynthesis, rpoSdependent orf, hypotheticalprotein putative oxidoreductase

Gene description Miscellaneous Open readingframes Open readingframes Cell processes Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes Miscellaneous Macromolecule metabolism Extrachromosomal Open readingframes Miscellaneous Metabolism ofsmallmolecules Open readingframes Extrachromosomal Miscellaneous Miscellaneous Macromolecule metabolism Open readingframes Miscellaneous

Functional category 1806 1806 1806 1806 1810 1809 1807 1804 1804 1802 1808 1803 1811 1805 1812 1805 1805 1805 1805 1812 1812 1812 1813 1812 1814 Operon ID b3069 b3068 b3051 b3071 b3070 b3052 b3072 b3056 b3055 b3054 b3053 b3073 b3057 b3074 b3058 b3075 b3059 b3060 b3061 b3062 b3063 b3064 b3066 b3065 b3067

B number ileX ygjF b3051 yqjI yqjH b3052 aer cca ygiM ygiF glnE ygjG bacA ygjH ygiG ebgR ygiH ygiP ttdA ttdB ygjE ygjD dnaG rpsU rpoD

Gene name + + + + + + + + + + + + + + ------Strand orientation 168 553 207 254 477 506 412 206 433 946 496 273 110 123 327 205 310 303 201 487 337 581 613 71 Protein length 14928 1480 1446 1797 1852 1441 1812 222 537 749 420 681 951 284 263 764 412 207 145 827 868 76 34 60 69 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P P mRNA present 10 25 10 25 12 17 40 24 23 22 10 16 20 16 16 28 19 9 6 5 5 9 8 3 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 3 0 0 1 3 3 1 1 0 0 1 0 0 0 0 0 0 0 0 0 4 0 0 2 # of tryptic peptides detected (total list) P P Protein detected - short list 3 1 0 2 6 1 1 2 0 0 1 0 0 0 0 0 0 0 0 0 4 0 0 2 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 3 0 0 1 3 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 4 0 0 2 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

PHD Membrane protein assignment orf, hypotheticalprotein temperatures RNA polymerase,sigma(70)factor;regulationofproteins inducedathigh orf, hypotheticalprotein tRNA-Ile putative membraneprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein adenylylating enzymeforglutaminesynthetase putative kinase aerotaxis sensorreceptor, flavoprotein tRNA probable ornithineaminotransferase bacitracin resistance;possiblyphosphorylatesundecaprenol putative tRNA synthetase putative kinase regulator ofebg operon orf, hypotheticalprotein putative transcriptionalregulatorLYSR-type L-tartrate dehydratase,subunitA L-tartrate dehydratase,subunitB orf, hypotheticalprotein 30S ribosomalsubunitproteinS21 putative O-sialoglycoproteinendopeptidase DNA biosynthesis;

Gene description Macromolecule metabolism Global functions Open readingframes tRNA Miscellaneous Open readingframes Open readingframes Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Cell processes Miscellaneous Metabolism ofsmallmolecules Metabolism of smallmolecules Open readingframes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Structural elements Miscellaneous Macromolecule metabolism

Functional category 1826 1825 1827 1814 1828 1816 1815 1815 1815 1829 1817 1830 1818 1831 1819 1832 1820 1821 1822 1822 1823 1825 1824 1825 Operon ID b3077 b3076 b3078 b3079 b3080 b3081 b3082 b3083 b3084 b3085 b3086 b3087 b3088 b3091 b3090 b3089 b3092 b3093 b3096 b3095 b3094 b3098 b3097 b3100 b3099

B number ebgC ebgA ygjI ygjJ ygjK ygjL ygjM ygjN ygjO ygjP ygjQ ygjR ygjT uxaA ygjV ygjU uxaC exuT yqjB yqjA exuR yqjD yqjC b3100 yqjE

Gene name + + + + + + + + + + + + + + + + + + + ------Strand orientation 1042 149 477 356 783 672 138 104 388 179 230 334 321 495 183 414 470 472 127 220 263 101 127 134 99 Protein length 11454 1065 1102 8519 3827 147 121 382 327 250 137 264 359 120 427 154 138 948 416 313 637 908 60 20 47 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 38 14 34 32 15 12 20 31 13 14 8 9 4 6 8 9 8 9 4 5 5 5 6 4 7 # of tryptic peptides predicted P P P P P Protein detected - total list 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 3 0 0 0 0 0 1 2 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt PHD PHD PHD PHD Membrane protein assignment evolved beta-D-galactosidase,alphasubunit;crypticgene evolved beta-D-galactosidase,betasubunit;crypticgene putative oxidoreductase orf, hypotheticalprotein putative isomerase putative NADPHdehydrogenase orf, hypotheticalprotein orf, hypotheticalprotein putative enzyme orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transportprotein orf, hypotheticalprotein putative transportprotein altronate hydrolase uronate isomerase negative regulatorofexuregulon,exuT,uxaAC,and uxuB transport ofhexuronates orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein orf, hypothetical protein orf, hypotheticalprotein

Gene description Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Open readingframes Miscellaneous Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Open readingframes Open readingframes Open readingframes Open reading frames Open reading frames Open readingframes

Functional category 1833 1833 1834 1835 1835 1836 1837 1837 1838 1839 1840 1841 1842 1844 1843 1845 1845 1847 1846 1848 1849 1848 1849 1849 1849 Operon ID b3101 b3102 b3103 b3104 b3105 b3106 b3108 b3107 b3109 b3110 b3111 b3112 b3113 b3114 b3115 b3116 b3117 b3118 b3119 b3120 b3121 b3124 b3123 b3122 b3125

B number yqjF yqjG yhaH yhaI yhaJ yhaK yhaM yhaL yhaN yhaO yhaP yhaQ yhaR tdcE tdcD tdcC tdcB tdcA tdcR yhaB yhaC yhaD rnpB b3122 yhaE

Gene name + + + + + + + + + + ------Strand orientation 160 328 121 118 298 233 188 187 425 275 140 150 746 406 443 329 312 114 186 395 408 299 56 54 Protein length 42169 1214 132 418 675 136 384 145 294 169 240 145 180 131 155 286 644 73 80 95 84 31 16 30 30 mRNA intensity A A A A A A A A A A A A A A P P P P P P P P P P P mRNA present 17 16 15 35 19 10 17 13 19 15 15 5 3 2 3 4 4 9 7 5 8 8 7 1 # of tryptic peptides predicted P P Protein detected - total list 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein putative transferase putative cytochrome putative cytochrome putative transcriptionalregulatorLYSR-type orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transportsystempermeaseprotein putative L-serinedehydratase putative L-serinedehydratase orf, hypotheticalprotein probable formateacetyltransferase3 putative kinase anaerobically inducibleL-threonine,L-serinepermease threonine dehydratase,catabolic transcriptional activatoroftdcoperon threonine dehydrataseoperonactivatorprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein putative dehydrogenase

Gene description Open readingframes Miscellaneous Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Macromolecule metabolism Metabolism of smallmolecules Metabolism of smallmolecules

Functional category 1850 1851 1852 1853 1854 1855 1855 1856 1857 1857 1858 1858 1859 1859 1859 1860 1860 1860 1861 1862 1863 1862 1864 1864 Operon ID b3141 b3140 b3139 b3135 b3134 b3126 b3143 b3142 b3136 b3127 b3144 b3137 b3128 b3145 b3138 b3130 b3129 b3146 b3131 b3150 b3149 b3148 b3147 b3132 b3133

B number agaI agaD agaC agaA agaW yhaF yraI yraH agaS yhaU yraJ agaY yhaG yraK agaB yhaV sohA yraL agaR yraP yraO yraN yraM agaZ agaV

Gene name + + + + + + + + + + + + + + + + + + + + + - - - - Strand orientation 251 263 267 167 133 256 231 194 384 444 838 286 523 363 158 154 111 286 269 191 196 131 678 426 169 Protein length 1760 1789 1974 1306 1102 123 283 267 326 119 622 427 989 285 47 45 90 76 98 93 65 31 89 18 26 mRNA intensity A A A A A A A A A A A A A P P P P P P P P P P P P mRNA present 13 10 14 12 12 27 10 24 14 14 12 30 15 8 4 9 1 6 7 7 5 9 8 8 7 # of tryptic peptides predicted

P P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3 0 0 detected (membrane sample) GenProt-PHD MP-GenProt

PHD PHD PHD Membrane protein assignment PTS system,N-acetylglucosamineenzymeIIDcomponent1 PTS systemN-acetylgalactosamine-specificIICcomponent1 1 (EIIB-AGA) PTS system,cytoplasmic,N-acetylgalactosamine-specificIIBcomponent PTS systemN-acetylgalactosameine-specificIICcomponent2 2 (EIIB-AGA) PTS system,cytoplasmic,N-acetylgalactosamine-specificIIBcomponent putative fimbrial-likeprotein putative galactosamine-6-phosphateisomerase putative N-acetylgalactosamine-6-phosphatedeacetylase orf, hypotheticalprotein putative chaperone putative tagatose-6-phosphatealdose/ketoseisomerase putative transportprotein putative outermembraneprotein tagatose-bisphosphate aldolase2 putative protease;htrAsuppressorprotein putative hydrolase putative fimbrialprotein orf, hypotheticalprotein putative periplasmic protein orf, hypothetical protein orf, hypotheticalprotein putative glycosylase orf, hypotheticalprotein putative DEOR-typetranscriptionalregulatorofagaoperon putative tagatose6-phosphatekinase2

Gene description Metabolism ofsmallmolecules Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Miscellaneous Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open readingframes Cell processes Miscellaneous Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open readingframes Miscellaneous Open reading frames Open readingframes Miscellaneous Open readingframes Miscellaneous Miscellaneous

Functional category 1869 1869 1869 1868 1868 1870 1869 1868 1864 1871 1868 1864 1871 1868 1866 1865 1871 1866 1873 1873 1873 1873 1872 1867 1868 Operon ID b3152 b3151 b3153 b3154 b3155 b3156 b3158 b3157 b3159 b3160 b3161 b3162 b3169 b3168 b3167 b3166 b3165 b3164 b3163 b3173 b3172 b3171 b3170 b3174 b3175

B number yraR yraQ yhbO yhbP yhbQ yhbS yhbU yhbT yhbV yhbW mtr deaD nusA infB rbfA truB rpsO pnp nlpI yhbX argG metY yhbC leuU secG

Gene name + + + + + + ------Strand orientation 226 346 186 147 100 167 331 174 298 335 414 646 495 890 133 314 734 294 547 447 152 110 89 Protein length 11021 1915 2918 1507 1448 3259 5346 3423 2077 8451 5822 2622 350 426 461 400 425 508 868 193 716 151 82 83 16 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 10 10 11 16 12 11 25 39 13 29 14 24 24 19 8 6 5 5 4 8 3 5 5 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 0 0 0 0 0 2 0 0 0 1 0 2 9 3 0 3 8 0 7 6 0 0 2 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 10 10 0 0 0 0 0 2 0 0 0 1 0 4 3 0 3 8 0 9 0 0 1 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 0 0 0 0 0 2 0 0 0 1 0 2 9 3 0 3 8 0 7 6 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 2 detected (membrane sample) GenProt-PHD MP-GenProt GenProt PHD PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative collagenase orf, hypotheticalprotein putative enzyme tryptophan-specific transportprotein protein chaininitiationfactorIF-2 ribosome-binding factorA tRNA pseudouridine5Ssynthase 30S ribosomalsubunitproteinS15 polynucleotide phosphorylase;cytidylatekinaseactivity Lipoprotein inducible ATP-independentRNAhelicase argininosuccinate synthetase tRNA-Met orf, hypotheticalprotein transcription pausing;Lfactor putative alkalinephosphatase I tRNA-Leu protein export -membraneprotein

Gene description Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Open readingframes Open readingframes Miscellaneous Cell processes Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Structural elements Macromolecule metabolism Cell processes Macromolecule metabolism Metabolism ofsmallmolecules tRNA Open readingframes Macromolecule metabolism Open readingframes tRNA Cell processes

Functional category 1874 1875 1876 1877 1878 1879 1879 1880 1880 1881 1882 1887 1886 1886 1885 1885 1884 1883 1889 1888 1887 1890 1891 Operon ID b3196 b3195 b3194 b3193 b3192 b3191 b3190 b3189 b3183 b3181 b3180 b3179 b3178 b3177 b3176 b3200 b3199 b3198 b3197 b3186 b3185 b3184 b3182 b3188 b3187

B number yrbG yrbF yrbE yrbD yrbC yrbB yrbA murA yhbZ greA yhbY ftsJ hflB folP mrsA yhbN yrbK yrbI yrbH rplU rpmA yhbE dacB nlp ispB

Gene name + + + + + + + + + ------Strand orientation 325 269 260 183 211 129 419 390 153 209 644 297 445 185 191 188 328 103 321 477 323 89 97 85 92 Protein length 53296 1343 3863 3960 1569 3056 1459 3551 4717 3175 1109 2106 2682 2178 2421 1492 6571 1911 984 890 679 925 104 839 328 mRNA intensity A A P P P P P P P P P P P P P P P P P P P P P P P mRNA present 10 11 13 21 10 32 16 23 10 15 10 15 10 21 6 2 3 9 4 7 8 4 6 5 5 # of tryptic peptides predicted P P P P P P P P P P P P P Protein detected - total list 0 1 1 0 1 1 1 1 8 3 4 0 0 1 4 0 0 0 0 0 3 0 0 1 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 0 1 0 0 3 1 1 5 3 6 0 0 2 5 0 0 0 0 0 2 0 0 2 0 # of tryptic peptides detected (short list) P P P P P P P P P P P P Protein detected - long list 0 0 1 0 1 1 1 1 2 3 4 0 0 1 4 0 0 0 0 0 3 0 0 1 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 1 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD MP-GenProt PHD PHD Membrane protein assignment putative ATP-bindingcomponentofatransportsystem orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein cell divisionprotein 7,8- similar tophosphoglucomutasesandphosphomannomutases orf, hypotheticalprotein carboxyvinyltransferase first stepinmureinbiosynthesis;UDP-N-glucosamine1- of phageMu regulatory factorofmaltosemetabolism;similartoNerrepressorprotein 4 D-alanyl-D-alanine carboxypeptidase,fractionB;penicillin-bindingprotein degrades sigma32,integralmembranepeptidase,celldivisionprotein orf, hypothetical protein orf, hypothetical protein orf, hypotheticalprotein putative isomerase orf, hypotheticalprotein 50S ribosomalsubunitproteinL27 putative GTP-bindingfactor transcription elongationfactor:cleaves3'nucleotideofpausedmRNA orf, hypotheticalprotein octaprenyl diphosphatesynthase 50S ribosomalsubunitproteinL21

Gene description Cell processes Open readingframes Cell processes Open readingframes Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Structural elements Metabolism ofsmallmolecules Structural elements Macromolecule metabolism Open reading frames Open reading frames Open readingframes Open readingframes Open readingframes Structural elements Miscellaneous Macromolecule metabolism Open readingframes Metabolism ofsmallmolecules Structural elements

Functional category 1903 1903 1903 1903 1902 1894 1893 1892 1892 1903 1901 1900 1896 1893 1904 1904 1904 1904 1904 1898 1897 1895 1897 1899 1898 Operon ID b3211 b3208 b3207 b3206 b3205 b3204 b3203 b3202 b3201 b3214 b3213 b3212 b3210 b3209 b3215 b3216 b3217 b3218 b3219 b3220 b3221 b3222 b3223 b3224 b3225

B number yhcC mtgA yrbL ptsO yhbJ ptsN yhbH rpoN yhbG gltF gltD gltB arcB yhbL yhcA yhcD yhcE trs5_10 yhcF yhcG yhcH nanK nanE nanT nanA

Gene name + + + + + + + + + + + + + + + ------Strand orientation 1517 309 242 210 284 163 477 241 254 472 776 220 224 793 159 338 238 375 154 302 229 506 297 90 95 Protein length 5524 1033 5109 6992 7108 2705 7485 9886 1071 404 203 156 183 868 127 167 104 375 493 244 39 75 76 94 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 14 13 13 12 25 73 15 34 10 26 14 18 12 10 10 12 4 9 7 3 9 8 4 8 3 # of tryptic peptides predicted P P P P P P Protein detected - total list 11 30 0 0 0 0 2 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P P Protein detected - short list 11 33 0 0 0 0 2 0 1 0 0 2 0 1 0 0 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 11 30 0 0 0 0 2 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD MP-GenProt

Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein systemenzymeIIA,regulatesNmetabolism probable sigma-54modulationprotein putative ATP-bindingcomponentofatransportsystem 12? N-acetylneuraminate lyase(aldolase);catabolism ofsialicacid;not K- kinase/phosphatase, sensorforarcA aerobic respirationsensor-responseprotein;histidineprotein phosphate withEnzymeI,Hpr phosphocarrier proteinHPr-likeNPr,nitrogenrelated,exchanges regulation RNA polymerase,sigma(54or60)factor;nitrogenandfermentation glutamate synthase,smallsubunit glutamate synthase,largesubunit orf, hypotheticalprotein sigma cross-reactingprotein27A(SCRP-27A) putative peptidoglycanenzyme regulator ofgltBDFoperon,inductionNtrenzymes putative chaperone putative outermembraneprotein orf, hypotheticalprotein IS5 transposase putative transcriptionalregulator orf, hypotheticalprotein orf, hypotheticalprotein ManNAc kinase ManNAc epimerase sialic acidtransporter

Gene description Open readingframes Open readingframes Cell processes Global functions Cell processes Structural elements Global functions Cell processes Global functions Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Miscellaneous Metabolism ofsmallmolecules Miscellaneous Miscellaneous Open readingframes Extrachromosomal Miscellaneous Open readingframes Open readingframes Miscellaneous Miscellaneous Cell processes

Functional category 1906 1905 1905 1904 1904 1916 1908 1905 1904 1910 1910 1909 1907 1907 1910 1911 1911 1911 1912 1913 1914 1915 1915 1915 1915 Operon ID b3227 b3226 b3230 b3229 b3228 b3231 b3232 b3234 b3233 b3235 b3236 b3238 b3237 b3243 b3241 b3240 b3239 b3244 b3242 b3245 b3246 b3247 b3249 b3248 b3250

B number dcuD nanR rpsI sspA sspB rplM yhcM degQ yhcB degS mdh yhcN argR yhcS yhcQ yhcP yhcO tldD yhcR yhdP yhdR rng mreD yhdE mreC

Gene name + + + + + + + ------Strand orientation 455 263 130 212 165 142 375 455 134 355 312 104 156 309 310 655 481 986 282 495 162 197 367 90 90 Protein length 15830 38878 18040 1068 4258 1618 2508 1556 1447 541 685 731 336 158 213 150 157 806 250 237 796 602 855 23 92 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 13 17 20 12 13 16 24 14 17 44 15 28 20 8 9 5 7 6 9 5 3 4 1 9 2 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 25 0 0 2 1 4 2 0 3 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 # of tryptic peptides detected (total list) P P Protein detected - short list 12 0 0 3 1 2 3 0 3 5 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 25 0 0 2 1 4 2 0 3 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 detected (membrane sample) GenProt-PHD GenProt-PHD MP-GenProt

PHD PHD Membrane protein assignment Nan regulator regulator oftranscription;stringentstarvationproteinA stringent starvationproteinB Cryptic C4-dicarboxylatecarrier 30S ribosomalsubunitproteinS9 50S ribosomalsubunitproteinL13 orf, hypotheticalprotein orf, hypotheticalprotein serine endoprotease protease repressor ofargregulon;cer-mediatedsitespecificrecombination malate dehydrogenase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transcriptionalregulatorLYSR-type putative membraneprotein suppresses inhibitoryactivityofCsrA orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein RNase G,maturationof16S RNA rod shape-determining protein rod shape-determining protein

Gene description Miscellaneous Global functions Global functions Cell processes Structural elements Structural elements Open readingframes Open readingframes Macromolecule metabolism Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Miscellaneous Macromolecule metabolism Open readingframes Open readingframes Cell processes Structural elements Structural elements

Functional category 1917 1919 1919 1918 1920 1920 1922 1921 1923 1923 1925 1924 1927 1926 1928 1928 1929 1928 1930 1931 1931 1932 1932 1933 1933 Operon ID b3267 b3266 b3262 b3258 b3255 b3254 b3253 b3252 b3251 b3268 b3264 b3263 b3259 b3257 b3256 b3269 b3265 b3261 b3260 b3270 b3271 b3272 b3274 b3273 b3275

B number yhdV acrF yhdJ panF accB b3254 yhdH yhdA mreB yhdW envR yhdU prmA yhdT accC yhdX acrE fis yhdG yhdY yhdZ rrfF rrfD thrV rrlD

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 1034 296 485 156 324 646 367 305 220 293 449 368 385 321 368 252 73 33 59 80 98 Protein length 10847 73907 92314 38677 1362 3268 2703 4945 5970 2475 257 179 316 180 204 536 77 15 24 11 10 29 77 8 5 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 13 17 25 15 29 22 11 18 18 12 20 12 13 2 1 2 2 6 9 9 2 # of tryptic peptides predicted P P P P P Protein detected - total list 0 3 5 0 1 0 0 0 0 0 0 9 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 0 5 6 0 0 0 0 0 1 0 0 7 0 1 0 1 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 0 3 5 0 0 0 0 0 0 0 0 9 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt

PHD PHD Membrane protein assignment orf, hypotheticalprotein putative dehydrogenase regulator offtsI,penicillinbindingprotein3,septationfunction integral transmembraneprotein;acridineresistance permeability transmembrane proteinaffectsseptumformationandcellmembrane trans activatorfortranscription site-specific DNAinversionstimulationfactor;DNA-bindingprotein;a orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative methyltransferase acetyl CoAcarboxylase,biotincarboxylasesubunit acetylCoA carboxylase,BCCPsubunit;carrierofbiotin sodium/pantothenate symporter putative periplasmicbindingtransportprotein putative transcriptionalregulator putative dehydrogenase methylase for50SribosomalsubunitproteinL11 putative transportsystempermeaseprotein putative transportsystempermeaseprotein putative ATP-bindingcomponentofatransportsystem tRNA-Thr 5S ribosomalRNA 5S ribosomal RNA 23S ribosomal RNA

Gene description Open readingframes Miscellaneous Cell processes Cell processes Structural elements Macromolecule metabolism Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Cell processes Miscellaneous Open readingframes Structural elements Cell processes Cell processes Cell processes tRNA Structural elements Structural elements Structural elements

Functional category 1936 1935 1933 1945 1945 1941 1938 1934 1946 1943 1942 1937 1937 1939 1947 1944 1940 1939 1947 1948 1948 Operon ID b3281 b3280 b3279 b3278 b3277 b3276 b3282 b3286 b3285 b3284 b3283 b3289 b3288 b3287 b3290 b3292 b3291 b3294 b3293 b3295 b3296 b3297 b3298 b3300 b3299

B number aroE yrdB yrdA rrsD ileU alaU yrdC smf_1 smf_2 smg yrdD rrmB fmt def trkA zntR mscL rplQ yhdN rpoA rpsD rpsK rpsM prlA rpmJ

Gene name + + + + + + ------Strand orientation 272 256 190 253 102 157 169 429 315 169 458 141 136 127 122 329 206 129 118 443 85 38 Protein length 79137 10334 33843 32646 48728 50514 45957 25184 1766 4924 4378 3050 3279 1246 1413 4813 2696 1210 215 479 895 160 802 218 510 mRNA intensity A P P P P P P P P P P P P P P P P P P P P P P P P mRNA present 14 12 11 13 19 15 17 10 4 9 0 7 7 6 5 7 8 4 6 1 7 9 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 12 10 0 2 0 2 0 0 0 0 4 1 0 0 0 0 0 5 5 0 9 2 # of tryptic peptides detected (total list) P P P P Protein detected - short list 10 10 0 1 0 2 0 0 0 0 4 1 1 0 0 0 0 3 3 0 6 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 12 10 0 2 0 2 0 0 0 0 4 1 0 0 0 0 0 5 5 0 9 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 4 0 0 2 2 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt PHD Membrane protein assignment orf, hypotheticalprotein putative transferase 16S rRNA tRNA-Ile tRNA-Asx dehydroshikimate reductase orf, fragment2 orf, hypotheticalprotein putative DNAtopoisomerase orf, hypotheticalprotein 10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase peptide deformylase orf, fragment1 16S rRNAm5C967methyltransferase transport ofpotassium mechanosensitive channel orf, hypotheticalprotein Zn(II)-responsive transcriptionalregulator 50S ribosomalsubunitproteinL17 RNA polymerase,alphasubunit 30S ribosomalsubunitproteinS4 30S ribosomalsubunitprotein S11 50S ribosomal subunitproteinL36 30S ribosomalsubunitprotein S13 putative ATPase subunitoftranslocase

Gene description Open readingframes Miscellaneous Structural elements tRNA tRNA Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Open readingframes Macromolecule metabolism Macromolecule metabolism Open readingframes Macromolecule metabolism Cell processes Cell processes Open readingframes Miscellaneous Structural elements Miscellaneous Structural elements Structural elements Structural elements Structural elements Cell processes

Functional category 1950 1949 1950 1951 1951 1950 1950 1953 1953 1952 1954 1954 1955 1956 1956 1957 1957 1957 1957 1958 1957 1958 Operon ID b3301 b3303 b3302 b3304 b3305 b3306 b3307 b3308 b3309 b3310 b3313 b3312 b3311 b3314 b3315 b3317 b3316 b3318 b3319 b3320 b3321 b3322 b3323 b3324 b3325

B number rplO rpsE rpmD rplR rplF rpsH rpsN rplE rplX rplN rplP rpmC rpsQ rpsC rplV rplB rpsS rplW rplD rplC rpsJ pinO yheD yheE yheF

Gene name + + ------Strand orientation 144 167 117 177 130 101 179 104 123 136 233 110 273 100 201 209 103 139 489 271 654 59 63 84 92 Protein length 21005 45038 27989 33740 39081 40833 30584 58952 46318 12209 15552 43789 26918 29916 42940 37295 29469 39328 40039 34128 41152 352 172 79 69 mRNA intensity A A P P P P P P P P P P P P P P P P P P P P P P P mRNA present 11 10 13 12 24 12 19 4 6 9 4 9 8 2 4 3 3 5 4 4 5 2 8 7 6 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P P P Protein detected - total list 10 12 10 1 4 4 2 2 4 5 3 0 6 2 1 5 6 1 7 6 6 0 0 0 0 # of tryptic peptides detected (total list) P P P P P P P P P P Protein detected - short list 1 4 3 2 8 3 2 7 4 2 0 4 2 9 1 4 4 0 4 4 3 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P P P P P P P P P P P P P Protein detected - long list 10 12 10 1 4 4 2 2 4 5 3 0 6 2 1 5 6 1 7 6 6 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 2 0 1 0 0 7 0 0 0 1 0 1 0 0 0 0 2 0 2 0 0 0 0 detected (membrane sample)

Membrane protein assignment 50S ribosomalsubunitproteinL30 50S ribosomalsubunitproteinL15 30S ribosomalsubunitproteinS5 50S ribosomalsubunitproteinL18 50S ribosomalsubunitproteinL6 30S ribosomalsubunitproteinS8,andregulator 30S ribosomalsubunitproteinS14 50S ribosomalsubunitproteinL5 50S ribosomalsubunitproteinL24 50S ribosomalsubunitproteinL29 30S ribosomalsubunitproteinS17 50S ribosomalsubunitproteinL14 50S ribosomalsubunitproteinL16 30S ribosomalsubunitproteinS3 30S ribosomalsubunitproteinS19 50S ribosomalsubunitproteinL22 50S ribosomalsubunitproteinL2 50S ribosomalsubunitproteinL23 50S ribosomalsubunitproteinL4,regulatesexpression ofS10operon 50S ribosomalsubunitproteinL3 30S ribosomalsubunitproteinS10 calcium-binding proteinrequired forinitiationofchromosomereplication putative exportproteinAfor generalsecretionpathway(GSP) putative general secretionpathwayforprotein export(GSP) putative general proteinsecretion

Gene description Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Structural elements Macromolecule metabolism Cell processes Open reading frames Open reading frames

Functional category 1958 1958 1958 1958 1958 1958 1958 1958 1958 1959 1959 1958 1959 1959 1959 1959 1959 1959 1959 1959 1959 1960 1960 1961 1961 Operon ID b3327 b3326 b3328 b3329 b3330 b3331 b3332 b3333 b3334 b3335 b3338 b3337 b3336 b3339 b3340 b3341 b3342 b3344 b3343 b3345 b3350 b3349 b3348 b3347 b3346

B number hofF yheG hofG hofH yheH yheI yheJ yheK pshM hofD yheB yheA bfr tufA fusA rpsG rpsL yheM yheL yheN kefB slyD slyX fkpA yheO

Gene name + + + + + + + + + + + ------Strand orientation 398 493 145 169 138 195 327 388 161 225 897 158 394 704 179 124 119 128 601 196 270 244 64 95 72 Protein length 55718 56613 35444 45358 1178 2892 5225 1049 1544 1788 125 200 150 130 124 229 627 591 881 690 96 73 14 87 86 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 22 18 13 11 10 32 22 32 13 19 1 3 5 7 3 4 4 9 6 5 5 4 5 4 8 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 36 29 0 0 0 0 0 0 0 0 0 0 3 0 0 8 0 5 0 0 1 0 6 1 0 # of tryptic peptides detected (total list) P P P P P Protein detected - short list 14 16 0 0 0 0 0 0 0 0 0 0 4 0 0 7 0 3 0 0 1 0 8 1 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 36 29 0 0 0 0 0 0 0 0 0 0 3 0 0 8 0 5 0 0 1 0 6 1 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD

Membrane protein assignment TRAFFIC WARDENATPASE) putative generalsecretionpathwayforproteinexport(GSP)(TYPEII putative generalproteinsecretion putative generalproteinsecretion putative generalproteinsecretion putative exportproteinforgeneralsecretionpathway(GSP) putative exportproteinIforgeneralsecretionpathway(GSP) putative exportproteinJforgeneralsecretionpathway(GSP) putative generalproteinsecretion putative generalsecretion orf, hypotheticalprotein bacterioferrin, anironstoragehomoprotein leader peptidase,integralmembraneprotein putative enzyme protein chainelongationfactorEF-Tu(duplicateoftufB) GTP-binding proteinchainelongationfactorEF-G 30S ribosomalsubunitproteinS7,initiatesassembly orf, hypotheticalprotein 30S ribosomalsubunitproteinS12 orf, hypotheticalprotein FKBP-type peptidyl-prolyl cis-transisomerase (rotamase) host factorforlysisofphiX174 infection FKBP-type peptidyl-prolyl cis-trans isomerase(rotamase) orf, hypotheticalprotein orf, hypotheticalprotein K+ efflux;NEM-activable K+/H+antiporter

Gene description Cell processes Open readingframes Open readingframes Miscellaneous Miscellaneous Miscellaneous Miscellaneous Open readingframes Miscellaneous Open readingframes Cell processes Macromolecule metabolism Miscellaneous Macromolecule metabolism Macromolecule metabolism Structural elements Open readingframes Structural elements Open readingframes Macromolecule metabolism Open readingframes Macromolecule metabolism Open readingframes Open readingframes Cell processes

Functional category 1961 1961 1961 1961 1961 1961 1961 1961 1961 1963 1962 1961 1964 1965 1965 1965 1966 1965 1966 1969 1968 1967 1966 1966 1970 Operon ID b3351 b3355 b3354 b3353 b3352 b3360 b3359 b3358 b3357 b3356 b3361 b3364 b3363 b3362 b3365 b3366 b3367 b3368 b3369 b3370 b3371 b3372 b3373 b3374 b3375

B number yheR prkB yheU yheT yheS pabA argD yhfK crp yhfA fic yhfC ppiA yhfG nirB nirD nirC cysG yhfL yhfM yhfN yhfO yhfP yhfQ yhfR

Gene name + + + + + + + + + + + + + + + + + + ------Strand orientation 184 289 340 637 187 406 696 210 134 200 393 190 847 108 184 457 462 347 149 134 261 265 72 55 55 Protein length 1701 2043 1400 1967 9299 2116 2058 420 609 316 431 658 811 209 105 100 241 143 254 106 395 57 61 11 57 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 16 33 18 13 27 10 45 22 10 13 13 8 3 9 7 6 2 8 3 2 5 3 6 4 8 # of tryptic peptides predicted P P P P P P P Protein detected - total list 0 0 0 1 1 3 6 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P P Protein detected - short list 0 0 0 2 1 4 6 1 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 0 0 0 1 1 3 6 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein putative ATP-bindingcomponentofatransportsystem putative NAD(P)Hoxidoreductase acetylornithine delta-aminotransferase cyclic AMPreceptorprotein orf, hypotheticalprotein probable orf, hypotheticalprotein p-aminobenzoate synthetase,componentII peptidyl-prolyl cis-transisomeraseA(rotamaseA) orf, hypotheticalprotein induced instationaryphase,recognizedbyrpoS,affectscelldivision putative transport nitrite reductase(NAD(P)H)subunit nitrite reductase(NAD(P)H)subunit nitrite reductaseactivity uroporphyrinogen IIImethylase;sirohaemebiosynthesis orf, hypotheticalprotein putative aminoacid/aminetransportprotein putative transportprotein orf, hypotheticalprotein orf, hypotheticalprotein putative kinase putative transcriptional regulator

Gene description Open readingframes Open readingframes Cell processes Miscellaneous Metabolism ofsmallmolecules Global functions Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism Open readingframes Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Open readingframes Cell processes Miscellaneous Open readingframes Open readingframes Miscellaneous Miscellaneous

Functional category 1971 1971 1971 1970 1976 1974 1973 1972 1975 1977 1978 1977 1977 1979 1980 1980 1980 1980 1981 1982 1982 1982 1983 1983 1983 Operon ID b3376 b3377 b3378 b3379 b3380 b3381 b3382 b3383 b3384 b3391 b3390 b3389 b3388 b3387 b3386 b3385 b3392 b3393 b3394 b3395 b3396 b3397 b3400 b3399 b3398

B number yhfS yhfT yhfU yhfV yhfW yhfX yhfY yhfZ trpS hofQ aroK aroB damX dam rpe gph yrfA yrfB yrfC yrfD mrcA yrfE hslR yrfG yrfF

Gene name + + + + ------Strand orientation 361 434 130 292 408 387 134 228 334 412 240 362 428 278 225 252 147 146 179 268 858 186 133 237 711 Protein length 5176 1128 2383 1506 2239 3910 2844 2524 269 233 100 101 223 171 858 307 226 122 110 516 619 233 56 67 98 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P P mRNA present 22 11 17 13 17 12 12 14 18 18 13 18 10 17 45 10 27 5 4 8 7 7 5 6 9 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 1 0 0 0 0 0 0 0 3 2 2 1 0 2 0 0 0 0 0 0 2 0 0 0 1 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 0 0 0 0 3 3 4 0 0 3 1 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 1 0 0 0 0 0 0 0 3 2 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 2 0 0 0 1 detected (membrane sample) GenProt-PHD MP-GenProt

PHD Membrane protein assignment orf, hypotheticalprotein putative transportsystempermeaseprotein orf, hypotheticalprotein putative hydrolase putative mutase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein shikimate kinaseI 3-dehydroquinate synthase DNA adeninemethylase D-ribulose-5-phosphate 3-epimerase phosphoglycolate phosphatase tryptophan tRNAsynthetase putative membraneprotein;interfereswithcelldivision putative transportportein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein peptidoglycan synthetase;penicillin-bindingprotein1A Hsp15. DNA/RNA bindingheatshockprotein putative phosphatase orf, hypotheticalprotein putative dehydrogenase

Gene description Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Cell processes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Structural elements Cell processes Open reading frames Open readingframes Miscellaneous

Functional category 1984 1984 1984 1984 1984 1984 1985 1985 1986 1986 1986 1986 1986 1986 1986 1987 1987 1987 1987 1987 1988 1990 1990 1989 1990 Operon ID b3406 b3405 b3401 b3409 b3408 b3407 b3404 b3403 b3402 b3411 b3410 b3412 b3415 b3414 b3413 b3416 b3418 b3417 b3419 b3420 b3421 b3422 b3425 b3424 b3423

B number greB ompR hslO feoB feoA yhgF envZ pckA yhgE yhgA yhgG bioH gntT yhgI yhgH malQ malT malP rtcA rtcA rtcB rtcR glpE glpG glpR

Gene name + + + + + + + + + + + + + ------Strand orientation 170 239 294 773 740 450 540 574 292 256 437 191 243 694 901 797 201 146 408 532 108 276 252 75 78 Protein length 1241 1632 1807 7786 4562 1938 1326 1814 1150 374 668 555 484 556 228 171 347 236 884 660 307 262 238 149 901 mRNA intensity A A P P P P P P P P P P P P P P P P P P P P P P P mRNA present 13 11 38 24 23 25 24 15 14 16 14 29 44 44 10 24 11 27 9 5 3 6 7 7 6 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 15 1 1 4 0 8 0 0 0 0 0 0 3 0 0 1 5 0 0 0 0 0 1 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 10 14 2 1 2 0 0 0 0 0 0 0 3 0 0 0 7 0 0 0 0 0 1 0 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 15 1 1 4 0 8 0 0 0 0 0 0 3 0 0 1 5 0 0 0 0 0 1 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD

PHD Membrane protein assignment ompF: outermembraneproteinsynthesis response regulator(sensor,EnvZ)affectingtranscriptionofompCand expression ofompFandompC protein histidinekinase/phosphatasesensorforOmpR,modulates ferrous irontransportproteinA orf, hypotheticalprotein transcription elongationfactorandtranscriptcleavage phosphoenolpyruvate carboxykinase Hsp33. Redoxregulatedchaperone putative transport orf, hypotheticalprotein ferrous irontransportproteinB orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein biotin biosynthesis;reactionpriortopimeloylCoA high-affinity transportofgluconate/permease maltodextrin phosphorylase 4-alpha-glucanotransferase (amylomaltase) positive regulatorofmalregulon RNA 3'-terminalphosphatecyclase RNA 3'-terminalphosphatecyclase Still Unknown protein ofglp regulon repressor oftheglpoperon Sigma54-dependent regulator ofrtcBAexpression protein ofglp regulon

Gene description Global functions Global functions Cell processes Macromolecule metabolism Macromolecule metabolism Metabolism ofsmallmolecules Cell processes Miscellaneous Open readingframes Cell processes Open readingframes Miscellaneous Miscellaneous Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Open readingframes Macromolecule metabolism Open readingframes Metabolism of smallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Metabolism of smallmolecules

Functional category 1993 1993 1996 1995 1994 1992 1990 1991 1997 1996 1998 2001 2000 1999 2002 2003 2003 2004 2005 2005 2005 2007 2007 2006 2007 Operon ID b3428 b3427 b3426 b3435 b3434 b3433 b3432 b3431 b3430 b3429 b3436 b3437 b3438 b3439 b3440 b3441 b3442 b3443 b3445 b3444 b3446 b3447 b3448 b3449 b3450

B number glgP yzgL glpD gntU_2 yhgN asd glgB glgX glgC glgA gntU_1 gntK gntR yhhW yhhX yhhY yhhZ yrhA insB_6 insA_6 yrhB ggt yhhA ugpQ ugpC

Gene name + + + + + + + + + ------Strand orientation 815 501 111 197 367 728 657 431 477 332 162 313 231 345 162 392 138 167 580 146 247 369 97 91 94 Protein length 7847 7201 4558 3007 3802 3110 128 669 132 191 108 529 356 921 201 748 912 673 769 72 26 20 76 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P mRNA present 30 36 12 31 28 20 15 14 10 13 15 26 12 2 4 3 9 6 9 9 5 9 6 7 9 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 23 12 0 5 1 0 3 4 0 0 0 0 0 0 4 0 0 0 0 0 0 3 0 0 1 # of tryptic peptides detected (total list) P P P P P P Protein detected - short list 20 0 5 7 1 0 4 0 0 0 0 0 0 0 5 0 0 0 0 0 0 4 0 0 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 23 12 0 5 1 0 3 0 0 0 0 0 0 0 4 0 0 0 0 0 0 3 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 12 0 0 0 1 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 detected (membrane sample) GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein sn-glycerol-3-phosphate dehydrogenase(aerobic) aspartate-semialdehyde dehydrogenase 1,4-alpha-glucan branchingenzyme part ofglycogenoperon,aglycosylhydrolase,debranchingenzyme glucose-1-phosphate adenylyltransferase glycogen synthase glycogen phosphorylase orf, hypotheticalprotein low-affinity gluconatetransportpermeaseprotein,fragment2 low-affinity gluconatetransportpermeaseprotein,interrupted 2,thermoresistant regulator ofgluconate(gnt)operon orf, hypotheticalprotein putative regulator orf, hypotheticalprotein orf, hypotheticalprotein IS1 proteinInsA orf, hypotheticalprotein IS1 proteinInsB orf, hypotheticalprotein gamma-glutamyltranspeptidase orf, hypotheticalprotein glycerophosphodiester phosphodiesterase, cytosolic ATP-binding component ofsn-glycerol3-phosphate transportsystem

Gene description Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Open readingframes Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Open readingframes Extrachromosomal Open readingframes Extrachromosomal Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism of smallmolecules Cell processes

Functional category 2009 2008 2011 2010 2010 2010 2010 2010 2012 2013 2013 2013 2014 2015 2016 2017 2017 2017 2017 2018 2019 2020 2021 2021 Operon ID b3465 b3464 b3462 b3459 b3458 b3457 b3456 b3453 b3452 b3451 b3467 b3466 b3463 b3460 b3455 b3454 b3469 b3468 b3461 b3473 b3472 b3471 b3470 b3474 b3475

B number yhhF ftsY ftsX yhhK livK livH livM ugpB ugpA ugpE yhhM yhhL ftsE livJ livG livF zntA yhhN rpoH yhhS b3472 yhhQ yhhP yhhT yhhU

Gene name + + + + + + + + + ------Strand orientation 198 497 352 127 369 308 425 438 295 281 119 222 386 255 241 732 208 284 419 203 221 376 195 89 81 Protein length 26232 2991 5530 3491 2830 1601 3665 4687 1059 2715 189 724 391 506 760 470 557 692 555 401 420 169 222 350 401 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 21 17 25 10 16 15 11 13 15 30 10 5 9 9 4 6 3 5 7 5 2 6 8 8 2 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 11 11 2 1 0 0 5 0 0 0 0 1 0 2 2 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 11 3 0 0 0 5 0 0 0 0 0 0 1 0 0 6 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 11 11 2 0 0 0 5 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 1 0 0 0 0 0 0 0 1 0 2 2 0 1 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt PHD PHD PHD MP Membrane protein assignment high-affinity leucine-specifictransportsystem;periplasmicbindingprotein cell divisionmembraneprotein cell division ATP-binding componentofamembrane-associatedcomplexinvolvedin temperatures RNA polymerase,sigma(32)factor;regulationofproteinsinducedathigh component high-affinity branched-chainaminoacidtransportsystem;membrane high-affinity branched-chainaminoacidtransport transport system ATP-binding componentofhigh-affinitybranched-chainaminoacid sn-glycerol 3-phosphatetransportsystem,integralmembraneprotein sn-glycerol 3-phosphatetransportsystem,integralmembraneprotein orf, hypotheticalprotein orf, hypotheticalprotein cell divisionmembraneprotein orf, hypotheticalprotein ATP-binding componentofleucinetransport sn-glycerol 3-phosphatetransportsystem;periplasmicbindingprotein putative receptor high-affinity aminoacidtransportsystem;periplasmicbindingprotein putative enzyme orf, hypotheticalprotein orf, hypotheticalprotein -transporting ATPase orf, hypotheticalprotein putative transport orf, hypothetical protein orf, hypothetical protein

Gene description Cell processes Cell processes Cell processes Global functions Cell processes Cell processes Cell processes Cell processes Cell processes Open readingframes Open readingframes Cell processes Open readingframes Cell processes Cell processes Miscellaneous Cell processes Miscellaneous Open readingframes Miscellaneous Cell processes Open readingframes Cell processes Miscellaneous Open reading frames

Functional category 2022 2026 2026 2025 2022 2022 2022 2021 2021 2027 2027 2026 2023 2022 2021 2028 2024 2029 2032 2031 2030 2032 2033 2034 2035 Operon ID b3476 b3477 b3479 b3478 b3480 b3481 b3484 b3483 b3482 b3485 b3486 b3488 b3487 b3489 b3490 b3492 b3491 b3494 b3493 b3495 b3496 b3497 b3498 b3499 b3500

B number nikA nikB nikD nikC nikE nikR yhhI yhhH rhsB yhhJ yhiH yhiJ yhiI yhiK yhiL yhiN yhiM yhiO pitA uspA yhiP yhiQ prlC yhiR gor

Gene name + + + + + + + + + + + + + + + ------Strand orientation 1411 524 314 254 277 268 133 378 122 375 894 540 355 123 412 400 383 111 499 144 489 250 680 280 450 Protein length 21127 2088 1547 2280 143 277 243 171 436 689 373 212 558 292 422 631 643 43 83 66 28 29 82 9 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 25 14 12 79 20 35 18 22 23 17 10 30 17 17 7 6 4 3 8 6 7 9 5 4 7 # of tryptic peptides predicted P P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 6 0 3 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 0 4 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 6 0 3 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

PHD Membrane protein assignment periplasmic bindingproteinfornickel transport ofnickel,membraneprotein transport ofnickel,membraneprotein ATP-binding proteinofnickeltransportsystem ATP-binding proteinofnickeltransportsystem orf, hypotheticalprotein rhsB proteininrhselement Nickel-responsive transcriptionalregulator putative receptor putative transporter putative membraneprotein putative ATP-bindingcomponentofatransportsystem,fragment1 orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein low-affinity phosphatetransport orf, hypotheticalprotein universal stressprotein;broadregulatoryfunction? putative transportprotein orf, hypotheticalprotein oligopeptidase A glutathione oxidoreductase orf, hypothetical protein

Gene description Cell processes Cell processes Cell processes Cell processes Cell processes Open readingframes Extrachromosomal Open readingframes Open readingframes Cell processes Miscellaneous Cell processes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Miscellaneous Cell processes Open readingframes Open readingframes Macromolecule metabolism Metabolism of smallmolecules Open reading frames

Functional category 2036 2036 2036 2036 2036 2038 2038 2037 2039 2040 2040 2040 2041 2042 2042 2043 2044 2045 2046 2047 2048 2049 2049 2051 2050 Operon ID b3501 b3503 b3502 b3504 b3505 b3507 b3506 b3508 b3510 b3509 b3512 b3511 b3513 b3515 b3514 b3516 b3517 b3518 b3519 b3520 b3521 b3524 b3523 b3522 b3525

B number arsR arsC arsB yhiS trs5_11 yhiF slp yhiD hdeA hdeB yhiE hdeD yhiU yhiW yhiV yhiX gadA yhjA treF yhjB yhjC yhjG yhjE yhjD yhjH

Gene name + + + + + + + + + + + + + + ------Strand orientation 1037 117 141 436 260 338 176 199 215 110 112 175 190 385 242 274 466 465 549 200 323 691 440 337 256 Protein length 21552 1442 3775 1407 317 356 121 396 982 102 332 314 901 830 107 361 194 315 245 464 225 92 59 45 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 14 13 29 21 12 15 20 23 24 11 17 13 29 11 6 7 8 7 9 9 7 6 2 3 5 # of tryptic peptides predicted P P P P P P P Protein detected - total list 0 0 0 0 0 5 0 1 0 2 0 0 0 0 0 0 0 0 1 0 0 4 1 1 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 1 1 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt MP-GenProt PHD PHD PHD Membrane protein assignment transcriptional repressorofchromosomalarsoperon arsenical pumpmembraneprotein arsenate reductase orf, hypotheticalprotein IS5 transposase outer membraneproteininducedaftercarbonstarvation orf, hypotheticalprotein orf, hypotheticalprotein putative transportATPase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative transportsystempermeaseprotein putative membraneprotein putative ARAC-typeregulatoryprotein putative ARAC-typeregulatoryprotein glutamate decarboxylaseisozyme putative cytochromeCperoxidase(EC1.11.1) cytoplasmic trehalase putative regulator putative transcriptionalregulatorLYSR-type putative transportprotein orf, hypotheticalprotein orf, hypothetical protein orf, hypothetical protein

Gene description Cell processes Cell processes Cell processes Open readingframes Extrachromosomal Structural elements Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Miscellaneous Miscellaneous Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Miscellaneous Miscellaneous Cell processes Open readingframes Open reading frames Open reading frames

Functional category 2052 2052 2052 2053 2054 2055 2056 2058 2057 2058 2059 2060 2061 2061 2062 2063 2064 2065 2066 2067 2068 2069 2068 2070 2071 Operon ID b3526 b3527 b3531 b3530 b3529 b3528 b3532 b3533 b3534 b3536 b3535 b3544 b3543 b3542 b3541 b3540 b3539 b3538 b3537 b3545 b3546 b3547 b3548 b3549 b3550

B number kdgK yhjJ bcsC yhjL yhjK dctA yhjN yhjO yhjQ yhjS yhjR dppA dppB dppC dppD dppF yhjV yhjU yhjT proK yhjW yhjX yhjY tag yiaC

Gene name + + + + + + + ------Strand orientation 1166 382 498 368 651 428 779 888 242 523 535 339 300 327 334 423 559 574 402 234 187 146 62 62 Protein length 13089 1130 2021 2028 3918 1835 571 559 748 171 384 160 193 639 174 503 635 241 254 527 893 427 96 22 69 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 11 69 24 19 25 35 36 10 22 17 16 24 12 24 10 8 4 3 6 5 9 2 5 7 # of tryptic peptides predicted P P P P P P P Protein detected - total list 15 2 0 1 1 0 0 0 0 0 0 0 0 2 0 3 3 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 15 2 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 15 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 1 0 0 0 0 0 0 0 0 2 0 3 3 0 2 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment ketodeoxygluconokinase putative oxidoreductasesubunit orf, hypotheticalprotein orf, hypotheticalprotein uptake ofC4-dicarboxylicacids Endo-1,4-D-glucanase orf, hypotheticalprotein putative cellulosesynthase orf, hypotheticalprotein orf, hypotheticalprotein putative ATP-bindingcomponentofdipeptidetransportsystem putative ATP-bindingcomponentofdipeptidetransportsystem orf, hypotheticalprotein putative protease dipeptide transportsystempermeaseprotein1 dipeptide transportsystempermeaseprotein2 putative transporterprotein orf, hypotheticalprotein dipeptide transportprotein tRNA-Pro orf, hypotheticalprotein putative resistanceprotein putative lipase 3-methyl-adenine DNAglycosylaseI,constitutive orf, hypothetical protein

Gene description Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Cell processes Macromolecule metabolism Open readingframes Miscellaneous Open readingframes Open readingframes Cell processes Cell processes Open readingframes Miscellaneous Cell processes Cell processes Cell processes Open readingframes Cell processes tRNA Open readingframes Cell processes Miscellaneous Macromolecule metabolism Open reading frames

Functional category 2072 2076 2073 2075 2074 2076 2076 2076 2076 2076 2079 2079 2077 2077 2079 2079 2078 2077 2079 2080 2081 2082 2083 2083 Operon ID b3573 b3551 b3574 b3552 b3575 b3557 b3556 b3555 b3554 b3553 b3558 b3564 b3563 b3562 b3561 b3560 b3559 b3565 b3566 b3567 b3568 b3569 b3571 b3570 b3572

B number yiaI bisC yiaJ yiaD yiaK yi5A cspA yiaG yiaF yiaE t150 xylB yiaB yiaA yiaH glyQ glyS xylA xylF xylG xylH xylR malS bax avtA

Gene name + + + + + + + + + + + + + + ------Strand orientation 157 739 282 219 332 173 276 328 283 484 117 146 331 303 689 440 330 513 393 392 676 274 417 70 96 Protein length 2139 1741 1432 4075 2239 8120 1365 433 449 726 289 149 100 513 247 141 144 231 196 94 71 17 45 89 72 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 31 14 10 13 16 14 10 36 22 20 13 28 10 15 13 10 28 6 4 5 7 6 4 2 7 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 18 0 0 0 1 0 2 3 1 0 0 0 0 4 0 0 0 1 1 0 0 0 0 3 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 20 0 0 0 1 0 1 4 0 0 0 0 0 3 0 0 0 1 1 0 0 0 0 4 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 18 0 0 0 1 0 1 3 0 0 0 0 0 4 0 0 0 1 1 0 0 0 0 3 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt PHD PHD PHD PHD Membrane protein assignment transaminase C alanine-alpha-ketoisovalerate (orvaline-pyruvate)transaminase, orf, hypotheticalprotein biotin sulfoxidereductase putative regulator cold shockprotein7.4,transcriptionalactivatorofhns orf, hypotheticalprotein orf, hypotheticalprotein putative dehydrogenase putative dehydrogenase putative outermembraneprotein IS150 hypotheticalprotein orf, hypotheticalprotein glycine tRNAsynthetase,alphasubunit glycine tRNAsynthetase,betasubunit IS150 putativetransposase orf, hypotheticalprotein orf, hypotheticalprotein D- isomerase xylose bindingproteintransportsystem putative ATP-bindingproteinofxylosetransportsystem putative xylosetransport,membranecomponent putative ATP-bindingprotein putative regulatorofxyloperon alpha-amylase

Gene description Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Miscellaneous Cell processes Open readingframes Open readingframes Miscellaneous Open reading frames Miscellaneous Extrachromosomal Open readingframes Macromolecule metabolism Macromolecule metabolism Extrachromosomal Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Cell processes Cell processes Miscellaneous Miscellaneous Macromolecule metabolism

Functional category 2098 2099 2084 2100 2089 2088 2087 2086 2101 2085 2090 2093 2091 2091 2090 2093 2092 2094 2094 2095 2095 2095 2096 2095 2097 Operon ID b3576 b3579 b3578 b3577 b3580 b3581 b3582 b3583 b3584 b3585 b3589 b3588 b3587 b3586 b3590 b3595 b3594 b3593 b3592 b3591 b3596 b3598 b3597 b3599 b3600

B number yiaL yiaO yiaN yiaM lyxK sgbH sgbU sgbE yiaT yiaU yiaY aldB yiaW yiaV selB yibJ yibA rhsA yibF selA yibG yibI yibH mtlA mtlD

Gene name + + + + + + + + + + + + + + + ------Strand orientation 1377 155 328 424 157 498 220 297 231 246 324 382 542 107 378 614 233 280 202 463 153 120 378 637 382 Protein length 1289 1357 1887 152 153 308 151 145 123 156 146 129 518 222 324 913 879 52 45 50 83 60 12 94 33 mRNA intensity A A A A A A A A A A A A A A A A P P P P P P P P P mRNA present 14 18 12 19 13 11 15 33 20 76 10 29 10 11 20 18 7 8 6 7 6 7 1 5 4 # of tryptic peptides predicted P P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 5 0 0 0 0 1 0 0 0 0 0 0 0 0 2 1 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 0 0 0 0 0 5 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD MP-GenProt PHD PHD PHD Membrane protein assignment putative lipase putative membraneprotein orf, hypotheticalprotein putative solute-bindingtransportprotein L-xylulose kinase,cryptic probable 3-hexulose6-phosphatesynthase probable 3-hexulose-6-phosphateisomerase putative epimerase/aldolase putative outermembraneprotein aldehyde dehydrogenaseB(lactaldehydedehydrogenase) putative transcriptionalregulatorLYSR-type orf, hypotheticalprotein putative membraneprotein putative oxidoreductase orf, hypotheticalprotein rhsA proteininrhselement putative S-transferase selenocysteine synthase:L-seryl-tRNA(Ser)seleniumtransferase selenocysteinyl-tRNA-specific translationfactor orf, hypotheticalprotein orf, hypotheticalprotein putative membraneprotein orf, hypotheticalprotein PTS system, mannitol-specific enzyme IIABC components mannitol-1-phosphate dehydrogenase

Gene description Open readingframes Miscellaneous Open readingframes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Metabolism ofsmallmolecules Miscellaneous Open readingframes Miscellaneous Miscellaneous Open readingframes Extrachromosomal Miscellaneous Macromolecule metabolism Macromolecule metabolism Open readingframes Open readingframes Miscellaneous Open readingframes Cell processes Metabolism of smallmolecules

Functional category 2101 2102 2102 2102 2102 2102 2102 2102 2103 2106 2104 2105 2105 2107 2110 2110 2109 2108 2108 2110 2111 2112 2112 2113 2113 Operon ID b3621 b3601 b3622 b3602 b3623 b3603 b3624 b3604 b3625 b3605 b3606 b3613 b3612 b3611 b3610 b3609 b3608 b3607 b3614 b3615 b3616 b3618 b3617 b3620 b3619

B number rfaC mtlR rfaL yibL rfaK lldP rfaZ lldR rfaY lldD yibK yibP yibO yibN grxC secB gpsA cysE yibQ yibD tdh htrL kbl rfaF rfaD

Gene name + + + + + + + + + + + + + ------Strand orientation 319 195 419 120 357 551 283 258 232 396 157 427 514 143 155 339 273 277 344 341 290 398 348 310 83 Protein length 11412 1790 4909 4678 3923 2834 1216 2052 4177 846 153 343 905 174 595 462 454 782 371 580 298 377 118 96 38 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 14 18 22 12 13 12 21 10 19 13 12 22 13 15 15 11 15 16 18 7 4 8 5 8 5 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 12 0 0 0 0 0 0 0 0 0 0 3 0 4 3 5 2 1 1 0 0 1 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 13 0 0 0 0 0 0 0 0 0 0 3 0 3 1 2 3 1 0 0 0 1 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 12 0 0 0 0 0 0 0 0 0 0 3 0 4 1 5 2 1 0 0 0 1 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 1 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt GenProt GenProt GenProt GenProt Membrane protein assignment biosynthesis ADP-heptose--lps heptosyltransferaseII;lipopolysaccharide core heptosyl transferaseI;lipopolysaccharidecorebiosynthesis repressor formtl O-antigen ligase;lipopolysaccharide corebiosynthesis orf, hypotheticalprotein probably hexosetransferase; lipopolysaccharidecorebiosynthesis L-lactate permease lipopolysaccharide corebiosynthesis transcriptional regulator lipopolysaccharide corebiosynthesis L-lactate dehydrogenase putative 2,3-bisphosphoglycerate-independentphosphoglyceratemutase orf, hypotheticalprotein glutaredoxin 3 protein export;molecularchaperone;maybindtosignalsequence glycerol-3-phosphate dehydrogenase(NAD+) serine acetyltransferase orf, hypotheticalprotein putative membraneprotein orf, hypotheticalprotein putative regulator 2-amino-3-ketobutyrate CoAligase(glycineacetyltransferase) threonine dehydrogenase ADP-L-glycero-D-mannoheptose-6-epimerase involved inlipopolysaccharidebiosynthesis

Gene description Macromolecule metabolism Macromolecule metabolism Metabolism ofsmallmolecules Macromolecule metabolism Open readingframes Macromolecule metabolism Cell processes Macromolecule metabolism Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Open readingframes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Miscellaneous Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Structural elements Miscellaneous

Functional category 2127 2127 2113 2127 2114 2128 2115 2128 2116 2128 2116 2122 2121 2120 2119 2119 2118 2117 2122 2123 2124 2125 2125 2127 2126 Operon ID b3631 b3629 b3628 b3627 b3626 b3632 b3630 b3634 b3633 b3635 b3638 b3637 b3636 b3642 b3641 b3640 b3639 b3643 b3645 b3644 b3647 b3646 b3650 b3649 b3648

B number rfaG rfaS rfaB rfaI rfaJ rfaQ rfaP coaD kdtA mutM radC rpmB rpmG pyrE ttk dut dfp rph dinD yicC yicF yicG spoT rpoZ gmk

Gene name + + + + + + + + + + + ------Strand orientation 374 311 369 339 338 344 265 159 425 269 224 213 212 151 430 228 278 287 562 223 702 207 78 55 91 Protein length 26656 18880 1278 2228 1867 3195 1083 1476 4820 2684 532 106 263 288 187 700 304 398 290 358 325 644 159 94 23 mRNA intensity A A P P P P P P P P P P P P P P P P P P P P P P P mRNA present 22 19 19 18 17 14 11 16 15 10 10 17 12 19 11 31 36 9 5 1 4 7 6 5 8 # of tryptic peptides predicted P P P P P P P Protein detected - total list 0 0 0 0 0 0 0 0 0 2 1 0 0 1 1 0 0 0 3 0 0 0 0 3 1 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 0 0 0 0 0 0 0 2 0 0 0 1 1 1 0 0 4 0 0 0 0 5 1 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 0 0 0 0 0 0 0 0 0 2 1 0 0 1 1 0 0 0 3 0 0 0 0 3 1 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt GenProt PHD PHD PHD Membrane protein assignment pyrophosphohydrolase (p)ppGpp synthetase II;alsoguanosine-3',5'-bis pyrophosphate3'- attaches phosphate-containingsubstratetoLPSco lipopolysaccharide corebiosynthesis;phosphorylationofheptose; galactosyltransferase UDP-D-galactose:(glucosyl)lipopolysaccharide-1,6- D- galactosyltransferase UDP-D-galactose:(glucosyl)lipopolysaccharide- alpha-1,3-D- UDP-D-glucose:(galactosyl)lipopolysaccharide glucosyltransferase glucosyltransferase I;lipopolysaccharidecorebiosynthesis lipopolysaccharide corebiosynthesis 3-deoxy-D-manno-octulosonic-acid transferase(KDOtransferase) lipopolysaccharide corebiosynthesis Phosphopantetheine adenylyltransferase 50S ribosomalsubunitproteinL28 50S ribosomalsubunitproteinL33 formamidopyrimidine DNAglycosylase putative transcriptionalregulator deoxyuridinetriphosphatase flavoprotein affectingsynthesisofDNAandpantothenatemetabolism DNA repairprotein orotate phosphoribosyltransferase putative alphahelixprotein RNase PH DNA-damage-inducible protein orf, hypotheticalprotein RNA polymerase, omegasubunit putative enzyme

Gene description Global functions Macromolecule metabolism Structural elements Structural elements Structural elements Macromolecule metabolism Macromolecule metabolism Structural elements Macromolecule metabolism Structural elements Structural elements Structural elements Macromolecule metabolism Miscellaneous Metabolism ofsmallmolecules Macromolecule metabolism Miscellaneous Metabolism ofsmallmolecules Miscellaneous Macromolecule metabolism Macromolecule metabolism Open readingframes Miscellaneous Metabolism ofsmallmolecules Miscellaneous

Functional category 2141 2128 2128 2128 2128 2128 2128 2129 2128 2129 2131 2131 2130 2134 2133 2133 2132 2135 2136 2135 2137 2138 2141 2140 2139 Operon ID b3673 b3672 b3671 b3670 b3652 b3651 b3674 b3653 b3675 b3654 b3655 b3656 b3657 b3658 b3659 b3662 b3661 b3660 b3663 b3664 b3665 b3666 b3667 b3668 b3669

B number emrD ivbL ilvB ilvN recG spoU yidF gltS yidG yicE yicH yicI yicJ selC yicK yicM nlpA yicL yicN yicO yicP uhpT uhpC uhpB uhpA

Gene name + + + + + + + + + ------Strand orientation 396 562 693 229 165 401 120 463 569 772 479 394 451 272 307 159 470 588 463 440 501 196 32 96 Protein length 12057 5136 2917 1020 1002 244 174 120 443 683 654 157 102 114 163 181 106 117 227 171 882 98 59 32 92 mRNA intensity A A A A A A A A A A A A A A P P P P P P P P P P P mRNA present 22 11 30 10 25 32 11 11 11 24 11 12 19 3 6 3 9 4 3 8 6 5 8 9 # of tryptic peptides predicted P P P Protein detected - total list 0 5 0 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P Protein detected - short list 0 5 1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 5 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt GenProt GenProt GenProt PHD PHD PHD Membrane protein assignment ilvB operonleaderpeptide acetolactate synthaseI,valine-sensitive,largesubunit acetolactate synthaseI,valinesensitive,smallsubunit putative RNAmethylase uhpB) response regulator,positiveactivatorofuhpTtranscription (sensor, 2-module integralmembrane pump;multidrugresistance DNA helicase,resolutionofHollidayjunctions,branchmigration putative transcriptional regulator orf, hypothetical protein glutamate transport putative transportprotein orf, hypotheticalprotein orf, hypotheticalprotein putative permease tRNA-OTHER two-module transportprotein lipoprotein-28 putative permeasetransporter putative transportprotein orf, hypotheticalprotein orf, hypotheticalprotein probable adeninedeaminase(synthesisxanthine) hexose phosphatetransportprotein regulator ofuhpT sensor histidineproteinkinasephosphorylatesUhpA

Gene description Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Cell processes Cell processes Macromolecule metabolism Open reading frames Open reading frames Cell processes Miscellaneous Open readingframes Open readingframes Cell processes tRNA Cell processes Macromolecule metabolism Miscellaneous Cell processes Open readingframes Open readingframes Metabolism ofsmallmolecules Cell processes Cell processes Cell processes

Functional category 2153 2153 2153 2141 2152 2154 2141 2155 2155 2142 2143 2144 2145 2145 2146 2148 2147 2149 2149 2149 2150 2151 2152 2152 Operon ID b3693 b3677 b3676 b3695 b3694 b3678 b3696 b3679 b3697 b3681 b3680 b3698 b3682 b3699 b3683 b3700 b3684 b3685 b3686 b3687 b3689 b3688 b3690 b3691 b3692

B number dgoK yidI yidH yidW b3694 yidJ yidX yidK yidA glvG yidL yidB glvB gyrB glvC recF yidP yidE ibpB ibpA yidR yidQ yidS dgoT dgoA

Gene name + + + + + + ------Strand orientation 292 149 115 128 497 223 571 270 212 307 135 161 804 455 357 238 561 144 137 416 135 361 445 587 98 Protein length 1965 455 131 177 317 405 115 509 199 670 983 124 577 356 177 653 213 126 56 96 48 93 66 87 99 mRNA intensity A A A A A A A A A A A P P P P P P P P P P P P P P mRNA present 13 20 11 17 12 10 40 11 18 13 11 19 22 10 23 6 5 3 4 9 4 7 8 6 8 # of tryptic peptides predicted P P P Protein detected - total list 0 0 0 0 0 0 0 0 1 0 0 0 0 6 0 0 0 0 0 1 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 0 0 0 0 1 0 0 0 0 8 0 0 0 0 0 1 0 0 0 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 0 0 0 0 1 0 0 0 0 6 0 0 0 0 0 1 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD PHD Membrane protein assignment dehydratase 2-oxo-3-deoxygalactonate 6-phosphatealdolaseand galactonate orf, hypotheticalprotein putative FADA-typetranscriptionalregulator 2-oxo-3-deoxygalactonate kinase orf, hypotheticalprotein regulator proteinfordgooperon putative sulfatase putative replicaseEC2.7.- putative cotransporter putative ARAC-typeregulatoryprotein orf, hypotheticalprotein probable 6-phospho-beta-glucosidase orf, hypotheticalprotein PTS system,arbutin-likeIIBcomponent DNA gyrasesubunit B,typeIItopoisomerase, ATPaseactivity PTS system,arbutin-likeIICcomponent ssDNA anddsDNA binding,ATPbinding putative transcriptionalregulator putative transportprotein heat shockprotein orf, hypotheticalprotein heat shockprotein orf, hypotheticalprotein orf, hypotheticalprotein D-galactonate transport

Gene description Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Miscellaneous Miscellaneous Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Cell processes Macromolecule metabolism Cell processes Macromolecule metabolism Miscellaneous Miscellaneous Cell processes Open readingframes Cell processes Open readingframes Open readingframes Cell processes

Functional category 2168 2155 2168 2168 2156 2168 2157 2169 2157 2158 2170 2159 2171 2159 2172 2159 2173 2160 2161 2162 2164 2163 2165 2166 2167 Operon ID b3725 b3709 b3708 b3707 b3706 b3705 b3704 b3703 b3702 b3701 b3710 b3711 b3712 b3713 b3714 b3715 b3716 b3717 b3718 b3719 b3720 b3721 b3722 b3723 b3724

B number pstB tnaB tnaA tnaL thdF yidC rnpA rpmH dnaA dnaN yidY yidZ yieE yieF yieG yieH yieI yieJ yieK yieL yieC bglB bglF bglG phoU

Gene name + + + + + + + + + + + + + + ------Strand orientation 257 415 476 454 548 119 467 366 391 319 253 188 445 221 155 195 213 400 538 470 625 278 241 24 46 Protein length 3771 1915 1311 1484 4617 8867 2218 111 994 889 694 488 843 462 108 176 124 591 50 78 34 38 42 48 40 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 14 22 24 14 13 27 13 16 29 21 10 15 13 2 6 1 6 5 9 7 5 9 4 5 8 # of tryptic peptides predicted P P P P P Protein detected - total list 0 8 0 3 0 0 1 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 8 0 3 0 0 2 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P Protein detected - long list 0 8 0 3 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-PHD GenProt PHD Membrane protein assignment tryptophanase leaderpeptide GTP-binding proteininthiopheneandfuranoxidation RNase P,proteincomponent;C5;processestRNA,4.5SRNA 50S ribosomalsubunitproteinL34 DNA polymeraseIII,beta-subunit system ATP-binding component ofhigh-affinity phosphate-specific transport metabolism negative regulatorforpho regulon andputativeenzymeinphosphate 60 KDinner-membraneprotein transcription regulator DNA biosynthesis;initiationofchromosomereplication;canbe low affinitytryptophanpermease putative transportprotein putative transcriptionalregulatorLYSR-type orf, hypotheticalprotein orf, hypotheticalprotein putative membrane/transportprotein putative phosphatase orf, hypotheticalprotein orf, hypotheticalprotein putative isomerase putative xylanase putative receptorprotein phospho-beta-glucosidase B;cryptic PTS systembeta-glucosides, enzymeII,cryptic positive regulationofbgloperon

Gene description Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Macromolecule metabolism Structural elements Macromolecule metabolism Cell processes Global functions Structural elements Macromolecule metabolism Cell processes Cell processes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Cell processes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules

Functional category 2178 2178 2176 2174 2174 2173 2187 2187 2175 2173 2178 2179 2179 2180 2180 2181 2182 2183 2183 2184 2185 2185 2186 2186 2186 Operon ID b3740 b3733 b3732 b3731 b3730 b3729 b3728 b3726 b3741 b3734 b3727 b3743 b3742 b3735 b3744 b3739 b3738 b3736 b3745 b3737 b3746 b3747 b3749 b3748 b3750

B number gidB atpG atpD atpC glmU glmS pstS pstA gidA atpA pstC asnC mioC atpH asnA atpI atpB atpF yieM atpE yieN kup rbsA rbsD rbsC

Gene name + + + + + ------Strand orientation 207 287 460 139 456 609 346 296 629 513 319 152 147 177 330 130 271 156 427 506 519 501 151 321 79 Protein length 11853 16689 36217 17285 35912 28649 5523 4613 3616 2008 2111 2650 4929 9855 1311 197 721 450 511 231 412 593 589 329 479 mRNA intensity P P P P P P P P P P P P P P P P P P P P P P P P P mRNA present 23 19 28 22 11 17 26 25 10 13 10 24 23 18 30 3 7 8 4 7 6 3 1 8 8 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 11 17 0 2 3 0 0 7 0 1 0 2 0 2 0 2 1 0 3 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 10 14 0 2 5 0 0 6 0 1 0 0 0 1 0 2 0 0 1 0 0 0 1 0 0 # of tryptic peptides detected (short list) P P P P P P P P P P Protein detected - long list 10 15 0 2 3 0 0 6 0 1 0 2 0 2 0 2 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 11 17 0 0 0 0 0 7 0 0 0 0 0 1 0 0 1 0 3 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt MP-GenProt MP-GenProt MP-GenProt MP-GenProt MP-GenProt MP-GenProt

Membrane protein assignment N-acetyl glucosamine-1-phosphateuridyltransferase L-glutamine:D-fructose-6-phosphate aminotransferase of atpB membrane-bound ATPsynthase,dispensableprotein,affectsexpression membrane-bound ATPsynthase,F1sector,beta-subunit membrane-bound ATPsynthase,F1sector,epsilon-subunit binding protein high-affinity phosphate-specifictransportsystem;periplasmicphosphate- component high-affinity phosphate-specifictransportsystem,cytoplasmicmembrane glucose-inhibited division;chromosomereplication? membrane-bound ATPsynthase,F1sector,gamma-subunit high-affinity phosphate-specifictransportsystem initiation ofchromosomereplication glucose-inhibited division;chromosomereplication? membrane-bound ATPsynthase,F1sector,alpha-subunit regulator forasnA,asnCandgidA membrane-bound ATPsynthase,F1sector,delta-subunit membrane-bound ATPsynthase,F0sector,subunita membrane-bound ATPsynthase,F0sector,subunitc asparagine synthetaseA membrane-bound ATPsynthase,F0sector,subunitb orf, hypotheticalprotein putative 2-componentregulator low affinitypotassiumtransport system D-ribose high-affinitytransport system;membrane-associatedprotein ATP-binding component ofD-ribosehigh-affinity transportsystem D-ribose high-affinity transportsystem

Gene description Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Cell processes Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Cell processes Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Cell processes Metabolism ofsmallmolecules Cell processes Open readingframes Miscellaneous Cell processes Cell processes Cell processes Cell processes

Functional category 2188 2188 2189 2189 2189 2187 2187 2190 2189 2187 2190 2190 2189 2191 2189 2189 2189 2192 2189 2193 2194 2195 2196 2196 2196 Operon ID b3751 b3752 b3753 b3754 b3755 b3762 b3761 b3760 b3759 b3758 b3757 b3756 b3763 b3765 b3764 b3773 b3772 b3771 b3770 b3769 b3768 b3767 b3766 b3774 b3775

B number rbsB rbsK rbsR yieO yieP yifA trpT aspT rrfC rrlC gltU rrsC pssR yifB yifE ilvY ilvA ilvD ilvE ilvM ilvG_2 ilvG_1 ilvL ilvC ppiC

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 296 309 330 475 181 198 133 516 112 297 514 605 309 327 491 87 32 93 Protein length 11090 90177 63267 38464 80812 21344 1838 1367 1018 1335 2177 1243 4402 4481 1060 876 294 107 409 300 903 639 299 75 84 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 13 13 12 22 31 25 13 10 11 28 8 5 7 9 8 4 1 6 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 23 3 0 0 0 0 0 0 1 0 1 6 5 0 1 0 0 2 # of tryptic peptides detected (total list) P P P Protein detected - short list 16 4 0 0 0 0 0 0 1 0 1 6 3 0 1 0 0 2 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 23 3 0 0 0 0 0 0 1 0 1 6 5 0 1 0 0 2 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD

Membrane protein assignment D-ribose periplasmicbindingprotein regulator forrbsoperon putative transportprotein tRNA-Trp tRNA-Sec 5S ribosomalRNA 23S ribosomalRNA tRNA-Val 16S ribosomalRNA orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein regulator ofpssA threonine deaminase(dehydratase) dihydroxyacid dehydratase branched-chain amino-acidaminotransferase acetolactate synthaseII,valineinsensitive,smallsubunit split gene,acetolactatesynthaseII,largesubunit,fragment 2,cryptic acetolactate synthaseII,largesubunit,cryptic,interrupted ilvGEDA operonleaderpeptide putative 2-componentregulator positive regulatorforilvC peptidyl-prolyl cis-transisomeraseC(rotamase C) ketol-acid reductoisomerase

Gene description Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes tRNA tRNA Structural elements Structural elements tRNA Structural elements Open readingframes Open readingframes Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Macromolecule metabolism Metabolism of smallmolecules

Functional category 2196 2196 2197 2198 2198 2199 2200 2199 2202 2202 2202 2202 2202 2201 2203 2205 2204 Operon ID b3799 b3798 b3797 b3796 b3795 b3794 b3788 b3787 b3785 b3778 b3777 b3776 b3800 b3789 b3786 b3779 b3790 b3784 b3783 b3782 b3781 b3780 b3791 b3793 b3792

B number proM leuT hisR argX yifK wecG rffG wecC wzzE rep yifN b3776 aslB rffH wecB gppA wecD rfe rho rhoL trxA rhlB wecE wecF wzxE

Gene name + + + + + + + + + + + + + + + + + + + + + - - - - Strand orientation 461 246 355 420 349 673 411 293 389 494 181 367 419 127 421 376 450 416 86 91 33 Protein length 13382 1015 8901 1563 1236 1018 2414 5763 2177 249 142 237 796 964 342 816 721 515 508 707 309 316 392 18 76 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 12 17 16 17 16 36 11 13 17 22 21 23 14 14 12 5 5 2 8 8 7 # of tryptic peptides predicted P P P P P P Protein detected - total list 11 0 0 0 0 0 0 1 0 0 0 2 0 0 5 3 0 0 2 0 0 # of tryptic peptides detected (total list)

P P Protein detected - short list 10 0 0 0 0 0 0 0 0 0 0 2 0 0 4 3 0 0 2 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 11 0 0 0 0 0 0 0 0 0 0 2 0 0 5 3 0 0 2 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 detected (membrane sample) GenProt GenProt GenProt GenProt PHD PHD Membrane protein assignment tRNA-Leu tRNA-His tRNA-Arg orf, hypotheticalprotein orf, hypotheticalprotein putative aminoacid/aminetransportprotein of enterobacterialcommonantigen(ECA) probable UDP-N-acetyl-D-mannosaminuronicacidtransferase; synthesis antigen (ECA) TDP-Fuc4NAc:lipidII transferase;synthesisofenterobacterial common enterobacterial commonantigen(ECA) UDP-N-acetyl-D-mannosaminuronic aciddehydrogenase;synthesisof common antigen(ECA) UDP-N-acetyl glucosamine-2-epimerase;synthesisofenterobacterial synthesis ofenterobacterialcommonantigen(ECA) UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphatetransferase; tRNA-Pro dTDP-glucose 4,6-dehydratase putative transportprotein rep helicase,asingle-strandedDNAdependentATPase putative regulator glucose-1-phosphate thymidylyltransferase transcription terminationfactorRho;polaritysuppressor rho operonleaderpeptide thioredoxin 1 putative ATP-dependentRNAhelicase guanosine pentaphosphatase;exopolyphosphatase orf, hypotheticalprotein putative regulator putative cytochrome

Gene description tRNA tRNA tRNA Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules tRNA Metabolism ofsmallmolecules Open readingframes Macromolecule metabolism Miscellaneous Metabolism ofsmallmolecules Macromolecule metabolism Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Global functions Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous

Functional category 2206 2206 2214 2213 2213 2212 2212 2212 2212 2212 2207 2215 2212 2211 2211 2210 2209 2208 2213 2213 2213 Operon ID b3812 b3801 b3813 b3806 b3805 b3804 b3803 b3802 b3814 b3810 b3809 b3808 b3807 b3815 b3811 b3816 b3819 b3818 b3817 b3820 b3821 b3822 b3823 b3824 b3825

B number yigB aslA uvrD cyaA hemC hemD hemX hemY b3814 yigA dapF yzcX cyaY yigE xerC corA rarD yigG yigF yigI pldA recQ rhtC rhtB pldB

Gene name + + + + + + + + + + + + ------Strand orientation 238 551 720 848 320 246 393 398 235 275 161 106 161 298 316 300 138 126 161 289 610 122 138 340 99 Protein length 2018 2129 2492 1460 3481 1552 1674 909 114 570 294 914 151 377 168 807 609 405 198 358 625 31 14 17 11 mRNA intensity A A A A A A A A P P P P P P P P P P P P P P P P P mRNA present 12 21 17 13 21 19 38 35 11 14 11 14 27 20 8 6 6 9 5 3 2 8 9 5 5 # of tryptic peptides predicted P P P P P P Protein detected - total list 0 0 0 1 5 1 0 2 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 1 1 1 1 0 2 0 2 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 0 0 0 1 1 1 0 2 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD MP-GenProt GenProt GenProt PHD PHD PHD PHD PHD Membrane protein assignment chromosome segregationatcelldivision site-specific recombinase,actsoncersequenceofColE1,effects putative phosphatase porphobilinogen deaminase=hydroxymethylbilanesynthase uroporphyrinogen IIIsynthase uroporphyrinogen IIImethylase a latestepofprotohemeIXsynthesis arylsulfatase DNA-dependent ATPaseIandhelicaseII diaminopimelate epimerase orf, hypotheticalprotein adenylate cyclase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein Mg2+ transport,systemI orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein outer membranephospholipaseA ATP-dependent DNAhelicase Amino acidexporter(threonine) Amino acidexporter (homoserine,HSL) lysophospholipase L(2)

Gene description Cell processes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Open readingframes Global functions Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Open readingframes Open readingframes Miscellaneous Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism Miscellaneous Miscellaneous Metabolism of smallmolecules

Functional category 2221 2221 2217 2217 2217 2217 2216 2222 2221 2219 2218 2220 2223 2221 2223 2224 2225 2225 2226 2226 2227 2228 2229 2230 2231 Operon ID b3848 b3847 b3845 b3844 b3843 b3835 b3834 b3826 b3849 b3846 b3840 b3839 b3838 b3837 b3836 b3828 b3827 b3850 b3841 b3829 b3842 b3830 b3833 b3832 b3831

B number yigZ pepQ fadA ubiB yigC aarF yigP yigL trkH fadB tatD tatC b3838 tatB tatA metR yigM hemG yigW_2 metE rfaH ysgA ubiE yigN udp

Gene name + + + + + + + + + + + + + + + + + + + + - - - - - Strand orientation 205 443 387 233 497 546 201 171 432 729 206 258 145 113 103 317 299 181 113 753 162 332 251 475 253 Protein length 12228 2496 2234 1827 1719 1041 2343 2194 3868 1085 2156 1535 814 764 822 714 429 894 592 631 301 383 190 633 383 mRNA intensity P P P P P P P P P P P P P P P P P P P P P P P P P mRNA present 20 15 20 15 25 10 30 10 13 13 31 17 12 10 33 7 7 3 8 3 6 7 4 7 8 # of tryptic peptides predicted P P P P P P Protein detected - total list 36 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 5 1 1 0 # of tryptic peptides detected (total list) P P Protein detected - short list 24 5 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 3 1 3 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 36 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 5 1 1 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 detected (membrane sample) GenProt GenProt GenProt PHD PHD Membrane protein assignment proline dipeptidase putative oxidoreductase orf, hypotheticalprotein CoA epimerase;delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase;enoyl- 4-enzyme protein:3-hydroxyacyl-CoAdehydrogenase; 3-hydroxybutyryl- oxidoreductase) ferrisiderophore reductase;flavinreductase(NADPH:flavin core, Fpilin,andhaemolysin transcriptional activatoraffectingbiosynthesisoflipopolysaccharide methoxy-1,4-benzoquinone 2-octaprenyl-6-methoxy-1,4-benzoquinone -->2-octaprenyl-3-methyl-6- orf, hypotheticalprotein thiolase I;3-ketoacyl-CoAthiolase;acetyl-CoAtransferase Essential componentoftranslocase orf, hypotheticalprotein Gene essentialforubiquinonebiosynthesis orf, hypotheticalprotein Essential componentoftranslocase Component oftranslocase orf, hypotheticalprotein protoporphyrin oxidase potassium uptake, requiresTrkE Possible componentoftranslocase regulator formetEandmetH orf, hypotheticalprotein tetrahydropteroyltriglutamate methyltransferase uridine phosphorylase putative enzyme putative alphahelixchain

Gene description Macromolecule metabolism Miscellaneous Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Miscellaneous Miscellaneous Metabolism ofsmallmolecules Open readingframes Cell processes Open readingframes Miscellaneous Metabolism of smallmolecules Cell processes Open readingframes Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Miscellaneous

Functional category 2243 2241 2239 2242 2241 2240 2239 2243 2242 2239 2239 2239 2232 2239 2239 2233 2244 2243 2239 2234 2239 2235 2237 2236 2238 Operon ID b3872 b3871 b3870 b3867 b3866 b3865 b3864 b3861 b3856 b3855 b3854 b3853 b3852 b3851 b3873 b3868 b3863 b3862 b3857 b3874 b3869 b3860 b3859 b3858 b3875

B number yihL yihK glnA hemN yihI yihA spf yihF mobB rrfA rrlA alaT ileT rrsA yihM glnG polA yihG mobA yihN glnL dsbA yihE yihD yshA

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 236 591 469 459 169 199 490 170 326 469 928 310 194 421 349 208 328 230 89 Protein length 78069 61006 76544 2901 3685 1118 1890 4030 4459 2297 2029 2651 342 404 104 364 144 451 827 154 537 856 56 51 7 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 20 20 10 11 13 22 21 18 42 13 22 10 16 11 15 12 8 7 5 # of tryptic peptides predicted P P P P P P P Protein detected - total list 12 9 0 0 0 0 0 0 0 5 0 0 4 1 1 1 0 0 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 10 12 0 1 0 0 0 0 0 7 0 0 6 2 1 2 0 0 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 12 9 0 0 0 0 0 0 0 5 0 0 4 1 1 1 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt PHD Membrane protein assignment putative GTP-bindingfactor orf, hypotheticalprotein GTPase essentialforcellcycle 5S ribosomalRNA 23S ribosomalRNA tRNA-Asx tRNA-Ile 16S ribosomalRNA NRII) histidine proteinkinasesensorforGlnGregulator(nitrogen regulatorII, exonuclease DNA polymeraseI,3'-->5'polymerase,and formate-dependent reduction protein disulfideisomeraseI,essentialforcytochromecsynthesisand putative transcriptionalregulator O2-independent coproporphyrinogenIIIoxidase putative GTP-bindingprotein molybdopterin-guanine dinucleotidebiosynthesisproteinB putative endonuclease orf, hypotheticalprotein response regulatorforgln(sensorglnL)(nitrogen I,NRI) orf, hypotheticalprotein orf, hypotheticalprotein molybdopterin --->molybdopterin-guaninedinucleotide,proteinAr putative resistance protein(transport) orf, hypothetical protein

Gene description Global functions Miscellaneous Metabolism ofsmallmolecules Open readingframes Open readingframes Structural elements Structural elements tRNA tRNA Structural elements Metabolism ofsmallmolecules Macromolecule metabolism Macromolecule metabolism Miscellaneous Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Open reading frames Open reading frames

Functional category 2255 2254 2252 2251 2254 2250 2247 2256 2253 2248 2245 2249 2256 2254 2247 2246 2245 2257 2258 Operon ID b3876 b3877 b3878 b3879 b3880 b3881 b3882 b3883 b3884 b3888 b3887 b3886 b3885 b3889 b3891 b3890 b3892 b3893 b3895 b3894 b3896 b3897 b3898 b3899 b3900

B number yihO yihP yihQ yihR yihS yihT yihU yihV yihW yiiD yihZ rbn yihX yiiE fdhE yiiF fdoI fdoH fdhD fdoG yiiG frvR frvX frvB frvA

Gene name + + + + + + + + + + ------Strand orientation 1016 487 468 678 308 418 292 298 300 269 329 145 290 206 309 211 300 277 351 582 356 485 148 81 80 Protein length 2870 1920 251 171 453 588 602 164 529 503 397 352 230 128 116 113 51 66 72 26 67 89 66 35 54 mRNA intensity A A A A A A A A A A A A A A P P P P P P P P P P P mRNA present 12 28 22 18 14 12 15 15 17 45 14 11 17 30 14 8 5 8 7 7 3 5 5 9 8 # of tryptic peptides predicted P P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 2 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt GenProt PHD PHD Membrane protein assignment putative permease putative permease putative glycosidase putative -1-epimerase(EC5.1.3.3) orf, hypotheticalprotein putative aldolase putative dehydrogenase putative kinase D-Tyr-tRNATyr deacyclase Unknown putative DEOR-typetranscriptionalregulator RNase BN Unknown orf, hypotheticalprotein orf, hypotheticalprotein affects formatedehydrogenase-N formate dehydrogenase,cytochromeB556(FDO)subunit formate dehydrogenase-O,majorsubunit formate dehydrogenase-O,iron-sulfursubunit affects formatedehydrogenase-N orf, hypotheticalprotein putative frvoperonregulatory protein frv operonprotein PTS system, fructose-like enzymeIIBC component PTS system, fructose-specific IIAcomponent

Gene description Cell processes Cell processes Open readingframes Miscellaneous Open readingframes Miscellaneous Miscellaneous Miscellaneous Cell processes Miscellaneous Miscellaneous Macromolecule metabolism Miscellaneous Open readingframes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Miscellaneous Open readingframes Cell processes Cell processes

Functional category 2258 2258 2258 2259 2260 2260 2260 2261 2262 2262 2261 2262 2262 2264 2263 2265 2265 2265 2265 2266 2267 2268 2268 2268 2268 Operon ID b3901 b3902 b3903 b3904 b3905 b3906 b3907 b3908 b3909 b3910 b3911 b3917 b3916 b3915 b3914 b3913 b3912 b3918 b3920 b3919 b3924 b3923 b3922 b3921 b3925

B number yiiL rhaD rhaA rhaB rhaS rhaR rhaT sodA kdgT yiiM cpxA sbp pfkA yiiP b3914 b3913 cpxR cdh yiiQ tpiA fpr yiiT yiiS yiiR glpX

Gene name + + + + + + + + + + + + + + ------Strand orientation 104 274 419 489 278 312 344 206 330 234 457 329 320 300 122 232 251 199 255 248 142 146 336 49 99 Protein length 20896 2928 1757 1521 2387 4548 7653 1041 1586 178 179 130 129 414 750 394 260 791 350 834 175 78 78 51 64 mRNA intensity A A A A A A P P P P P P P P P P P P P P P P P P P mRNA present 22 13 11 16 11 23 18 19 16 10 11 12 17 6 9 6 8 6 8 8 0 8 3 4 4 # of tryptic peptides predicted P P P P P P P P Protein detected - total list 0 0 0 0 0 0 0 9 0 1 0 2 0 2 0 1 0 0 1 0 0 0 1 0 1 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 0 0 0 6 0 1 0 1 0 2 0 1 0 0 3 0 0 0 1 0 1 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 0 0 0 0 0 0 0 9 0 1 0 2 0 2 0 1 0 0 1 0 0 0 1 0 1 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

PHD Membrane protein assignment orf, hypotheticalprotein rhamnulose-phosphate aldolase L-rhamnose isomerase positive regulatorforrhaBADoperon positive regulatorforrhaRSoperon rhamnose transport superoxide dismutase,manganese 2-keto-3-deoxy-D-gluconate transportsystem orf, hypotheticalprotein 6-phosphofructokinase I orf, hypotheticalprotein orf, hypotheticalprotein transcriptional regulatorin2-componentsystem probable sensorprotein(histidinekinase),actingonarcA putative transportsystempermeaseprotein periplasmic sulfate-bindingprotein triosephosphate isomerase CDP-diacylglycerol phosphotidylhydrolase putative regulator orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein unknown function inglycerolmetabolism ferredoxin-NADP reductase

Gene description Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Cell processes Cell processes Open readingframes Metabolism ofsmallmolecules Open readingframes Cell processes Miscellaneous Global functions Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Metabolism of smallmolecules

Functional category 2269 2270 2270 2270 2271 2271 2272 2273 2274 2275 2279 2277 2277 2276 2276 2278 2280 2282 2281 2285 2285 2283 2284 2287 2286 Operon ID b3926 b3927 b3930 b3929 b3928 b3934 b3933 b3932 b3931 b3935 b3937 b3936 b3940 b3939 b3938 b3943 b3942 b3941 b3944 b3946 b3945 b3947 b3948 b3949 b3950

B number glpK glpF menA menG yiiU cytR ftsN hslV hslU priA yiiX rpmE metL metB metJ yijE katG metF yijF talC gldA ptsA yijI frwC frwB

Gene name + + + + + + + + + + ------Strand orientation 502 281 308 161 341 319 176 443 732 202 810 386 105 312 726 296 205 220 380 711 109 359 106 81 70 Protein length 17449 25772 10849 2640 1607 1193 3959 1558 1221 2490 2050 2803 466 886 138 134 506 301 139 217 190 120 123 34 13 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 28 16 26 14 35 10 40 34 16 10 12 13 33 6 5 4 5 6 3 9 4 8 4 8 4 # of tryptic peptides predicted P P P P P P P P P P P P P Protein detected - total list 22 15 1 1 2 0 1 1 7 0 3 0 4 1 0 4 5 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P P P P Protein detected - short list 19 14 0 1 2 0 0 1 9 0 1 0 4 0 0 6 5 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P P P P Protein detected - long list 22 15 0 1 2 0 0 1 7 0 3 0 4 1 0 4 5 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 3 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD PHD PHD PHD Membrane protein assignment menaquinone biosynthesis,unknown orf, hypotheticalprotein facilitated diffusionofglycerol heat shockproteinhslVU,proteasome-relatedpeptidasesubunit heat shockproteinhslVU,ATPasesubunit,homologoustochaperones 1,4-dihydroxy-2-naphthoate -->dimethylmenaquinone essential celldivisionprotein regulator fordeooperon,udp,cdd,tsx,nupC,andnupG 50S ribosomalsubunitproteinL31 primosomal proteinN'(=factorY)(putativehelicase) cystathionine gamma-synthase repressor ofallmetgenesbutmetF orf, hypotheticalprotein catalase; hydroperoxidaseHPI(I) 5,10-methylenetetrahydrofolate reductase aspartokinase IIandhomoserinedehydrogenase orf, hypotheticalprotein orf, hypotheticalprotein glycerol dehydrogenase,(NAD) putative transaldolase PEP-protein phosphotransferase systemenzymeI orf, hypotheticalprotein PTS system, fructose-like enzymeIIcomponent PTS systemfructose-like IIBcomponent 1

Gene description Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Cell processes Macromolecule metabolism Cell processes Metabolism ofsmallmolecules Cell processes Global functions Structural elements Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Miscellaneous Cell processes Open readingframes Cell processes Metabolism of smallmolecules

Functional category 2288 2290 2289 2288 2291 2291 2290 2292 2293 2295 2294 2298 2297 2296 2300 2299 2298 2301 2302 2303 2303 2303 2304 2305 2305 Operon ID b3974 b3972 b3971 b3970 b3969 b3968 b3967 b3951 b3975 b3973 b3952 b3953 b3954 b3960 b3959 b3958 b3957 b3956 b3955 b3961 b3965 b3964 b3963 b3962 b3966

B number coaA murB rrfB rrlB gltT rrsB murI pflD b3975 birA pflC frwD yijO argH argB argC argE ppc yijP oxyR trmA yijD yijC udhA btuB

Gene name + + + + + + + + + + + + + + + ------Strand orientation 316 342 289 765 321 292 113 283 457 258 334 383 883 577 305 366 119 234 444 614 51 Protein length 84342 72643 37454 78206 4288 2642 2692 2997 1033 2217 2520 448 784 557 104 262 227 180 981 943 566 590 299 35 15 mRNA intensity A A A P P P P P P P P P P P P P P P P P P P P P P mRNA present 16 15 14 41 16 17 14 13 10 13 47 22 29 15 10 24 19 31 3 6 2 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 18 0 2 0 0 0 0 0 0 0 5 3 2 8 1 2 0 0 6 0 4 # of tryptic peptides detected (total list) P P P P Protein detected - short list 20 0 2 0 0 0 0 0 0 0 5 3 2 9 0 3 0 0 7 0 0 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 18 0 2 0 0 0 0 0 0 0 5 3 2 8 0 2 0 0 6 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 4 detected (membrane sample) MP-GenProt PHD PHD Membrane protein assignment 5S ribosomalRNA 23S rRNA tRNA-Val 16S rRNA repressor biotin-[acetylCoA carboxylase] holoenzymesynthetaseandbiotinoperon peptidoglycan glutamate racemase,requiredforbiosynthesisofD-glutamate and bacteriophage BF23 outer membranereceptorfortransportofvitaminB12,Ecolicins,and UDP-N-acetylenolpyruvoylglucosamine reductase formate acetyltransferase2 orf, hypothetical protein probable pyruvateformatelyaseactivatingenzyme2 PTS systemfructose-likeIIBcomponent2 N-acetyl-gamma-glutamylphosphate reductase acetylornithine deacetylase phosphoenolpyruvate carboxylase putative ARAC-typeregulatoryprotein Required forinvasionofbrainmicrovascularendothelialcells argininosuccinate lyase orf, hypotheticalprotein orf, hypotheticalprotein Soluble pyridinenucleotidetranshydrogenase activator, hydrogenperoxide-induciblegenes tRNA (uracil-5-)-methyltransferase

Gene description Structural elements Structural elements tRNA Structural elements Metabolism ofsmallmolecules Structural elements Structural elements Metabolism of smallmolecules Structural elements Metabolism ofsmallmolecules Open reading frames Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Global functions Macromolecule metabolism

Functional category 2317 2317 2317 2318 2317 2306 2319 2306 2307 2312 2312 2311 2310 2308 2309 2312 2315 2315 2314 2313 2316 Operon ID b3980 b3979 b3978 b3977 b3976 b3983 b3982 b3981 b3984 b3985 b3986 b3989 b3988 b3987 b3998 b3997 b3996 b3995 b3994 b3993 b3992 b3991 b3990 b3999 b4000

B number tufB thrT glyT tyrU thrU rplK nusG secE rplA rplJ rplL htrC rpoC rpoB nfi hemE yjaD yjaE thiC thiE thiF thiG thiH yjaG hupA

Gene name + + + + + + + + + + + + + + + + + + + ------Strand orientation 1407 1342 394 142 181 127 234 165 121 179 225 354 257 158 631 211 245 281 377 196 90 Protein length 11618 15681 26738 55718 33966 28105 34311 23694 16031 7543 5933 5586 1198 8885 1145 1328 2346 5841 4076 2362 4139 3797 918 736 97 mRNA intensity A P P P P P P P P P P P P P P P P P P P P P P P P mRNA present 22 10 12 63 63 10 14 16 29 13 20 11 11 5 6 8 5 5 9 9 4 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P Protein detected - total list 36 30 31 5 1 4 9 7 6 0 0 0 1 7 2 3 3 0 1 4 1 # of tryptic peptides detected (total list) P P P P P P P P P Protein detected - short list 14 10 29 31 3 0 4 6 4 0 0 0 1 9 3 3 3 1 1 4 1 # of tryptic peptides detected (short list) P P P P P P P P P P P P P P P P Protein detected - long list 36 30 31 5 0 4 9 7 6 0 0 0 1 7 2 3 3 0 1 4 1 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 3 0 1 0 3 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD

PHD Membrane protein assignment tRNA-Thr tRNA-Gly tRNA-Tyr tRNA-Thr component intranscriptionantitermination protein chainelongationfactorEF-Tu(duplicateoftufA) preprotein translocase 50S ribosomalsubunitproteinL11 50S ribosomalsubunitproteinL1,regulatessynthesisofL1andL11 50S ribosomalsubunitproteinL10 RNA polymerase,betaprimesubunit RNA polymerase,betasubunit 50S ribosomalsubunitproteinL7/L12 uroporphyrinogen decarboxylase orf, hypotheticalprotein putative transcriptionalregulator thiamin biosynthesis,pyrimidinemoiety thiamin biosynthesis,thiazolemoiety thiamin biosynthesis,thiazolemoiety thiamin biosynthesis,thiazolemoiety thiamin biosynthesis,thiazolemoiety heat shockproteinhtrC Endonuclease V DNA-binding protein HU-alpha(HU-2) orf, hypothetical protein

Gene description tRNA tRNA tRNA tRNA Macromolecule metabolism Macromolecule metabolism Cell processes Structural elements Structural elements Structural elements Miscellaneous Miscellaneous Structural elements Metabolism ofsmallmolecules Open readingframes Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Macromolecule metabolism Macromolecule metabolism Open reading frames

Functional category 2322 2320 2321 2323 2323 2324 2325 2325 2324 2329 2329 2328 2327 2327 2327 2327 2327 2326 2329 2330 2329 Operon ID b4021 b4020 b4011 b4010 b4009 b4008 b4007 b4001 b4022 b4012 b4002 b4024 b4023 b4014 b4013 b4003 b4025 b4015 b4004 b4017 b4016 b4006 b4005 b4018 b4019

B number pepE yjbB yjaA rrfE rrlE gltV rrsE yjaH yjbC yjaB yjaI lysC yjbD aceB metA hydH pgi aceA hydG arp aceK purH purD iclR metH

Gene name + + + + + + + + + + + + + + + ------Strand orientation 1227 229 543 127 231 290 147 188 449 533 309 465 549 434 441 728 578 529 429 287 90 Protein length 74275 66355 34705 70767 42160 30099 3034 4150 1064 3168 1053 1355 466 391 385 829 465 279 754 244 260 316 74 97 33 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 20 17 16 21 26 26 15 20 19 31 28 17 34 15 58 8 8 7 2 6 8 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 14 11 34 10 15 1 0 0 0 1 0 0 0 4 4 0 0 0 5 0 0 # of tryptic peptides detected (total list) P P P P P P P Protein detected - short list 13 10 14 13 13 1 0 0 0 1 2 0 0 3 9 0 0 0 5 0 0 # of tryptic peptides detected (short list) P P P P P P P P P P Protein detected - long list 14 11 34 10 15 1 0 0 0 1 0 0 0 4 4 0 0 0 5 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD

PHD Membrane protein assignment 5S ribosomalRNA 23S ribosomalRNA tRNA-Sec 16S rRNA putative alphahelixprotein repressor ofmetEandmetF B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase, formyltransferase; IMPcyclohydrolase phosphoribosylaminoimidazolecarboxamideformyltransferase =AICAR peptidase E,adipeptidasewhereamino-terminalresidue isaspartate orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein homoserine transsuccinylase orf, hypotheticalprotein orf, hypotheticalprotein glucosephosphate isomerase aspartokinase III,lysinesensitive malate synthaseA sensor kinaseforHydG,hydrogenase3activity isocitrate dehydrogenasekinase/phosphatase phosphoribosylglycinamide synthetase=GAR response regulatorofhydrogenase3activity(sensorHydH) regulator ofacetylCoAsynthetase repressor ofaceBAoperon

Gene description Structural elements Structural elements tRNA Structural elements Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Open readingframes Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Miscellaneous Metabolism of smallmolecules Metabolism of smallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules

Functional category 2342 2341 2334 2343 2335 2330 2345 2344 2337 2336 2331 2347 2346 2338 2332 2338 2338 2334 2333 2339 2340 Operon ID b4038 b4037 b4036 b4035 b4026 b4040 b4039 b4027 b4041 b4028 b4044 b4043 b4042 b4029 b4046 b4045 b4030 b4047 b4031 b4048 b4033 b4032 b4049 b4034 b4050

B number yjbI malM lamB malK yjbE ubiA ubiC yjbF plsB yjbG dinF lexA dgkA yjbH yjbK yjbJ yjbA yjbL xylE yjbM malF malG yjbN malE yjbO

Gene name + + + + + + + + + + + + + + + + + + + ------Strand orientation 442 306 446 371 290 202 222 827 245 459 202 122 698 191 136 491 235 514 296 345 396 150 80 69 84 Protein length 1039 3422 1416 2404 1002 1344 3061 483 272 712 717 221 120 506 105 114 630 535 488 187 19 58 59 24 49 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 17 17 26 10 41 12 10 11 28 14 24 21 8 0 5 9 6 3 9 7 6 9 9 8 5 # of tryptic peptides predicted P P P P P Protein detected - total list 1 1 0 0 0 0 0 0 3 0 0 0 1 0 0 0 0 0 0 0 0 0 3 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 2 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 3 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 3 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 1 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt GenProt PHD PHD Membrane protein assignment periplasmic proteinofmalregulon ATP-binding componentoftransportsystemformaltose phage lambdareceptorprotein;maltosehigh-affinity and chemotaxis periplasmic maltose-bindingprotein;substraterecognitionfortransport orf, hypotheticalprotein orf, hypotheticalprotein 4-hydroxybenzoate-octaprenyltransferase orf, hypotheticalprotein regulator forSOS(lexA)regulon glycerol-3-phosphate acyltransferase orf, hypotheticalprotein orf, hypotheticalprotein DNA-damage-inducible proteinF orf, hypotheticalprotein putative regulator orf, hypotheticalprotein orf, hypotheticalprotein part ofmaltosepermease,innermembrane xylose-proton symport orf, hypotheticalprotein part ofmaltosepermease,periplasmic orf, hypothetical protein orf, hypothetical protein

Gene description Metabolism ofsmallmolecules Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Global functions Macromolecule metabolism Open readingframes Metabolism ofsmallmolecules Open readingframes Cell processes Open readingframes Miscellaneous Open readingframes Open readingframes Cell processes Cell processes Open readingframes Cell processes Open reading frames Open reading frames

Functional category 2353 2353 2353 2352 2355 2354 2348 2355 2349 2358 2356 2349 2357 2359 2358 2349 2360 2350 2361 2352 2351 2361 2352 2362 2362 Operon ID b4053 b4052 b4051 b4055 b4054 b4058 b4057 b4056 b4061 b4060 b4059 b4063 b4062 b4065 b4064 b4066 b4070 b4069 b4068 b4067 b4071 b4072 b4074 b4073 b4075

B number alr dnaB qor aphA tyrB uvrA yjbR yjbQ yjcC yjcB ssb soxR soxS yjcE yjcD yjcF nrfA acs yjcH yjcG nrfB nrfC nrfE nrfD nrfF

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 359 471 327 237 397 940 118 138 528 116 178 154 107 549 449 430 478 652 104 549 190 223 552 318 127 Protein length 1658 1555 1196 1408 1821 2312 1677 8103 3316 3605 516 478 202 157 440 607 249 212 141 320 97 79 19 81 82 mRNA intensity A A A A A A A A A P P P P P P P P P P P P P P P P mRNA present 28 17 15 17 40 30 15 17 27 25 11 18 8 5 5 7 3 4 8 6 5 9 9 8 3 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 18 1 2 1 5 0 1 0 3 3 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 18 2 4 1 7 0 2 0 3 3 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P P Protein detected - long list 18 1 2 1 5 0 1 0 3 3 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt PHD PHD PHD Membrane protein assignment replicative DNAhelicase;partofprimosome quinone oxidoreductase tyrosine aminotransferase,repressible alanine racemase1 orf, hypotheticalprotein orf, hypotheticalprotein diadenosine tetraphosphatase ssDNA-binding protein excision nucleasesubunitA orf, hypotheticalprotein regulation ofsuperoxideresponseregulon orf, hypotheticalprotein redox-sensing activatorofsoxS orf, hypotheticalprotein orf, hypotheticalprotein acetyl-CoA synthetase orf, hypotheticalprotein orf, hypotheticalprotein putative transportprotein periplasmic cytochromec(552):playsaroleinnitrite reduction formate-dependent nitritereductase;apenta-haeme cytochromec formate-dependent nitrate reductase complex;transmembraneprotein formate-dependent nitritereductase; Fe-Scenters formate-dependent nitritereductase;possible assemblyfunction part offormate-dependent nitritereductase complex

Gene description Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism Macromolecule metabolism Open readingframes Global functions Open readingframes Global functions Open readingframes Cell processes Metabolism ofsmallmolecules Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism of smallmolecules Metabolism of smallmolecules

Functional category 2364 2363 2366 2365 2368 2368 2367 2370 2369 2371 2373 2372 2374 2375 2376 2379 2378 2377 2378 2380 2380 2380 2380 2380 2380 Operon ID b4076 b4077 b4078 b4079 b4080 b4082 b4081 b4083 b4084 b4085 b4086 b4087 b4088 b4089 b4090 b4091 b4092 b4093 b4094 b4095 b4096 b4097 b4098 b4099 b4100

B number nrfG gltP yjcO fdhF yjcP yjcR yjcQ yjcS yjcT yjcU yjcV yjcW yjcX rpiR rpiB phnQ phnP phnO phnN phnM phnL phnK phnJ phnI phnH

Gene name + + + ------Strand orientation 198 437 229 715 488 343 636 665 309 231 326 510 311 307 149 135 252 144 185 378 226 252 281 354 194 Protein length 111 223 275 167 129 318 353 161 262 112 101 331 434 674 108 212 638 390 147 538 112 28 56 27 36 mRNA intensity A A A A A A A A A A A A A P P P P P P P P P P P P mRNA present 11 34 24 21 19 29 14 26 17 11 16 12 13 14 15 4 9 8 4 8 7 8 6 8 4 # of tryptic peptides predicted

Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD MP-GenProt GenProt GenProt PHD PHD Membrane protein assignment part offormate-dependentnitritereductasecomplex glutamate-aspartate symportprotein orf, hypotheticalprotein selenopolypeptide subunitofformatedehydrogenaseH putative enzyme putative enzyme putative membraneprotein orf, hypotheticalprotein putative NAGC-liketranscriptionalregulator putative epimerase putative transportsystempermeaseprotein putative ATP-bindingcomponentofatransportsystem putative LACI-typetranscriptionalregulator transcriptional repressorofrpiBexpression ribose 5-phosphateisomeraseB orf, hypotheticalprotein phosphonate metabolism putative regulator,phnoperon ATP-binding componentofphosphonatetransport phosphonate metabolism ATP-binding componentofphosphonatetransport ATP-binding componentof phosphonatetransport phosphonate metabolism phosphonate metabolism phosphonate metabolism

Gene description Metabolism ofsmallmolecules Cell processes Open readingframes Metabolism ofsmallmolecules Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Miscellaneous Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Metabolism of smallmolecules Metabolism of smallmolecules

Functional category 2380 2381 2382 2383 2384 2384 2385 2386 2387 2387 2387 2387 2388 2389 2390 2391 2391 2391 2391 2391 2391 2391 2391 2391 2391 Operon ID b4115 b4114 b4101 b4116 b4102 b4117 b4104 b4103 b4118 b4105 b4119 b4106 b4120 b4107 b4122 b4121 b4109 b4108 b4123 b4110 b4124 b4112 b4111 b4125 b4113

B number yjdE yjdB phnG adiY phnF adiA phnE b4103 melR phnD melA phnC melB phnB fumB yjdF yjdA phnA dcuB yjcZ dcuR basS proP dcuS basR

Gene name + + + + + ------Strand orientation 445 557 150 253 241 756 206 302 338 451 262 469 147 548 209 742 111 446 281 239 363 500 543 222 73 Protein length 2675 2032 273 174 154 145 145 517 120 575 261 136 243 340 271 591 591 34 41 48 42 39 43 35 9 mRNA intensity A A A A A A A A A A A A A A P P P P P P P P P P P mRNA present 10 17 10 12 13 31 15 16 16 12 10 32 42 12 16 10 16 26 2 4 9 4 3 6 6 # of tryptic peptides predicted

P Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

P Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt PHD PHD PHD PHD Membrane protein assignment orf, hypotheticalprotein system, transcriptional regulatoryprotein,memberof2-component putative aminoacid/aminetransportprotein,cryptic phosphonate metabolism putative ARAC-typeregulatoryprotein putative transcriptionalregulator orf, hypotheticalprotein biodegradative argininedecarboxylase membrane channelproteincomponentofPntransporter regulator ofmelibioseoperon periplasmic bindingproteincomponentofPntransporter alpha-galactosidase ATP-binding componentofphosphonatetransport orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein melibiose permeaseII fumarase B=fumaratehydratase ClassI;anaerobicisozyme putative vimentin anaerobic dicarboxylatetransport orf, hypotheticalprotein low-affinity transportsystem;prolinepermeaseII Cognate response regulator sensor proteinforbasR Fumarate sensor protein

Gene description Open readingframes Macromolecule metabolism Miscellaneous Metabolism ofsmallmolecules Miscellaneous Miscellaneous Open readingframes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Cell processes Open readingframes Open readingframes Open readingframes Cell processes Metabolism ofsmallmolecules Miscellaneous Cell processes Open readingframes Cell processes Metabolism of smallmolecules Macromolecule metabolism Metabolism of smallmolecules

Functional category 2397 2396 2398 2391 2399 2391 2391 2399 2391 2400 2391 2401 2391 2393 2392 2402 2401 2403 2394 2404 2394 2395 2405 2396 2405 Operon ID b4145 b4144 b4143 b4128 b4127 b4126 b4146 b4129 b4148 b4147 b4130 b4150 b4149 b4131 b4132 b4133 b4134 b4136 b4135 b4138 b4137 b4140 b4139 b4142 b4141

B number yjeJ yjeI mopA yjdK yjdJ yjdI yjeK lysU sugE efp yjdL ampC blc cadA cadB cadC pheU dsbD yjdC dcuA cutA fxsA aspA mopB yjeH

Gene name + + + + + + + + + ------Strand orientation 289 128 548 342 505 155 188 485 377 177 715 444 512 565 199 433 112 125 493 418 98 90 76 97 Protein length 10097 35460 4386 1087 1579 6703 1023 2805 1606 1704 151 400 394 279 282 295 281 641 793 338 479 35 40 40 8 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 15 26 15 25 13 19 33 19 12 14 20 4 4 4 4 4 5 5 6 4 4 6 4 6 # of tryptic peptides predicted P P P P P P P P P P Protein detected - total list 13 1 0 0 0 0 0 1 2 0 2 0 0 0 0 0 2 1 0 1 3 5 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 17 1 0 0 0 0 0 0 2 0 0 0 0 0 0 0 2 0 0 0 5 4 0 0 # of tryptic peptides detected (short list) P P P P P P Protein detected - long list 13 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 2 0 0 0 3 5 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 1 0 0 0 4 0 0 0 0 0 2 0 0 0 0 0 0 1 0 1 0 1 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt

PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein protein GroEL, chaperoneHsp60,peptide-dependentATPase, heatshock its ATPaseactivity GroES, 10KdchaperonebindstoHsp60inpres.Mg-ATP, suppressing orf, hypotheticalprotein orf, hypotheticalprotein elongation factorP(EF-P) orf, hypotheticalprotein lysine tRNAsynthetase,inducible;heatshockprotein putative peptidetransporter outer membrane lipoprotein(lipocalin) suppresses groEL,maybe chaperone beta-lactamase; penicillinresistance lysine decarboxylase1 transport oflysine/cadaverine transcriptional activatorofcadoperon orf, hypotheticalprotein tRNA-Phe divalent cationtoleranceprotein;cytochromecbiogenesis thiol:disulfide interchangeprotein;coppertolerance aspartate ammonia-lyase(aspartase) anaerobic dicarboxylatetransport Suppressor ofFexclusionbacteriophageT7. putative transport

Gene description Open readingframes Open readingframes Open readingframes Cell processes Cell processes Open readingframes Open readingframes Macromolecule metabolism Open readingframes Macromolecule metabolism Cell processes Macromolecule metabolism Cell processes Cell processes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Open readingframes tRNA Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Open readingframes Miscellaneous

Functional category 2417 2406 2406 2416 2416 2418 2407 2420 2419 2408 2409 2422 2421 2423 2410 2410 2410 2411 2411 2411 2413 2412 2414 2415 Operon ID b4175 b4174 b4173 b4153 b4152 b4151 b4155 b4154 b4156 b4157 b4161 b4160 b4159 b4158 b4162 b4166 b4165 b4164 b4163 b4168 b4167 b4169 b4170 b4171 b4172

B number hflC hflK hflX frdB frdC frdD yjeA frdA yjeM yjeN yjeQ psd yjeP yjeO yjeR yjeS glyY glyX glyV yjeE yjeF amiB mutL miaA hfq

Gene name + + + + + + + + + + + + + + + + + ------Strand orientation 1107 334 419 426 244 131 119 335 602 514 104 337 322 104 204 379 153 515 445 615 316 102 Protein length 21261 11884 2685 4830 5821 1593 1157 7948 9224 8003 1328 883 272 506 206 111 417 821 835 118 697 778 601 18 68 mRNA intensity A A A A P P P P P P P P P P P P P P P P P P P P P mRNA present 16 17 24 32 16 13 48 12 16 18 16 18 26 19 9 5 5 5 5 8 6 4 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 4 5 2 2 0 0 1 0 0 1 0 4 1 0 2 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 1 4 3 0 0 0 1 0 0 0 0 1 2 0 3 1 0 0 1 0 0 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 1 3 2 0 0 0 1 0 0 0 0 1 1 0 2 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 4 5 0 2 0 0 0 0 0 1 0 4 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD GenProt PHD Membrane protein assignment protease specific forphagelambdacII repressor protease specific forphagelambdacII repressor GTP -bindingsubunitofprotease specificforphagelambdacIIrepressor protein host factorIforbacteriophage Qbetareplication,agrowth-related fumarate reductase,anaerobic,membraneanchorpolypeptide fumarate reductase,anaerobic,membraneanchorpolypeptide fumarate reductase,anaerobic,flavoproteinsubunit fumarate reductase,anaerobic,iron-sulfurproteinsubunit putative lysyl-tRNAsynthetase putative transport putative periplasmicbindingprotein orf, hypotheticalprotein phosphatidylserine decarboxylase;phospholipidsynthesis orf, hypotheticalprotein orf, hypotheticalprotein tRNA-Gly tRNA-Gly tRNA-Gly orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein N-acetylmuramoyl-l-alanine amidaseII;amureinhydrolase enzyme inmethyl-directedmismatchrepair delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase

Gene description Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Extrachromosomal Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Miscellaneous Miscellaneous Open readingframes Macromolecule metabolism Open readingframes Open readingframes tRNA tRNA tRNA Open readingframes Open readingframes Open readingframes Open readingframes Structural elements Macromolecule metabolism Macromolecule metabolism

Functional category 2433 2433 2433 2433 2424 2424 2424 2424 2425 2426 2428 2427 2428 2427 2429 2430 2432 2431 2432 2433 2433 2433 Operon ID b4178 b4177 b4176 b4180 b4179 b4181 b4182 b4183 b4185 b4184 b4186 b4187 b4188 b4190 b4189 b4191 b4192 b4193 b4194 b4195 b4196 b4197 b4198 b4200 b4199

B number yjeB purA yjeT yjfH vacB yjfI yjfJ yjfK yjfM yjfL yjfC aidB yjfN yjfP yjfO yjfQ yjfR sgaT sgaB ptxA sgaH sgaU sgaE rpsF yjfY

Gene name + + + + + + + + + + + + + + + + + + + + - - - - - Strand orientation 141 432 243 827 133 232 219 212 132 387 546 100 249 142 251 356 484 101 154 216 284 228 131 65 91 Protein length 23491 2778 1123 1496 144 509 173 310 457 434 308 102 222 247 259 365 179 55 61 75 30 96 85 46 83 mRNA intensity A A A A A A A A A A A A A A A P P P P P P P P P P mRNA present 21 41 11 10 18 21 10 11 20 14 3 7 9 2 9 2 2 6 8 5 4 9 9 4 7 # of tryptic peptides predicted P P P P Protein detected - total list 15 0 0 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 # of tryptic peptides detected (total list) P P Protein detected - short list 15 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 # of tryptic peptides detected (short list) P P P P Protein detected - long list 15 0 0 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample)

PHD Membrane protein assignment adenylosuccinate synthetase orf, hypotheticalprotein putative enzyme orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative alphahelicalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative synthetase/amidase putative acylcoenzymeAdehydrogenase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative DEOR-typetranscriptionalregulator orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative PTSsystemenzymeIIAcomponent probable hexulose-6-phosphatesynthase putative hexulose-6-phosphate isomerase orf, hypothetical protein putative epimerase/aldolase 30S ribosomal subunitproteinS6

Gene description Metabolism ofsmallmolecules Open readingframes Macromolecule metabolism Open readingframes Macromolecule metabolism Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous Miscellaneous Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Miscellaneous Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open reading frames Open readingframes Structural elements

Functional category 2435 2434 2436 2436 2437 2438 2438 2439 2439 2439 2439 2440 2442 2441 2443 2444 2445 2446 2446 2446 2446 2446 2447 2446 2448 Operon ID b4215 b4201 b4220 b4219 b4218 b4217 b4216 b4204 b4203 b4202 b4225 b4224 b4223 b4222 b4221 b4205 b4206 b4209 b4208 b4207 b4210 b4211 b4212 b4213 b4214

B number ytfI priB ytfM msrA ytfL ytfK ytfJ yjfZ rplI rpsR chpB chpS yjfA ytfP ytfN ytfA ytfB ytfE cycA fklB ytfF ytfG ytfH cpdB cysQ

Gene name + + + + + + + + + + + + + + + ------Strand orientation 1259 166 104 577 212 447 184 264 149 116 113 108 224 220 470 259 324 286 156 647 246 81 75 85 89 Protein length 14218 23556 1447 1019 2574 2322 1002 2038 3787 635 347 103 353 398 546 971 204 273 102 524 464 36 74 38 62 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 10 10 27 15 60 11 10 10 15 31 10 4 3 5 7 7 4 9 6 4 3 3 9 5 7 # of tryptic peptides predicted P P P P P P P P P Protein detected - total list 0 0 4 0 2 0 5 0 1 0 0 0 2 0 0 0 0 0 4 0 0 1 0 2 1 # of tryptic peptides detected (total list) P P Protein detected - short list 0 0 2 0 2 0 6 0 0 0 0 0 2 0 0 0 0 0 5 0 0 0 0 3 3 # of tryptic peptides detected (short list) P P P P P P P P Protein detected - long list 0 0 4 0 2 0 5 0 0 0 0 0 2 0 0 0 0 0 4 0 0 1 0 2 1 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 3 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD MP-PHD GenProt PHD Membrane protein assignment sulfite synthesis affects poolof3'-phosphoadenosine-5'-phosphosulfateinpathway peptide methioninesulfoxidereductase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein 50S ribosomalsubunitproteinL9 30S ribosomalsubunitproteinS18 primosomal replicationproteinN putative transportprotein suppressor of inhibitoryfunctionofChpB, PemI-like,autoregulated orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein probable growth inhibitor,PemK-like,autoregulated orf, hypotheticalprotein FKBP-type 22KDpeptidyl-prolylcis-transisomerase(rotamase) orf, hypotheticalprotein transport ofD-alanine,D-serine,andglycine orf, hypotheticalprotein putative transmembranesubunit putative oxidoreductase orf, hypotheticalprotein 2':3'-cyclic-nucleotide 2'-phosphodiesterase

Gene description Metabolism ofsmallmolecules Macromolecule metabolism Open readingframes Open readingframes Open readingframes Structural elements Structural elements Macromolecule metabolism Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Macromolecule metabolism Open readingframes Cell processes Open readingframes Open readingframes Miscellaneous Open readingframes Metabolism ofsmallmolecules

Functional category 2459 2464 2462 2461 2460 2448 2448 2448 2463 2467 2466 2465 2465 2465 2449 2467 2450 2452 2451 2453 2454 2455 2456 2457 2458 Operon ID b4227 b4226 b4228 b4230 b4229 b4231 b4233 b4232 b4236 b4235 b4234 b4237 b4238 b4239 b4241 b4240 b4242 b4243 b4244 b4245 b4247 b4246 b4248 b4249 b4250

B number ytfQ ppa ytfR ytfT ytfS yjfF yjfG fbp cybC pmbA yjgA nrdG nrdD treC treR treB mgtA yjgF pyrI pyrB yjgG pyrL yjgH yjgI b4250

Gene name + + + + + + + + + + + ------Strand orientation 318 176 417 341 323 457 332 100 450 183 154 712 551 315 473 898 141 153 311 110 131 237 90 44 54 Protein length 11796 36636 39294 3081 2607 1085 1513 1253 908 185 336 116 908 313 126 357 423 175 721 941 622 153 96 30 98 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 11 13 23 14 17 25 27 22 15 31 19 11 3 7 6 7 5 9 8 7 9 2 5 4 4 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 14 4 2 0 0 0 0 3 1 2 1 0 0 0 1 2 0 0 2 8 0 0 0 0 0 # of tryptic peptides detected (total list) P P P P Protein detected - short list 10 3 1 0 0 0 0 6 0 4 2 0 0 0 1 0 0 0 3 7 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P P P P P P Protein detected - long list 14 4 2 0 0 0 0 3 1 2 1 0 0 0 1 0 0 0 2 8 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 2 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt GenProt PHD Membrane protein assignment inorganic pyrophosphatase putative LACI-typetranscriptionalregulator putative ATP-bindingcomponentofatransportsystem putative ATP-bindingcomponentofatransportsystem putative transportsystempermeaseprotein fructose-bisphosphatase putative transportsystempermeaseprotein maturation ofantibioticMccB17,seetldgenes putative alphahelixprotein putative ligase cytochrome b(562) anaerobic ribonucleotidereductaseactivatingprotein anaerobic ribonucleoside-triphosphatereductase trehalase 6-Phydrolase PTS systemenzymeII,trehalosespecific repressor oftreA,B,C Mg2+ transportATPase,P-type1 orf, hypotheticalprotein aspartate carbamoyltransferase,regulatorysubunit pyrBI operonleaderpeptide aspartate carbamoyltransferase,catalyticsubunit orf, hypotheticalprotein orf, hypotheticalprotein orf, hypothetical protein putative oxidoreductase

Gene description Metabolism ofsmallmolecules Cell processes Cell processes Cell processes Cell processes Metabolism ofsmallmolecules Cell processes Macromolecule metabolism Miscellaneous Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Cell processes Cell processes Cell processes Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Open readingframes Open reading frames Miscellaneous

Functional category 2468 2469 2470 2470 2470 2471 2470 2474 2473 2472 2475 2476 2477 2478 2478 2479 2480 2481 2482 2483 2482 2484 2485 2487 2486 Operon ID b4252 b4251 b4253 b4257 b4256 b4255 b4254 b4263 b4262 b4261 b4260 b4259 b4258 b4264 b4265 b4266 b4267 b4268 b4269 b4270 b4271 b4272 b4273 b4274 b4275

B number yjgK yjgJ yjgL yjgN b4256 yjgD argI yjgR yjgQ yjgP pepA holC valS idnR idnT idnO idnD idnK yjgB leuX intB yi21_6 yi22_6 yjgW yjgX

Gene name + + + + + + + + + + + + + ------Strand orientation 153 616 393 138 334 500 361 366 503 147 951 332 439 254 343 187 353 396 136 301 111 148 84 97 Protein length 6166 2198 2469 2370 1977 146 399 326 100 691 267 626 204 382 270 243 352 228 166 262 17 39 20 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P mRNA present 36 15 21 47 13 29 15 11 12 13 15 11 20 16 4 8 4 1 6 6 9 8 6 7 # of tryptic peptides predicted P P P P P P Protein detected - total list 16 0 0 0 0 1 4 4 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 15 0 0 0 0 0 4 4 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P P P P Protein detected - long list 16 0 0 0 0 1 4 4 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD

PHD PHD Membrane protein assignment orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein ornithine carbamoyltransferase1 orf, hypotheticalprotein aminopeptidase A/I DNA polymeraseIII,chisubunit valine tRNAsynthetase orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein L-Idonate regulator L-Idonate transporter 5-Keto-D-gluconate 5-reductase L-Idonate 5-dehydrogenase D-Gluconate kinase putative oxidoreductase tRNA-Leu prophage P4integrase IS2 hypotheticalprotein IS2 hypotheticalprotein orf, hypothetical protein orf, hypothetical protein

Gene description Open readingframes Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Open readingframes Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Open readingframes Open readingframes Open readingframes Open readingframes Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Miscellaneous tRNA Extrachromosomal Open readingframes Miscellaneous Open reading frames Open reading frames

Functional category 2488 2489 2493 2492 2491 2490 2496 2495 2495 2494 2497 2497 2498 2499 2500 2501 2501 2502 2503 2504 2505 2505 2506 2507 Operon ID b4292 b4277 b4276 b4293 b4278 b4295 b4294 b4279 b4296 b4280 b4297 b4281 b4298 b4283 b4282 b4299 b4284 b4300 b4285 b4286 b4287 b4288 b4289 b4290 b4291

B number fecR yjgZ yjgY fecI yi41 yjhU insA_7 yjhB yjhF yjhC yjhG yjhD yjhH yi91b yjhE yjhI tra8_3 sgcR b4285 b4286 fecE fecD fecC fecB fecA

Gene name + + + + + + + + ------Strand orientation 317 109 149 173 442 266 425 449 377 655 124 319 100 262 383 260 198 137 255 318 332 302 774 91 67 Protein length 175 110 140 287 557 200 485 129 243 146 143 295 204 101 128 151 188 152 180 211 53 97 52 51 mRNA intensity A A A A A A A A A A A A A A P P P P P P P P P P mRNA present 16 10 21 13 10 10 13 22 16 19 16 13 13 13 10 31 7 8 5 5 1 7 5 6 6 # of tryptic peptides predicted

Protein detected - total list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list)

Protein detected - long list 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt GenProt GenProt PHD PHD PHD Membrane protein assignment membrane receptor outer membranereceptor;citrate-dependentirontransport, orf, hypotheticalprotein orf, hypotheticalprotein regulator forfecoperon,periplasmic IS1 proteinInsA probable RNApolymerasesigmafactor IS4 hypotheticalprotein orf, hypotheticalprotein putative transportprotein putative transportsystempermease putative dehydrogenase putative dehydratase orf, hypotheticalprotein orf, hypotheticalprotein putative lyase/synthase IS911 hypotheticalprotein(IS911B) putative regulator IS30 transposase putative DEOR-type transcriptionalregulator putative transposase orf, hypotheticalprotein ATP-binding componentofcitrate-dependentiron(III)transportprotein citrate-dependent irontransport,membrane-boundprotein citrate-dependent iron(III)transportprotein,cytosolic citrate-dependent irontransport,periplasmicprotein

Gene description Cell processes Open readingframes Open readingframes Cell processes Extrachromosomal Global functions Extrachromosomal Open readingframes Cell processes Cell processes Open readingframes Miscellaneous Open readingframes Open readingframes Open readingframes Extrachromosomal Miscellaneous Extrachromosomal Miscellaneous Miscellaneous Open readingframes Cell processes Cell processes Cell processes Cell processes

Functional category 2517 2507 2508 2517 2518 2517 2509 2519 2510 2520 2510 2521 2512 2511 2521 2513 2521 2514 2522 2515 2516 2517 2517 2517 2517 Operon ID b4318 b4301 b4319 b4302 b4320 b4303 b4321 b4304 b4322 b4305 b4323 b4306 b4324 b4307 b4325 b4309 b4308 b4310 b4311 b4312 b4313 b4314 b4316 b4315 b4317

B number fimF sgcE fimG sgcA fimH sgcQ gntP sgcC uxuA sgcX uxuB yjhP uxuR yjhQ yjiC yjhS yjhR yjhT yjhA fimB fimE fimA fimC fimI fimD

Gene name + + + + + + + + + + + + + ------Strand orientation 176 210 167 143 300 268 447 437 394 383 486 248 257 181 276 326 338 404 241 200 198 182 241 215 878 Protein length 10286 1048 207 218 290 356 292 173 189 558 155 432 268 232 192 122 120 275 255 596 114 17 59 89 67 mRNA intensity A A A A A A A A A A P P P P P P P P P P P P P P P mRNA present 11 23 14 19 12 19 10 10 22 10 12 11 10 13 32 4 7 5 2 7 8 9 9 9 2 # of tryptic peptides predicted P P P Protein detected - total list 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 # of tryptic peptides detected (total list)

Protein detected - short list 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD MP-GenProt

PHD Membrane protein assignment interrupted outer membraneprotein;exportandassemblyoftype 1fimbriae, fimbrial morphology putative epimerase fimbrial morphology putative PTSsystemenzymeIIAcomponent minor fimbrialsubunit,D-mannosespecificadhesin putative nucleosidetriphosphatase gluconate transportsystempermease3 putative PTSsystemenzymeIICcomponent mannonate hydrolase putative lyase/synthase D-mannonate oxidoreductase putative methyltransferase regulator foruxu operon putative frameshiftsuppressor orf, hypotheticalprotein orf, hypothetical protein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein recombinase involvedinphasevariation;regulatorforfimA recombinase involvedinphasevariation;regulatorforfimA fimbrial protein major type1subunitfimbrin(pilin) periplasmic chaperone,requiredfortype1fimbriae

Gene description Structural elements Structural elements Miscellaneous Structural elements Cell processes Structural elements Miscellaneous Cell processes Miscellaneous Metabolism ofsmallmolecules Cell processes Metabolism ofsmallmolecules Miscellaneous Metabolism of smallmolecules Miscellaneous Open readingframes Open reading frames Open readingframes Open readingframes Open readingframes Structural elements Structural elements Structural elements Structural elements Structural elements

Functional category 2530 2530 2522 2530 2522 2530 2523 2531 2523 2532 2524 2532 2525 2533 2527 2526 2534 2528 2529 2529 2530 2530 2530 2530 2530 Operon ID b4346 b4326 b4347 b4327 b4348 b4328 b4350 b4349 b4329 b4331 b4330 b4333 b4332 b4334 b4335 b4337 b4336 b4338 b4339 b4340 b4342 b4341 b4343 b4344 b4345

B number mcrB yjiD yjiW yjiE hsdS iadA hsdR hsdM yjiG kptA yjiH yjiK yjiJ yjiL yjiM yjiO yjiN yjiP yjiQ yjiR yjiT yjiS yjiU mcrD mcrC

Gene name + + + + + + + + ------Strand orientation 1188 465 133 132 303 464 390 529 153 218 231 323 392 257 390 410 426 103 186 470 521 513 420 348 54 Protein length 1232 220 162 148 321 266 224 196 254 154 253 100 357 248 110 179 551 209 105 90 85 91 65 76 48 mRNA intensity A A A A A A A A A A A A A P P P P P P P P P P P P mRNA present 19 15 69 28 19 32 15 16 13 16 21 21 26 26 22 16 5 7 4 6 4 8 8 9 3 # of tryptic peptides predicted P P Protein detected - total list 0 0 0 0 1 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 0 0 1 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (short list) P P Protein detected - long list 0 0 0 0 1 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD PHD PHD PHD PHD Membrane protein assignment of sequencesrestricted component ofMcrBC5-methylcytosinerestrictionsystem, expandsrange component ofMcrBC5-methylcytosinerestrictionsystem orf, hypotheticalprotein orf, hypotheticalprotein putative transcriptionalregulatorLYSR-type host restriction; endonucleaseR host modification; DNAmethylaseM specificity determinantfor hsdM andhsdR isoaspartyl dipeptidase orf, hypotheticalprotein orf, hypotheticalprotein 2'-phosphotransferase putative transportprotein orf, hypotheticalprotein putative enzyme orf, hypotheticalprotein orf, hypotheticalprotein putative transportprotein orf, hypotheticalprotein orf, hypotheticalprotein orf, hypotheticalprotein putative regulator orf, hypotheticalprotein orf, hypotheticalprotein inhibits McrE5-methylcytosinerestrictionsystem

Gene description Macromolecule metabolism Macromolecule metabolism Open readingframes Open readingframes Miscellaneous Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Open readingframes Open readingframes Metabolism ofsmallmolecules Miscellaneous Open readingframes Open readingframes Open readingframes Open readingframes Cell processes Open readingframes Open readingframes Open readingframes Miscellaneous Open readingframes Open readingframes Macromolecule metabolism

Functional category 2548 2548 2535 2549 2536 2551 2550 2550 2537 2537 2537 2538 2539 2540 2541 2541 2542 2542 2543 2543 2545 2544 2546 2547 2547 Operon ID b4374 b4351 b4375 b4352 b4355 b4354 b4353 b4356 b4357 b4358 b4359 b4360 b4361 b4362 b4363 b4364 b4365 b4366 b4368 b4367 b4371 b4370 b4369 b4373 b4372

B number yjjG mrr prfC yjiA tsr yjiY yjiX yjiZ yjjM yjjN mdoB yjjA dnaC dnaT yjjB yjjP yjjQ bglJ leuV fhuF rsmC leuQ leuP rimI holD

Gene name + + + + + + + + + ------Strand orientation 225 304 529 284 551 721 453 268 345 750 165 245 179 108 277 241 225 262 343 148 137 67 Protein length 1117 1576 2164 1103 1749 2453 1781 272 824 859 359 123 140 219 177 717 698 441 618 109 192 994 510 56 46 mRNA intensity A A A A A P P P P P P P P P P P P P P P P P P P P mRNA present 17 23 10 19 29 11 14 17 31 11 11 12 12 13 16 7 3 6 8 2 9 7 # of tryptic peptides predicted P P P P Protein detected - total list 0 0 3 1 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 1 0 0 # of tryptic peptides detected (total list)

P Protein detected - short list 0 0 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # of tryptic peptides detected (short list) P P P Protein detected - long list 0 0 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 # of tryptic peptides detected (long list) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt GenProt PHD PHD Membrane protein assignment terminal alanine acyltransferase for30Sribosomal subunitproteinS18;acetylationofN- peptide chain releasefactorRF-3 putative phosphatase restriction ofmethylatedadenine orf, hypotheticalprotein orf, hypotheticalprotein putative carbonstarvationprotein methyl-accepting chemotaxisproteinI,serinesensorreceptor putative transportprotein,cryptic,orf,joinsformeryjiZandyjjL orf, hypotheticalprotein putative oxidoreductase phosphoglycerol transferaseI putative glycoprotein/receptor chromosome replication;initiationandchainelongation DNA biosynthesis;primosomalproteini orf, hypotheticalprotein putative structuralprotein putative regulator orf, hypotheticalprotein 2-component transcriptionalregulator tRNA-Leu tRNA-Leu tRNA-Leu DNA polymeraseIII,psisubunit 16S RNAm2G1207Methylase

Gene description Structural elements Macromolecule metabolism Open reading frames Macromolecule metabolism Open readingframes Open readingframes Miscellaneous Cell processes Miscellaneous Open readingframes Miscellaneous Cell processes Miscellaneous Cell processes Macromolecule metabolism Open readingframes Miscellaneous Miscellaneous Metabolism ofsmallmolecules Metabolism ofsmallmolecules tRNA tRNA tRNA Macromolecule metabolism Macromolecule metabolism

Functional category 2567 2567 2567 2552 2554 2553 2554 2555 2556 2557 2558 2559 2560 2561 2561 2562 2563 2564 2565 2564 2567 2566 Operon ID b4400 b4378 b4377 b4376 b4379 b4380 b4381 b4382 b4385 b4384 b4383 b4386 b4387 b4389 b4388 b4390 b4392 b4391 b4393 b4394 b4395 b4398 b4397 b4396 b4399

B number creD yjjV yjjU osmY yjjW yjjI deoC deoA yjjJ deoD deoB lplA smp sms serB nadR slt yjjK trpR yjjX gpmB creB creA rob creC

Gene name + + + + + + + + + + + + + + + + + + ------Strand orientation 450 211 357 201 287 516 259 440 443 239 407 338 214 460 322 417 654 555 108 173 215 229 157 289 474 Protein length 1127 6115 3617 2940 1030 2248 1120 1097 112 368 126 113 533 863 340 884 927 912 746 591 401 568 437 59 13 mRNA intensity A A A A A A A P P P P P P P P P P P P P P P P P P mRNA present 15 10 14 13 24 14 25 14 19 16 17 10 16 21 23 30 41 11 11 19 7 6 6 6 9 # of tryptic peptides predicted P P P P P P P P P P P Protein detected - total list 16 0 3 0 0 0 0 3 1 4 7 0 0 0 1 1 0 4 0 0 1 0 1 0 0 # of tryptic peptides detected (total list) P P P Protein detected - short list 17 0 4 0 0 0 0 3 2 2 8 0 0 0 1 1 0 3 0 0 2 1 2 0 0 # of tryptic peptides detected (short list) P P P P P P P P P P P Protein detected - long list 16 0 3 0 0 0 0 3 1 4 7 0 0 0 1 1 0 4 0 0 1 0 1 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt Membrane protein assignment orf, hypotheticalprotein hyperosmotically inducibleperiplasmicprotein regulon catabolite repressionsensor kinaseforPhoB;alternativesensorpho orf, hypotheticalprotein tolerance tocolicin E2 putative activatingenzyme orf, hypotheticalprotein 2-deoxyribose-5-phosphate aldolase purine-nucleoside phosphorylase phosphopentomutase thymidine phosphorylase orf, hypotheticalprotein lipoate-protein ligaseA 3-phosphoserine phosphatase orf, hypotheticalprotein probable ATP-dependentprotease putative ATP-bindingcomponentofatransportsystem probable nadABtranscriptionalregulator soluble lyticmureintransglycosylase regulator fortrpoperonandaroH;aporepressor orf, hypotheticalprotein orf, hypotheticalprotein right origin-bindingprotein phosphoglyceromutase 2 catabolic regulationresponse regulator

Gene description Open readingframes Cell processes Global functions Open readingframes Extrachromosomal Metabolism ofsmallmolecules Open readingframes Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Metabolism ofsmallmolecules Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Miscellaneous Macromolecule metabolism Cell processes Metabolism ofsmallmolecules Structural elements Metabolism ofsmallmolecules Open readingframes Open readingframes Macromolecule metabolism Metabolism ofsmallmolecules Global functions

Functional category 2568 2567 2581 2569 2581 2570 2570 2571 2571 2571 2571 2572 2573 2574 2573 2574 2575 2574 2576 2577 2578 2581 2580 2579 2581 Operon ID b4403 b4402 b4401 b4405 b4404

B number lasT yjjY arcA yifM_2 yifM_1 present onGeneChips)-2826. All genes-4405.Protein-coding4291; genesexcluded:86tRNAgenes,25stableRNAs, Membrane proteinassignment(seepaper):MP-list#1,GenProt#2,PHD#3. 66 geneshadnoprobesonGeneChipswhichisindicatedbyblankcellsformRNAsignal andmRNApresent. detected. TufA andTufBproteinsdifferbyonlyoneaminoacidthuscannotbedifferentiated byeithermRNAorproteinanalysis.Bothgenesandproteinswereconsidered Two genes-ilvG_2(b3768)andyifM_2(b4405)havenocategoryassignmentwere notconsideredinanycalculations. operon organizationwaschangedbasedonnewinformation;suchoperonshaveapatterned background.Non-proteincodinggenesareshownonagreen All 4405E.coligenesareshown.Genessortedbybnumbers.Differentoperons denotedbyalternatingwhite-yellowbackgroundcolor.Inseveralcasesthe assigned asdefinedbyRileyandLabedan(1996). Annotation informationwastakenfromthe

Gene name + + + + - Strand orientation 228 238 204 46 74 Protein length 2126 172 561 mRNA intensity P P P mRNA present 11 14 11 1 4 # of tryptic peptides predicted

P Protein detected - total list E.coli 0 2 0 0 0 # of tryptic peptides detected (total list) EntryPointdatabase.TheannotationinthedatabaseisbasedonBlattneretal(1997). Functionalcategoriesare Protein detected - short list 0 2 0 0 0 # of tryptic peptides detected (short list)

P Protein detected - long list 0 2 0 0 0 # of tryptic peptides detected (long list)

Proteins detected - membrane sample

# of tryptic peptides 0 0 0 0 0 detected (membrane sample)

rnpB, spf,dicF Membrane protein assignment orf, hypotheticalprotein ArcB andCpxA) negative responseregulatorofgenesinaerobicpathways,(sensors, orf, conceptualtranslationinSwissProtisfusedwithb4405 orf, hypotheticalprotein orf, conceptualtranslationinSwissProtisfusedwithb4404 genes.Expressedprotein-codinggenes(called

Gene description Open readingframes Global functions Open readingframes Open readingframes

Functional category 2583 2582 2213 2584 2213 Operon ID