b0053 b0052 b0051 b0050 b0033 b0032 b0029 b0027 b0026 b0015 b0078 b0014 b0077 b0008 b0076 b0004 b0075 b0074 b0003 b0002 b0073 b0072 b0071 b0001

B number surA pdxA ksgA apaG carB carA lytB lspA ileS dnaJ ilvH dnaK ilvI talB leuO thrC leuL leuA thrB thrA leuB leuC leuD thrL

Gene Name + + + + + + + + + + + + + + + ------Strand orientation 32 32 32 32 24 24 20 20 20 11 45 11 45 45 44 44 44 44 44 5 1 1 1 1 Operon ID 13283 20561 15039 11143 13624 10273 10437 3825 1543 2240 2140 7656 9312 1331 3643 4036 4492 2778 3201 1458 6781 1344 4770 158 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 mRNA present 19 13 10 48 14 16 46 13 32 20 27 15 18 28 39 12 18 10 5 6 9 1 9 1 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P Protein detected - total list 17 13 23 13 10 18 4 0 1 0 8 2 0 4 2 2 0 0 3 7 8 0 9 9 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P Protein detected - short list 19 14 24 16 11 18 5 0 2 0 8 2 0 6 5 2 0 0 3 7 8 0 7 7 # of tryptic peptides detected (short list) P P P P P P P P P P P P P P P P P P Protein detected - long list 17 13 23 13 10 18 4 0 1 0 8 2 0 4 2 2 0 0 3 7 8 0 9 9 # 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 1 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt Membrane protein assignment pyridoxine biosynthesis S-adenosylmethionine-6-N',N'-adenosyl (rRNA)dimethyltransferase orf, hypotheticalprotein carbamoyl-phosphate synthaselargesubunit carbamoyl-phosphate synthetase,glutamine(small)subunit control ofstringentresponse;involvedinpenicillintolerance prolipoprotein signalpeptidase(SPaseII) isoleucine tRNAsynthetase chaperone withDnaK;heatshockprotein chaperone Hsp70;DNAbiosynthesis;autoregulatedheatshockproteins acetolactate synthase III,valinesensitive, smallsubunit transaldolase B acetolactate synthaseIII,valine sensitive,largesubunit probable transcriptionalactivator forleuABCDoperon threonine synthase leu operonleaderpeptide homoserine kinase 2-isopropylmalate synthase aspartokinase I,homoserinedehydrogenaseI 3-isopropylmalate dehydrogenase thr operonleaderpeptide 3-isopropylmalate isomerase(dehydratase)subunit isopropylmalate isomerasesubunit membrane proteins(1stmodule) peptidyl-prolyl cis-transisomerase(PPIase),involved inmaturationofouter

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

Functional category b0194 b0193 b0185 b0170 b0169 b0167 b0166 b0165 b0164 b0163 b0161 b0154 b0134 b0116 b0115 b0133 b0114 b0126 b0118 b0113 b0098 b0095 b0094 b0093

B number proS yaeF accA tsf rpsB glnD dapD b0165 yaeI yaeH htrA hemL panB lpdA aceF panC aceE yadF acnB pdhR secA ftsZ ftsA ftsQ

Gene Name + + + + + + + + + + + + + ------Strand orientation 109 109 104 95 95 93 93 93 93 92 90 85 74 59 59 74 59 68 61 59 51 48 48 48 Operon ID 22176 21822 15349 17436 1361 1969 9865 4162 1127 1016 1274 5716 8150 1978 4087 1587 9268 4248 3716 982 508 312 311 33 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 29 12 18 18 11 51 17 13 11 17 15 34 44 15 41 46 22 18 10 1 7 6 8 8 # 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 11 13 10 15 13 24 22 0 6 0 9 0 0 5 4 5 3 5 4 0 3 6 0 0 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P P Protein detected - short list 12 10 12 24 19 0 5 9 8 0 9 0 0 7 5 7 2 6 5 0 6 7 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 Protein detected - long list 11 13 10 15 13 24 22 0 6 0 9 0 0 5 4 5 3 5 4 0 3 6 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 4 0 1 0 1 0 0 0 0 0 1 2 detected (membrane sample) GenProt-PHD GenProt Membrane protein assignment proline tRNA synthetase orf, hypotheticalprotein acetylCoA carboxylase,carboxytransferase component,alphasubunit protein chainelongationfactor EF-Ts 30S ribosomalsubunitproteinS2 protein PII;uridylyltransferaseactsonregulatorofglnA 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase orf, hypotheticalprotein orf, hypotheticalprotein putative structuralprotein glutamate-1-semialdehyde aminotransferase(aminomutase) 3-methyl-2-oxobutanoate hydroxymethyltransferase pyruvate dehydrogenase(dihydrolipoyltransacetylasecomponent) periplasmic serineproteaseDo;heatshockproteinHtrA pantothenate synthetase pyruvate dehydrogenase(decarboxylasecomponent) putative carbonicanhdrase(EC4.2.1.1) transcriptional regulatorforpyruvatedehydrogenasecomplex aconitate hydraseB preprotein translocase;secretionprotein cell divisionprotein;ingrowthofwallatseptum pyruvate complexes;L-proteinofglycinecleavagecomplex lipoamide dehydrogenase(NADH);componentof2-oxodehydrogenaseand GTPase cell division;formscircumferentialring;tubulin-likeGTP-bindingproteinand associated withjunctionsofinnerandoutermembranes ATP-binding celldivisionprotein,septationprocess,complexeswithFtsZ,

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

Functional category b0437 b0436 b0426 b0337 b0336 b0325 b0273 b0522 b0243 b0494 b0474 b0493 b0473 b0242 b0605 b0492 b0439 b0237 b0578 b0526 b0523 b0480 b0438 b0222

B number clpP tig yajQ codA codB yahK argF purK proA tesA adk ybbO htpG proB ahpC ybbN lon pepD nfnB cysS purE ushA clpX gmhA

Gene Name + + + + + + + + + + + + + + + + ------Strand orientation 262 261 256 202 202 193 161 319 142 304 289 304 288 142 372 304 263 137 354 321 319 295 262 126 Operon ID 38698 4300 7545 3822 6804 8160 2065 3188 1507 1200 7814 2446 2692 3719 1500 2638 3543 1930 2012 3000 794 879 970 745 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 mRNA present 24 10 12 16 13 12 20 12 13 22 14 37 12 37 19 11 21 22 10 19 7 4 9 5 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P P P P Protein detected - total list 17 14 0 3 5 1 5 6 2 4 1 4 1 0 4 8 8 9 4 0 4 8 4 4 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P P P P Protein detected - short list 12 16 11 1 5 5 0 7 5 4 5 2 4 3 0 6 8 7 6 4 1 5 4 4 # 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 17 14 0 3 5 0 5 6 2 4 1 4 1 0 4 8 8 9 4 0 4 8 4 4 # 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 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD

PHD Membrane protein assignment trigger factor;amolecularchaperoneinvolvedincelldivision orf, hypotheticalprotein cytosine deaminase cytosine permease/transport putative oxidoreductase ornithine carbamoyltransferase2,chainF gamma-glutamylphosphate reductase acyl-CoA thioesteraseI;alsofunctionsasprotease I gamma-glutamate kinase putative oxidoreductase chaperone Hsp90,heatshockproteinC62.5 putative thioredoxin-likeprotein DNA-binding, ATP-dependentproteaseLa;heatshockK-protein aminoacyl-histidine dipeptidase(peptidaseD) alkyl hydroperoxide reductase,C22subunit; detoxificationofhydroperoxides oxygen-insensitive NAD(P)H nitroreductase UDP-sugar hydrolase(5'-nucleotidase) ATP-dependent specificitycomponentofclpPserineprotease,chaperone phosphoheptose isomerase cysteine tRNAsynthetase subunit phosphoribosylaminoimidazole carboxylase=AIRcarboxylase,catalytic subunit phosphoribosylaminoimidazole carboxylase=AIRcarboxylase, CO(2)-fixing acyltransferase activity adenylate kinaseactivity;pleiotropiceffectsonglycerol-3-phosphate protein F21.5 ATP-dependent proteolyticsubunitofclpA-clpPserineprotease,heatshock

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

Functional category b0724 b0723 b0722 b0721 b0720 b0661 b0714 b0713 b0660 b0712 b0659 b0711 b0655 b0710 b0642 b0688 b0641 b0687 b0640 b0680 b0674 b0639 b0638 b0606

B number sdhB sdhA sdhD sdhC gltA miaB nei ybgL ybeZ ybgK ybeY ybgJ gltI ybgI leuS pgm rlpB seqA holA glnS asnB ybeN phpB ahpF

Gene Name + + + + + + + + + + + + + ------Strand orientation 437 437 437 437 436 404 432 432 403 432 403 432 400 432 391 416 391 416 391 410 407 391 391 372 Operon ID 18927 16326 12121 11527 5467 1450 3091 1289 2321 1335 5452 3721 3675 1043 3178 4865 1049 1254 1131 3105 215 950 736 212 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 mRNA present 15 27 29 17 12 18 10 13 14 41 24 10 10 14 31 24 30 3 5 1 6 9 4 5 # 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 11 12 12 11 3 1 3 0 5 0 3 0 1 5 4 6 0 3 0 6 0 6 5 0 # of tryptic peptides detected (total list) P P P P P P P P P P P P Protein detected - short list 12 13 5 5 0 0 8 0 6 0 3 0 1 4 4 7 0 3 0 7 0 6 7 0 # of tryptic peptides detected (short list) P P P P P P P P P P P P P P P Protein detected - long list 12 12 11 3 3 0 0 0 5 0 3 0 1 5 4 6 0 3 0 6 0 6 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 11 11 0 1 3 2 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 succinate dehydrogenase, ironsulfurprotein succinate dehydrogenase, flavoproteinsubunit citrate synthase succinate dehydrogenase, hydrophobicsubunit succinate dehydrogenase, cytochromeb556 endonuclease VIIIandDNAN-glycosylasewithanAP lyaseactivity putative ATP-bindingproteininphoregulon putative lactamutilizationprotein putative carboxylase orf, hypotheticalprotein putative carboxylase glutamate/aspartate transportsystemperiplasmicbindingprotein orf, hypotheticalprotein leucine tRNAsynthetase phosphoglucomutase a minorlipoprotein negative modulatorofinitiationreplication DNA polymeraseIII,deltasubunit glutamine tRNAsynthetase orf, hypotheticalprotein asparagine synthetaseB homolog ofSalmonellacobC,aphosphohistidineprotein module) involved inmethylthiolationofisopentenylatedA37derivativestRNA(2nd hydroperoxides alkyl hydroperoxidereductase,F52asubunit;detoxificationof

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

Functional category b0811 b0810 b0809 b0801 b0800 b0799 b0767 b0760 b0759 b0758 b0757 b0737 b0756 b0754 b0729 b0740 b0728 b0755 b0742 b0741 b0739 b0738 b0727 b0726

B number glnH glnP glnQ ybiC ybiB dinG ybhE modF galE galT galK tolQ galM aroG sucD tolB sucC gpmA ybgF pal tolA tolR sucB sucA

Gene Name + + + + + + + + + + + + + + + ------Strand orientation 486 486 486 479 478 478 459 454 453 453 453 445 453 451 439 445 439 452 446 446 445 445 439 439 Operon ID 16120 40902 13638 20532 11040 4090 3281 2836 3144 1742 1657 3273 1325 4960 5196 7268 6246 5169 6035 1400 1031 952 229 501 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 mRNA present 14 12 13 17 39 11 21 15 16 12 13 17 15 15 24 13 14 15 39 6 9 8 5 7 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P P P P Protein detected - total list 21 13 12 5 1 2 3 5 0 3 2 2 1 5 1 6 5 5 5 3 0 0 5 5 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P Protein detected - short list 19 13 7 0 0 4 5 0 4 4 5 1 3 0 7 5 9 6 9 4 0 0 1 3 # of tryptic peptides detected (short list) P P P P P P P P P P P P P P P P P P Protein detected - long list 21 13 12 5 0 0 3 5 0 3 2 2 1 5 0 6 5 5 5 3 0 0 1 5 # 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 0 1 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 3 0 5 1 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD MP-GenProt MP-GenProt GenProt Membrane protein assignment periplasmic glutamine-binding protein;permease glutamine high-affinitytransport system;membranecomponent ATP-binding componentof glutaminehigh-affinitytransportsystem putative dehydrogenase putative enzyme probably ATP-dependenthelicase putative isomerase ATP-binding componentofmolybdatetransportsystem UDP-galactose-4-epimerase galactose-1-phosphate uridylyltransferase galactokinase galactose-1-epimerase (mutarotase) succinyl-CoA synthetase,alphasubunit phosphoglyceromutase 1 orf, hypotheticalprotein succinyl-CoA synthetase,betasubunit membrane spanningprotein,requiredforouterintegrity 2-oxoglutarate dehydrogenase(dihydrolipoyltranssuccinaseE2component) peptidoglycan-associated lipoprotein 2-oxoglutarate dehydrogenase(decarboxylasecomponent) phenylalanine repressible) 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase(DAHPsynthetase, colicins periplasmic proteininvolvedinthetonb-independentuptakeofgroupA group Acolicins putative innermembraneprotein,involvedinthetonB-independentuptakeof envelope; tolerancetogroupAcolicins inner membraneprotein,membrane-spanning,maintainsintegrityofcell

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

Functional category b0889 b0888 b0882 b0881 b0871 b0870 b0869 b0864 b0863 b0862 b0861 b0860 b0838 b0832 b0831 b0830 b0829 b0828 b0827 b0893 b0826 b0892 b0891 b0812

B number lrp trxB clpA yljA poxB itaA ybjT artP artI artQ artM artJ yliJ b0832 b0831 b0830 b0829 ybiK moeA serS moeB ycaJ lolA dps

Gene Name + + + + + + + + + + + ------Strand orientation 538 537 533 533 525 525 525 521 521 521 521 521 505 500 500 500 500 500 499 541 499 540 540 487 Operon ID 22609 3450 1462 2333 5279 3121 1509 4200 4421 1447 1059 4456 1655 1054 1782 1231 2667 761 443 792 772 643 193 561 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 mRNA present 12 40 23 17 23 12 12 11 21 32 14 15 22 12 25 12 9 7 5 5 7 6 8 9 # of tryptic peptides predicted P P P P P P P P P P P P P P Protein detected - total list 3 4 5 0 4 1 0 0 2 0 0 6 2 0 0 3 0 1 4 9 3 0 0 6 # of tryptic peptides detected (total list) P P P P P P P P P P P P Protein detected - short list 4 5 8 0 4 1 0 0 4 0 0 7 4 0 0 4 0 1 6 9 5 0 0 7 # of tryptic peptides detected (short list) P P P P P P P P P P P P P P Protein detected - long list 3 4 5 0 4 1 0 0 2 0 0 6 2 0 0 3 0 1 4 9 3 0 0 6 # 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 GenProt-PHD GenProt-PHD PHD PHD Membrane protein assignment thioredoxin reductase ATP-binding componentofserineprotease orf, hypotheticalprotein pyruvate oxidase L-allo-threonine aldolase,PLP-dependent putative dTDP-glucoseenzyme ATP-binding componentof3rdargininetransportsystem arginine 3rdtransportsystemperiplasmicbindingprotein arginine 3rdtransportsystempermeaseprotein arginine 3rdtransportsystempermeaseprotein arginine 3rdtransportsystemperiplasmicbindingprotein putative transferase putative transportsystempermeaseprotein putative transportsystempermeaseprotein putative transportprotein putative ATP-bindingcomponentofatransportsystem L-asparaginase molybdopterin biosynthesis serine tRNAsynthetase; alsochargesselenocystein tRNAwithserine molybdopterin biosynthesis putative polynucleotideenzyme global regulator,starvationconditions to outer periplasmic proteineffects translocationoflipoproteinsfrominnermembrane acid transportsystem regulator forleucine(orlrp) regulonandhigh-affinitybranched-chainamino

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

Functional category b1004 b1003 b1002 b0957 b0932 b0931 b0930 b0928 b0924 b0923 b0922 b0921 b1049 b0918 b1048 b0917 b0911 b1035 b0908 b1034 b0907 b0903 b1033 b0902

B number wrbA yccJ agp ompA pepN pncB asnS aspC mukB mukE mukF smtA mdoH kdsB mdoG ycaR rpsA ycdY aroA ycdX serC pflB ycdW pflA

Gene Name + + + + + + + + + + + + + + + + ------Strand orientation 607 607 606 580 567 566 565 563 560 560 560 560 630 557 630 557 554 622 551 622 551 547 621 547 Operon ID 36891 29325 6589 2597 2197 1962 1464 8281 2884 2195 2010 3791 3950 1307 3622 1904 5838 5044 2446 670 954 994 976 875 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 mRNA present 15 16 37 22 23 23 75 30 11 15 32 25 23 19 11 17 38 17 14 9 5 9 5 8 # 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 19 13 12 16 20 10 15 7 2 6 5 6 0 0 0 2 2 7 2 5 3 2 4 0 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P Protein detected - short list 15 10 16 14 14 5 3 6 7 5 6 1 0 0 4 1 9 3 4 3 2 9 4 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 13 12 16 20 10 15 7 2 6 5 5 6 0 0 0 2 1 7 2 5 3 2 4 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 19 0 0 1 0 0 1 0 0 0 0 0 0 2 0 0 3 0 0 0 0 1 0 0 detected (membrane sample) MP-GenProt-PHD MP-GenProt

Membrane protein assignment orf, hypotheticalprotein periplasmic glucose-1-phosphatase outer membraneprotein3a(II*;G;d) aminopeptidase N nicotinate phosphoribosyltransferase asparagine tRNAsynthetase aspartate aminotransferase kinesin-like celldivisionproteininvolvedinchromosomepartitioning putative killingproteinsuppressor mukF protein(killingfactorKICB) S-adenosylmethionine-dependent methyltransferase CTP:CMP-3-deoxy-D-manno-octulosonate transferase periplasmic glucansbiosynthesis protein orf, hypotheticalprotein 30S ribosomalsubunitproteinS1 putative oxidoreductasecomponent 5-enolpyruvylshikimate-3-phosphate synthetase putative DNApolymerasesubunit 3-phosphoserine aminotransferase formate acetyltransferase1 putative dehydrogenase pyruvate formatelyaseactivatingenzyme1 oligosaccharide (MDO) membrane glycosyltransferase; synthesis ofmembrane-derived operator trp repressorbindingprotein;affectsassociationof repressorand

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

Functional category b1174 b1136 b1131 b1130 b1129 b1126 b1125 b1124 b1123 b1114 b1093 b1092 b1091 b1200 b1084 b1199 b1198 b1064 b1197 b1062 b1176 b1059 b1175 b1058

B number minE icdA purB phoP phoQ potA potB potC potD mfd fabG fabD fabH dhaK1 rne dhaK2 ycgC grxB treA pyrC minC solA minD yceO

Gene Name + + + + ------Strand orientation 698 676 674 673 673 670 670 670 670 666 655 655 655 718 648 718 718 641 717 639 698 636 698 636 Operon ID 42636 24478 2930 2271 6704 1143 1171 3389 5107 1102 8101 5633 3466 1642 3006 8708 1352 4514 6644 5617 698 618 770 5 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 mRNA present 21 22 11 22 19 14 63 10 11 13 15 43 10 12 21 27 16 11 19 14 6 7 2 2 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P Protein detected - total list 13 2 7 8 0 0 0 0 2 4 4 2 4 5 5 2 7 7 3 5 0 6 5 0 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P Protein detected - short list 10 10 1 6 8 0 0 0 0 5 4 5 3 3 6 2 4 6 6 4 0 8 7 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 Protein detected - long list 13 2 7 8 0 0 0 0 2 4 4 2 4 5 5 2 7 7 3 5 0 6 5 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 3 0 0 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt PHD MP Membrane protein assignment isocitrate dehydrogenase,specificforNADP+ adenylosuccinate lyase transcriptional regulatoryprotein sensor proteinPhoQ ATP-binding componentofspermidine/putrescinetransport spermidine/putrescine transportsystempermease spermidine/putrescine transportsystempermease spermidine/putrescine periplasmictransportprotein transcription-repair couplingfactor;mutationfrequencydecline 3-oxoacyl-[acyl-carrier-protein] reductase malonyl-CoA-[acyl-carrier-protein] transacylase 3-oxoacyl-[acyl-carrier-protein] synthaseIII;acetylCoAACPtransacylase putative dihydroxyacetone kinase(EC2.7.1.2) RNase E,membraneattachment,mRNAturnover,maturation5SRNA putative dihydroxyacetone kinase(EC2.7.1.2) glutaredoxin 2 putative PTSsystemenzyme I trehalase, periplasmic dihydro-orotase cell divisioninhibitor,inhibitsftsZringformation N-methyltryptophan oxidase,FADbinding(1stmodule) cell divisioninhibitor,amembraneATPase,activates minC orf, hypotheticalprotein formation cell divisiontopologicalspecificityfactor,reversesMinC inhibitionofftsZring

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

Functional category b1241 b1237 b1236 b1215 b1214 b1213 b1286 b1212 b1276 b1211 b1274 b1262 b1246 b1210 b1245 b1265 b1261 b1244 b1207 b1264 b1263 b1260 b1243 b1203

B number adhE hns galU kdsA ychA b1213 rnb hemK acnA prfA topA trpC oppD hemA oppC trpL trpB oppB prsA trpE trpD trpA oppA ychF

Gene Name + + + + + + + + + + + + + ------Strand orientation 744 741 740 727 727 727 773 727 765 727 763 757 746 727 746 757 757 746 725 757 757 757 746 721 Operon ID 34541 4865 1036 2855 3833 1671 3784 1533 2301 2589 7588 3242 2638 2693 3403 1889 7098 1146 946 395 328 626 570 897 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 mRNA present 41 13 15 12 32 12 34 20 23 20 44 17 18 12 19 15 14 26 19 7 7 5 0 9 # of tryptic peptides predicted P P P P P P P P P P P P P P P P Protein detected - total list 24 10 18 4 4 4 0 0 9 0 0 4 0 5 0 0 0 4 1 4 6 2 9 6 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P Protein detected - short list 22 13 10 16 4 4 4 0 0 9 0 0 5 0 7 0 0 0 6 0 6 8 3 6 # of tryptic peptides detected (short list) P P P P P P P P P P P P P P P Protein detected - long list 24 10 18 4 4 4 0 0 9 0 0 4 0 5 0 0 0 4 0 4 6 2 9 6 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

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

PHD Membrane protein assignment DNA-binding proteinHLP-II(HU,BH2,HD,NS);pleiotropicregulator glucose-1-phosphate uridylyltransferase 2-dehydro-3-deoxyphosphooctulonate aldolase orf, hypotheticalprotein orf, hypotheticalprotein RNase II,mRNA degradation possible protoporphyrinogenoxidase aconitate hydrase1 peptide chainreleasefactorRF-1 DNA topoisomerasetypeI, omegaprotein enzyme inalternatepathofsynthesis5-aminolevulinate homolog ofSalmonellaoligopeptidetransportpermeaseprotein trp operonleaderpeptide tryptophan synthase,betaprotein phosphoribosylpyrophosphate synthetase oligopeptide transportpermeaseprotein anthranilate synthasecomponentI tryptophan synthase,alphaprotein oligopeptide transport;periplasmicbindingprotein putative GTP-bindingprotein phosphoribosylanthranilate transferase anthranilate synthasecomponentII,glutamineamidotransferase and synthetase N-(5-phosphoribosyl)anthranilate isomeraseandindole-3-glycerolphosphate system homolog ofSalmonellaATP-bindingproteinoligopeptideABCtransport dehydrogenase; pyruvate-formate-lyasedeactivase CoA-linked acetaldehydedehydrogenaseandiron-dependentalcohol

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

Functional category b1647 b1637 b1614 b1613 b1612 b1604 b1603 b1602 b1538 b1493 b1482 b1479 b1452 b1449 b1444 b1443 b1442 b1329 b1441 b1440 b1324 b1415 b1378 b1288

B number b1647 tyrS ydgA manA fumA b1604 pntA pntB dcp gadB osmC sfcA b1452 yncB b1444 b1443 b1442 mppA b1441 b1440 tpx aldA nifJ fabI

Gene Name + + + + + + + + + + + + + ------Strand orientation 1006 998 983 982 981 975 974 974 931 901 896 893 875 872 868 868 868 796 868 868 791 846 826 775 Operon ID 18004 1511 2372 3778 1536 4018 1185 3267 1113 3972 5905 1814 2465 1015 7051 8892 5468 884 746 383 457 676 598 648 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 mRNA present 13 17 26 18 31 19 21 13 25 20 26 15 17 20 27 17 22 23 11 48 6 6 7 7 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P P P P Protein detected - total list 12 10 19 2 7 4 6 5 6 4 6 6 9 6 2 3 0 0 1 0 9 5 5 3 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P P P P P P Protein detected - short list 13 13 4 8 4 7 9 5 0 6 7 6 9 6 4 4 0 0 4 0 5 6 4 4 # 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 12 10 19 2 7 3 6 5 0 4 6 6 9 6 2 3 0 0 1 0 9 5 5 3 # 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 4 1 0 0 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

Membrane protein assignment orf, hypothetical protein tyrosine tRNAsynthetase orf, hypotheticalprotein mannose-6-phosphate isomerase fumarase A=fumaratehydrataseClassI;aerobicisozyme orf, hypotheticalprotein pyridine nucleotidetranshydrogenase,alphasubunit pyridine nucleotidetranshydrogenase,betasubunit dipeptidyl carboxypeptidaseII glutamate decarboxylaseisozyme osmotically inducibleprotein NAD-linked malatedehydrogenase(malicenzyme) putative receptor putative oxidoreductase putative aldehydedehydrogenase putative transportsystempermeaseprotein putative transportsystempermeaseprotein putative ATP-bindingcomponentofatransportsystem thiol peroxidase putative transportprotein aldehyde dehydrogenase,NAD-linked enoyl-[acyl-carrier-protein] reductase(NADH) putative pyruvate-flavodoxinoxidoreductase,Fe-Ssubunit(2ndmodule) multiple antibioticresistance periplasmic mureintripeptidetransportprotein,alsonegativeregulatorof

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

Functional category b1780 b1779 b1761 b1740 b1732 b1723 b1719 b1718 b1717 b1716 b1715 b1714 b1711 b1710 b1709 b1702 b1687 b1686 b1685 b1713 b1676 b1664 b1661 b1648

B number yeaD gapA gdhA nadE katE pfkB thrS infC rpmI rplT pheM pheS btuC btuE btuD ppsA ydiJ b1686 b1685 pheT pykF b1664 cfa b1648

Gene Name + + + + + + + + ------Strand orientation 1087 1086 1075 1064 1060 1051 1048 1048 1048 1048 1047 1047 1045 1045 1045 1038 1029 1029 1029 1047 1025 1020 1017 1006 Operon ID 41263 34009 19377 10398 1358 2794 2929 2791 4224 8201 4824 4088 2419 1013 2862 1795 1375 3969 2979 334 975 925 199 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 mRNA present 11 20 23 15 30 16 35 18 10 36 47 35 27 14 21 8 1 5 9 6 2 5 6 3 # 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 13 14 12 13 5 8 8 7 3 7 3 0 3 8 6 0 5 0 0 0 0 4 4 0 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P P Protein detected - short list 10 11 16 17 14 4 7 7 4 7 5 0 3 8 5 0 4 0 0 0 0 4 4 0 # of tryptic peptides detected (short list) P P P P P P P P P P P P P P P P P Protein detected - long list 13 14 12 13 5 8 8 7 3 7 3 0 3 8 6 0 2 0 0 0 0 4 4 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) Proteins detected - membrane sample

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

Membrane protein assignment orf, hypothetical protein glyceraldehyde-3-phosphate dehydrogenaseA NADP-specific glutamatedehydrogenase NAD synthetase,prefersNH3 overglutamine catalase; hydroperoxidaseHPII(III) 6-phosphofructokinase II;suppressorofpfkA threonine tRNAsynthetase protein chaininitiationfactorIF-3 50S ribosomalsubunitproteinA phenylalanine tRNAsynthetase,alpha-subunit vitamin B12transport ATP-binding componentofvitaminB12transportsystem phosphoenolpyruvate synthase orf, hypotheticalprotein 50S ribosomalsubunitproteinL20,andregulator phenylalanyl-tRNA synthetase(pheST)operonleaderpeptide phenylalanine tRNAsynthetase,beta-subunit putative oxidase orf, hypotheticalprotein pyruvate kinaseI(formerlyF),fructosestimulated vitamin B12transportpermeaseprotein possible enzyme cyclopropane fattyacylphospholipidsynthase orf, hypotheticalprotein

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

Functional category b2022 b2021 b2020 b2019 b2000 b1982 b1973 b1920 b1919 b1918 b1917 b1897 b1896 b1876 b1866 b1854 b1852 b1849 b1831 b1830 b2025 b2024 b2023 b1783

B number hisB hisC hisD hisG flu amn b1973 fliY yedO yecS yecC otsB otsA argS aspS pykA zwf purT proQ prc hisF hisA hisH yeaG

Gene Name + + + + + + + + + + + + + + ------Strand orientation 1240 1240 1240 1240 1225 1214 1208 1178 1178 1178 1178 1165 1165 1157 1152 1144 1142 1140 1127 1127 1240 1240 1240 1090 Operon ID 3091 2631 3584 5358 1273 5516 1906 1087 4018 3503 1782 2415 1843 3318 1360 3366 4310 2569 3833 565 912 759 689 89 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 mRNA present 16 18 12 14 39 18 18 13 10 14 21 29 33 22 28 17 35 15 13 36 8 8 2 9 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P P P P P Protein detected - total list 13 12 15 3 3 5 2 3 4 3 6 3 0 2 2 7 5 4 0 6 2 1 1 9 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P P P Protein detected - short list 11 13 14 4 4 6 5 5 4 4 9 4 0 0 2 7 7 4 0 6 2 1 3 9 # 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 P Protein detected - long list 13 12 15 3 3 5 2 3 4 3 6 3 0 0 2 7 5 4 0 6 2 1 1 9 # of tryptic peptides detected (long list) P(m) P(m) Proteins detected - membrane sample

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

MP Membrane protein assignment histidinol-phosphate aminotransferase L-histidinal:NAD+ oxidoreductase;L-histidinol:NAD+ oxidoreductase ATP phosphoribosyltransferase outer membranefluffingprotein,similartoadhesin AMP nucleosidase orf, hypotheticalprotein putative periplasmicbindingtransportprotein putative 1-aminocyclopropane-1-carboxylatedeaminase putative transportsystempermeaseprotein(formeryecC) putative ATP-bindingcomponentofatransportsystem trehalose-6-phosphate phophatase,biosynthetic trehalose-6-phosphate synthase arginine tRNAsynthetase aspartate tRNAsynthetase pyruvate kinaseII,glucosestimulated glucose-6-phosphate dehydrogenase phosphoribosylglycinamide formyltransferase2 Activation ofsolutetransporterProP carboxy-terminal proteaseforpenicillin-bindingprotein3 orf, hypotheticalprotein 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

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

Functional category b2114 b2097 b2096 b2095 b2094 b2093 b2092 b2091 b2090 b2081 b2041 b2040 b2039 b2038 b2037 b2036 b2035 b2034 b2033 b2032 b2031 b2030 b2029 b2026

B number metG b2097 gatY gatZ gatA gatB gatC gatD gatR_2 yegQ rfbB rfbD rfbA rfbC rfbX glf wbbH wbbI wbbJ wbbK yefJ trs5_7 gnd hisI

Gene Name + + + ------Strand orientation 1279 1269 1268 1268 1268 1268 1268 1268 1268 1264 1245 1245 1245 1245 1245 1244 1244 1244 1244 1244 1244 1244 1243 1240 Operon ID 10583 47588 56901 51189 43258 31493 1194 8850 3175 2839 2723 3609 1393 1058 1578 2265 1838 4998 1384 574 956 690 530 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 mRNA present 34 16 13 17 12 21 19 11 17 20 16 24 14 24 12 10 8 4 9 5 9 7 9 4 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P Protein detected - total list 11 19 8 7 5 4 4 5 5 0 2 9 2 7 7 5 1 0 0 0 1 0 0 1 # of tryptic peptides detected (total list) P P P P P P P P P P P P Protein detected - short list 13 10 19 6 7 4 5 1 1 5 0 4 4 8 7 0 0 1 0 0 2 0 0 2 # 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 11 19 8 7 5 4 4 1 5 0 2 9 2 7 7 0 0 0 0 0 1 0 0 1 # 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 2 1 1 0 0 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 0 detected (membrane sample) GenProt-PHD GenProt-PHD

PHD PHD Membrane protein assignment methionine tRNA synthetase orf, hypotheticalprotein tagatose-bisphosphate aldolase 1 tagatose 6-phosphatealdolase 2,subunitwithGatY galactitol-specific enzymeIIAofphosphotransferase system galactitol-specific enzymeIIBofphosphotransferase system PTS systemgalactitol-specificenzymeIIC galactitol-1-phosphate dehydrogenase split galactitolutilizationoperonrepressor,fragment 2 orf, hypotheticalprotein dTDP-glucose 4,6dehydratase dTDP-6-deoxy-L-mannose-dehydrogenase glucose-1-phosphate thymidylyltransferase UDP-galactopyranose mutase putative glucosetransferase putative creatinase(EC3.5.-) IS5 transposase gluconate-6-phosphate dehydrogenase,decarboxylating dTDP-6-deoxy-D-glucose-3,5 epimerase putative O-antigentransporter O-antigen polymerase putative Galftransferase putative O-acetyltransferase phosphoribosyl-amp cyclohydrolase;phosphoribosyl-ATPpyrophosphatase

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

Functional category b2242 b2241 b2240 b2239 b2235 b2281 b2280 b2279 b2278 b2277 b2276 b2234 b2231 b2186 b2148 b2243 b2154 b2150 b2149 b2133 b2128 b2131 b2130 b2129

B number glpB glpA glpT glpQ nrdB nuoI nuoJ nuoK nuoL nuoM nuoN nrdA gyrA yejK mglC glpC yeiG mglB mglA dld yehW yehZ yehY yehX

Gene Name + + + + + + + ------Strand orientation 1353 1353 1352 1352 1348 1348 1373 1373 1373 1373 1373 1373 1345 1325 1353 1301 1298 1287 1298 1298 1285 1285 1285 1285 Operon ID 12296 3240 1921 5247 1563 2428 6191 4869 5100 5120 2636 3640 1303 1059 1441 2088 1830 7569 1844 1068 543 224 974 571 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 mRNA present 14 27 15 18 19 35 11 11 40 16 27 13 35 20 33 15 13 2 2 4 7 6 8 2 # 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 10 11 12 1 6 4 2 9 2 0 0 2 1 1 4 0 3 4 1 0 0 0 2 0 # of tryptic peptides detected (total list) P P P P P P P P P Protein detected - short list 12 12 11 2 7 0 9 3 2 0 0 0 0 0 5 0 5 5 0 0 0 0 4 0 # of tryptic peptides detected (short list) P P P P P P P P P P P P Protein detected - long list 10 11 12 1 6 0 2 9 2 0 0 0 0 0 4 0 3 4 0 0 0 0 2 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 0 0 4 1 0 0 0 0 0 0 1 2 1 1 0 0 1 0 0 1 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD MP-GenProt GenProt GenProt Membrane protein assignment sn-glycerol-3-phosphate dehydrogenase(anaerobic), largesubunit sn-glycerol-3-phosphate permease glycerophosphodiester phosphodiesterase,periplasmic ribonucleoside-diphosphate reductase1,betasubunit,B2 ribonucleoside diphosphatereductase1,alphasubunit,B1 DNA gyrase,subunitA,typeIItopoisomerase Present inspermidinenucleoids NADH dehydrogenase Ichain NADH dehydrogenaseIchain J NADH dehydrogenaseIchain K NADH dehydrogenaseIchain L NADH dehydrogenaseIchainM NADH dehydrogenaseIchainN sn-glycerol-3-phosphate dehydrogenase(anaerobic), K-smallsubunit putative esterase(EC3.1.1.-). D-lactate dehydrogenase,FADprotein,NADHindependent galactose-binding transportprotein;receptorforgalactosetaxis ATP-binding componentofmethyl-galactosidetransportandgalactosetaxis methyl-galactoside transportandgalactosetaxis subunit sn-glycerol-3-phosphate dehydrogenase(anaerobic), membraneanchor betaine cholinetransportforosmoprotection) putative ABCsuperfamily(peri_bind)transportprotein(possiblyglycine putative transportsystempermeaseprotein putative ATP-bindingcomponentofatransportsystem putative transportsystempermeaseprotein

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

Functional category b2421 b2417 b2416 b2414 b2400 b2388 b2323 b2320 b2313 b2312 b2311 b2310 b2309 b2297 b2296 b2294 b2293 b2288 b2287 b2286 b2285 b2284 b2283 b2282

B number cysM crr ptsI cysK gltX glk fabB pdxB cvpA purF ubiX argT hisJ pta ackA b2294 yfbT nuoA nuoB nuoC nuoE nuoF nuoG nuoH

Gene Name + + + + + ------Strand orientation 1455 1452 1452 1450 1442 1434 1400 1397 1392 1392 1392 1391 1390 1381 1380 1378 1378 1373 1373 1373 1373 1373 1373 1373 Operon ID 20122 26197 10132 11188 15463 1725 8031 1430 1515 7891 4417 1384 3551 6475 1290 5299 8848 1242 9713 8616 8178 7672 792 145 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 mRNA present 16 28 13 23 13 13 20 15 12 21 31 15 10 10 33 21 40 6 7 9 4 9 7 9 # 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 15 10 10 2 5 8 7 7 6 0 6 4 5 0 9 3 1 3 0 2 1 5 8 0 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P P Protein detected - short list 10 10 10 11 1 4 8 6 6 0 8 6 5 0 5 1 4 0 2 8 1 9 8 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 15 10 2 5 8 7 7 6 0 6 4 5 0 9 3 1 3 0 2 6 1 5 8 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 10 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 3 5 detected (membrane sample) MP-GenProt-PHD GenProt-PHD GenProt-PHD

Membrane protein assignment cysteine synthase B,O-acetylserinesulfhydrolase B PTS system,glucose-specific IIAcomponent PEP-protein phosphotransferase systemenzymeI cysteine synthaseA,O-acetylserine sulfhydrolaseA glutamate tRNAsynthetase,catalyticsubunit glucokinase 3-oxoacyl-[acyl-carrier-protein] synthaseI membrane proteinrequiredforcolicinVproduction amidophosphoribosyltransferase =PRPPamidotransferase lysine-, arginine-,ornithine-bindingperiplasmicprotein histidine-binding periplasmicproteinofhigh-affinityhistidinetransportsystem erythronate-4-phosphate dehyrogenase 3-octaprenyl-4-hydroxybenzoate carboxy-lyase phosphotransacetylase acetate kinase orf, hypotheticalprotein putative phosphatase NADH dehydrogenaseIchainA NADH dehydrogenaseIchainB NADH dehydrogenaseIchainC,D NADH dehydrogenaseIchainE NADH dehydrogenaseIchainF NADH dehydrogenaseIchainG NADH dehydrogenaseIchainH

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

Functional category b2521 b2518 b2516 b2515 b2514 b2513 b2512 b2508 b2507 b2500 b2499 b2498 b2476 b2480 b2465 b2479 b2478 b2477 b2464 b2463 b2425 b2424 b2423 b2422

B number sseA ndk yfgA gcpE hisS b2513 yfgL guaB guaA purN purM upp purC bcp tktB gcvR dapA nlpB talA maeB cysP cysU cysW cysA

Gene Name + + + + + + + ------Strand orientation 1504 1502 1500 1500 1499 1499 1499 1496 1496 1490 1490 1489 1481 1483 1473 1483 1473 1482 1482 1472 1455 1455 1455 1455 Operon ID 19329 2053 3428 1419 3338 2958 1897 5523 2859 3201 3990 6828 6714 5167 2244 3742 7999 8978 3434 4835 3266 1361 1423 2069 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 mRNA present 13 22 23 10 15 17 27 11 10 13 10 24 21 11 17 34 21 19 6 9 9 7 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 P Protein detected - total list 10 11 12 12 6 3 6 9 1 5 5 0 5 4 6 5 1 6 2 4 8 0 0 1 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P Protein detected - short list 12 10 12 10 6 5 2 7 1 0 7 1 5 5 8 5 1 6 5 0 9 0 0 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 10 11 12 12 6 0 6 9 0 0 5 0 5 4 6 5 1 6 2 0 8 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 0 0 0 0 0 0 0 3 1 5 1 0 0 0 0 0 0 0 0 0 0 0 4 1 detected (membrane sample) GenProt-PHD GenProt-PHD MP-PHD GenProt PHD Membrane protein assignment putative thiosulfate sulfurtransferase nucleoside diphosphatekinase orf, hypotheticalprotein histidine tRNAsynthetase IMP dehydrogenase GMP synthetase(glutamine-hydrolyzing) phosphoribosylglycinamide formyltransferase1 putative membraneprotein orf, hypotheticalprotein putative serine/threonineproteinkinase phosphoribosylaminoimidazole synthetase=AIR uracil phosphoribosyltransferase thiol peroxidase,thioredoxindependent transketolase 2isozyme transcriptional regulationofgcvoperon transaldolase A dihydrodipicolinate synthase multimodular MaeB:putativemalicoxidoreductase thiosulfate bindingprotein lipoprotein-34 sulfate, thiosulfatetransportsystempermeaseTprotein sulfate transportsystempermeaseWprotein ATP-binding componentofsulfatepermeaseAprotein;chromateresistance synthetase phosphoribosylaminoimidazole-succinocarboxamide synthetase=SAICAR

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

Functional category b2688 b2679 b2678 b2677 b2669 b2664 b2663 b2662 b2661 b2660 b2659 b2610 b2609 b2608 b2592 b2579 b2569 b2557 b2551 b2533 b2530 b2529 b2528 b2523

B number gshA proX proW proV stpA ygaE gabP gabT gabD ygaF b2659 ffh rpsP rimM clpB yfiD lepA purL glyA suhB iscS iscU iscA pepB

Gene Name + + + + + + + + + + ------Strand orientation 1606 1600 1600 1600 1595 1591 1591 1591 1591 1591 1591 1558 1557 1557 1548 1541 1533 1525 1511 1520 1508 1508 1508 1506 Operon ID 19104 37205 10756 4821 6568 5333 4860 4742 1277 1841 2332 3553 1281 1726 1606 1535 1010 5845 6702 5460 3045 396 394 479 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 mRNA present 21 11 13 16 12 21 22 21 18 21 46 25 56 19 16 22 25 3 9 3 9 9 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 14 19 14 16 4 7 2 4 4 0 0 5 6 0 0 3 5 1 5 4 6 9 5 3 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P P Protein detected - short list 16 22 17 5 8 0 1 4 0 0 7 8 0 3 4 3 4 7 5 8 6 9 5 1 # 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 Protein detected - long list 14 19 14 16 4 7 1 0 4 0 0 5 6 0 0 3 5 1 5 4 6 9 5 3 # 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 2 4 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 detected (membrane sample) GenProt-PHD GenProt-PHD PHD MP Membrane protein assignment gamma-glutamate-cysteine ligase high-affinity transportsystem forglycinebetaineandproline high-affinity transportsystem forglycinebetaineandproline ATP-binding componentof transportsystemforglycine,betaineandproline DNA-binding protein;H-NS-likechaperoneactivity; RNAsplicing? putative transcriptionalregulator transport permeaseproteinofgamma-aminobutyrate 4-aminobutyrate aminotransferaseactivity succinate-semialdehyde dehydrogenase,NADP-dependent activity orf, hypotheticalprotein orf, hypotheticalprotein GTP-binding exportfactorbindstosignalsequence,GTPandRNA 30S ribosomalsubunitproteinS16 16S rRNAprocessingprotein heat shockprotein putative formateacetyltransferase GTP-binding elongationfactor,maybeinnermembraneprotein phosphoribosylformyl-glycineamide synthetase=FGAM serine hydroxymethyltransferase cysteine desulfurase(tRNAsulfurtransferase)PLP-dependent(1stmodule) putative FeSassemblyprotein putative regulatorbelievedtobeinvolvedinFe-Sproteinformationorrepair aminopeptidase B,acyteinylglycinase(2ndmodule) modulate RNAseIIIlethalaction enhances synthesisofsigma32inmutant;extragenicsuppressor,may

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

Functional category b2904 b2903 b2901 b2898 b2925 b2913 b2909 b2908 b2907 b2906 b2905 b2891 b2890 b2829 b2780 b2779 b2764 b2763 b2762 b2752 b2751 b2750 b2699 b2697

B number gcvH gcvP bglA ygfZ fba serA ygfB pepP ubiH visC gcvT prfB lysS ptsP pyrG eno cysJ cysI cysH cysD cysN cysC recA alaS

Gene Name + + ------Strand orientation 1714.5 1723 1723 1721 1718 1736 1727 1724 1724 1724 1724 1723 1714 1674 1649 1648 1641 1641 1641 1637 1636 1636 1611 1609 Operon ID 11093 6996 1912 1971 8676 5147 8054 6563 2528 2003 1501 1003 7990 6797 5071 4375 9053 5046 1667 3341 6894 536 807 531 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 mRNA present 37 24 16 17 19 12 13 17 13 27 34 27 24 31 12 12 21 15 49 18 18 3 3 8 # 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 15 14 12 14 15 13 0 6 6 6 4 1 2 0 2 7 9 8 4 9 1 6 0 0 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P P P P Protein detected - short list 13 10 12 15 10 10 15 0 6 9 7 4 9 1 4 2 4 7 7 4 2 6 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 15 14 12 14 15 13 0 6 6 6 4 1 2 0 2 7 9 8 4 9 1 6 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 2 0 0 0 0 0 0 0 1 0 0 2 detected (membrane sample)

Membrane protein assignment glycine decarboxylase,Pproteinofcleavage system 6-phospho-beta-glucosidase A;cryptic orf, hypotheticalprotein peptide chainreleasefactorRF-2 D-3-phosphoglycerate dehydrogenase orf, hypotheticalprotein proline aminopeptidasePII PTS system,enzymeI,transcriptionalregulator(withNPRandNTRproteins) CTP synthetase enolase sulfite reductase(NADPH),flavoproteinbetasubunit sulfite reductase,alphasubunit 3'-phosphoadenosine 5'-phosphosulfatereductase ATP:sulfurylase (ATP:sulfateadenylyltransferase),subunit2 adenosine 5'-phosphosulfatekinase alanyl-tRNA synthetase fructose-bisphosphate aldolase,classII 2-octaprenyl-6-methoxyphenol--> 2-octaprenyl-6-methoxy-1, 4-benzoquinone orf, hypotheticalprotein cleavage system aminomethyltransferase (Tprotein;tetrahydrofolate-dependent) ofglycine bound lipoylcofactor in glycinecleavagecomplex,carrierofaminomethyl moiety viacovalently RNA lysine tRNAsynthetase,constitutive;suppressorofColE1mutationinprimer GTPase ATP-sulfurylase (ATP:sulfateadenylyltransferase),subunit1,probablya ATP-dependent coprotease DNA strandexchangeandrenaturation,DNA-dependentATPase,DNA-

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

Functional category b3067 b3066 b3065 b3054 b3053 b3052 b3176 b3012 b2942 b2938 b2935 b3172 b2927 b3169 b3168 b3165 b3164 b3162 b3008 b2979 b2978 b2977 b2976 b2926

B number rpoD dnaG rpsU ygiF glnE b3052 mrsA yqhE metK speA tktA argG epd nusA infB rpsO pnp deaD metC glcD glcF glcG glcB pgk

Gene Name + + + + + + + ------Strand orientation 1825 1825 1825 1815 1815 1815 1791 1745 1892 1889 1741 1738 1787 1736 1887 1887 1885 1885 1883 1767 1767 1767 1767 1736 Operon ID 14928 11021 16984 1812 1852 1441 1421 2768 2106 2077 1472 1912 1992 1647 2918 3259 5346 1129 5137 1082 868 749 716 543 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 mRNA present 19 28 17 40 25 14 20 23 24 22 20 18 18 24 18 39 29 32 30 25 23 3 3 4 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P P Protein detected - total list 19 2 0 4 1 1 3 4 8 4 6 2 9 5 0 7 9 3 8 0 0 8 2 0 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P Protein detected - short list 10 10 15 10 11 2 0 4 1 2 6 4 6 4 8 5 0 9 3 8 0 0 4 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 Protein detected - long list 19 2 0 4 1 1 3 4 8 4 6 2 9 5 0 7 9 3 8 0 0 8 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 0 0 0 1 1 0 0 detected (membrane sample)

Membrane protein assignment DNA biosynthesis;primase 30S ribosomalsubunitproteinS21 orf, hypotheticalprotein adenylylating enzymeforglutaminesynthetase putative kinase 2,5-diketo-D-gluconate reductaseA similar tophosphoglucomutases andphosphomannomutases argininosuccinate synthetase biosynthetic argininedecarboxylase transketolase 1isozyme cystathionine beta-lyase(beta-cystathionase) D-erythrose 4-phosphatedehydrogenase transcription pausing;Lfactor phosphoglycerate kinase 30S ribosomalsubunitproteinS15 glycolate oxidaseiron-sulfursubunit orf, hypotheticalprotein malate synthaseG protein chaininitiationfactor IF-2 polynucleotide phosphorylase;cytidylatekinaseactivity inducible ATP-independentRNAhelicase glycolate oxidasesubunitD temperatures RNA polymerase,sigma(70)factor;regulationofproteins inducedathigh propylamine donor,corepressorofmetgenes methionine adenosyltransferase1(AdoMetsynthetase);methyland

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

Functional category b3299 b3298 b3297 b3296 b3295 b3294 b3288 b3287 b3256 b3255 b3250 b3249 b3253 b3251 b3236 b3235 b3234 b3214 b3213 b3212 b3181 b3179 b3178 b3177

B number rpmJ rpsM rpsK rpsD rpoA rplQ fmt def accC accB mreC mreD yhdH mreB mdh degS degQ gltF gltD gltB greA ftsJ hflB folP

Gene Name + + + + + + + + + + ------Strand orientation 1958 1957 1957 1957 1957 1957 1953 1953 1937 1937 1935 1933 1933 1933 1924 1923 1923 1910 1910 1910 1895 1893 1893 1892 Operon ID 50514 45957 48728 32646 33843 10334 10847 18040 1413 4813 2703 1362 3268 7485 9886 4717 3175 1109 855 602 731 685 183 925 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 mRNA present 10 17 13 22 13 20 13 17 12 20 25 73 10 32 16 10 1 7 6 4 6 6 2 8 # of tryptic peptides predicted 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 25 11 30 0 9 5 5 4 1 9 0 3 2 0 5 0 2 0 1 8 3 4 # of tryptic peptides detected (total list) P P P P P P P P P P P P P Protein detected - short list 10 10 12 11 33 0 6 3 3 4 1 7 1 5 0 0 6 0 5 0 1 5 3 5 # of tryptic peptides detected (short list) P P P P P P P P P P P P P P P P P P Protein detected - long list 10 12 25 11 30 0 9 5 5 4 1 9 0 3 0 0 5 0 2 0 1 2 3 4 # 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 2 0 4 0 1 0 0 0 0 0 0 0 2 2 0 0 0 1 0 0 0 0 8 detected (membrane sample) GenProt-PHD MP-GenProt

Membrane protein assignment 50S ribosomal subunitproteinL36 30S ribosomalsubunitprotein S13 30S ribosomalsubunitprotein S11 30S ribosomalsubunitprotein S4 RNA polymerase,alphasubunit 50S ribosomalsubunitproteinL17 10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase peptide deformylase acetyl CoAcarboxylase,biotincarboxylasesubunit acetylCoA carboxylase,BCCPsubunit;carrierofbiotin putative dehydrogenase rod shape-determiningprotein malate dehydrogenase rod shape-determiningprotein regulator offtsI,penicillinbindingprotein3,septationfunction protease serine endoprotease regulator ofgltBDFoperon,inductionNtrenzymes glutamate synthase,smallsubunit glutamate synthase,largesubunit cell divisionprotein 7,8-dihydropteroate synthase transcription elongationfactor:cleaves3'nucleotideofpausedmRNA degrades sigma32,integralmembranepeptidase,celldivisionprotein

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

Functional category b3339 b3336 b3321 b3320 b3319 b3318 b3317 b3316 b3315 b3314 b3313 b3312 b3311 b3310 b3309 b3308 b3307 b3306 b3305 b3304 b3303 b3302 b3301 b3300

B number tufA bfr rpsJ rplC rplD rplW rplB rpsS rplV rpsC rplP rpmC rpsQ rplN rplX rplE rpsN rpsH rplF rplR rpsE rpmD rplO prlA

Gene Name ------Strand orientation 1965 1962 1959 1959 1959 1959 1959 1959 1959 1959 1959 1959 1959 1958 1958 1958 1958 1958 1958 1958 1958 1958 1958 1958 Operon ID 55718 41152 34128 40039 39328 29469 42940 37295 29916 26918 12209 15552 43789 46318 58952 30584 40833 39081 33740 27989 21005 45038 25184 2892 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 mRNA present 22 10 12 13 10 11 7 8 2 4 5 4 3 3 5 4 2 8 9 4 9 4 6 9 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P P P P P P Protein detected - total list 36 10 12 10 3 6 6 7 1 6 1 5 2 3 0 6 5 4 2 2 4 1 4 2 # of tryptic peptides detected (total list) P P P P P P P P P P P P Protein detected - short list 14 4 3 4 4 0 4 1 4 9 2 2 0 4 4 7 2 3 8 2 3 1 4 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 P P Protein detected - long list 36 10 12 10 3 6 6 7 1 6 1 5 2 3 0 6 5 4 2 2 4 1 4 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 3 0 2 0 2 0 0 0 0 1 0 0 0 1 0 7 0 0 1 0 2 0 0 2 detected (membrane sample) GenProt-PHD

Membrane protein assignment protein chain elongation factorEF-Tu(duplicate oftufB) bacterioferrin, anironstorage homoprotein 30S ribosomalsubunitprotein S10 50S ribosomalsubunitprotein L3 50S ribosomalsubunitproteinL4,regulatesexpression ofS10operon 50S ribosomalsubunitproteinL23 50S ribosomalsubunitproteinL2 30S ribosomalsubunitproteinS19 50S ribosomalsubunitproteinL22 30S ribosomalsubunitproteinS3 50S ribosomalsubunitproteinL16 50S ribosomalsubunitproteinL29 30S ribosomalsubunitproteinS17 50S ribosomalsubunitproteinL14 50S ribosomalsubunitproteinL24 50S ribosomalsubunitproteinL5 30S ribosomalsubunitproteinS14 30S ribosomalsubunitproteinS8,andregulator 50S ribosomalsubunitproteinL6 50S ribosomalsubunitproteinL18 30S ribosomalsubunitproteinS5 50S ribosomalsubunitproteinL30 50S ribosomalsubunitproteinL15 putative ATPasesubunitoftranslocase

Gene description Macromolecule metabolism Cell processes 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 Cell processes

Functional category b3433 b3432 b3431 b3430 b3429 b3428 b3426 b3417 b3416 b3407 b3403 b3390 b3389 b3388 b3387 b3386 b3385 b3384 b3359 b3357 b3347 b3342 b3341 b3340

B number asd glgB glgX glgC glgA glgP glpD malP malQ yhgF pckA aroK aroB damX dam rpe gph trpS argD crp fkpA rpsL rpsG fusA

Gene Name + + + + ------Strand orientation 2011 2010 2010 2010 2010 2010 2008 2003 2003 1995 1992 1986 1986 1986 1986 1986 1986 1986 1976 1974 1967 1965 1965 1965 Operon ID 45358 35444 56613 7201 4558 3007 3802 3110 7847 1326 1807 7786 5176 1128 2383 1506 2239 3910 1967 9299 1544 669 884 858 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 mRNA present 12 31 28 20 15 30 36 44 29 38 24 14 18 18 13 18 12 13 13 32 8 7 5 9 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P P P P Protein detected - total list 12 23 15 29 1 0 3 4 5 5 1 8 2 2 1 0 2 0 3 3 6 6 5 8 # of tryptic peptides detected (total list) P P P P P P P P P P P P P Protein detected - short list 20 10 14 16 7 1 0 4 0 5 7 0 3 4 0 0 3 1 4 3 6 8 3 7 # 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 Protein detected - long list 12 23 15 29 1 0 3 0 5 5 1 8 2 2 0 0 2 0 3 3 6 6 5 8 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 12 0 0 1 0 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 detected (membrane sample) MP-GenProt

Membrane protein assignment aspartate-semialdehyde dehydrogenase part ofglycogenoperon,a glycosylhydrolase,debranchingenzyme 1,4-alpha-glucan branching enzyme glucose-1-phosphate adenylyltransferase glycogen synthase glycogen phosphorylase sn-glycerol-3-phosphate dehydrogenase(aerobic) maltodextrin phosphorylase 4-alpha-glucanotransferase (amylomaltase) orf, hypotheticalprotein phosphoenolpyruvate carboxykinase shikimate kinaseI 3-dehydroquinate synthase DNA adeninemethylase D-ribulose-5-phosphate 3-epimerase phosphoglycolate phosphatase acetylornithine delta-aminotransferase putative membraneprotein;interfereswithcelldivision tryptophan tRNAsynthetase cyclic AMPreceptorprotein FKBP-type peptidyl-prolylcis-transisomerase(rotamase) 30S ribosomalsubunitproteinS12 30S ribosomalsubunitproteinS7,initiatesassembly GTP-binding proteinchainelongationfactorEF-G

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

Functional category b3560 b3559 b3553 b3544 b3543 b3542 b3541 b3540 b3500 b3498 b3497 b3460 b3458 b3457 b3456 b3455 b3454 b3453 b3452 b3451 b3450 b3449 b3447 b3440

B number glyQ glyS yiaE dppA dppB dppC dppD dppF gor prlC yhiQ livJ livK livH livM livG livF ugpB ugpA ugpE ugpC ugpQ ggt yhhX

Gene Name + + ------Strand orientation 2091 2091 2086 2079 2079 2079 2079 2079 2051 2049 2049 2024 2022 2022 2022 2022 2022 2021 2021 2021 2021 2021 2019 2015 Operon ID 13089 26232 4075 2239 1432 2021 2028 3918 1835 2280 5530 3491 2830 3665 4687 631 422 760 470 557 769 673 748 921 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 mRNA present 10 36 13 24 17 16 17 13 17 15 11 30 10 25 12 26 13 6 5 5 9 4 6 9 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P Protein detected - total list 18 15 11 11 4 3 2 0 3 3 3 1 0 2 2 6 0 5 0 0 1 0 3 4 # of tryptic peptides detected (total list) P P P P P P P P P P Protein detected - short list 20 15 11 3 4 0 0 1 0 4 6 0 0 1 0 6 0 5 0 0 0 0 4 5 # of tryptic peptides detected (short list) P P P P P P P P P P P P Protein detected - long list 18 15 11 11 4 3 0 0 0 0 3 0 0 1 0 6 0 5 0 0 0 0 3 4 # 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 0 0 0 2 0 2 3 3 0 1 0 0 0 0 1 2 2 0 0 0 0 0 0 1 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD GenProt-PHD GenProt-PHD

Membrane protein assignment glycine tRNA synthetase, alphasubunit glycine tRNAsynthetase,beta subunit putative dehydrogenase dipeptide transportprotein dipeptide transportsystempermeaseprotein1 dipeptide transportsystempermeaseprotein2 putative ATP-bindingcomponentofdipeptidetransport system putative ATP-bindingcomponentofdipeptidetransport system glutathione oxidoreductase high-affinity aminoacidtransportsystem;periplasmicbindingprotein high-affinity leucine-specifictransportsystem;periplasmicbindingprotein oligopeptidase A orf, hypotheticalprotein high-affinity branched-chainaminoacidtransport ATP-binding componentofleucinetransport sn-glycerol 3-phosphatetransportsystem;periplasmicbindingprotein sn-glycerol 3-phosphatetransportsystem,integralmembraneprotein sn-glycerol 3-phosphatetransportsystem,integralmembraneprotein glycerophosphodiester phosphodiesterase,cytosolic gamma-glutamyltranspeptidase putative regulator component high-affinity branched-chainaminoacidtransportsystem;membrane system ATP-binding componentofhigh-affinitybranched-chainaminoacidtransport ATP-binding componentofsn-glycerol3-phosphatetransportsystem

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

Functional category b3734 b3733 b3732 b3731 b3730 b3729 b3709 b3708 b3650 b3707 b3699 b3672 b3671 b3649 b3670 b3661 b3652 b3644 b3620 b3622 b3651 b3621 b3619 b3572

B number atpA atpG atpD atpC glmU glmS tnaB tnaA spoT tnaL gyrB ivbL ilvB rpoZ ilvN nlpA recG yicC rfaF rfaL spoU rfaC rfaD avtA

Gene Name + + + + + + + + + + + + + ------Strand orientation 2178 2189 2189 2189 2189 2188 2188 2178 2141 2178 2172 2141 2153 2153 2153 2148 2141 2136 2127 2127 2141 2127 2127 2098 Operon ID 16689 11853 12057 5523 4613 3616 2008 1915 1476 1311 4820 5136 2917 1002 1083 2052 1020 4177 1365 111 983 174 343 846 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 mRNA present 25 17 23 19 28 22 36 40 22 11 19 16 30 18 11 18 10 14 3 6 2 5 3 6 # of tryptic peptides predicted P P P P P P P P P P P P P Protein detected - total list 17 11 12 7 0 2 3 0 8 0 0 3 6 0 5 0 3 3 0 0 0 0 3 0 # of tryptic peptides detected (total list) P P P P P P P P P P P P Protein detected - short list 14 10 13 6 0 2 5 0 8 0 0 5 8 0 5 1 4 4 0 0 0 0 4 0 # of tryptic peptides detected (short list) P P P P P P P P P P P P P Protein detected - long list 15 10 12 6 0 2 3 0 8 0 0 3 6 0 5 0 3 3 0 0 0 0 3 0 # of tryptic peptides detected (long list) P(m) P(m) P(m) P(m) Proteins detected - membrane sample

# of tryptic peptides 17 11 7 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 MP-GenProt MP-GenProt MP-GenProt GenProt GenProt Membrane protein assignment membrane-bound ATPsynthase,F1sector, alpha-subunit N-acetyl glucosamine-1-phosphateuridyltransferase L-glutamine:D-fructose-6-phosphate aminotransferase membrane-bound ATPsynthase, F1sector,gamma-subunit membrane-bound ATPsynthase, F1sector,beta-subunit membrane-bound ATPsynthase, F1sector,epsilon-subunit low affinitytryptophanpermease tryptophanase tryptophanase leaderpeptide RNA polymerase,omegasubunit DNA gyrasesubunitB,typeIItopoisomerase,ATPaseactivity ilvB operonleaderpeptide acetolactate synthaseI,valine-sensitive,largesubunit acetolactate synthaseI,valinesensitive,smallsubunit putative alphahelixprotein lipoprotein-28 DNA helicase,resolutionofHollidayjunctions,branchmigration O-antigen ligase;lipopolysaccharidecorebiosynthesis putative RNAmethylase ADP-L-glycero-D-mannoheptose-6-epimerase heptosyl transferaseI;lipopolysaccharidecorebiosynthesis pyrophosphohydrolase (p)ppGpp synthetaseII;alsoguanosine-3',5'-bispyrophosphate3'- biosynthesis ADP-heptose--lps heptosyltransferaseII;lipopolysaccharidecore transaminase C alanine-alpha-ketoisovalerate (orvaline-pyruvate)transaminase,

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

Functional category b3863 b3849 b3848 b3847 b3829 b3783 b3782 b3781 b3774 b3771 b3770 b3769 b3767 b3766 b3752 b3751 b3750 b3739 b3749 b3738 b3748 b3737 b3736 b3735

B number polA trkH yigZ pepQ metE rho rhoL trxA ilvC ilvD ilvE ilvM ilvG_1 ilvL rbsK rbsB rbsC atpI rbsA atpB rbsD atpE atpF atpH

Gene Name + + + + + + + + + + + + + + + + + + + - - - - - Strand orientation 2250 2243 2243 2243 2235 2211 2211 2210 2204 2202 2202 2202 2202 2202 2196 2196 2196 2196 2189 2196 2189 2189 2189 2189 Operon ID 12228 13382 21344 11090 17285 35912 28649 36217 2496 2414 5763 1335 2177 1243 4402 4481 1311 4929 9855 827 429 814 876 479 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 mRNA present 42 20 31 21 28 25 13 10 13 13 30 10 7 7 2 8 4 1 8 6 3 8 1 7 # of tryptic peptides predicted P P P P P P P P P P P P P Protein detected - total list 36 11 23 5 0 0 5 0 5 6 5 0 1 0 0 3 0 0 0 1 0 0 3 2 # of tryptic peptides detected (total list) P P P P P P P P Protein detected - short list 24 10 16 7 0 0 5 0 4 6 3 0 1 0 0 4 0 0 0 0 1 0 1 1 # of tryptic peptides detected (short list) P P P P P P P P P P P P Protein detected - long list 36 11 23 5 0 0 5 0 5 6 5 0 1 0 0 3 0 0 0 0 0 0 1 2 # 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 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 3 1 detected (membrane sample) MP-GenProt-PHD MP-GenProt-PHD MP-GenProt-PHD GenProt-PHD MP-GenProt MP-GenProt MP-GenProt GenProt Membrane protein assignment DNA polymerase I,3'-->5'polymerase, 5'-->3'andexonuclease potassium uptake,requires TrkE orf, hypotheticalprotein proline dipeptidase tetrahydropteroyltriglutamate methyltransferase transcription terminationfactorRho;polaritysuppressor rho operonleaderpeptide thioredoxin 1 ketol-acid reductoisomerase dihydroxyacid dehydratase branched-chain amino-acidaminotransferase acetolactate synthaseII,valineinsensitive,smallsubunit acetolactate synthaseII,largesubunit,cryptic,interrupted ilvGEDA operonleaderpeptide ribokinase D-ribose periplasmicbindingprotein D-ribose high-affinitytransportsystem ATP-binding componentofD-ribosehigh-affinitytransportsystem membrane-bound ATPsynthase,F0sector,subunita D-ribose high-affinitytransportsystem;membrane-associatedprotein membrane-bound ATPsynthase,F0sector,subunitc membrane-bound ATPsynthase,F0sector,subunitb membrane-bound ATPsynthase,F1sector,delta-subunit atpB membrane-bound ATPsynthase,dispensableprotein,affectsexpressionof

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

Functional category b3987 b3986 b3985 b3984 b3983 b3980 b3962 b3960 b3959 b3958 b3956 b3942 b3941 b3940 b3939 b3932 b3931 b3927 b3926 b3908 b3871 b3870 b3869 b3868

B number rpoB rplL rplJ rplA rplK tufB udhA argH argB argC ppc katG metF metL metB hslV hslU glpF glpK sodA yihK glnA glnL glnG

Gene Name + + + + + + + + + + + + + + + ------Strand orientation 2325 2324 2324 2323 2323 2320 2314 2312 2312 2312 2310 2300 2299 2298 2298 2291 2291 2288 2288 2273 2255 2254 2254 2254 Operon ID 23694 34311 28105 33966 55718 25772 17449 20896 8885 2520 4288 2642 2997 2050 2803 1221 3959 1558 2901 3685 981 506 856 451 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 mRNA present 63 12 22 24 22 13 10 47 34 16 40 28 26 20 20 15 22 5 8 6 9 6 6 8 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P P P P P P Protein detected - total list 31 36 18 15 22 12 6 7 9 4 6 8 5 3 5 4 4 1 1 7 9 9 0 4 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P P P P P P Protein detected - short list 31 10 14 20 14 19 10 12 4 6 4 7 9 5 3 5 6 4 0 1 9 6 0 6 # 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 P P Protein detected - long list 31 36 18 15 22 12 6 7 9 4 6 8 5 3 5 4 4 0 1 7 9 9 0 4 # 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 0 1 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 1 3 0 0 3 0 0 detected (membrane sample) GenProt-PHD GenProt Membrane protein assignment RNA polymerase, betasubunit 50S ribosomalsubunitprotein L7/L12 50S ribosomalsubunitprotein L10 50S ribosomalsubunitprotein L1,regulatessynthesisofL1andL11 50S ribosomalsubunitproteinL11 protein chainelongationfactorEF-Tu(duplicateoftufA) Soluble pyridinenucleotidetranshydrogenase argininosuccinate lyase acetylglutamate kinase N-acetyl-gamma-glutamylphosphate reductase phosphoenolpyruvate carboxylase catalase; hydroperoxidaseHPI(I) 5,10-methylenetetrahydrofolate reductase aspartokinase IIandhomoserinedehydrogenase cystathionine gamma-synthase heat shockproteinhslVU,proteasome-relatedpeptidasesubunit heat shockproteinhslVU,ATPasesubunit,homologoustochaperones glycerol kinase facilitated diffusionofglycerol superoxide dismutase,manganese putative GTP-bindingfactor glutamine synthetase histidine proteinkinasesensorforGlnGregulator(nitrogenII,NRII) response regulatorforgln(sensorglnL)(nitrogenI,NRI)

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

Functional category b4019 b4006 b4005 b4142 b4139 b4069 b4016 b4001 b4170 b4169 b4054 b4051 b4015 b4000 b3994 b3993 b3992 b3991 b3990 b4143 b4025 b4024 b4014 b3988

B number metH purH purD mopB aspA acs aceK yjaH mutL amiB tyrB qor aceA hupA thiC thiE thiF thiG thiH mopA pgi lysC aceB rpoC

Gene Name + + + + + + + + + + + + + ------Strand orientation 2341 2334 2416 2338 2334 2330 2433 2413 2379 2433 2366 2338 2330 2363 2327 2327 2327 2327 2416 2347 2338 2327 2325 2346 Operon ID 35460 30099 16031 10097 42160 1355 3168 1064 1053 1704 8103 1196 1555 5841 4076 2362 4139 4150 3797 1198 385 601 778 754 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 mRNA present 58 28 31 17 20 27 26 20 17 18 17 29 13 26 26 26 20 63 21 6 7 4 9 9 # of tryptic peptides predicted P P P P P P P P P P P P P P P P P P P Protein detected - total list 15 10 18 34 13 14 11 30 5 0 5 0 3 0 4 5 0 2 7 2 3 3 0 4 # of tryptic peptides detected (total list) P P P P P P P P P P P P P P P P Protein detected - short list 13 13 18 14 17 13 10 29 4 0 5 0 5 0 4 7 1 4 9 3 3 3 1 9 # 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 Protein detected - long list 15 10 18 34 13 14 11 30 5 0 5 0 3 0 4 5 0 2 7 2 3 3 0 4 # of tryptic peptides detected (long list) 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 0 7 0 0 0 0 0 0 0 4 0 0 2 0 detected (membrane sample)

PHD Membrane protein assignment isocitrate dehydrogenasekinase/phosphatase phosphoribosylglycinamide synthetase=GAR orf, hypotheticalprotein aspartate ammonia-lyase(aspartase) acetyl-CoA synthetase enzyme inmethyl-directed mismatchrepair DNA-binding proteinHU-alpha(HU-2) tyrosine aminotransferase,repressible isocitrate lyase N-acetylmuramoyl-l-alanine amidaseII;amureinhydrolase quinone oxidoreductase thiamin biosynthesis,pyrimidinemoiety thiamin biosynthesis,thiazolemoiety thiamin biosynthesis,thiazolemoiety thiamin biosynthesis,thiazolemoiety malate synthaseA GroEL, chaperoneHsp60, peptide-dependentATPase,heatshockprotein glucosephosphate isomerase thiamin biosynthesis,thiazolemoiety RNA polymerase,betaprimesubunit aspartokinase III,lysinesensitive ATPase activity GroES, 10Kdchaperonebinds toHsp60inpres.Mg-ATP,suppressingits repressor ofmetEandmetF B12-dependent homocysteine-N5-methyltetrahydrofolatetransmethylase, formyltransferase; IMPcyclohydrolase phosphoribosylaminoimidazolecarboxamideformyltransferase =AICAR

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

Functional category b4372 b4349 b4348 b4260 b4259 b4258 b4254 b4245 b4244 b4235 b4232 b4207 b4203 b4202 b4201 b4200 b4179 b4178 b4177 b4175 b4174 b4173 b4172 b4171

B number holD hsdM hsdS pepA holC valS argI pyrB pyrI pmbA fbp fklB rplI rpsR priB rpsF vacB yjeB purA hflC hflK hflX hfq miaA

Gene Name + + + + + + + + + + + + + + + ------Strand orientation 2567 2550 2550 2496 2495 2495 2491 2482 2482 2474 2471 2452 2448 2448 2448 2448 2436 2436 2435 2433 2433 2433 2433 2433 Operon ID 39294 36636 14218 23556 23491 11884 21261 1781 1232 2469 2370 1977 2198 1085 2607 3787 2574 1123 2778 2685 4830 5821 266 509 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 mRNA present 32 21 47 15 28 19 25 14 10 10 41 21 16 17 24 19 7 6 9 3 5 7 7 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 16 14 15 0 4 4 0 4 0 8 2 3 4 5 4 0 2 5 0 4 5 2 0 0 # of tryptic peptides detected (total list) P P P P P P P P P P P P P Protein detected - short list 15 10 15 0 5 4 0 4 0 7 4 6 5 6 2 0 2 6 0 1 4 3 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 Protein detected - long list 16 14 15 0 4 4 0 4 0 8 2 3 4 5 4 0 2 5 0 1 3 2 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 2 0 0 0 0 3 0 0 0 0 0 0 4 5 0 0 0 detected (membrane sample)

Membrane protein assignment DNA polymerase III,psisubunit host modification;DNAmethylase M aminopeptidase A/I DNA polymeraseIII,chisubunit valine tRNAsynthetase ornithine carbamoyltransferase1 specificity determinantfor hsdM andhsdR aspartate carbamoyltransferase,catalyticsubunit aspartate carbamoyltransferase,regulatorysubunit maturation ofantibioticMccB17,seetldgenes fructose-bisphosphatase FKBP-type 22KDpeptidyl-prolylcis-transisomerase(rotamase) 50S ribosomalsubunitproteinL9 30S ribosomalsubunitproteinS18 primosomal replicationproteinN 30S ribosomalsubunitproteinS6 putative enzyme orf, hypotheticalprotein adenylosuccinate synthetase protease specificforphagelambdacIIrepressor protease specificforphagelambdacIIrepressor GTP -bindingsubunitofproteasespecificforphagelambdacIIrepressor host factorIforbacteriophageQbetareplication,agrowth-relatedprotein delta(2)-isopentenylpyrophosphate tRNA-adenosinetransferase

Gene description Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Metabolism ofsmallmolecules Macromolecule metabolism Metabolism ofsmallmolecules Macromolecule metabolism Structural elements Structural elements Macromolecule metabolism Structural elements Macromolecule metabolism Open readingframes Metabolism ofsmallmolecules Macromolecule metabolism Macromolecule metabolism Macromolecule metabolism Extrachromosomal Macromolecule metabolism

Functional category b4391 b4384 b4383 b4382 b4381 b4376 b4375 b4374 b4373

B number yjjK deoD deoB deoA deoC osmY prfC yjjG rimI Membrane proteinassignment(seepaper): MP-list#1,GenProt#2,PHD#3. TufA andTufBproteinsdifferbyonlyoneamino acidandthuscannotbedifferentiatedbyiethermRNAorproteinanalysis.Bothgenes andproteinswereconsidereddetected. Different operonsaredenotedbyalternatingwhite-greybackgroundcolor. The originallistof404proteinsidentifiedintheshortprotienwasexpandedtoinclude allmembersofcorrespondingoperons(681genesoverall). defined byRileyandLabedan(1996). Annotation informationwastakenfromthe

Gene Name + + + + + + + + - Strand orientation 2575 2571 2571 2571 2571 2567 2567 2567 2567 Operon ID 2248 3617 2940 6115 1117 2453 863 533 272 mRNA intensity A P P P P P P P P mRNA present 30 14 19 25 14 23 7 9 7 # of tryptic peptides predicted P P P P P P P Protein detected - total

E.coli list 16 4 7 1 3 3 3 0 0 # of tryptic peptides

Entry Pointdatabase.TheannotationinthedatabaseisbasedonBlattneretal(1997). Functionalcategoriesareassignedas detected (total list) P P P P Protein detected - short list 17 2 8 2 3 4 5 0 0 # of tryptic peptides detected (short list) P P P P P P P Protein detected - long list 16 4 7 1 3 3 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 detected (membrane sample)

Membrane protein assignment putative ATP-bindingcomponentofatransportsystem purine-nucleoside phosphorylase phosphopentomutase thymidine phosphorylase 2-deoxyribose-5-phosphate aldolase hyperosmotically inducibleperiplasmicprotein peptide chainreleasefactorRF-3 putative phosphatase terminal alanine acyltransferase for30SribosomalsubunitproteinS18;acetylationofN-

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

Functional category