Additional file 1

Table S1. Proteins identified on the reference map Spot no. 1 1-2 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 29-2

STM no. STM1959 STM2771 STM2884 STM1290 STM3359 STM0781 STM3069 STM0217 STM2681 STM2433 STM4055 STM3453 STM3169 STM0890 STM1796 STM4403 STM2166 STM0964 STM0092 STM3551 STM0007 STM3068 STM1210 STM1431 STM1044 STM0665 STM3884 STM1954 STM2884 STM3557 STM0748

Gene type fliC fljB sipC gapA mdh modA pgk tsf grpE crr sodA fkpA stm3169 artI treA cpdB bglX dmsA surA ggt talB fba ycfP sodB sodC gltI rbsB fliY sipC ugpB tolB

30 31

STM3310 STM2165

yrbC yehZ

32 33 34 35 36 37 38 39 40 40-2 41 42 43 44 45 46 47 48 49 50 50-2 51 52 53 53-2 54 54-2 55 56 57 58 59 60 61 62 63 64 65 66 66-2 67

STM2354 STM2355 STM0168 STM1679 STM2494 STM0209 STM1165 STM4232 STM2638 STM1478 STM1375 STM3857 STM4582 STM1091 STM0617 STM4148 STM4570 STM0837 STM3355 STM1891 STM4077 STM3106 STM2282 STM3567 STM0977 STM4007 STM3136 STM0224 STM1746 STM2090 STM1746 STM0849 STM3557 STM2861 STM1091 STM0665 STM4319 STM2324 STM1780 STM2190 STM1815

hisJ argT yacK mppA stm2494 htrA grxB malM rseB ydgH ynhG pstS slt sopB rna nusG deoD ybiS stm3355 znuA yneA ansB glpQ livJ serC glnA stm3136 yaeT oppA rfbH oppA yliB ugpB sitA sopB gltI phoN nuoF prsA mglB minD

68 69 69-2 70 71 72 73 73-2 74 75 76 77 77-2 78 79 80

STM3342 STM3630 STM0609 STM1117 STM3142 STM0209 STM2771 STM1959 STM0012 STM0772 STM2190 STM3630 STM3867 STM4229 STM0830 STM0154

sspA dppA ahpF agp stm3142 htrA fljB fliC dnaK gpmA mglB dppA atpA malE glnH lpdA

80-2 81 82

STM1255 STM2952 STM1238

stm1255 eno icdA

Alternative gene symbol flagellar biosynthesis; flagellin, filament structural protein Flagellar synthesis: phase 2 flagellin (filament structural protein) cell invasion protein glyceraldehyde-3-phosphate dehydrogenase A malate dehydrogenase ABC superfamily (peri_perm), molybdate transporter phosphoglycerate kinase protein chain elongation factor EF-Ts molecular chaparone; heat shock protein PTS family, glucose-specific IIA component superoxide dismutase, manganese FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase) putative dicarboxylate-binding periplasmic protein ABC superfamily (bind_prot), arginine transport system trehalase, periplasmic 2':3'-cyclic-nucleotide 2'-phosphodiesterase beta-D-glucoside glucohydrolase, periplasmic anaerobic dimethyl sulfoxide reductase, subunit A peptidyl-prolyl cis-trans isomerase, survival protein gamma-glutamyltranspeptidase transaldolase B fructose-bisphosphate aldolase putative esterase superoxide dismutase, iron Gifsy-2 prophage: superoxide dismutase precursor (Cu-Zn) ABC superfamily (bind_prot), glutamate/aspartate transporter ABC superfamily (peri_perm), D-ribose transport protein putative periplasmic binding transport protein cell invasion protein ABC superfamily (peri_perm), sn-glycerol 3-phosphate transport protein tol protein required for outer membrane integrity, uptake of group A colicins, and translocation of phage DNA to cytoplasm, may be part of multiprotein peptidoglycan recycling complex (Two domains)

Mwa 51593 52517 42965 35568 32457 27502 41114 30339 21882 18229 23061 28926 36198 26978 63491 70498 83374 90328 47232 61702 35153 39138 21059 21289 18352 34114 30944 28787 42965 48374 46130

Scoreb 140.4 90.0 204.3 295.8 213.2 226.0 237.4 86.1 103.7 99.1 109.2 178.0 94.5 114.1 220.1 201.9 290.7 194.0 229.4 228.1 153.6 129.9 56.1 67.9 53.3 119.4 172.3 230.4 193.4 130.3 105.4

Seq. cov. (%)c 31.3 21.7 45.2 53.2 44.9 61.1 57.1 47.3 32.1 42.6 39.8 40.8 26.9 32.9 32.5 30.1 33.2 21.3 49.8 31.0 48.6 30.4 28.9 21.2 48.0 40.9 49.0 61.7 45.0 27.2 28.4

putative ABC superfamily (atp&memb), transport protein putative ABC superfamily (bind_prot) transport protein (possibly glycine betaine choline transport for osmoprotection) ABC superfamily (bind_prot), histidine transport protein ABC superfamily (bind_prot), lysine/arginine/ornithine transport protein putative multicopper oxidase periplasmic murein tripeptide transport protein, also negative regulator of mulitple antibiotic resistance putative inner membrane or exported periplasmic serine protease Do, heat shock protein glutaredoxin 2 periplasmic protein of mal regulon anti sigma E (sigma 24) factor, negative regulator putative periplasmic protein putative LysM domain ABC superfamily (bind_prot), high-affinity phosphate transporter lytic murein transglycosylase, soluble Salmonella outer protein: homologous to ipgD of Shigella RNase I, cleaves phosphodiester bond between any two nucleotides component in transcription antitermination purine-nucleoside phosphorylase putative periplasmic protein putative tartrate dehydratase alpha subunit ABC superfamily (bind_prot) high affinity Zn transport protein putative ABC superfamily (peri_perm), sugar transport protein periplasmic L-asparaginase II glycerophosphodiester phosphodiesterase, periplasmic ABC superfamily (bind_prot), branched-chain amino acid transporter, high-affinity 3-phosphoserine aminotransferase / phosphohydroxythreonine transaminase glutamine synthetase putative D-mannonate oxidoreductase putative outer membrane antigen ABC superfamily (periplasm), oligopeptide transport protein with chaperone properties LPS side chain defect: CDP-6deoxy-D-xylo-4-hexulose-3-dehydrase ABC superfamily (periplasm), oligopeptide transport protein with chaperone properties putative ABC transporter periplasmic binding protein ABC superfamily (peri_perm), sn-glycerol 3-phosphate transport protein Salmonella iron transporter: fur regulated Salmonella outer protein: homologous to ipgD of Shigella ABC superfamily (bind_prot), glutamate/aspartate transporter non-specific acid phosphatase NADH dehydrogenase I chain F phosphoribosylpyrophosphate synthetase ABC superfamily (peri_perm), galactose transport protein cell division inhibitor, a membrane ATPase, activates MinC, directs division apparatus to middle of cell by oscillating from one half to other stringent starvation protein A, regulator of transcription ABC superfamily (peri_perm), dipeptide transport protein alkyl hydroperoxide reductase, F52a subunit; detoxification of hydroperoxides glucose-1-phosphatase putative ferrichrome-binding periplasmic protein periplasmic serine protease Do, heat shock protein Flagellar synthesis: phase 2 flagellin (filament structural protein) flagellar biosynthesis; flagellin, filament structural protein chaperone Hsp70 in DNA biosynthesis/cell division phosphoglyceromutase 1 ABC superfamily (peri_perm), galactose transport protein ABC superfamily (peri_perm), dipeptide transport protein membrane-bound ATP synthase, F1 sector, alpha-subunit ABC superfamily (bind_prot) maltose transport protein, substrate recognition for transport and chemotaxis ABC superfamily (bind_prot), glutamine high-affinity transporter lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L protein of glycine cleavage complex second part putative ABC transporter periplasmic binding protein enolase isocitrate dehydrogenase in e14 prophage, specific for NADP+

23986 32739

156.8 149.2

50.7 24.9

28361 28181 58607 59859 53722 49297 24413 31805 35749 33897 36111 36798 75066 61916 29509 20527 25959 33274 32224 36459 36741 36908 40406 38769 39814 51767 53989 89508 65517 48085 65517 56520 48374 33704 61916 34114 28364 49227 34166 35795 29481

127.4 139.8 79.1 257.5 140.0 187.3 128.5 136.4 128.9 75.2 98.6 168.6 213.0 184.0 63.8 158.1 102.2 160.9 64.5 129.1 55.4 248.0 176.5 105.4 54.1 147.4 52.6 192.0 254.5 168.6 196.1 228.1 248.3 225.0 199.2 75.9 71.6 144.0 139.6 73.1 149.9

37.7 37.7 17.2 43.9 29.6 33.7 41.4 28.2 31.8 27.1 30.3 48.3 30.3 37.1 18.7 57.5 24.7 42.8 24.4 25.2 23.2 50.0 41.0 40.5 16.0 27.1 11.0 26.9 28.2 30.2 34.7 45.9 42.0 45.6 31.2 29.9 20.0 28.3 45.1 30.1 50.0

24230 60201 55931 45540 39616 49297 52517 51593 69240 28475 35795 60201 55094 43465 27244 50621

137.8 128.4 43.2 128.5 169.7 169.5 153.7 107.3 221.2 161.1 173.4 199.8 114.5 209.5 139.2 186.9

52.8 27.5 10.7 25.2 44.3 27.2 37.4 26.7 34.0 40.8 40.4 36.8 20.7 54.6 53.2 39.9

60010 45580 45769

75.0 200.0 240.0

14.7 35.2 48.6

83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 99-2 100 101 102 103 103-2 104 105 106 106-2 107 108 108-2 109 110 111 112 113 113-2 114 115 116 117 118 119

STM0981 STM4055 STM2445 STM0890 STM3287 STM2786 STM0133 STM1431 STM2884 STM1478 STM0219 STM2444 STM1586 STM1700 STM0213 STM0232 STM0242 STM0487 STM3613 STM3446 STM4330 STM3445 STM4146 STM1117 STM4561 STM3997 STM4561 STM0402 STM0435 STM1440 STM4055 STM4249 STM4081 STM0488 STM1231 STM2355 STM0738 STM3415 STM4184 STM0152 STM0737 STM2660

rpsA sodA ucpA artI nusA stm2786 ftsZ sodB sipC ydgH frr cysP stm1586 fabI dapD accA proS htpG yhjJ fusA mopA tufA tufB agp osmY dsbA osmY stm0402 yajQ sodC sodA aphA tpiA adk phoP argT sucC rpoA aceA aceE sucB clpB

120 121 122 123 124 125 126 127 127-2 128 129 129-2 130 131 132 133 134 135 136 137 138 139 139-2

STM3380 STM0504 STM0007 STM3903 STM1599 STM1119 STM3472 STM1150 STM1679 STM2259 STM4242 STM3188 STM2267 STM1572 STM4077 STM2861 STM0216 STM0735 STM3968 STM4342 STM3043 STM4055 STM1884

accC ybbN talB ilvE pdgL wraB ppiA mdoG mppA napA stm4242 ygiC ompC nmpC yneA sitA rpsB sdhB udp frdB dsbC sodA eda

139-3 140 141 142 142-2 143 144 145 146 146-2 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 165-2 166 167 167-2

STM1451 STM2433 STM0608 STM3063 STM4334 STM2498 STM0578 STM4190 STM1690 STM0711 STM1729 STM3551 STM1251 STM2817 STM0961 STM1070 STM3318 STM4405 STM0734 STM3500 STM0421 STM3090 STM0785 STM3348 STM1310 STM0186 STM1682 STM0536 STM0739 STM1772 STM4078 STM3359 STM2430

gst crr ahpC rpiA efp upp nfnB pepE pspA stm0711 yciF ggt stm1251 luxS lolA ompA yhbN ytfJ sdhA pckA yajO metK ybhE degQ nadE dksA tpx ppiB sucD kdsA yneB mdh cysK

30S ribosomal subunit protein S1 superoxide dismutase, manganese putative oxidoreductase ABC superfamily (bind_prot), arginine transport system transcription pausing; L factor tricarboxylic transport tubulin-like GTP-binding protein and GTPase, forms circumferential ring in cell division superoxide dismutase, iron cell invasion protein putative periplasmic protein ribosome releasing factor ABC superfamily (bind_prot), thiosulfate transport protein putative periplasmic protein enoyl-[acyl-carrier-protein] reductase (NADH) 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase acetylCoA carboxylase, carboxytransferase component, alpha subunit proline tRNA synthetase chaperone Hsp90, heat shock protein C 62.5 putative Zn-dependent peptidase protein chain elongation factor EF-G, GTP-binding chaperone Hsp60 with peptide-dependent ATPase activity, affects cell division protein chain elongation factor EF-Tu (duplicate of tufB) protein chain elongation factor EF-Tu (duplicate of tufA) glucose-1-phosphatase hyperosmotically inducible periplasmic protein, RpoS-dependent stationary phase gene periplasmic protein disulfide isomerase I hyperosmotically inducible periplasmic protein, RpoS-dependent stationary phase gene putative thiol - alkyl hydroperoxide reductase putative cytoplasmic protein copper/zinc superoxide dismutase superoxide dismutase, manganese non-specific acid phosphatase/phosphotransferase, class B triosephosphate isomerase adenylate kinase response regulator in two-component regulatory system with PhoQ, transcribes genes expressed under low Mg+ concentration (OmpR family) ABC superfamily (bind_prot), lysine/arginine/ornithine transport protein succinyl-CoA synthetase, beta subunit RNA polymerase, alpha subunit isocitrate lyase pyruvate dehydrogenase, decarboxylase component 2-oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component) ATP-dependent protease, Hsp 100, part of novel multi-chaperone system with DnaK, DnaJ, and GrpE acetyl CoA carboxylase, biotin carboxylase subunit paral putative thioredoxin protein transaldolase B branched-chain amino-acid aminotransferase periplasmic dipeptidase for D-ala-D-ala digestion in peptidoglycan trp-repressor binding protein peptidyl-prolyl cis-trans isomerase A (rotamase A) periplasmic glucans biosynthesis protein periplasmic murein tripeptide transport protein, also negative regulator of mulitple antibiotic resistance periplasmic nitrate reductase, large subunit, in complex with NapB putative outer membrane or exported putative glutathionylspermidine synthase outer membrane protein 1b (ib;c), porin new outer membrane protein; predicted bacterial porin putative ABC superfamily (peri_perm), sugar transport protein Salmonella iron transporter: fur regulated 30S ribosomal subunit protein S2 succinate dehydrogenase, Fe-S protein uridine phosphorylase fumarate reductase, anaerobic, Fe-S protein subunit protein disulfide isomerase II superoxide dismutase, manganese multifunctional:2-keto-3-deoxygluconate 6-phosphate aldolase; 2-keto-4-hydroxyglutarate aldolase; oxaloacetate decarboxylase

61155 23061 27851 26978 55407 35461 40305 21289 42965 33897 20505 37564 38485 27742 29834 35325 63521 72390 55162 77581 57267 43233 43265 45540 21431 22893 21431 22299 19003 17719 23061 26296 26898 23469 25615 28181 41462 36493 47544 99561 43839 95418

205.6 150.0 139.2 74.7 156.4 102.9 178.6 53.4 158.3 177.8 90.5 233.9 130.8 162.8 198.6 75.5 145.9 128.3 207.7 284.5 192.4 225.3 212.0 159.1 168.8 132.4 55.8 150.8 113.2 64.8 133.3 98.7 141.1 164.5 107.4 75.0 239.4 186.9 139.6 164.8 197.9 264.1

33.8 30.1 47.9 22.6 25.8 22.5 48.6 21.2 42.1 59.2 35.1 61.8 32.0 54.6 44.2 29.2 24.8 22.9 40.6 44.6 24.3 37.3 37.3 27.6 57.1 45.4 23.9 62.0 41.4 33.5 37.4 40.5 30.2 57.9 42.0 31.2 42.8 48.6 29.7 14.9 38.3 34.3

49244 31796 35153 34034 28977 20849 20314 57826 59859 92855 46927 44962 41220 39661 36741 33704 26740 26846 27121 27157 25817 23061 22168

185.1 96.8 143.8 84.9 64.4 96.5 72.9 108.6 95.6 160.6 54.5 38.2 78.8 55.0 182.7 164.8 135.8 146.2 106.8 129.4 128.5 75.1 71.7

33.6 25.4 39.4 23.9 17.2 44.4 22.1 25.2 22.2 20.3 16.1 8.0 17.2 13.8 56.5 43.6 34.9 55.2 34.4 42.6 49.4 33.0 25.4

glutathionine S-transferase PTS family, glucose-specific IIA component alkyl hydroperoxide reductase, C22 subunit; detoxification of hydroperoxides ribosephosphate isomerase, constitutive elongation factor P (EF-P) uracil phosphoribosyltransferase dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase (alpha)-aspartyl dipeptidase phage shock protein; negative regulatory gene for the psp opreon putative cytoplasmic protein putative cytoplasmic protein gamma-glutamyltranspeptidase putative molecular chaperone (small heat shock protein) quorum sensing protein, produces autoinducer - acyl-homoserine lactone-signaling molecules periplasmic protein effects translocation of lipoproteins from inner membrane to outer membrane putative hydrogenase, membrane component putative ABC superfamily (bind_prot) transport protein putative transcriptional regulator succinate dehydrogenase, flavoprotein subunit phosphoenolpyruvate carboxykinase putative oxidoreductase / K + channel protein methionine adenosyltransferase 1 (AdoMet synthetase) putative 3-carboxymuconate cyclase serine endoprotease NAD synthetase, prefers NH3 over glutamine dnaK suppressor protein thiol peroxidase peptidyl-prolyl cis-trans isomerase B (rotamase B) succinyl-CoA synthetase, alpha subunit 3-deoxy-D-manno-octulosonic acid 8-P synthetase putative fructose-1,6-bisphosphate aldolase malate dehydrogenase subunit of cysteine synthase A and O-acetylserine sulfhydrolase A

22424 18229 20729 22877 20605 22515 23937 24751 25505 26927 18634 61702 17532 19290 22594 37497 20040 20558 64443 59558 36143 41934 36318 47308 30465 17497 18007 18122 29757 30777 31724 32457 34517

64.7 108.0 135.1 53.3 40.5 106.8 114.6 76.3 99.5 43.5 105.7 58.8 86.7 54.3 107.2 148.7 128.8 168.4 182.6 211.4 170.9 107.1 86.7 187.4 115.2 54.7 94.1 64.8 117.5 80.8 127.9 115.8 113.9

35.8 46.2 50.8 22.8 21.8 45.7 46.5 34.9 39.6 25.5 43.1 11.2 52.3 22.8 61.8 21.1 52.2 37.3 29.3 40.1 41.7 26.3 23.3 35.4 29.5 17.9 23.8 52.4 29.1 20.1 40.9 36.5 43.0

168 168-2 169 170 171 172 173 174 175 176 177 178 179 180 180-2 181 182 183 183-2

STM0076 STM2016 STM1163 STM4062 STM2555 STM4086 STM4091 STM3710 STM3374 STM1752 STM0372 STM3069 STM0773 STM1337 STM3708 STM2578 STM1222 STM3557 STM0748

fixB cobT pyrC pfkA glyA glpK hslU rfaD mreB galU hemB pgk galM pheS tdh pdxJ potD ugpB tolB

putative electron transfer flavoprotein, carnitine metabolism nicotinate-nucleotide dimethylbenzimidazole-P phophoribosyl transferase dihydro-orotase 6-phosphofructokinase I serine hydroxymethyltransferase glycerol kinase ATPase component of the HslUV protease ADP-L-glycero-D-mannoheptose-6-epimerase rod shape-determining protein; HSP70 class molecular chaperones involved in cell morphogenesis glucose-1-phosphate uridylyltransferase 5-aminolevulinate dehydratase ( porphobilinogen synthase) phosphoglycerate kinase galactose-1-epimerase (mutarotase) phenylalanine tRNA synthetase, alpha-subunit threonine 3-dehydrogenase carries out condensation and ring closure step after PdxA in pyridoxine biosynthesis ABC superfamily (peri_perm), spermidine/putrescine transporter ABC superfamily (peri_perm), sn-glycerol 3-phosphate transport protein tol protein required for outer membrane integrity, uptake of group A colicins, and translocation of phage DNA to cytoplasm, may be part of multiprotein peptidoglycan recycling complex (Two domains)

37115 36594 38587 34897 45436 56045 49649 34831 36934 32888 35529 41114 38497 36736 37194 26325 39003 48374 46130

104.4 32.1 72.7 125.1 116.0 188.1 187.7 228.9 137.1 87.1 64.7 84.9 75.1 92.2 73.0 82.6 158.3 81.2 53.2

26.6 8.4 20.1 35.6 24.5 36.9 37.7 41.9 37.8 21.5 20.7 18.6 19.7 23.9 17.6 32.9 39.1 21.2 13.3

184 185 186 187 188 189 190 191 191-2 192 193 193-2 194 195 196 196-2 197 198 199 199-2 200

STM3348 STM2061 STM3282 STM3446 STM0158 STM0153 STM0228 STM3868 STM4561 STM0803 STM3483 STM0171 STM1720 STM3165 STM1493 STM1599 STM0684 STM1302 STM4404 STM1358 STM4598

degQ sbmC pnp fusA acnB aceF lpxA atpH osmY moaB rpe yadF yciO yqhE stm1493 pdgL nagB xthA cysQ aroD arcA

47308 18044 77002 77581 93479 66122 28038 19394 21431 18521 24473 24803 23088 30977 33865 28977 29613 30767 27472 27307 27273

136.4 50.8 140.6 125.8 147.9 177.4 84.5 49.1 46.7 97.0 39.4 31.5 32.1 115.9 113.3 42.3 43.2 111.0 85.5 53.9 105.1

24.2 24.5 21.2 20.2 16.8 21.3 29.8 23.2 15.6 34.7 6.7 7.7 11.2 21.8 25.3 16.0 18.0 31.7 28.5 22.2 21.0

201 201-2 202 202-2 203 203-2 204 205 206 206-2 207 207-2 208 208-2 209 209-2 210 211 211-2 212 213 214 214-1 215 216 217 218 219 220 221 222

STM1731 STM1970 STM2883 STM0145 STM1953 STM0958 STM1070 STM3539 STM3164 STM1976 STM3339 STM2307 STM1328 STM1700 STM1960 STM3597 STM1305 STM4077 STM4460 STM1290 STM1796 STM0494 STM0683 STM2487 STM3063 STM2335 STM1567 STM2354 STM2433 STM3487 STM3502

stm1731 fliG sipD nadC yedO trxB ompA asd yqhD fliM nanA menB stm1328 fabI fliD gor astD yneA pyrB gapA treA ushA nagA purC rpiA yfbU adhP hisJ crr aroK ompR

31828 36833 37094 32541 34893 34666 37497 40118 42065 37840 32437 31675 34789 27742 49816 48674 52999 36741 34366 35568 63491 60538 41092 26889 22877 19506 35522 28361 18229 19451

74.6 31.8 95.8 40.1 115.1 54.2 136.9 62.6 75.0 41.7 85.8 52.5 74.4 48.6 181.3 71.9 43.2 86.2 74.7 153.6 74.2 97.5 53.9 63.6 67.0 103.7 80.9 111.5 42.8 74.3

19.5 5.1 28.3 11.1 24.7 16.1 35.4 8.4 17.6 11.1 18.2 15.1 13.8 16.4 33.0 10.2 9.3 24.1 20.9 28.1 10.5 12.4 14.6 13.9 11.0 37.8 18.2 22.3 24.3 42.2

27335

83.8

30.1

223 224 225 226 226-2 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 243-2 244 245

STM2211 STM1157 STM2262 STM3445 STM4146 STM2378 STM0310 STM4561 STM1730 STM1746 STM0653 STM4152 STM4152 STM4152 STM3591 STM3591 STM4391 STM1751 STM4329 STM4329 STM1652 STM4391 STM1652 STM0211 STM0211

yeiP yceI eco tufA tufB fabB ghmA osmY yciE oppA ybeL rplL rplL rplL uspA uspA rpsF hns mopB mopB ynaF rpsF ynaF yaeH yaeH

serine endoprotease DNA gyrase inhibitor polynucleotide phosphorylase, member of mRNA degradosome protein chain elongation factor EF-G, GTP-binding aconitate hydratase 2 pyruvate dehydrogenase, dihydrolipoyltransacetylase component UDP-N-acetylglucosamine acetyltransferase membrane-bound ATP synthase, F1 sector, delta-subunit hyperosmotically inducible periplasmic protein, RpoS-dependent stationary phase gene molybdopterin biosynthesis, protein B D-ribulose-5-phosphate 3-epimerase putative carbonic anhydrase putative translation factor 2,5-diketo-D-gluconate reductase A putative periplasmic component, ABC transport system Periplasmic dipeptidase for D-ala-D-ala digestion in peptidoglycan glucosamine-6-phosphate deaminase exonuclease III, may repair singlet oxygen induced lesions affects pool of 3'-phosphoadenosine-5'-phosphosulfate in pathway of sulfite synthesis 3-dehydroquinate dehydratase response regulator (OmpR family) in two-component regulatory system with ArcB (or CpxA), regulates genes in aerobic pathways putative catalase flagellar biosynthesis, component of motor switching and energizing cell invasion protein quinolinate phosphoribosyltransferase putative 1-cyclopropane-carboxylate deaminase thioredoxin reductase putative hydrogenase, membrane component aspartate-semialdehyde dehydrogenase putative alcohol dehydrogenase flagellar biosynthesis, component of motor switch and energizing N-acetylneuraminate lyase (aldolase) dihydroxynaphtoic acid synthetase putative outer membrane protein enoyl-[acyl-carrier-protein] reductase (NADH) flagellar biosynthesis; filament capping protein; enables filament assembly glutathione oxidoreductase succinylglutamic semialdehyde dehydrogenase putative ABC superfamily (peri_perm), sugar transport protein aspartate carbamoyltransferase, catalytic subunit glyceraldehyde-3-phosphate dehydrogenase A trehalase, periplasmic UDP-sugar hydrolase 5'-nucleotidase N-acetylglucosamine-6-phosphate deacetylase phosphoribosylaminoimidazole-succinocarboxamide synthetase (SAICAR synthetase) ribosephosphate isomerase, constitutive putative cytoplasmic protein alcohol dehydrogenase, propanol preferring ABC superfamily (bind_prot), histidine transport protein PTS family, glucose-specific IIA component shikimate kinase I response regulator in two-component regulatory system with EnvZ, affecting transcription of ompC and ompF (OmpR family) putative elongation factor putative secreted protein ecotin, a serine protease inhibitor protein chain elongation factor EF-Tu (duplicate of tufB) protein chain elongation factor EF-Tu (duplicate of tufA) 3-oxoacyl-[acyl-carrier-protein] synthase I phosphoheptose isomerase hyperosmotically inducible periplasmic protein, RpoS-dependent stationary phase gene putative cytoplasmic protein ABC superfamily (periplasm), oligopeptide transport protein with chaperone properties putative cytoplasmic protein 50S ribosomal subunit protein L7/L12 50S ribosomal subunit protein L7/L12 50S ribosomal subunit protein L7/L12 universal stress protein A universal stress protein A 30S ribosomal subunit protein S6 DNA-binding protein HLP-II (HU, BH2, HD, NS); pleiotropic regulator chaperone Hsp10, affects cell division chaperone Hsp10, affects cell division putative universal stress protein 30S ribosomal subunit protein S6 putative universal stress protein putative cytoplasmic protein putative cytoplasmic protein

29925 21004 18199 43233 43265 42355 20877 21431 18954 65517 18392 12281 12281 12281 16062 16062 15154 15524 10299 10299 15696 15154 15696 15076 15076

69.9 52.9 37.6 121.8 116.0 52.7 80.7 31.6 21.1 184.4 58.4 74.9 63.5 52.5 23.5 32.4 32.2 63.0 61.4 60.7 71.4 63.7 41.8 142.0 142.0

18.0 21.5 13.4 19.5 19.5 10.9 28.6 9.8 4.8 20.4 17.2 27.3 36.4 36.4 16.7 16.7 15.3 29.9 53.6 53.6 23.6 23.7 13.2 78.9 78.9

246 247 247-2 248 248-2 249 250 251 251-2 252 252-2 253 254 255 256 257 258 259 260 261 261-2 262 263 264 264-2 265 266 267 268 269 270 271

STM4394 STM3439 STM1195 STM3439 STM3310 STM2795 STM1044 STM4458 STM2646 STM2646 STM4458 STM2646 STM0417 STM1563 STM0653 STM3915 STM2526 STM2526 STM2262 STM0317 STM2262 STM4151 STM3176 STM0803 STM4561 STM3318 STM3426 STM0225 STM1855 STM4405 STM4405 STM0959

rplI rplD fabG rplD yrbC ygaU sodC yjgF yfiD yfiD yjgF yfiD ribH osmC ybeL trxA ndk ndk eco gpt eco rplJ ygiW moaB osmY yhbN rpsH hlpA sopE2 ytfJ ytfJ lrp

272 273 274 275 276 276-2 277 277-2 278 279 280 281 282 283 284 285 286 287 288 289 289-2 290 291 292 293 294 295 296 297 297-2 298 299 300 301 302 303 304 305 306 307 307-2

STM4587 STM3701 STM0366 STM0219 STM1682 STM1730 STM3176 STM3108 STM0694 STM1196 STM1196 STM1196 STM1431 STM2061 STM2433 STM2433 STM3379 STM1070 STM0961 STM4148 STM1210 STM3428 STM3428 STM1920 STM3915 STM1118 STM0186 STM0435 STM1751 STM2491 STM2491 STM3487 STM1652 STM4391 STM4151 STM1837 STM3864 STM1157 STM0506 STM2799 STM4149

creA secB yahO frr tpx yciE ygiW yggL fldA acpP acpP acpP sodB sbmC crr crr accB ompA lolA nusG ycfP rplE rplE cheW trxA yccJ dksA yajQ hns bcp bcp aroK ynaF rpsF rplJ cspC atpC yceI tesA stpA rplK

Theoritical molecular weight calculated from the amino acid sequence. The highest score of SEQUEST search in the most likely candidate. Accordance rate of peptides confirmed by MS/MS analyses in amino acid sequences of candidate proteins

a b c

50S ribosomal subunit protein L9 50S ribosomal subunit protein L4, regulates expression of S10 operon 3-oxoacyl-[acyl-carrier-protein] reductase 50S ribosomal subunit protein L4, regulates expression of S10 operon putative ABC superfamily (atp&memb), transport protein putative LysM domain Gifsy-2 prophage: superoxide dismutase precursor (Cu-Zn) putative translation initiation inhibitor putative formate acetyltransferase putative formate acetyltransferase putative translation initiation inhibitor putative formate acetyltransferase riboflavin synthase, beta chain putative resistance protein, osmotically inducible putative cytoplasmic protein thioredoxin 1, redox factor nucleoside diphosphate kinase nucleoside diphosphate kinase ecotin, a serine protease inhibitor guanine-hypoxanthine phosphoribosyltransferase ecotin, a serine protease inhibitor 50S ribosomal subunit protein L10 putative outer membrane protein molybdopterin biosynthesis, protein B hyperosmotically inducible periplasmic protein, RpoS-dependent stationary phase gene putative ABC superfamily (bind_prot) transport protein 30S ribosomal subunit protein S8, and regulator histone-like protein, located in outer membrane TypeIII-secreted protein effector: invasion-associated protein putative transcriptional regulator putative transcriptional regulator regulator for lrp regulon and high-affinity branched-chain amino acid transport system; mediator of of leucine response (AsnC family) putative periplasmic protein molecular chaperone in protein export putative periplasmic protein ribosome releasing factor thiol peroxidase putative cytoplasmic protein putative outer membrane protein putative cytoplasmic protein flavodoxin 1 acyl carrier protein acyl carrier protein acyl carrier protein superoxide dismutase, iron DNA gyrase inhibitor PTS family, glucose-specific IIA component PTS family, glucose-specific IIA component acetylCoA carboxylase, BCCP subunit, carrier of biotin putative hydrogenase, membrane component periplasmic protein effects translocation of lipoproteins from inner membrane to outer membrane component in transcription antitermination putative esterase 50S ribosomal subunit protein L5 50S ribosomal subunit protein L5 purine-binding chemotaxis protein; regulation thioredoxin 1, redox factor putative cytoplasmic protein dnaK suppressor protein putative cytoplasmic protein DNA-binding protein HLP-II (HU, BH2, HD, NS); pleiotropic regulator thiol peroxidase, thioredoxin dependent thiol peroxidase, thioredoxin dependent shikimate kinase I putative universal stress protein 30S ribosomal subunit protein S6 50S ribosomal subunit protein L10 cold shock protein, multicopy suppresses mukB mutants, putative regulator membrane-bound ATP synthase, F1 sector, epsilon-subunit putative secreted protein multifunctional acyl-CoA thioesterase I; also functions as protease I, lysophospholipaseL(I) DNA-binding protein with chaperone activity 50 S ribosomal subunit protein L11

15766 22068 25527 22068 23986 16103 18352 13557 14326 14326 13557 14326 15990 15084 18392 11788 15503 15503 13876 16951 18199 17782 13926 18521 21431 20040 14108 17855 26398 20558 20558

115.3 60.6 31.5 60.3 43.9 68.6 44.4 60.9 52.8 84.2 61.3 122.3 21.5 42.0 42.3 29.3 43.3 37.4 31.7 37.5 37.5 32.6 29.1 45.9 21.1 57.3 33.9 21.2 83.9 68.9 62.9

56.4 14.9 11.9 19.4 12.8 41.6 14.7 25.0 25.2 33.9 25.0 53.5 15.4 14.0 14.6 11.0 33.6 19.6 11.5 11.8 8.5 4.2 8.5 15.3 12.7 17.4 23.1 13.7 22.5 15.1 24.3

18838

123.9

40.9

17184 17227 9901 20505 18007 18954 13926 12776 16918 8621 8621 8621 21289 18044 18229 18229 16669 37497 22594 20527 21059 20299 20299 18030 11788 13876 17497 19003 15524 17590 17590 19451 15696 15154 16028 7384 15046 21004 23033 15469 14857

81.7 21.3 21.7 63.8 38.1 21.1 37.8 21.2 40.0 41.9 42.0 31.1 31.7 81.6 64.2 84.6 51.0 120.8 72.0 49.8 21.6 88.9 71.7 71.5 31.6 21.1 52.7 113.9 71.9 53.9 80.4 168.9 52.9 64.1 31.9 52.1 31.4 71.9 84.9 68.7 42.8

31.8 14.2 23.1 23.2 14.9 4.8 19.2 24.1 11.4 12.8 12.8 12.8 8.3 24.5 23.1 43.8 30.8 18.6 25.0 17.1 13.9 31.8 12.0 27.5 26.6 17.7 34.4 42.0 29.2 25.0 30.1 75.7 18.8 23.7 30.8 62.3 5.8 25.7 27.5 23.3 12.7