1 SUPPLEMENTARY DATA

TABLE S1. Primers used in this study ______Primer Primer sequence (5’  3’) Application ______

aceA del-F TCGCTTACTGGCTTAATTCACCACATA- aceA deletion ACAATATGTGTAGGCTGGAGCTGCTTC aceA del-R GTTCGCTTATCCGGCCTACGCTATCTG- aceA deletion TAGGCCCATATGAATATCCTCCTTA aceA-check-F ACGTCTGATGGAGCAAATCACCAC aceA deletion confirmation aceA-check-R AAAGCCTTGCAGGATGGTTTGAGC aceA deletion confirmation aceA-F GGCGATTTATCTTTCAGGCT aceA real-time PCR aceA-R ATCTGATCTGCACGACGAAA aceA real-time PCR aceB del-F GATGTATCTGGATCAACAACGAGGAGC- aceB deletion TGCATGTGTGTAGGCTGGAGCTGCTTC aceB del-R TATTGTTATGTGGTGAATTAAGCCAGT- aceB deletion AAGCGACATATGAATATCCTCCTTA aceB-check-F AGCATGTTGAATCAGGCACCTTCG aceB deletion confirmation aceB-check-R ACTGGATCTGATCTGCACGACGAA aceB deletion confirmation aceB-F TCCAGCAACAGCAGGATATT aceB real-time PCR aceB-R TGCGTTCAGGGCATTAATCA aceB real-time PCR sitA-F ACGTTTACCGTTATTGCCGA sitA real-time PCR sitA-R TTCAGACCATTCGCGAGGATAA sitA real-time PCR gudT-F TTCATGGGCCTATGTTATCGGGCA gudT real-time PCR gudT-R AGACCAACCAGGAAACGAAGCGTA gudT real-time PCR garK-F TTACCGCGAATACTTTGGCT garK real-time PCR garK-R TGAATGTCGACGTAAAGACG garK real-time PCR glnH-F TCGCGAAAGAACTGAAGCTGGACT glnH real-time PCR glnH-R TTGTTGGCTTTCACCATCACGAGC glnH real-time PCR mgtA-F TTATCGCCCTGATGGTCGGTATCT mgtA real-time PCR mgtA-R ATAATATCGCCGGGCACCAGTTGA mgtA real-time PCR STM0649.S-F CAATGTTCATTGGCGAACGCGAGA STM0649.S real-time PCR STM0649.S-R GCGGCCAATGGATTCGCCATATTT STM0649.S real-time PCR invG-F CCCAATCAGCTTGGTGTAAA invG real-time PCR invG-R TGGCGTGTCATTAAACCAGT invG real-time PCR ssaJ-F TCCGCATAGGCAGTTTACAA ssaJ real-time PCR ssaJ-R TCATAAGTCGGTAGCGCAAT ssaJ real-time PCR virK-F ACCAGTTCGTTCAGTCCTTT virK real-time PCR virK-R AACGGCGTATCATTGAAGCA virK real-time PCR prpE-F ATCCATTCGGTGGTCTTTGG prpE real-time PCR prpE-R AGAACGTGTTTCGGCTGAT prpE real-time PCR gyrB-F CGGGTTCATTTCACCCAGACCTTT real-time PCR internal control gyrB-R TACGCATGGCGTGGATACCGATTA real-time PCR internal control ______

2 TABLE S2. Comparison of gene expression ratios from microarrays and real-time PCR of selected H2-affected genes. ______

LOCUS ID§ Gene§ Expression Ratio Microarrays Real-time PCR ______Up-regulated STM2861 sitA 13.1 15.6 STM2962 gudT 5.7 8.2 STM4183 aceB 5.3 4.5 STM3159 exbB 5.2 5.2 STM4184 aceA 3.6 5.2 STM3247 garK 3.4 4.4 STM0380 glnH 2.6 2.5

Down-regulated STM2463 eutE 0.01 0.001 STM4172 zraP 0.01 0.001 STM0371 prpE 0.03 0.01 STM2781 virK 0.04 0.02 STM1409 ssaJ 0.06 0.02 STM2898 invG 0.09 0.09 STM0649.S 0.18 0.02 STM4456 mgtA 0.38 0.05 ______§Based on the published genome of S. enterica serovar Typhimurium strain LT2 using the NCBI Genbank database.

3 2 TABLE S3. Microarray-identified H2-stimulated genes in S. enterica serovar Typhimurium JSG210.

______

LOCUS ID§ Gene§ Function§ Expression Ratio ______Up-regulated

STM0191 fhuA outer membrane protein receptor / transporter 15.2 STM2861 sitA Salmonella iron transporter: fur regulated 13.1 STM2862 sitB Salmonella iron transporter: fur regulated 8.2 STM4055 sodA superoxide dismutase, manganese 8.2 STM1729 yciF putative cytoplasmic protein 6.7 STM4550 fhuF ferric hydrozamate transport 6.6 STM0756 nadA quinolinate synthetase, A protein 6.4 STM2962 gudT putative MFS superfamily, D-glucarate permease 5.7 STM4183 aceB malate synthase A 5.3 STM3159 exbB uptake of enterochelin; tonB-dependent uptake of B colicins 5.2 STM3248 garR tartronate semialdehyde reductase (TSAR) 4.9 STM1731 putative catalase 4.9 STM1730 yciE putative cytoplasmic protein 4.8 STM0761 fumarate hydratase Class I anaerobic 4.7 STM0586 fes enterochelin esterase 4.7 STM0762 fumarate hydratase, alpha subunit 4.5 STM0791 hutH histidine ammonia lyase 4.3 STM2342 putative inner membrane protein 4.1 STM4330 mopA chaperone Hsp60 with peptide-dependent ATPase activity 4.1 STM0999 ompF outer membrane protein, porin 4.0 STM3249 garL 2-Dehydro-3-Deoxy-Galactarate Aldolase 3.9 STM1586 putative periplasmic protein 3.8 STM3106 ansB periplasmic L-asparaginase II 3.8 STM0597 entB 2,3-dihydro-2,3-dihydroxybenzoate synthetase, isochorismatase 3.8 STM4077 yneA putative ABC superfamily (peri_perm), sugar transport protein 3.6 STM4184 aceA isocitrate lyase 3.6 STM2863 sitC Salmonella iron transporter: fur regulated 3.6 STM4519 putative NAD-dependent aldehyde dehydrogenase 3.6 STM2960 gudD d-glucarate dehydratase 3.5 STM1125 putP SSS family, major sodium/proline symporter 3.5 STM0794 bioB biotin synthetase 3.4 STM4452 nrdD anaerobic ribonucleoside-triphosphate reductase 3.4 STM3247 garK glycerate kinase 3.4 STM0487.S htpG chaperone Hsp9 3.3 STM4231 lamB phage lambda receptor protein; maltose high-affinity receptor 3.3 STM3355 putative tartrate dehydratase alpha subunit 3.3 STM3506 feoB FeoB family, ferrous iron transport protein B 3.2 STM0012 dnaK chaperone Hsp70 in DNA biosynthesis/cell division 3.2 STM3321 yhbH putative sigma N modulation factor 3.1 STM0757 pnuC NMN family, nucleoside/purine/pyrimidine transporter 3.1 STM1513 putative cytoplasmic protein 3.1 STM4087 glpF MIP channel, glycerol diffusion 3.1 STM1177 flgE flagellar biosynthesis, hook protein 3.0 STM_PSLT040 spvA Salmonella plasmid virulence: outer membrane protein 3.0 STM3663 bax gene transcribed divergently from malS 3.0

4 3 STM4078 yneB putative fructose-1,6-bisphosphate aldolase 3.0 STM4165 rsd regulator of sigma D, binds to the major sigma subunit of RNAP 3.0 STM2141 fbaB 3-oxoacyl-[acyl-carrier-protein] synthase I 3.0 STM1070 ompA putative hydrogenase, membrane component 3.0 STM0585 fepA outer membrane porin, receptor for ferric enterobactin and colicins 2.9 STM3809.S ibpA small heat shock protein 2.9 STM1131 putative outer membrane protein 2.9 STM3865 atpD membrane-bound ATP synthase, F1 sector, β-subunit 2.9 STM4187 iclR acetate operon transcriptional repressor 2.9 STM2277 nrdA ribonucleoside diphosphate reductase 1, α- subunit 2.9 STM1558 putative glycosyl hydrolase 2.9 STM3466 crp catabolite activator protein (CAP), cAMP receptor protein 2.8 STM3709 kbl 2-amino-3-ketobutyrate CoA ligase (glycine acetyltransferase) 2.8 STM3433 rplP 50S ribosomal subunit protein L16 2.8 STM0772 gpmA phosphoglyceromutase 1 2.8 STM3867 atpA membrane-bound ATP synthase, F1 sector, α-subunit 2.7 STM3850 yieF putative oxidoreductase 2.7 STM1176 flgD flagellar biosynthesis, initiation of hook assembly 2.7 STM1973 fliJ flagellar fliJ protein 2.6 STM2340 putative transketolase 2.6 STM1796 treA trehalase, periplasmic 2.6 STM1157 yceI putative secreted protein 2.6 STM1143 csgB minor curlin subunit precursor 2.6 STM0890 artI ABC superfamily, arginine transport system 2.6 STM0830 glnH ABC superfamily, glutamine high-affinity transporter 2.6 STM3511 yhgI putative Thioredoxin-like proteins and domain 2.6 STM2087 rfbV LPS side chain defect: abequosyltransferase 2.6 STM3557 ugpB ABC superfamily, sn-glycerol 3-phosphate transport protein 2.6 STM2085 rfbN LPS side chain defect: rhamnosyl transferase 2.6 STM2074 hisB imidazoleglycerol-phosphate dehydratase; histidinol-phosphatase 2.6 STM3708 tdh threonine 3-dehydrogenase 2.6 STM3866 atpG membrane-bound ATP synthase, F1 sector, γ-subunit 2.6 STM0523 allB allantoinase 2.5 STM3434 rpsC 30S ribosomal subunit protein S3 2.5 STM1728 yciG putative cytoplasmic protein 2.5 STM4289 phnA putative alkylphosphonate uptake protein in phosphonate metabolism 2.5 STM3327 yhbL sigma cross-reacting protein 27A 2.5 STM1572 nmpC new outer membrane protein; predicted bacterial porin 2.5 STM1607 putative outer membrane lipoprotein 2.5 STM2086 rfbU LPS side chain defect: mannosyl transferase 2.5 STM1190 yceD putative metal-binding 2.5 STM1179 flgG flagellar biosynthesis, cell-distal portion of basal-body rod 2.5 STM3963 yigM paral putative transport protein 2.5 STM2832 srlA PTS family, glucitol/sorbitol-specific enzyme IIC component 2.4 STM4503 putative inner membrane protein 2.4 STM3511 yhgI putative Thioredoxin-like proteins and domain 2.4 STM1130 putative inner membrane protein 2.4 STM3884 rbsB ABC superfamily, D-ribose transport protein 2.4 STM2190 mglB ABC superfamily, galactose transport protein 2.4 STM1955 fliZ putative regulator of FliA 2.4 STM1568 fdnI formate dehydrogenase-N, cytochrome γ-subunit, nitrate-inducible 2.4 STM1831 manY Sugar Specific PTS family, mannose-specific enzyme IIC 2.4 STM4458 yjgF putative translation initiation inhibitor 2.4 STM1178 flgF flagellar biosynthesis, cell-proximal portion of basal-body rod 2.4 STM1737 tonB energy transducer; uptake of iron, cyanocobalimin, colicins 2.4 STM2807 nrdE ribonucleoside diphosphate reductase 2, α-subunit 2.4

5 4 STM2072 hisD histidinal dehydrogenase (also histidinol dehydrogenase activity) 2.4 STM2077 hisF imidazole glycerol phosphate synthase, subunit with HisH 2.4 STM1830 manX Sugar Specific PTS family, mannose-specific enzyme IIAB 2.3 STM2084 rfbM LPS side chain defect: mannose-1-phosphate guanylyltransferase 2.3 STM3068 fba fructose-bisphosphate aldolase 2.3 STM2641 nadB quinolinate synthetase, B protein 2.3 STM4007 glnA glutamine synthetase 2.3 STM4477 pepA aminopeptidase A 2.3 STM2278 nrdB ribonucleoside-diphosphate reductase 1, beta subunit 2.3 STM2089 rfbJ LPS side chain defect: CDP-abequose synthase 2.3 STM2555 glyA serine hydroxymethyltransferase 2.3 STM3421 rplO 50S ribosomal subunit protein L15 2.3 STM3868 atpH membrane-bound ATP synthase, F1 sector, delta-subunit 2.3 STM0687 ybfM putative outer membrane protein 2.3 STM3416 rpsD 30S ribosomal subunit protein S4 2.3 STM2341 putative transketolase 2.3 STM2090 rfbH LPS side chain defect: CDP-6deoxy-D-xylo-4-hexulose-3-dehydrase 2.3 STM4080 putative ribulose-5-phosphate 3-epimerase 2.3 STM2430 cysK subunit of cysteine synthase A and O-acetylserine sulfhydrolase A 2.3 STM2083 rfbK LPS side chain defect: phosphomannomutase 2.3 STM4360 miaA delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase 2.3 STM3214 yqjH putative transporter 2.3 STM4325 dcuA Dcu family, anaerobic dicarboxylate transport protein 2.3 STM1174 flgB flagellar biosynthesis, cell-proximal portion of basal-body rod 2.3 STM2078 hisI phosphoribosyl-AMP cyclohydrolase; -ATP pyrophosphatase 2.3 STM3422 rpmD 50S ribosomal subunit protein L30 2.2 STM4074 ego putative ABC-type sugar, aldose transport system 2.2 STM3870 atpE membrane-bound ATP synthase, F0 sector, subunit c 2.2 STM0041 putative glycosyl hydrolase 2.2 STM1173 flgA flagellar biosynthesis; assembly of basal-body periplasmic P ring 2.2 STM0013 dnaJ heat shock protein 2.2 STM1175 flgC flagellar biosynthesis, cell-proximal portion of basal-body rod 2.2 STM0615 ybdR putative dehydrogenase 2.2 STM1191 rpmF 50S ribosomal subunit protein L32 2.2 STM0685 nagE Sugar Specific PTS family, n-acetylglucosamine-specific 2.2 STM0210 yaeG putative inner membrane protein 2.2 STM1624 putative cytoplasmic protein 2.2 STM2082 rfbP undecaprenol-PO4 galactosephosphotransferase, O-antigen transfer 2.2 STM3322 ptsN sugar specific PTS family, enzyme IIA 2.2 STM3997 dsbA periplasmic protein disulfide isomerase I 2.2 STM0592 fepD ABC superfamily ferric enterobactin (enterochelin) transporter 2.1 STM4327 fxsA suppresses F exclusion of bacteriophage T7 2.1 STM3347 yhcB putative periplasmic protein 2.1 STM0363 putative transcription regulator, AraC family 2.1 STM4486 yjgB putative alcohol dehydrogenase 2.1 STM3348 degQ serine endoprotease 2.1 STM1569 fdnH formate dehydrogenase-N, Fe-S beta subunit, nitrate-inducible 2.1 STM4075 ydeY putative ABC superfamily (membrane), sugar transport protein 2.1 STM2076 hisA isomerase 2.1 STM0594 fepB ABC superfamily, ferric enterobactin (enterochelin) tranporter 2.1 STM4076 ydeZ putative ABC superfamily (membrane), sugar transport protein 2.1 STM4154 rpoC RNA polymerase, beta prime subunit 2.1 STM0310 ghmA phosphoheptose isomerase 2.1 STM3326 mtgA peptidoglycan transglycosylase, biosynthetic 2.1 STM3650 putative periplasmic or exported protein 2.1 STM2075 hisH glutamine amidotransferase, subunit with HisF 2.1

6 5 STM0829 glnP ABC superfamily (membrane), glutamine high-affinity transporter 2.1 STM0828 glnQ ABC superfamily (atp_bind), glutamine high-affinity transporter 2.1 STM4500 yjhP putative SAM-dependent methyltransferase 2.0 STM1960 fliD flagellar biosynthesis; filament capping ; filament assembly 2.0 STM3158 exbD uptake of enterochelin; tonB-dependent uptake of B colicins 2.0 STM0598 entA 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase 2.0 STM1752 galU glucose-1-phosphate uridylyltransferase 2.0 STM3684 yibF putative glutathione S-transferase 2.0 STM0002 thrA bifunctional: aspartokinaseI; homoserine dehydrogenase I 2.0 STM4391 rpsF 30S ribosomal subunit protein S6 2.0 STM2071 hisG ATP phosphoribosyltransferase 2.0 STM1815 minD cell division inhibitor 2.0 STM2651 yfiQ putative acetyl-CoA synthetase 2.0 STM0758 ybgR putative CDF family transport protein 2.0 STM4393 rpsR 30S ribosomal subunit protein S18 2.0 STM0193 fhuD ABC superfamily, hydroxamate-dependent iron uptake 2.0 STM2969 ygdH putative nucleotide binding 2.0 STM4392 priB primosomal replication protein N 2.0

Down-regulated

STM2463 eutE putative aldehyde oxidoreductase in ethanolamine utilization 0.01 STM2462 eutJ paral putative heatshock protein (Hsp70) 0.01 STM4172 zraP zinc-resistance associated protein 0.01 STM2464 eutN putative detox protein in ethanolamine utilization 0.01 STM2457 eutC ethanolamine ammonia-lyase, light chain 0.01 STM2460 eutH putative transport protein, ethanolamine utilization 0.01 STM2458 eutB ethanolamine ammonia-lyase, heavy chain 0.01 STM2468 eutQ putative ethanolamine utilization protein 0.01 STM2467 eutT putative cobalamin adenosyltransferase, ethanolamine utilization 0.02 STM2459 eutA CPPZ-55 prophage; chaperonin in ethanolamine utilization 0.02 STM2469 eutP putative ethanolamine utilization protein 0.02 STM2470 eutS putative carboxysome structural protein, ethanol utilization 0.02 STM0370 prpD putative protein in propionate catabolism 0.03 STM0371 prpE putative acetyl-CoA synthetase, propionate catabolism operon 0.03 STM2461 eutG paral putative transport protein in ethanolamine utilization 0.03 STM0368 prpB putative carboxyphosphonoenolpyruvate mutase 0.03 STM2455 eutK putative carboxysome structural protein, ethanolamine utilization 0.04 STM2798 ygaP putative rhodanese-related sulfurtransferase 0.04 STM0622 citE citrate lyase beta chain (acyl lyase subunit) 0.04 STM2558 cadB APC family, lysine/cadaverine transport protein 0.04 STM2781 virK virulence gene; homologous sequence to virK in Shigella 0.04 STM0620 citX putative cytoplasmic protein 0.04 STM2456 eutL putative carboxysome structural protein, ethanolamine utilization 0.05 STM0618 citT DASS family, citrate:succinate transport (antiport) protein 0.05 STM0369 prpC putative citrate synthase 0.05 STM2465 eutM putative detox protein in ethanolamine utilization 0.05 STM4171 yjaH putative inner membrane protein 0.06 STM0621 citF bifunctional citrate lyase alpha chain/citrate-ACP transferase 0.06 STM1409 ssaJ Secretion system apparatus 0.06 STM0623 citD citrate lyase acyl carrier protein (gamma chain) 0.06 STM0624 citC citrate lyase synthetase (citrate (pro-3S)-lyase ligase 0.06 STM2466 eutD putative phosphotransacetylase in ethanolamine utilization 0.07 STM2287 putative cytoplasmic protein 0.07 STM1398 sseB Secretion system effector 0.07 STM0650 putative hydrolase C-terminus 0.08

7 6 STM1410 putative cytoplasmic protein 0.09 STM2898 invG invasion protein; outer membrane 0.09 STM0972 homologous to secreted protein sopD 0.09 STM1698 putative inner membrane protein 0.10 STM0705 kdpB P-type ATPase, high-affinity potassium transport system, B chain 0.10 STM0061 citF2 putativ bifunctional citrate lyase alpha chain/citrate-ACP transferase 0.10 STM1412 ssaL Secretion system apparatus 0.10 STM2454 eutR putative regulator ethanolamine operon (AraC/XylS family) 0.10 STM2559 cadA lysine decarboxylase 1 0.10 STM1214 ycfR putative outer membrane protein 0.10 STM1224 sifA lysosomal glycoprotein (lgp)-containing structures 0.11 STM2548 asrA anaerobic sulfide reductase 0.11 STM1399 sscA Secretion system chaparone 0.12 STM1419 yscR Secretion system apparatus: homology with yscR of Yersinia 0.13 STM1091 sopB Salmonella outer protein: homologous to ipgD of Shigella 0.13 STM1246 pagC PhoP regulated: reduced macrophage survival 0.13 STM4173 hydH sensory kinase in two component regulatory system with HydG 0.14 STM2797 putative regulatory protein, arsR family 0.14 STM0309 yafH putative acyl-CoA dehydrogenase 0.14 STM2187 yeiA putative dihydropyrimidine dehydrogenase 0.15 STM1397 sseA Secretion system effector 0.15 STM2177 putative flutathione S-transferase 0.15 STM2899 invF invasion protein 0.16 STM1602 sifB Salmonella translocated effector: translocated by SPI-2 0.16 STM0704 kdpC P-type ATPase, high-affinity potassium transport system, C chain 0.16 STM0708 ybfA putative periplasmic protein 0.17 STM2186 putative NADPH-dependent glutamate synthase oxidoreductase 0.17 STM0708 ybfA putative periplasmic protein 0.18 STM0649.S putative hydrolase 0.18 STM1411 ssaK Secretion system apparatus 0.18 STM2176 putative glutathione S-transferase 0.18 STM1402 sseE Secretion system effector 0.18 STM2874 prgH cell invasion protein 0.18 STM2780 homologue of pipB, putative pentapeptide repeats (8 copies) 0.18 STM1395 ssaD Secretion system apparatus 0.19 STM0060 citE2 putative citrate lyase beta chain (acyl lyase subunit) 0.19 STM1407 ssaH Secretion system apparatus 0.19 STM2892 invJ surface presentation of antigens; secretory proteins 0.20 STM1328 putative outer membrane protein 0.20 STM1403 sscB Secretion system chaparone 0.20 STM1562 putative periplasmic transport protein 0.20 STM1401 sseD Secretion system effector 0.20 STM2867 hilC bacterial regulatory helix-turn-helix proteins, araC family 0.20 STM1408 ssaI Secretion system apparatus 0.20 STM2550 asrC anaerobic sulfide reductase 0.20 STM2549 asrB anaerobic sulfide reductase 0.20 STM0059 citD2 putative citrate lyase acyl carrier protein (gamma chain) 0.20 STM4174 hydG response regulator in two-component reguatory system with HydH 0.20 STM4258 putative methyl-accepting chemotaxis protein 0.21 STM2178 putative 1,2-dioxygenase protein 0.21 STM0853 yliH putative cytoplasmic protein 0.22 STM2175 putative monooxygenase 0.22 STM2869 orgA putative flagellar biosynthesis/type III secretory pathway protein 0.22 STM0058 citC2 putative citrate lyase synthetase (citrate (pro-3S)-lyase ligase 0.23 STM2882 sipA cell invasion protein 0.23 STM2868 putative cytoplasmic protein 0.23

8 7 STM2896 invA invasion protein 0.23 STM1400 sseC Secretion system effector 0.24 STM1392 ssrA Secretion system regulator:Sensor component 0.24 STM2883 sipD cell invasion protein 0.24 STM2885 sipB cell invasion protein 0.24 STM1415 ssaN Secretion system apparatus: homology with the YscN family proteins 0.24 STM2893 invI surface presentation of antigens; secretory proteins 0.24 STM2895 invB surface presentation of antigens; secretory proteins 0.25 STM1392 ssrA Secretion system regulator:Sensor component 0.25 STM2395 pgtE Phosphoglycerate transport: outer membrane protein E 0.25 STM1421 ssaT Secretion system apparatus: homology with YscT of Yersinia 0.25 STM2886 sicA surface presentation of antigens; secretory proteins 0.25 STM1548.s putative S-adenosylmethionine/tRNA-ribosyltransferase-isomerase 0.26 STM2897 invE invasion protein 0.26 STM1283 yeaJ putative Methyl-accepting chemotaxis protein 0.26 STM2360 putative diaminopimelate decarboxylase 0.26 STM0703 kdpD sensory kinase in two-component regulatory system wtih KdpE 0.26 STM0062 citX2 putative cytoplasmic protein 0.26 STM3138 putative methyl-accepting chemotaxis protein 0.27 STM1094 pipD Pathogenicity island encoded protein: SPI3 0.27 STM2627 Gifsy-2 prophage; probable regulatory protein 0.27 STM2139 putative inner membrane protein 0.27 STM1391 ssrB Secretion system regulator: transcriptonal activator 0.27 STM1588 yncC putative regulatory protein, gntR family 0.27 STM2782 mig-14 putative transcription activator 0.27 STM2530 putative anaerobic dimethylsulfoxide reductase 0.27 STM1538 putative hydrogenase-1 large subunit 0.27 STM2894 invC surface presentation of antigens; secretory proteins 0.27 STM0439 cyoE protohaeme IX farnesyltransferase (haeme O biosynthesis) 0.28 STM2389 yfcY paral putative acetyl-CoA acetyltransferase 0.28 STM0707 putative outer membrane protein 0.28 STM1539 putative hydrogenase-1 small subunit 0.28 STM3982 fadA 3-ketoacyl-CoA thiolase 0.28 STM1601 ugtL putative membrane protein 0.28 STM1482 ydgF putative membrane transporter of cations and cationic drugs 0.28 STM3763 mgtB Mg2+ transport protein 0.28 STM1414 ssaV Secretion system apparatus: homology with the LcrD family proteins 0.28 STM2884 sipC cell invasion protein 0.28 STM1394 ssaC Secretion system apparatus 0.29 STM3238 yhaN putative inner membrane protein 0.29 STM4259 putative ABC exporter outer membrane component homolog 0.29 STM1867 pagK PhoPQ-activated gene 0.29 STM4319 phoN non-specific acid phosphatase 0.30 STM1786 hydrogenase-1 small subunit 0.30 STM0062 citX2 putative cytoplasmic protein 0.30 STM2891 spaO surface presentation of antigens; secretory proteins 0.30 STM1088 pipB Pathogenicity island encoded protein: SPI3 0.30 STM1306 astB succinylarginine dihydrolase 0.31 STM0699 putative cytoplasmic protein 0.31 STM2360 putative diaminopimelate decarboxylase 0.31 STM2330 lrhA NADH dehydrogenase transcriptional repressor (LysR family) 0.32 STM2435 pdxK pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase 0.32 STM1786 hydrogenase-1 small subunit 0.32 STM2399 pgtP Phosphoglycerate transport: transporter 0.32 STM2887 spaS surface presentation of antigens; secretory proteins 0.33 STM0063 citG2 putative modifier of citrate lyase protein 0.33

9 8 STM1782 ychH putative inner membrane protein 0.33 STM3983 fadB 3-hydroxyacyl-coA dehydrogenase of 4-enzyme FadB protein 0.33 STM3218 oat putative acetylornithine aminotransferase 0.33 STM3239 yhaO putative HAAAP family transport protein 0.33 STM2388 yfcX paral putative dehydrogenase 0.34 STM1367 ydiH putative cytoplasmic protein 0.34 STM2066 sopA Secreted effector protein of Salmonella dublin 0.34 STM1413 ssaM Secretion system apparatus 0.34 STM2936 iap aminopeptidase in alkaline phosphatase isozyme conversion 0.34 STM0454 ybaW putative esterase 0.34 STM4260 membrane permease, predicted cation efflux pump 0.34 STM1781 ychM putative SulP family transport protein 0.35 STM0700 potE APC family, putrescine/ornithine antiporter 0.35 STM2873 prgI cell invasion protein; cytoplasmic 0.35 STM2401 ddg cold shock-induced palmitoleoyl transferase 0.35 STM3552 yhhA putative outer membrane protein 0.35 STM0625 dpiB sensory histidine kinase in TCRS with DpiA 0.35 STM0870 putative transport protein 0.35 STM4424.S putative endonuclease 0.35 STM1305 astD succinylglutamic semialdehyde dehydrogenase 0.35 STM1940 putative cell wall-associated hydrolase 0.36 STM2944 ygcB putative helicase 0.36 STM3280.S deaD cysteine sulfinate desulfinase 0.36 STM3798 emrD MFS family, multidrug tranport protein 0.36 STM3764 mgtC Mg2+ transport protein 0.36 STM4261 putative inner membrane protein 0.36 STM4315 putative AraC-type DNA-binding domain-containing protein 0.36 STM2197 putative phosphoserine phosphatase 0.36 STM3244 tdcB threonine dehydratase, catabolic 0.36 STM1536 putative hydrogenase maturation protease 0.37 STM1532 putative dehydrogenase protein 0.37 STM0701 speF ornithine decarboxylase isozyme, inducible 0.37 STM4295 adiY transcriptional activator of adiA (AraC/XylS family) 0.37 STM3219 fadH 2,4-dieonyl-coa reductase 0.37 STM1537 putative Ni/Fe-hydrogenase 1 b-type cytochrome subunit 0.37 STM2138 putative cytoplasmic protein 0.37 STM0968 ycaD putative MFS family transport protein 0.38 STM1631 sseJ Salmonella translocated effector: regulated by SPI-2 0.38 STM2890 spaP surface presentation of antigens; secretory proteins 0.38 STM4456 mgtA P-type ATPase, Mg2+ ATPase transporter 0.38 STM1851 putative cytoplasmic protein 0.38 STM1533 putative hydrogenase 0.38 STM2871 prgK cell invasion protein; lipoprotein, may link inner and outer membranes 0.38 STM1011 Gifsy-2 prophage 0.38 STM3197 glgS glycogen biosynthesis, rpoS dependent 0.38 STM1909 argS arginine tRNA synthetase 0.38 STM1449 tyrS tyrosine tRNA synthetase 0.39 STM2220 yejG putative cytoplasmic protein 0.39 STM4433 putative thiamine pyrophosphate-requiring enzyme 0.39 STM0440 cyoD cytochrome o ubiquinol oxidase subunit IV 0.39 STM4418 sugar (and other) transporter 0.39 STM0057 putative citrate-sodium symport 0.39 STM1984 yodD putative cytoplasmic protein 0.39 STM1282 yeaK putative cytoplasmic protein 0.39 STM2179 putative sugar transporter 0.39 STM0356 putative inner membrane protein 0.39

10 9 STM4257 putative inner membrane or exported 0.39 STM2596 Gifsy-1 prophage: similar to minor tail protein 0.40 STM2872 prgJ cell invasion protein; cytoplasmic 0.40 STM2374 putatiave helix-turn-helix regulatory protein 0.40 STM2621 Gifsy-2 prophage 0.40 STM0859 putative transcriptional regulator, LysR family 0.40 STM2434 putative cytoplasmic protein 0.40 STM1907 cutC copper homeostasis protein 0.41 STM1121 ymdF putative cytoplasmic protein 0.41 STM2876 hilA invasion genes transcription activator 0.41 STM1855 sopE2 TypeIII-secreted protein effector: invasion-associated protein 0.41 STM1935 ftn cytoplasmic ferritin 0.41 STM1089 putative inner membrane protein 0.41 STM1999 putative cytoplasmic protein 0.41 STM1941 putative inner membrane protein 0.41 STM0626 dpiA response regulator in TCRS with DpiB 0.41 STM1818 fadD acyl-CoA synthetase (long-chain-fatty-acid--CoA ligase) 0.41 STM2425 yfeH putative Na+-dependent transporter 0.42 STM0619 citG putative modifier of citrate lyase protein 0.42 STM0366 yahO putative periplasmic protein 0.42 STM4425 putative dehydrogenase 0.42 STM1244 pagD PhoP regulated 0.42 STM1396 ssaE Secretion system effector 0.42 STM2866 sprB transcriptional regulator 0.42 STM2903 putative cytoplasmic protein 0.42 STM1535 putative hydrogenase protein 0.42 STM2605 Gifsy-1 prophage: similar to head-tail preconnector gp5 of phage 21 0.42 STM3083 putative Mannitol dehydrogenase 0.43 STM2711 Fels-2 prophage: similar to gpS for completion of tail, in phage P2 0.43 STM0382 putative permease 0.43 STM1671 putative bacterial regulatory helix-turn-helix proteins, araC family 0.43 STM1483 ydgE putative membrane transporter of cations and cationic drugs 0.43 STM4594 sthA putative fimbrial chaparone protein 0.43 STM2888 spaR surface presentation of antigens; secretory proteins 0.43 STM1705 osmB osmotically inducible lipoprotein 0.43 STM2738 Fels-2 prophage: similar to E. coli retron 0.43 STM2889 spaQ surface presentation of antigens; secretory proteins 0.43 STM4156 putative cytoplasmic protein 0.43 STM1797 ymgE putative transglycosylase-associated protein 0.43 STM2706 Fels-2 prophage: similar to invertase (pin) in phage E14 0.43 STM0609 ahpF alkyl hydroperoxide reductase, F52a subunit 0.43 STM2436 ptsJ putative regulatory protein, gntR family 0.43 STM0914 Fels-1 prophage; putative phage tail component 0.43 STM2373 putative cytoplasmic protein 0.43 STM0281 putative cytoplasmic protein 0.43 STM0920 Fels-1 prophage; ail and ompX homologue 0.43 STM2881 iacP putative acyl carrier protein 0.44 STM1320 ydjN part of a kinase, putative domain shared with transporter 0.44 STM2420.1n hypothetical protein 0.44 STM1417 ssaP Secretion system apparatus 0.44 STM0903 Fels-1 prophage; putative chaparone 0.44 STM2209 putative inner membrane protein 0.44 STM2721 Fels-2 prophage: similar to gpO, capsid scaffold, in phage P2 0.44 STM1304 astA arginine succinyltransferase 0.44 STM1422 ssaU Secretion system apparatus: homology with YscU of Yersinia 0.44 STM4504 putative cytoplasmic protein 0.44

11 10 STM1712 acnA aconitate hydratase 1 0.44 STM2169 yohC paral putative transport protein 0.44 STM1416 ssaO Secretion system apparatus 0.44 STM1329 putative inner membrane protein 0.44 STM2701 Fels-2 prophage: similar to tail sheath proteins in phage P2 0.44 STM2202 yeiH putative inner membrane protein 0.44 STM2585 Gifsy-1 prophage: similar to transpose 0.44 STM2359 putative amino acid transporter 0.44 STM1418 ssaQ Secretion system apparatus 0.45 STM2607 Gifsy-1 prophage: similar to head to tail joining protein 0.45 STM2358 putative cytoplasmic protein 0.45 STM2710 Fels-2 prophage: similar to gpV, base plate of tail, in phage P2 0.45 STM1420 ssaS Secretion system apparatus: homology with YscS of Yersinia 0.45 STM1327 ydiY putative salt-induced outer membrane protein 0.45 STM4312 putative phage protein 0.45 STM2731 Fels-2 prophage: similar to protein in phage 186 0.45 STM1344 ydiV putative Diguanylate cyclase/phosphodiesterase domain 1 0.45 STM1840 yobG putative inner membrane protein 0.45 STM3325 yrbL putative cytoplasmic protein 0.45 STM1636 putative ABC-type transport system; membrane spanning protein 0.45 STM2702 Fels-2 prophage: DNA invertase Pin homolog 0.45 STM1584 ansP ABC family, L-asparagine transport protein 0.45 STM1669 homology to invasin C of Yersinia; intimin 0.45 STM1406 ssaG Secretion system apparatus 0.45 STM2732 Fels-2 prophage: similar to protein in phage 186 0.46 STM1239 putative cytoplasmic protein 0.46 STM1583 putative cytoplasmic protein 0.46 STM2529 putative anaerobic dimethylsulfoxide reductase 0.46 STM2850 hycD hydrogenase 3, membrane subunit (part of FHL complex) 0.46 STM2038 pduA Propanediol utilization: polyhedral bodies 0.46 STM2707 Fels-2 prophage: similar to tail fiber protein (gpH) in phage P2 0.46 STM1278 yeaN putative MFS family transport protein (amino acid/amine transport) 0.46 STM3301 yhbZ putative GTP-binding protein 0.46 STM2900 invH invasion protein 0.46 STM2718 Fels-2 prophage: similar to gpQ in phage 186 0.46 STM3623 yhjT putative inner membrane protein 0.46 STM1404 sseF Secretion system effector 0.46 STM2137 putative cytoplasmic protein 0.46 STM0341 putative inner membrane protein 0.46 STM0937 hcp hybrid cluster protein; similar to prismane-protein homolog 0.47 STM0929 putative inner membrane protein 0.47 STM0305 putative cytoplasmic protein 0.47 STM2231 homologue of msgA; ssrB-regulated factor 0.47 STM0019 putative hydroxymethyltransferase 0.47 STM2390 yfcZ putative cytoplasmic protein 0.47 STM1330 putative DNA/RNA non-specific endonuclease 0.47 STM1047 Gifsy-2 prophage; probable tail assembly protein 0.47 STM1803 dadA D-amino acid dehydrogenase subunit 0.47 STM3671 yiaM putative transporter 0.47 STM2875 hilD regulatory helix-turn-helix proteins, araC family 0.47 STM0902 Fels-1 prophage 0.47 STM2237 putative inner membrane protein 0.47 STM2244 homolog of virulence protein MsgA 0.47 STM3956 yigI putative protein PaaI 0.47 STM1457 putative respiratory-chain NADH dehydrogenase 0.47 STM2982 gcvA regulator of gcv operon (LysR family) 0.47

12 11 STM3133 putative amidohydrolase 0.47 STM4520 putative cytoplasmic protein 0.47 STM1788 putative Ni/Fe-hydrogenase 1 b-type cytochrome subunit 0.47 STM2751 putative PTS enzyme III glucitol 0.47 STM1994 putative inner membrane protein 0.47 STM1307 astE succinylglutamate desuccinylase 0.47 STM2696 Fels-2 prophage: similar to genes in phage phiCTX 0.47 STM2704 Fels-2 prophage: similar to genes in P2-like phages 0.47 STM1534 putative hydrogenase 0.47 STM1996 cspB putative cold-shock protein 0.47 STM1810 putative cytoplasmic protein 0.47 STM0921 Fels-1 prophage; putative minor tail protein 0.47 STM2198 putative regulatory protein 0.47 STM1284 yeaH putative cytoplasmic protein 0.47 STM4214 putative cytoplasmic protein 0.48 STM0895 Fels-1 prophage 0.48 STM1090 pipC Pathogenicity island encoded protein: homologous to ipgE of Shigella 0.48 STM2119 yegH putative inner membrane protein 0.48 STM3260 PTS family galactitol-specific enzyme IIC 0.48 STM2799 stpA DNA-binding protein with chaperone activity 0.48 STM1868 mig-3 Homology to phage-tail assembly proteins 0.48 STM0610 putative component of anaerobic dehydrogenases 0.48 STM4426 srfJ activated by transcription factor SsrB 0.48 STM0904 Fels-1 prophage 0.48 STM0721 putative glycosyl transferase 0.48 STM2800 putative inner membrane protein 0.48 STM1110 putative cytoplasmic protein 0.48 STM2603 Gifsy-1 prophage: similar to head protein gp7 of phage 21 0.48 STM0893 Fels-1 prophage; putative integrase 0.48 STM2757 putative cytoplasmic protein 0.48 STM0910 Fels-1 prophage 0.48 STM2400 putative inner membrane protein 0.48 STM1118 yccJ putative cytoplasmic protein 0.48 STM3154 putative ATP-dependent RNA helicase-like protein 0.48 STM1128 putative sodium/glucose cotransporter 0.48 STM2724 Fels-2 prophage: hypothetical protein 0.48 STM1373 sufS selenocysteine lyase 0.48 STM3256 putative phosphotransferase system mannitol/fructose-specific domain 0.48 STM4547 yjjQ putative transcriptional regulator (LuxR/UhpA family) 0.48 STM0860 putative inner membrane protein 0.49 STM2713 Fels-2 prophage: similar to protein from phage CTX 0.49 STM1269 putative chorismate mutase 0.49 STM4013.S putative membrane-associated metal-dependent hydrolase 0.49 STM0295 putative cytoplasmic protein 0.49 STM3690 putative inner membrane lipoprotein 0.49 STM0905 Fels-1 prophage 0.49 STM4313 putative cytoplasmic protein 0.49 STM2560 yjdL putative POT family, di-/tripeptide transport protein 0.49 STM4575 putative outer membrane protein 0.49 STM2236 putative phage protein 0.49 STM0896 hypothetical protein, Fels-1 prophage 0.49 STM0279 putative cytoplasmic protein 0.49 STM2200 lysP APC family, lysine-specific permease 0.49 STM2511 guaB IMP dehydrogenase 0.49 STM0913 hypothetical protein 0.49 STM2730 Fels-2 prophage: similar to retron in E. coli 0.49

13 12 STM0809 putative inner membrane protein 0.49 STM1531 putative hydrogenase 0.49 STM2877 iagB cell invasion protein 0.49 STM0114 leuL leu operon leader peptide 0.49 STM2609 Gifsy-1 prophage: similar to DNA packaging protein Nu1 of phage 21 0.49 STM3168 ygiR putative Fe-S oxidoreductase family 2 0.49 STM3258 Sugar specific- PTS family protein, galactitol-specific enzyme IIA 0.49 STM0384 psiF induced by phosphate starvation 0.49 STM3363 yhcO putative cytoplasmic protein 0.49 STM3079.S putative hydrolase/acyltransferase 0.49 STM2405 putative thiamine pyrophosphate enzymes 0.49 STM1138 ycdZ putative inner membrane protein 0.49 STM0632 ybeC putative Sec-independent protein secretion pathway component 0.49 STM1882 yebG DNA damage-inducible gene in SOS regulon 0.49 STM1405 sseG Secretion system effector 0.49 STM0348 putative inner membrane protein 0.49 STM2595 Gifsy-1 prophage: similar to minor tail protein 0.49 STM2136 yegQ putative protease 0.49 STM2245 putative outer membrane protein 0.49 STM1159 yceO putative inner membrane protein 0.49 STM0954 putative inner membrane protein 0.49 STM1603 yncJ putative periplasmic protein 0.49 STM2723 Fels-2 prophage: similar to gpQ, portal vertex protein, in phage P2 0.49 STM0917 Fels-1 prophage; putative minor tail protein 0.49 STM1791 putative hydrogenase-1 protein 0.50 STM0365 yahN paral putative transport protein 0.50 STM1253 putative inner membrane protein 0.50 STM2728 Fels-2 prophage: hypothetical protein 0.50 STM0334 putative cytoplasmic protein 0.50 STM4070 putative cytoplasmic protein 0.50 STM2631 Gifsy-2 prophage 0.50 STM2034 cibB synthesis of vitamin B12 adenosyl cobalamide precursor 0.50 STM2703 Fels-2 prophage: similar to invertase (pin) in phage E14 0.50 STM4206 putative phage glucose translocase 0.50 STM1869 Homology to phage-tail assembly proteins 0.50 STM1790 putative thiol-disulfide isomerase and thioredoxins 0.50 STM3796 ilvB acetolactate synthase I, large subunit, valine sensitive 0.50 STM4218 putative inner membrane protein 0.50 STM1345 ydiU putative cytoplasmic protein 0.50 STM2618 Gifsy-1 prophage 0.50 STM2727 Fels-2 prophage: similar to phage 186 protein, and to retron in E. coli 0.50 STM1303 astC succinylornithine transaminase 0.50 STM3362 putative periplasmic protein 0.50 STM1793 putative cytochrome oxidase, subunit II 0.50 STM3940 putative inner membrane protein 0.50 STM1863 putative inner membrane protein 0.50 STM4389 yjfY putative outer membrane protein 0.50 STM1272 yoaG putative cytoplasmic protein 0.50 STM0294 putative cytoplasmic protein 0.50 STM3392 yhdV putative outer membrane lipoprotein 0.50 ______§Based on the published genome of S. enterica serovar Typhimurium strain LT2 using the NCBI Genbank database.

14 13 15 14