Supporting Online Material: Supplemental Table 1

Typhoid Supplemental Tables Libby, et al.

Supporting Online Material: Supplemental Table 2. Complete List of Additional Transposon Insertions Surveyed in this Study.

Ty2 Symbol Gene Name Description t0006 yaaJ putative amino-acid transport protein t0007 talB transaldolase B t0010 hypothetical protein t0013 dnaJ chaperone protein t0015 hypothetical protein t0018 putative chitinase t0020 hypothetical protein t0022 bcfA fimbrial subunit t0024 bcfC t0029 hypothetical protein t0035 putative secreted 5'-nucleotidase t0036 hypothetical protein t0037 putative secreted sulfatase t0040 sulfatase t0043 putative glycosyl hydrolase t0044 putative transport protein t0047 ribF bifunctional riboflavin kinase/FMN adenylyltransferase t0051 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase t0055 citA sensor kinase t0059 citC citrate-sodium symporter t0059 - t0060 t0063 citF citrate lyase alpha chain t0068 carB carbamoyl phosphate synthase large subunit t0069 caiF transcriptional activator t0070 caiE carnitine operon protein t0072 caiC putative crotonobetaine/carnitine-CoA ligase t0073 caiB crotonobetainyl-CoA:carnitine CoA-transferase t0075 caiT L-carnitine/gamma-butyrobetaine antiporter t0076 fixA putative electron transfer flavoprotein t0078 fixC putative oxidoreductase t0080 yaaU putative metabolite transport protein t0082 hypothetical protein t0083 hypothetical protein t0083 - t0084 t0086 putative sulfatase t0087 hypothetical protein t0087 - t0088 t0089 kefC glutathione-regulated potassium-efflux system protein t0094 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase t0096 - t0097 t0097 djlA DnaJ-like membrane chaperone protein t0098 rluA 23S rRNA/tRNA pseudouridine synthase A t0099 hepA ATP-dependent helicase t0100 polB DNA polymerase II t0106 araA L-arabinose isomerase t0107 araB ribulokinase

1 Typhoid Supplemental Tables Libby, et al. t0108 araC transcriptional regulator t0110 thiQ thiamine transporter ATP-binding subunit t0112 tbpA thiamine transporter substrate binding subunit t0113 yabN transcriptional regulator SgrR t0114 leuD isopropylmalate isomerase small subunit t0115 leuC isopropylmalate isomerase large subunit t0119 - t0120 t0120 ilvI acetolactate synthase 3 catalytic subunit t0121 ilvH acetolactate synthase 3 regulatory subunit t0122 - t0123 t0123 mraZ cell division protein t0133 murC UDP-N-acetylmuramate--L-alanine ligase t0140 secA preprotein translocase subunit t0141 mutT nucleoside triphosphate pyrophosphohydrolase t0148 hofC type IV pilin biogenesis protein t0150 ppdD putative major pilin subunit t0154 putative glycosyl hydrolase t0156 aroP aromatic amino acid transporter t0163 yacH hypothetical protein bifunctional aconitate hydratase 2/2-methylisocitrate t0164 acnB dehydratase t0165 hypothetical protein t0171 speE spermidine synthase t0180 yadE hypothetical protein 2-amino-4-hydroxy-6-hydroxymethyldihyropteridine t0191 folK pyrophosphokinase t0192 pcnB poly(A) polymerase I t0192 - t0193 t0193 yadB glutamyl-Q tRNA(Asp) synthetase t0195 sfsA sugar fermentation stimulation protein A t0198 mrcB penicillin-binding protein 1b t0198 – t0199 t0199 fhuA t0202 fhuB iron-hydroxamate transporter permease subunit t0204 yadQ chloride channel protein t0209 dgt deoxyguanosinetriphosphate triphosphohydrolase t0210 htrA serine endoprotease t0212 yaeH hypothetical protein t0215 glnD PII uridylyl-transferase t0217 - t0218 t0219 pyrH uridylate kinase t0222 undecaprenyl pyrophosphate synthase t0225 yaeT outer membrane protein assembly factor t0229 lpxA UDP-N-acetylglucosamine acyltransferase t0232 dnaE DNA polymerase III subunit alpha t0235 t0242 yaeJ hypothetical protein t0246 yaeB hypothetical protein t0247 rcsF outer membrane lipoprotein t0247 - t0248

2 Typhoid Supplemental Tables Libby, et al. t0248 metQ DL-methionine transporter substrate-binding subunit t0252 16S ribosomal RNA t0254 23S ribosomal RNA t0263 ung uracil-DNA glycosylase t0265 yfiK neutral amino-acid efflux protein t0268 yfiC hypothetical protein t0269 nadB L-aspartate oxidase t0271 rseA anti-RNA polymerase sigma factor t0272 rseB periplasmic negative regulator of sigmaE t0274 lepA GTP-binding protein t0275 lepB type I signal peptidase I t0282 putative transcriptional regulator t0283 putative transmembrane transport protein t0284 2-dehydropantoate 2-reductase t0286 murQ N-acetylmuramic acid-6-phosphate etherase t0288 yfhB hypothetical protein t0289 - t0290 t0290 yfhD putative transglycosylase t0296 putative transmembrane transport protein t0297 cadA lysine decarboxylase t0297 - t0298 t0298 cadB lysine/cadaverine antiporter t0299 cadC transcriptional activator t0303 csiE stationary phase inducible protein t0303 - t0304 t0305 t0306 asrC anaerobic sulfite reductase subunit C t0308 asrA anaerobic sulfite reductase subunit A t0308 - t0309 t0309 hypothetical protein t0310 suhB inositol monophosphatase t0313 cysteine desulfurase t0323 sseA 3-mercaptopyruvate sulfurtransferase t0324 putative lipoprotein t0325 pbpC penicillin-binding protein 1C t0328 putative anaerobic reductase component t0329 putative polyferredoxin t0329 - t0330 t0331 - t0332 t0332 yfgA hypothetical protein t0337 engA GTP-binding protein t0338 - t0339 t0339 sivH t0342 ratB t0343 ratC hypothetical protein t0344 shdA t0346 guaB inositol-5-monophosphate dehydrogenase t0354 hypothetical protein t0356 ppk polyphosphate kinase t0357 purN phosphoribosylglycinamide formyltransferase

3 Typhoid Supplemental Tables Libby, et al. t0358 - t0359 t0363 - t0364 t0367 hypothetical protein t0369 gcvR glycine cleavage system transcriptional repressor t0371 nlpB lipoprotein t0379 narQ nitrate/nitrite sensor protein t0381 hypothetical protein t0381 - t0382 t0383 hypothetical protein t0385 tktB transketolase t0392 putative cobalamin adenosyltransferase t0394 eutN putative ethanolamine utilization protein t0395 eutE putative aldehyde dehydrogenase t0400 eutB ethanolamine ammonia-lyase heavy chain t0401 eutC ethanolamine ammonia-lyase small subunit t0405 hypothetical protein t0410 hypothetical protein t0412 hypothetical protein t0412 - t0413 t0413 yfeF short chain dehydrogenase t0416 cysW sulfate/thiosulfate transporter permease subunit t0421 ptsJ putative transcriptional regulator t0423 pdxK pyridoxal kinase t0434 yfeN hypothetical protein t0435 xapA purine nucleoside phosphorylase t0436 xapB xanthosine permease t0438 + t0439 t0439 tRNA-Val t0442 gltX glutamyl-tRNA synthetase t0447 yfeA hypothetical protein t0448 nupC nucleoside permease t0453 hypothetical protein t0456 - t0457 t0457 lipid A biosynthesis palmitoleoyl acyltransferase t0459 pgtP phosphoglycerate transporter protein t0459 - t0460 t0461 pgtB phosphoglycerate transport system sensor protein PgtB t0463 pgtE outer membrane protease t0463 - t0464 t0471 yfdC hypothetical protein t0471 - t0472 t0472 vacJ lipoprotein precursor t0476 fadJ multifunctional fatty acid oxidation complex subunit alpha t0478 hypothetical protein t0482 yfcA hypothetical protein t0487 hypothetical protein t0490 putative DNA-binding protein t0492 hypothetical protein t0494 pdxB erythronate-4-phosphate dehydrogenase t0497 dedA hypothetical protein

4 Typhoid Supplemental Tables Libby, et al. t0497 - t0498 t0498 accD acetyl-CoA carboxylase subunit beta t0499 folC bifunctional folylpolyglutamate synthase/ dihydrofolate synthase t0500 dedD hypothetical protein t0501 cvpA colicin V production protein t0502 purF amidophosphoribosyltransferase t0503 putative transcriptional regulator t0504 putative amino acid decarboxylase t0504 - t0505 t0505 putative amino acid transporter t0506 hypothetical protein t0506 - t0507 t0507 putative amino acid permease t0508 ubiX 3-octaprenyl-4-hydroxybenzoate carboxy-lyase t0509 argT lysine-arginine-ornithine-binding periplasmic protein precursor t0511 hisQ histidine transport system permease protein t0512 hisM histidine transport system permease t0517 phosphodiesterase t0519 putative transcriptional regulator t0520 putative sugar phosphotransferase component II A t0526 pta phosphate acetyltransferase t0524 putative transketolase C-terminal section t0531 putative sodium/sulphate transporter t0532 - t0533 t0537 nuoB NADH dehydrogenase subunit B t0538 nuoC bifunctional NADH:ubiquinone oxidoreductase subunit C/D t0540 nuoF NADH dehydrogenase I subunit F t0541 nuoG NADH dehydrogenase subunit G t0542 nuoH NADH dehydrogenase subunit H t0543 nuoI NADH dehydrogenase subunit I t0546 nuoL NADH dehydrogenase subunit L t0553 menF menaquinone-specific isochorismate synthase t0558 menE O-succinylbenzoic acid--CoA ligase t0567 ais Ais protein t0568 hypothetical protein t0569 hypothetical protein t0570 competence damage-inducible protein A t0570 - t0571 t0571 putative transcriptional regulator t0573 putative transport protein t0574 putative aldolase t0575 hypothetical protein t0578 glpC sn-glycerol-3-phosphate dehydrogenase subunit C t0580 glpA sn-glycerol-3-phosphate dehydrogenase subunit A t0582 glpQ glycerophosphodiester phosphodiesterase t0582 - t0583 t0583 putative transcriptional regulator t0583 - t0584 t0584 putative transmembrane transport protein t0590

5 Typhoid Supplemental Tables Libby, et al. t0591 putative MR-MLE-family protein t0591 - t0592 t0594 – t0595 phosphotransfer intermediate protein in two-component t0596 yojN regulatory system with RcsBC t0598 apbE thiamine biosynthesis lipoprotein ApbE multidrug transporter membrane component/ATP-binding t0601 yojI component t0605 napA nitrate reductase t0608 napB diheme cytochrome c550 t0609 napC cytochrome c-type protein t0609 + t0608 t0610 ccmA cytochrome c biogenesis protein t0618 – t0619 t0620 homolog of virulence protein MsgA t0621 t0621 - t0622 t0622 t0623 sspH secreted effector protein t0632 yejD 16S rRNA pseudouridylate synthase A t0636 yejF putative ABC transporter ATP-binding protein t0638 yejB putative binding-protein-dependent transporter t0639 yejA putative transport system periplasmic binding protein t0640 rtn hypothetical protein t0641 - t0642 t0642 hypothetical protein t0643 - t0644 t0647 hypothetical protein t0650 fruB bifunctional fructose-specific PTS IIA/HPr protein t0651 fruA fructose-specific PTS system IIBC component t0654 – t0655 t0656 cirA colicin I receptor t0657 t0658 putative hydrolase t0658 - t0659 t0659 sdaC putative L-serine dehydratase t0664 galS transcriptional regulator t0664 - t0665 t0665 mglB D-galactose-binding periplasmic protein precursor t0666 mglA t0667 mglC beta-methylgalactoside transporter inner membrane component t0668 yeiA hypothetical protein t0678 FAA-hydrolase-family protein t0680 salicylate hydroxylase t0681 - t0682 t0682 hypothetical protein t0685 yohD hypothetical protein t0688 dld D-lactate dehydrogenase t0689 bglX periplasmic beta-glucosidase precursor t0692 yehY putative permease transmembrane component

6 Typhoid Supplemental Tables Libby, et al. t0693 yehW putative permease transmembrane component t0696 yehU putative two-component system sensor kinase t0696 + t0697 t0697 yehT putative response-regulator t0699 putative lipoprotein t0699 - t0700 t0702 mrp putative ATPase t0702 - t0703 t0703 yehE hypothetical protein t0705 stcB putative fimbrial chaperone protein t0706 stcC t0710 thiD phosphomethylpyrimidine kinase t0712 putative sugar kinase t0714 putative nucleoside permease t0715 fbaB fructose-bisphosphate aldolase t0716 t0716 - t0717 t0717 hypothetical protein t0718 hypothetical protein t0719 hypothetical protein t0719 - t0720 t0720 putative protease t0737 hypothetical protein t0738 hypothetical protein t0739 hypothetical protein t0740 hypothetical protein t0743 yegB multidrug efflux system protein t0744 mdtC multidrug efflux system subunit MdtC t0745 mdtB multidrug efflux system subunit MdtB t0752 asmA putative assembly protein t0753 yegH hypothetical protein t0754 wza putative polysaccharide export protein t0756 wzc tyrosine kinase t0757 wcaA glycosyl transferase t0760 wcaD t0761 wcaE putative glycosyl transferase t0762 wcaF putative colanic acid biosynthesis acetyltransferase t0763 gmd GDP-mannose 4,6-dehydratase t0764 wcaH putative O-antigen biosynthesis protein t0769 wcaJ putative UDP-glucose lipid carrier transferase t0770 wzxC colanic acid exporter t0771 wcaK t0772 putative glycosyl transferase t0773 putative colanic acid biosynthesis protein t0773 - t0774 t0774 galF UTP--glucose-1-phosphate uridylyltransferase subunit t0775 rfbB dTDP-glucose 4,6 dehydratase t0777 rfbA TDP-glucose pyrophosphorylase t0778 + t0777 t0779 rfbI CDP-6-deoxy-delta-3,4-glucoseen reductase

7 Typhoid Supplemental Tables Libby, et al. t0781 rfbG CDP-glucose 4,6-dehydratase t0788 rfbN putative rhamnosyltransferase t0791 - t0792 t0792 gnd 6-phosphogluconate dehydrogenase t0793 ugd UDP-glucose 6-dehydrogenase t0796 hisF imidazole glycerol phosphate synthase subunit t0805 – t0806 t0808 sopA t0809 phsA thiosulfate reductase precursor t0811 phsC thiosulfate reductase cytochrome b subunit t0813 sbmC DNA gyrase inhibitor t0816 pduX hypothetical protein t0820 pduT putative propanediol utilization protein t0821 pduS putative ferredoxin t0828 pduK putative propanediol utilization protein t0830 pduH PduH protein t0831 pduG PduG protein t0834 pduC glycerol dehydratase large subunit t0836 pduA putative propanediol utilization protein t0836 - t0837 t0837 pduF propanediol diffusion facilitator t0838 pocR pdu/cob regulatory protein t0842 cbiD cobalt-precorrin-6A synthase t0845 cbiF precorrin-4 C11-methyltransferase t0855 cbiP cobyric acid synthase t0859 erfK hypothetical protein t0862 hypothetical protein t0863 - t0864 t0868 amn AMP nucleosidase t0882 - t0883 t0883 ompS outer membrane protein S1 t0884 hypothetical protein t0884 - t0885 t0885 yedJ hypothetical protein t0886 dcm DNA cytosine methylase t0888 yedA hypothetical protein t0888 - t0889 t0889 t0890 hypothetical protein t0890 - t0891 t0896 fliR flagellar biosynthesis protein t0897 fliQ flagellar biosynthesis protein t0905 fliI flagellum-specific ATP synthase t0907 fliG flagellar motor switch protein G t0910 hypothetical protein t0910 - t0911 t0911 yedF hypothetical protein t0914 amyA cytoplasmic alpha-amylase t0918 fliC flagellin t0919

8 Typhoid Supplemental Tables Libby, et al. t0921 fliZ protein FliZ t0925 yecC putative amino-acid ABC transporter ATP-binding protein t0926 sdiA transcriptional activator t0927 yecF hypothetical protein t0929 sirA response regulator t0930 uvrC excinuclease ABC subunit C t0931 pgsA phosphatidylglycerophosphate synthetase t0934 - t0935 t0937 hypothetical protein t0937 - t0938 t0939 hypothetical protein t0939 - t0940 t0940 yecA hypothetical protein t0943 ftnA ferritin t0947 - t0948 t0952 flhD transcriptional activator FlhD t0953 flhC transcriptional activator FlhC t0961 cheY chemotaxis regulatory protein CheY t0966 hypothetical protein t0969 hypothetical protein t0976 aspS aspartyl-tRNA synthetase t0977 ntpA dATP pyrophosphohydrolase t0980 yebB hypothetical protein t0982 ruvA Holliday junction DNA helicase motor protein t0984 znuB high-affinity zinc transporter membrane component t0986 znuA high-affinity zinc transporter periplasmic component t0989 pykA pyruvate kinase t0991 zwf glucose-6-phosphate 1-dehydrogenase t0992 edd phosphogluconate dehydratase keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate t0993 aldolase t0994 purT phosphoribosylglycinamide formyltransferase 2 t0996 yebF hypothetical protein t0998 opdB protease 2 t1000 hypothetical protein t1003 putative cation transporter t1016 - t1017 t1022 hypothetical protein t1024 hypothetical protein t1025 pphA serine/threonine protein phosphatase 1 t1036 kdgR transcriptional regulator t1037 hypothetical protein t1038 hypothetical protein t1038 - t1039 t1039 hypothetical protein t1045 hypothetical protein t1046 manZ mannose-specific PTS system protein IID t1047 manY phosphotransferase enzyme II, C component t1050 - t1051 t1051 sdaA L-serine deaminase 1

9 Typhoid Supplemental Tables Libby, et al. t1053 pabB para-aminobenzoate synthase component 1 t1056 putative ATP-dependent helicase t1057 hypothetical protein t1059 fadD long-chain fatty acid CoA ligase t1067 hypothetical protein t1069 hypothetical protein t1071 nhaB sodium/proton antiporter t1073 hypothetical protein t1073 - t1074 t1074 dadA D-amino acid dehydrogenase small subunit t1075 dadX alanine racemase t1081 treA t1082 gdhA glutamate dehydrogenase t1083 appB cytochrome oxidase subunit II t1088 hyaC hydrogenase 1 b-type cytochrome subunit t1090 - t1091 t1092 translation-associated GTPase t1093 pth peptidyl-tRNA hydrolase t1095 ychM putative sulfate transporter N5-glutamine S-adenosyl-L-methionine-dependent t1101 hemK methyltransferase t1104 - t1105 t1105 tnpA transposase for insertion sequence element IS200 t1114 envE putative lipoprotein t1119 pagC outer membrane invasion protein t1120 hypothetical protein t1120 - t1121 t1121 tRNA-Arg t1122 hypothetical protein t1125 hypothetical protein t1126 putative lipoprotein t1128 putative heat shock protein t1130 hypothetical protein t1131 putative cytochrome t1132 putative lipoprotein t1132 - t1133 t1138 hypothetical protein t1144 - t1145 t1145 hypothetical protein t1147 aroQ chorismate mutase t1149 hypothetical protein t1150 hypothetical protein t1151 hypothetical protein t1151 - t1152 t1153 - t1154 t1154 tnpA transposase for insertion sequence element IS200 t1155 hypothetical protein t1156 hypothetical protein t1159 + t1160 t1161 hypothetical protein

10 Typhoid Supplemental Tables Libby, et al. t1162 t1162 - t1163 t1163 hypothetical protein t1166 t1168 yeaD t1177 topB DNA topoisomerase III t1181 xthA exonuclease III t1181 - t1182 bifunctional succinylornithine transaminase/acetylornithine t1182 argD transaminase t1184 astD aldehyde dehyrogenase t1185 astB succinylarginine dihydrolase t1190 osmE transcriptional activator N,N'-diacetylchitobiose-specific PTS system transporter subunit t1192 celB IIC N,N'-diacetylchitobiose-specific PTS system transporter subunit t1193 celC IIA t1199 - t1200 t1200 putative sodium::dicarboxylate symporter t1203 hypothetical protein t1204 hypothetical protein t1205 hypothetical protein t1206 pfkB 6-phosphofructokinase 2 t1206 - t1207 t1207 putative outer membrane protein t1208 putative outer membrane protein t1210 t1211 hypothetical protein t1222 btuE putative glutathione peroxidase t1226 hypothetical protein t1227 hypothetical protein t1228 aroH phospho-2-dehydro-3-deoxyheptonate aldolase t1229 hypothetical protein t1233 FAD-binding protein t1235 - t1236 t1236 putative transporter t1240 sufD cysteine desulfurase activator complex subunit t1241 selenocysteine lyase t1243 ynhG t1250 - t1251 t1253 ttrB tetrathionate reductase subunit B t1254 ttrS hypothetical protein t1258 putative transcriptional regulator t1258 - t1259 t1263 ssaD putative SPI-2 pathogenicity island protein t1264 - t1265 t1270 sseE putative SPI-2 pathogenicity island effector protein t1271 sscB putative SPI-2 pathogenicity island protein t1272 sseF putative SPI-2 pathogenicity island effector protein t1273 sseG putative SPI-2 pathogenicity island effector protein

11 Typhoid Supplemental Tables Libby, et al. t1280 ssaL putative SPI-2 secretion system protein t1282 ssaV SPI-2 secretion system apparatus protein SsaV t1283 ssaN SPI-2 secretion system ATPase t1286 ssaQ SPI-2 secretion system protein t1290 ssaU SPI-2 secretion system apparatus protein SsaU t1290 - t1291 t1293 ydhE multidrug efflux protein t1295 cfa cyclopropane fatty acyl phospholipids synthase t1296 ydhC inner membrane transport protein t1297 ydhB putative transcriptional regulator t1303 gloA glyoxalase I t1304 nemA N-ethylmaleimide reductase t1307 putative oxidoreductase t1309 hypothetical protein t1313 - t1314 t1318 pdxY pyridoxamine kinase t1320 tppB putative tripeptide transporter permease t1320 - t1321 t1321 nth endonuclease III t1325 electron transport complex protein RnfC t1327 Na(+)-translocating NADH-quinone reductase subunit E t1330 putative oxidoreductase t1334 hypothetical protein t1338 tus DNA replication terminus site-binding protein t1339 rstB sensor protein t1340 hypothetical protein t1341 outer membrane protein t1345 putative amino acid permease t1398 hypothetical protein t1399 pntA NAD(P) transhydrogenase subunit alpha t1400 pntB pyridine nucleotide transhydrogenase t1401 - t1402 t1402 mdtJ multidrug efflux system protein t1404 putative secreted protein t1405 - t1406 t1409 putative regulatory protein t1415 - t1416 t1417 dmsC putative dimethyl sulfoxide reductase subunit t1418 dmsB putative dimethyl sulfoxide reductase subunit t1419 dmsA putative dimethyl sulfoxide reductase subunit t1421 t1426 rspA starvation sensing protein t1427 rspB starvation sensing protein t1428 putative membrane transport protein t1430 - t1431 t1432 3-hydroxy acid dehydrogenase t1432 - t1433 t1433 dcp dipeptidyl carboxypeptidase II t1435 - t1436 t1436 hypothetical protein

12 Typhoid Supplemental Tables Libby, et al. t1436 - t1437 t1437 ydeE putative MFS-type transporter t1441 marR transcriptional repressor t1445 putative aldehyde-dehydrogenase t1449 - t1450 t1452 hyaF hydrogenase-1 operon protein HyaF2 t1455 hyaD hydrogenase 1 maturation protease t1458 hyaA uptake hydrogenase small subunit t1459 putative secreted hydrolase t1462 membrane transport protein t1463 pqaA hypothetical protein t1464 putative multidrug efflux protein t1468 hypothetical protein t1469 t1470 putative aminotransferase t1470 - t1471 t1473 putative hydrolase t1481 sfcA malate dehydrogenase t1485 smvA methyl viologen resistance protein t1487 narU nitrite extrusion protein t1488 narZ respiratory nitrate reductase 2 alpha chain t1489 narY respiratory nitrate reductase 2 beta chain t1491 hypothetical protein t1492 - t1493 t1493 hypothetical protein t1496 ATP-binding protein t1497 TonB-dependent receptor t1498 putative transcriptional regulator t1498 - t1499 t1500 putative acetyltransferase t1501 hypothetical protein t1503 srfA putative virulence effector protein t1504 srfB putative virulence effector protein t1505 srfC putative virulence effector protein t1505 - t1506 t1506 gamma-aminobutyraldehyde dehydrogenase t1507 putative regulatory protein t1508 pcgL D-alanyl-D-alanine dipeptidase t1508 - t1509 t1509 hypothetical protein t1513 putative peptidase t1518 tehA potassium-tellurite ethidium and proflavin transporter t1519 putative transferase t1523 putative phosphotransferase enzyme t1526 ribulose-phosphate 3-epimerase t1527 putative regulatory protein t1529 putative glycolate oxidase t1530 hypothetical protein t1531 mdoD glucan biosynthesis protein D t1532 putative carboxylesterase

13 Typhoid Supplemental Tables Libby, et al. t1535 hypothetical protein t1536 putative periplasmic amino acid-binding protein t1538 ABC transporter ATP-binding subunit t1540 hypothetical protein t1543 hypothetical protein t1545 acpD azoreductase t1546 hypothetical protein t1551 hslJ heat-inducible protein t1559 dbpA t1559 - t1560 t1560 zntB zinc transporter t1562 hypothetical protein t1564 fnr fumarate/nitrate reduction transcriptional regulator t1565 uspE universal stress protein t1566 hypothetical protein t1570 hypothetical protein t1571 putative thiol peroxidase t1574 putative lipoprotein t1576 hypothetical protein t1577 putative lipoprotein t1580 putative oxidoreductase t1581 putative transcriptional regulator t1583 mppA periplasmic murein peptide-binding protein t1585 muconate lactonizing enzyme family protein t1589 hypothetical protein t1597 sapA peptide transport periplasmic protein SapA precursor t1597 + t1598 t1611 hypothetical protein t1611 - t1612 t1612 hypothetical protein t1612 - t1613 t1613 fabI enoyl-(acyl carrier protein) reductase t1615 rnb exoribonuclease II t1616 RNase II stability modulator t1616 - t1617 t1617 putative regulatory protein t1625 acnA aconitate hydratase t1625 - t1626 t1626 cysB transcriptional regulator t1630 short chain dehydrogenase t1632 23S rRNA pseudouridylate synthase B t1634 trpH hypothetical protein bifunctional indole-3-glycerol phosphate t1637 trpC synthase/phosphoribosylanthranilate isomerase t1638 trpB tryptophan synthase subunit beta t1642 hypothetical protein t1643 hypothetical protein t1644 ompW outer membrane protein W t1644 - t1645 t1645 hypothetical protein

14 Typhoid Supplemental Tables Libby, et al. t1654 oppF oligopeptide transport ATP-binding protein t1655 + t1656 t1657 oppB oligopeptide transporter permease t1660 adh bifunctional acetaldehyde-CoA/alcohol dehydrogenase t1664 regulator of RpoS t1671 narJ respiratory nitrate reductase 1 delta chain t1673 narG respiratory nitrate reductase 1 alpha chain t1675 narL transcriptional regulator t1677 hypothetical protein t1679 - t1680 t1680 chaA calcium/sodium:proton antiporter t1689 phoP transcriptional regulator t1693 pepT peptidase T t1695 potB spermidine/putrescine ABC transporter membrane protein t1696 sifA secreted effector protein t1704 mfd transcription-repair coupling factor t1705 hypothetical protein t1706 putative secreted protein t1711 beta-hexosaminidase t1712 thiK thiamine kinase t1716 fhuE t1717 ptsG glucose-specific PTS system IIBC components t1718 putative metallodependent hydrolase t1719 holB DNA polymerase III subunit delta' t1720 tdk thymidylate kinase t1720 + t1721 t1721 hypothetical protein t1722 pabC 4-amino-4-deoxychorismate lyase t1731 maf Maf-like protein t1734 rne ribonuclease E t1735 tnpA transposase for insertion sequence element IS200 t1736 flgL flagellar hook-associated protein t1737 flgK flagellar hook-associated protein t1750 mviN virulence factor t1751 mviM putative virulence factor t1753 rimJ ribosomal-protein-S5-alanine N-acetyltransferase t1754 multidrug resistance protein t1755 grxB glutaredoxin 2 t1764 hypothetical protein t1768 hypothetical protein t1769 mdoH glucosyltransferase t1771 mdoC glucans biosynthesis protein t1774 hypothetical protein t1775 putative autoagglutination protein t1776 csgA cryptic curlin major subunit t1777 csgB curlin minor subunit t1781 csgG assembly/transport component in curli production t1782 hypothetical protein putative 2-hydroxyacid dehydrogenase in phoH-csgG intergenic t1785 region

15 Typhoid Supplemental Tables Libby, et al. t1786 - t1787 t1788 putative sialic acid transporter t1790 - t1791 t1791 N-acetylmannosamine-6-phosphate 2-epimerase t1792 putative membrane transporter t1792 - t1793 t1793 putative membrane transporter t1794 putative transcriptional regulator t1795 - t1796 t1796 putP sodium/proline symporter trifunctional transcriptional regulator/proline t1797 putA dehydrogenase/pyrroline-5-carboxylate dehydrogenase t1803 agp glucose-1-phosphatase/inositol phosphatase t1804 scsD secreted copper-sensitivity suppressor D t1805 scsC secreted copper-sensitivity suppressor C t1806 scsB membrane protein, suppressor for copper-sensitivity B precursor t1807 scsA membrane protein, suppressor for copper-sensitivity A t1808 cbpA curved DNA-binding protein t1810 hypothetical protein 4-hydroxyphenylacetate 3-monooxygenase operon regulatory t1811 hpaA protein t1817 hpcC t1818 hpaG 2-hydroxyhepta-2,4-diene-1,7-dioate decarboxylase t1820 hpaB 4-hydroxyphenylacetate 3-monooxygenase t1821 hpaC 4-hydroxyphenylacetate 3-monooxygenase coupling protein t1822 hypothetical protein t1824 copS histidine kinase t1825 pipD putative secreted peptidase t1827 - t1828 t1828 sigD cell invasion protein t1829 sigE cell invasion protein t1836 putative acylphosphatase t1835 + t1836 t1838 t1848 hypothetical protein t1850 ompA outer membrane protein A t1852 hypothetical protein t1856 pqiB paraquat-inducible protein B t1857 pqiA putative inner membrane protein t1858 ABC transporter ATPase component t1859 23S rRNA m(2)G2445 methyltransferase t1861 hypothetical protein t1863 pepN aminopeptidase N t1863 - t1864 t1902 putative lipoprotein t1903 - t1904 t1904 putative prophage antitermination protein t1905 hypothetical protein t1906 putative bacteriophage protein t1917 putative replication protein

16 Typhoid Supplemental Tables Libby, et al. t1918 hypothetical protein t1918 - t1919 t1931 putative ion:amino acid symporter t1932 t1932 - t1933 t1935 ompF outer membrane protein F precursor t1939 ycbB hypothetical protein t1939 - t1940 t1949 lpxK tetraacyldisacharide 4’-kinase t1950 msbA lipid transporter ATP-binding/permease protein t1951 ycaI hypothetical protein t1953 rpsA 30S ribosomal protein S1 t1954 cmk cytidylate kinase t1957 serC phosphoserine aminotransferase t1958 hypothetical protein t1960 focA formate transporter t1961 pflB formate acetyltransferase 1 t1964 pflA pyruvate formate lyase-activating enzyme 1 t1964 - t1965 t1965 ycaM transport protein t1966 ycaD MFS family transporter t1968 dmsC anaerobic dimethyl sulfoxide reductase chain C t1969 dmsB anaerobic dimethyl sulfoxide reductase chain B t1970 dmsA anaerobic dimethyl sulfoxide reductase chain A precursor t1971 serS seryl-tRNA synthetase t1981 acT transcriptional activator t1982 putative pirin-related protein t1984 tRNA-Ser t1988 clpA ATP-dependent Clp protease ATP-binding subunit t1989 clpS ATP-dependent Clp protease adaptor protein t1991 ybjZ macrolide transporter ATP-binding /permease protein t1992 ybjY macrolide transporter subunit MacA t1995 hypothetical protein t1997 hcr HCP oxidoreductase, NADH-dependent t1998 poxB pyruvate dehydrogenase t1999 ybjU L-threonine aldolase t2010 sulfatase t2011 putative phosphotransferase enzyme II, B component t2011 + t2012 t2012 ulaA ascorbate-specific PTS system enzyme IIC t2014 rumB 23S rRNA methyluridine methyltransferase t2015 hypothetical protein t2016 potI putrescine ABC transporter membrane protein t2018 potG putrescine transporter ATP-binding subunit t2019 - t2020 t2020 hypothetical protein t2023 ybjC hypothetical protein t2026 hypothetical protein t2027 TetR family transcriptional regulator t2028 hypothetical protein

17 Typhoid Supplemental Tables Libby, et al. t2030 mdfA multidrug translocase t2030 - t2031 t2031 ybjG undecaprenyl pyrophosphate phosphatase t2032 deoR transcriptional repressor t2038 yliD ABC transporter permease t2039 yliC ABC transporter permease t2040 yliB putative ABC transporter periplasmic binding protein t2041 glutathione transporter ATP-binding protein t2042 ybiK L-asparaginase t2045 ybiY putative pyruvate formate-lyase 3 activating enzyme t2046 ybiW putative formate acetyltransferase 3 t2048 hypothetical protein t2049 ybiT ABC transporter ATP-binding protein t2051 ybiR hypothetical protein t2052 mntR manganese transport regulator t2053 ybiP hypothetical protein t2056 ybiF threonine and homoserine efflux system t2059 glnP glutamine ABC transporter permease protein t2061 hypothetical protein t2067 t2068 rhlE ATP-dependent RNA helicase t2069 ybiH putative transcriptional regulator t2071 ybhF ABC transporter ATP-binding protein t2074 hypothetical protein t2076 ybhO cardiolipin synthase 2 t2077 ybhN hypothetical protein t2085 moaA molybdenum cofactor biosynthesis protein A t2087 slrP t2088 hypothetical protein t2089 uvrB excinuclease ABC subunit B t2089 - t2090 t2090 bioD dithiobiotin synthetase t2094 - t2095 t2095 ybhB putative kinase inhibitor protein t2096 hutH histidine ammonia-lyase t2097 hutU urocanate hydratase t2100 hutI imidazolonepropionase t2101 ybhC putative pectinesterase t2105 modB molybdate ABC transporter permease protein t2106 - t2107 t2107 ybhT hypothetical protein t2109 modF putative molybdenum transport ATP-binding protein t2110 hypothetical protein t2111 galE UDP-galactose-4-epimerase t2118 aroG phospho-2-dehydro-3-deoxyheptonate aldolase t2120 ybgR zinc transporter ZitB t2121 pnuC nicontinamide riboside transporter t2127 pal peptidoglycan-associated outer membrane lipoprotein t2128 tolB translocation protein TolB t2131 tolQ colicin uptake protein TolQ

18 Typhoid Supplemental Tables Libby, et al. t2132 ybgC acyl-CoA thioester hydrolase YbgC t2136 - t2137 t2138 sucC succinyl-CoA synthetase subunit beta t2139 sucB dihydrolipoamide acetyltransferase t2140 kgd alpha-ketoglutarate decarboxylase t2142 sdhA succinate dehydrogenase flavoprotein subunit t2144 - t2145 t2146 gltA type II citrate synthase t2146 - t2147 putative polysaccharide export ABC transporter ATP-binding t2153 protein t2157 - t2158 t2160 DNA recombinase t2161 hypothetical protein t2161 - t2162 t2165 putative hydrolase-oxidase t2168 ybfA hypothetical protein t2169 kdpA potassium-transporting ATPase subunit A t2170 kdpB potassium-transporting ATPase B chain t2172 kdpE transcriptional activator t2174 speF t2175 potE putrescine transporter t2175 - t2176 t2176 5-nitroimidazole antibiotic resistance t2177 pgm phosphoglucomutase t2186 citA citrate-proton symporter t2192 nagA N-acetylglucosamine-6-phosphate deacetylase t2195 asnB asparagine synthetase B t2202 ubiF 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase t2206 hemolysin-related protein t2212 rihA ribonucleoside hydrolase 1 t2215 putative sigma-54 dependent transcriptional regulator t2216 2-keto-3-deoxygluconate permease t2220 rlpB LPS-assembly lipoprotein t2220 + t2221 t2227 pbpA penicillin-binding protein 2 t2228 mrdB cell wall shape-determining protein t2229 rlpA rare lipoprotein A t2230 dacA D-alanyl-D-alanine carboxypeptidase fraction A t2231 - t2232 t2235 tatE twin arginine translocase protein E t2238 cspE cold shock protein t2239 pagP palmitoyl transferase for Lipid A t2239 - t2240 t2240 dcuC C4-dicarboxylate transporter t2241 dpiA response regulator t2241 + t2242 t2242 dpiB sensor kinase t2251 rnk nucleoside diphosphate kinase regulator t2252 ybdR zinc-dependant alcohol dehydrogenase

19 Typhoid Supplemental Tables Libby, et al. t2253 ybdQ hypothetical protein molybdopterin-containing oxidoreductase membrane anchor t2254 subunit t2259 ahpF alkyl hydroperoxide reductase F52A protein subunit F t2261 dsbG disulfide isomerase/thiol-disulfide oxidase t2264 hypothetical protein t2265 putative aminotransferase t2266 ybdH hypothetical protein t2268 cstA carbon starvation protein A t2273 entC isochorismate synthase t2275 entS enterobactin exporter t2279 fepE t2283 fepA outer membrane receptor phosphopantetheinyltransferase component of enterobactin t2284 entD synthase multienzyme complex t2285 carboxylate-amine ligase t2287 - t2288 t2289 ybdF hypothetical protein t2292 ybdG hypothetical protein t2293 - t2294 t2296 ykgB hypothetical protein t2297 hypothetical protein t2300 cusS t2303 gtrA bactoprenol-linked glucose translocase t2304 hypothetical protein t2304 - t2306 t2305 gtrB bactoprenol glucosyltransferase t2306 t2306 + t2307 t2308 t2311 fimW fimbriae w protein t2312 hypothetical protein t2312 + t2313 t2313 fimY fimbriae Y protein t2316 fimH FimH protein precursor t2318 fimC fimbrial chaperone protein t2319 fimI hypothetical protein t2320 fimA Type-1 fimbrial protein, a chain precursor t2323 ybcI hypothetical protein t2328 purK phosphoribosylaminoimidazole carboxylase ATPase subunit t2330 hypothetical protein t2332 fdrA membrane protein t2332 - t2333 t2334 allC allantoate amidohydrolase t2335 hypothetical protein t2336 glxK glycerate kinase II t2338 allB allantoinase t2339 - t2340 t2340 metabolite transport protein t2342 hyi hydroxypyruvate isomerase

20 Typhoid Supplemental Tables Libby, et al. t2343 gcl glyoxylate carboligase t2344 allR transcriptional repressor t2355 ybbO short chain dehydrogenase t2357 hypothetical protein t2362 ybaR copper exporting ATPase t2362 - t2363 t2366 ushA t2373 htpG heat shock protein 90 t2382 kefA potassium efflux protein t2382 - t2383 t2383 acrR DNA-binding transcriptional repressor t2384 acrA acriflavin resistance protein A precursor t2385 acrB acriflavin resistance protein B t2388 maA maltose O-acetyltransferase t2390 rpmJ 50S ribosomal protein L36 t2392 ylaB hypothetical protein t2393 ybaZ putative methylated DNA methyltransferase t2396 amtB ammonium transporter t2397 glnK nitrogen regulatory protein P-II 2 t2396 + t2397 t2409 hupB transcriptional regulator HU subunit beta t2414 - t2415 t2416 ampG muropeptide transporter t2416 - t2417 t2417 cyoA cytochrome o ubiquinol oxidase subunit II t2418 cyoB cytochrome o ubiquinol oxidase subunit I t2420 cyoD cytochrome o ubiquinol oxidase subunit IV t2425 hypothetical protein t2427 major facilitator transporter t2431 phnX phosphonoacetaldehyde hydrolase t2433 - t2434 t2436 phnU membrane component of 2-aminoethylphosphonate transporter t2438 thiI thiamine biosynthesis protein ThiI t2439 xseB exodeoxyribonuclease VII small subunit t2440 ispA geranyltranstransferase t2441 dxs 1-deoxy-D-xylulose-5-phosphate synthase t2444 thiamine monophosphate kinase t2450 tsx nucleoside-specific channel-forming protein tsx precursor t2452 yajD hypothetical protein t2453 DeoR family transcriptional regulator t2455 secF preprotein translocase subunit t2456 secD preprotein translocase subunit t2458 tgt queuine tRNA-ribosyltransferase t2462 malZ maltodextrin glucosidase t2463 proY putative proline-specific permease t2465 brnQ branched chain amino acid transport system II carrier protein t2467 phoB transcriptional regulator t2468 sbcD exonuclease subunit t2470 araJ t2473 yaiE hypothetical protein

21 Typhoid Supplemental Tables Libby, et al. t2474 aroM t2474 - t2475 t2476 aroL shikimate kinase II t2478 proC pyrroline-5-carboxylate reductase t2479 adrA diguanylate cyclase t2480 - t2481 t2481 yaiB hypothetical protein t2481 - t2482 t2482 efflux pump t2486 hypothetical protein t2489 ampH beta-lactamase/D-alanine carboxypeptidase t2490 putative transcriptional regulator t2491 - t2492 t2492 hemB delta-aminolevulinic acid dehydratase t2493 prpE propionyl-CoA synthetase t2494 prpD 2-methylcitrate dehydratase t2497 prpR propionate catabolism operon regulatory protein t2498 hypothetical protein t2499 RhtC-like transporter t2500 foxA ferrioxamine B receptor precursor t2503 terminal oxidase subunit II t2504 terminal oxidase subunit I t2506 res t2507 mod Type III restriction-modification system StyLTI enzyme mod t2508 putative metabolite transport protein t2510 hypothetical protein t2511 t2512 lipoprotein t2514 transcriptionl regulator t2516 hypothetical protein t2517 transmembrane regulator t2518 putative rtn protein t2521 stbA fimbrial protein t2522 stbB fimbrial chaperone protein t2525 stbE fimbrial chaperone protein t2527 tRNA-Thr t2529 proB gamma-glutamyl kinase t2532 frsA fermentation/respiration switch protein t2534 pepD aminoacyl-histidine dipeptidase precursor t2536 - t2537 t2537 dinP DNA polymerase IV t2537 - t2538 t2540 gmhA phosphoheptose isomerase t2541 fadE acyl-CoA dehydrogenase t2542 - t2543 t2543 hypothetical protein t2555 - t2556 t2557 safD putative fimbrial structural subunit t2558 safC outer-membrane fimbrial usher protein t2559 safB periplasmic fimbrial chaperone protein

22 Typhoid Supplemental Tables Libby, et al. t2569 Rhs-family protein t2570 hypothetical protein t2571 Rhs-family protein t2574 hypothetical protein t2573 + t2574 t2577 sciT SPI-6, hypothetical protein t2578 t2581 hypothetical protein t2587 t2591 ClpB-like protein t2593 hypothetical protein t2594 sciE SPI-6, hypothetical protein t2596 + t2597 t2597 sciC SPI-6, hypothetical protein t2600 tRNA-Asp t2605 mltD membrane-bound lytic murein transglycosylase D t2610 dkgB 2,5-diketo-D-gluconate reductase B t2610 - t2611 t2611 tRNA-Asp t2612 23S ribosomal RNA t2615 16S ribosomal RNA t2615 - t2616 t2616 clpB protein disaggregation chaperone t2618 rluD 23S rRNA pseudouridine synthase D t2621 - t2622 t2627 yfiN hypothetical protein t2630 rimM 16S rRNA-processing protein t2634 corB hypothetical protein t2634 - t2635 t2635 hypothetical protein t2642 smpB SsrA-binding protein t2642 - t2643 t2643 large repetitive protein t2644 putative type I secretion protein t2645 putative type I ATP-binding secretion protein t2667 - t2668 t2668 iroB putative glycosyl transferase t2669 iroC putative ABC transporter protein t2670 iroD putative ferric enterochelin esterase t2671 iroE hypothetical protein t2672 iroN outer membrane receptor FepA t2673 hypothetical protein t2673 - t2674 t2674 hypothetical protein t2674 - t2675 t2676 mig-14 putative transcriptional regulator t2676 - t2677 t2677 t2682 hypothetical protein t2685 ygaF hypothetical protein

23 Typhoid Supplemental Tables Libby, et al. t2688 gabP t2689 ygaE transcriptional regulator CsiR t2690 ygaU t2694 hypothetical protein t2695 stpA DNA binding protein, nucleoid-associated t2697 ygaC hypothetical protein t2704 nrdE ribonucleotide-diphosphate reductase subunit alpha t2705 nrdF ribonucleotide-diphosphate reductase subunit beta t2706 proV t2706 + t2707 t2709 - t2710 t2710 emrR transcriptional repressor t2712 emrB multidrug resistance protein B t2713 putative glycoporin t2713 - t2714 t2715 gshA glutamate--cysteine ligase t2716 hypothetical protein t2729 recX recombination regulator t2736 srlD sorbitol-6-phosphate dehydrogenase t2740 gutQ D-arabinose 5-phosphate isomerase t2741 ygaA anaerobic nitric oxide reductase transcription regulator t2742 norV anaerobic nitric oxide reductase flavorubredoxin t2751 hycE formate hydrogenlyase subunit 5 t2753 hycC formate hydrogenlyase subunit 3 t2755 - t2756 t2760 hypE hydrogenase isoenzyme formation protein t2761 fhlA transcriptional activator of the formate hydrogenlyase system t2762 ygbA hypothetical protein t2769 sprA AraC family transcription regulator t2771 orgA oxygen-regulated invasion protein t2774 prgJ pathogenicity 1 island effector protein t2775 prgI pathogenicity 1 island effector protein t2776 - t2777 t2777 AraC family transcription regulator t2778 iagA invasion protein regulator t2779 iagB cell invasion protein t2780 stpA tyrosine phosphatase t2783 sipF acyl carrier protein t2784 sipA SPI-1 pathogenicity island effector protein t2785 sipD SPI-1 pathogenicity island effector protein t2786 sipC SPI-1 pathogenicity island effector protein t2787 sipB SPI-1 pathogenicity island effector protein t2788 spaT hypothetical protein t2788 - t2789 t2789 spaS surface presentation of antigens protein t2790 spaR virulence-associated secretory protein t2792 spaP surface antigen presentation protein SpaP t2796 spaI ATP synthase SpaL t2797 spak virulence-associated secretory protein t2800 invG SPI-1 virulence-associated secretory protein

24 Typhoid Supplemental Tables Libby, et al. t2800 + t2801 t2801 invF AraC family transcription regulator t2802 - t2803 t2807 serine/threonine-specific protein phosphatase 2 t2807 - t2808 t2810 mutS DNA mismatch repair protein t2813 LysR family transcriptional regulator t2814 permease t2815 hypothetical protein t2817 putative aldolase t2822 decarboxylase t2825 rpoS RNA polymerase sigma factor RpoS t2826 nlpD lipoprotein NlpD t2827 pcm protein-L-isoaspartate O-methyltransferase t2828 surE stationary phase survival protein SurE t2835 cysN sulfate adenylyltransferase subunit 1 t2836 cysD sulfate adenylyltransferase subunit 2 t2836 - t2837 t2837 iap alkaline phosphatase isozyme conversion aminopeptidase t2846 sopD hypothetical protein t2847 cysH phosphoadenosine phosphosulfate reductase t2848 cysI sulfite reductase subunit beta t2850 putative 6-pyruvoyl tetrahydrobiopterin synthase t2851 - t2852 t2852 hypothetical protein t2854 - t2855 t2855 mazG nucleoside triphosphate pyrophosphohydrolase t2856 steA t2868 - t2869 t2871 ygcZ glucarate transporter t2874 yqcC hypothetical protein t2875 syd SecY interacting protein t2876 queF 7-cyano-7-deazaguanine reductase t2878 sdaC putative serine transporter t2879 sdaB L-serine dehydratase 2 t2881 fucO L-1,2-propanediol oxidoreductase t2882 fucA L-fuculose phosphate aldolase t2885 fucK L-fuculokinase t2888 ygdE putative RNA 2'-O-ribose methyltransferase t2889 ygdD hypothetical protein t2891 lipoprotein t2892 cysteine sulfinate desulfinase t2893 hypothetical protein t2899 N-acetylmuramoyl-L-alanine amidase t2903 ptr protease III precursor t2904 recC exonuclease V subunit gamma t2907 ppdB hypothetical protein t2908 ppdA hypothetical protein t2910 thyA thymidylate synthase t2911 lgt prolipoprotein diacylglyceryl transferase

25 Typhoid Supplemental Tables Libby, et al.

fused phosphoenolpyruvate-protein phosphotransferase t2912 ptsP PtsP/GAF domain-containing protein t2915 - t2916 t2917 putative aldo-keto reductase bifunctional acyl-[acyl carrier protein] synthetase/2- t2919 aas acylglycerophosphoethanolamine acyltransferase t2921 galR DNA-binding transcriptional regulator t2922 regulatory protein t2923 lysA diaminopimelate decarboxylase t2925 ygeA putative racemase t2925 - t2926 t2928 kduI 5-keto-4-deoxyuronate isomerase t2929 yqeF acetyl-CoA acetyltransferase t2931 hypothetical protein t2932 amino acid ABC transporter t2933 hypothetical protein t2934 t2935 hypothetical protein t2936 hypothetical protein t2937 hypothetical protein t2937 + t2938 t2939 stdB outer membrane fimbrial usher protein t2940 stdA fimbrial protein t2942 - t2943 t2945 endonuclease fragment t2946 hypothetical protein t2946 - t2947 t2955 tRNA-Gly t2956 lipoprotein t2958 lysS lysyl-tRNA synthetase t2969 bglA 6-phospho-beta-glucosidase t2970 hypothetical protein t2971 gcvP glycine dehydrogenase t2982 iciA chromosome replication initiation inhibitor protein t2985 mechanosensitive channel MscS t2985 - t2986 t2986 tnpA transposase for insertion sequence element IS200 t2987 fba fructose-bisphosphate aldolase t2989 epd erythrose 4-phosphate dehydrogenase t2996 tktA transketolase t2999 speA arginine decarboxylase t3002 metK S-adenosylmethionine synthetase t3003 galP galactose-proton symport t3004 hypothetical protein t3005 endA endonuclease I t3011 pilT Type II secretion, ATP-binding, protein t3020 hypothetical protein t3021 hypothetical protein t3022 trmB tRNA (guanine-N(7))-methyltransferase t3023 mutY adenine DNA glycosylase

26 Typhoid Supplemental Tables Libby, et al. t3027 speC t3046 LysR family transcriptional regulator t3046 - t3047 t3048 amino acid ABC transporter t3049 hypothetical protein t3050 ordL putative oxidoreductase t3051 aldehyde dehydrogenase t3051 - t3052 t3052 - t3053 t3053 hypothetical protein t3053 + t3054 t3054 hydrolase t3054 - t3055 t3055 exuT hexuronate transporter t3055 - t3056 t3056 uxuA mannonate dehydratase t3058 uxaC glucuronate isomerase t3058 - t3059 t3061 putative glutathione S-transferase YghU t3068 hybC hydrogenase 2 large subunit t3073 t3073 - t3074 t3074 hypothetical protein t3076 - t3077 t3077 oxidoreductase t3081 metC cystathionine beta-lyase t3082 yghB DedA family integral membrane protein t3084 alcohol dehydrogenase t3086 membrane transporter t3095 parC DNA topoisomerase IV subunit A t3099 sensor protein QseC t3101 hypothetical protein t3106 nudF ADP-ribose pyrophosphatase t3109 hypothetical protein t3110 hypothetical protein t3112 assT putative arylsulfate sulfotransferase t3113 dsbA disulfide isomerase t3114 dsbB putative disulfide oxidoreductase t3116 hypothetical protein t3118 hypothetical protein bifunctional heptose 7-phosphate kinase/heptose 1-phosphate t3120 rfaE adenyltransferase t3123 putative signal transduction protein multifunctional tRNA nucleotidyl transferase/2'3'-cyclic t3124 cca phosphodiesterase/2'nucleotidase/phosphatase t3127 putative glycerol-3-phosphate acyltransferase PlsY t3128 - t3129 t3130 dnaG DNA primase t3132 mug G/U mismatch-specific DNA glycosylase t3134 hypothetical protein

27 Typhoid Supplemental Tables Libby, et al. t3136 cheM methyl-accepting chemotaxis protein II t3138 putrescine--2-oxoglutarate aminotransferase t3144 drug efflux protein t3144 - t3145 t3156 hypothetical protein t3158 hypothetical protein t3159 t3160 tdcG L-serine dehydratase t3161 tdcE formate acetyltransferase t3162 tdcD propionate/acetate kinase t3163 tdcC t3164 tdcB threonine dehydratase t3165 tdcA transcriptional activator t3167 glycerate kinase I t3169 - t3170 t3170 garD D-galactarate dehydratase t3174 carbohydrate kinase t3180 gatC galactitol-specific IIC component of PTS system t3196 hypothetical protein t3200 pnp polynucleotide phosphorylase/polyadenylase t3202 truB tRNA pseudouridine synthase B t3204 infB translation initiation factor IF-2 t3212 folP dihydropteroate synthase t3214 rrmJ 23s rRNA methyltransferase J t3218 obgE GTPase t3230 putative ABC transporter ATP-binding protein YrbF t3230 putative ABC transporter ATP-binding protein YrbF t3230 - t3231 t3232 D-arabinose 5-phosphate isomerase t3238 putative sigma(54) modulation protein t3238 - t3239 t3239 ptsN sugar-specific enzyme IIA component of PTS t3242 hypothetical protein t3245 arcB aerobic respiration control sensor protein ArcB t3246 hypothetical protein t3247 gltB glutamate synthase subunit alpha t3247 + t3248 t3248 gltD glutamate synthase subunit beta t3252 hypothetical protein t3255 nanT putative sialic acid transporter t3264 degQ serine endoprotease t3265 - t3266 t3268 oadG oxaloacetate decarboxylase subunit gamma t3268 - t3269 t3269 ttdB L(+)-tartrate dehydratase subunit beta t3271 membrane transporter t3273 GntR family transcriptional regulator t3278 - t3279 t3279 yhcP p-hydroxybenzoic acid efflux subunit AaeB t3284 hypothetical protein

28 Typhoid Supplemental Tables Libby, et al. t3286 maf Maf-like protein t3288 mreC cell wall structural complex MreBCD transmembrane component t3291 yhdH oxidoreductase t3291 - t3292 t3296 hypothetical protein t3297 panF sodium/panthothenate symporter t3298 prmA ribosomal protein L11 methyltransferase t3299 yhdG hypothetical protein t3302 hypothetical protein t3302 + t3303 t3304 acrF t3304 - t3305 t3305 yhdV lipoprotein t3312 trkH potassium transporter t3313 yigZ hypothetical protein t3315 fadB multifunctional fatty acid oxidation complex subunit alpha t3316 fadA 3-ketoacyl-CoA thiolase t3317 transferase t3319 yigC 3-octaprenyl-4-hydroxybenzoate decarboxylase t3325 ubiB putative ubiquinone biosynthesis protein t3330 ysgA putative hydrolase t3331 putative regulatory protein t3334 yigM hypothetical protein t3335 yigL putative sugar phosphatase t3339 recQ ATP-dependent DNA helicase t3340 pldA phospholipase A t3342 rarD chloramphenicol-sensitive protein t3344 yigF hypothetical protein t3345 corA magnesium/nickel/cobalt transporter t3346 uvrD DNA-dependent helicase II t3350 dapF diaminopimelate epimerase t3353 hypothetical protein t3355 hypothetical protein t3356 hypothetical protein t3357 hypothetical protein t3358 cyaA adenylate cyclase t3364 tRNA-Leu t3369 rffT putative entero common antigen polymerase t3370 4-alpha-L-fucosyltransferase t3378 lipopolysaccharide biosynthesis protein WzzE putative undecaprenyl-phosphate alpha-N- t3379 rfe acetylglucosaminyltransferase t3382 rhlB ATP-dependent RNA helicase t3390 ilvY transcriptional regulator t3391 hypothetical protein t3392 hypothetical protein t3393 ilvA threonine dehydratase t3394 ilvD dihydroxy-acid dehydratase t3395 ilvE branched-chain amino acid aminotransferase t3448 yifE hypothetical protein

29 Typhoid Supplemental Tables Libby, et al. t3450 tRNA-Trp bifunctional phosphoribosylaminoimidazolecarboxamide t3455 purH formyltransferase/IMP cyclohydrolase t3458 hydH sensor protein ZraS t3462 yjaG hypothetical protein t3463 nfi endonuclease V t3472 - t3473 t3474 rpoB DNA-directed RNA polymerase subunit beta t3480 secE preprotein translocase subunit t3481 tuf elongation factor Tu t3487 coaA pantothenate kinase t3490 23S ribosomal RNA t3494 murI glutamate racemase t3495 - t3496 t3498 yijC transcriptional repressor FabR t3499 udhA soluble pyridine nucleotide transhydrogenase t3503 argC N-acetyl-gamma-glutamyl-phosphate reductase t3504 argE acetylornithine deacetylase t3504 - t3505 t3506 yijP hypothetical protein t3510 katG catalase t3515 hypothetical protein t3516 hypothetical protein t3516 - t3517 t3518 metB cystathionine gamma-synthase t3518 - t3519 t3520 t3520 - t3521 t3524 cytR transcriptional regulator t3527 hslU ATP-dependent protease ATP-binding subunit t3528 menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase t3531 glpF glycerol uptake facilitator protein t3534 fpr ferredoxin-NADP reductase t3536 yiiQ hypothetical protein t3539 lsrG autoinducer-2 (AI-2) modifying protein t3540 yneB aldolase t3540 + t3541 t3541 putative ABC transport protein, solute-binding component t3542 ydeZ putative ABC transporter, membrane component t3544 putative ABC transporter ATP-binding protein t3552 aminoimidazole riboside kinase t3554 hypothetical protein t3555 - t3556 t3556 sbp sulfate transporter subunit t3560 cpxR transcriptional regulator t3561 cpxA two-component sensor protein t3569 rhaT rhamnose-proton symporter t3580 yiiG putative lipoprotein t3581 putative lipoprotein t3583 fdoG formate dehydrogenase-O major subunit

30 Typhoid Supplemental Tables Libby, et al. t3584 fdoH formate dehydrogenase-O beta subunit t3585 fdoI formate dehydrogenase-O subunit gamma t3586 fdhE formate dehydrogenase accessory protein t3595 yihX phosphatase t3595 - t3596 t3596 yihW DeoR family transcriptional regulator t3598 yihU putative oxidoreductase t3600 + t3601 t3602 yihQ alpha-glucosidase t3604 putative membrane permease t3605 ompL outer membrane porin L t3606 hypothetical protein t3610 t3610 + t3611 t3611 hypothetical protein t3612 hypothetical protein t3614 glnA glutamine synthetase t3621 polA DNA polymerase I t3622 yihG putative acyltransferase t3633 rbsR transcriptional repressor t3633 + t3634 t3634 - t3635 t3636 rbsC ribose ABC transporter permease t3637 rbsA D-ribose transporter ATP binding protein t3640 yieN regulatory ATPase RavA t3643 asnC transcriptional regulator t3652 atpA F0F1 ATP synthase subunit alpha t3654 atpD F0F1 ATP synthase subunit beta t3665 PTS system permease t3668 pstA phosphate transporter permease subunit t3671 6-phosphogluconate phosphatase t3676 yidY multidrug efflux system protein MdtL t3677 trmE tRNA modification GTPase t3679 rnpA ribonuclease P t3685 LysR family transcriptional regulator t3688 yidA sugar phosphatase t3692 torS hybrid sensory histidine kinase t3694 - t3695 t3696 torA trimethylamine-N-oxide reductase precursor t3699 ccmA cytochrome c biogenesis protein t3698 + t3699 t3700 ccmB heme exporter protein B2 t3701 ccmC heme exporter protein C2 t3702 ccmD heme exporter protein D2 t3703 ccmE cytochrome c-type biogenesis protein t3704 ccmF cytochrome c-type biogenesis protein F2 t3704 + t3705 t3705 dsbE thiol:disulfide interchange protein t3707 yidR putative ATP/GTP-binding protein t3707 + t3708

31 Typhoid Supplemental Tables Libby, et al. t3708 hypothetical protein t3711 yidE hypothetical protein t3714 yidF hypothetical protein t3715 dsdA D-serine dehydratase t3719 emrD multidrug resistance protein D t3722 ilvB acetolactate synthase catalytic subunit t3725 putative carbohydrate kinase t3726 permease t3730 uhpC regulatory protein t3733 GntR family transcriptional regulator t3734 hypothetical protein t3736 putative IIC component of PTS system t3737 putative carbohydrate kinase t3738 t3739 putative phosphocarrier protein of PTS system t3744 putative secreted protein t3745 t3748 + t3749 t3749 putative PTS system protein t3750 putative transferase t3753 yicL hypothetical protein t3753 - t3754 t3754 - t3755 t3755 mgtB magnesium transport ATPase, P-type 2 t3755 - t3756 t3756 cigR t3756 - t3757 t3759 fidL SPI-3 hypothetical protein t3760 misL t3764 putative DNA-binding protein t3766 - t3767 t3767 hypothetical protein t3769 yicJ putative transporter t3770 yicI alpha-xylosidase t3771 yicH hypothetical protein t3772 putative purine permease t3773 gltS glutamate permease bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis t3776 spoT pyrophosphate 3'-pyrophosphohydrolase t3782 putative regulatory protein t3784 rph ribonuclease PH bifunctional phosphopantothenoylcysteine t3788 dfp decarboxylase/phosphopantothenate synthase t3797 waaP lipopolysaccharide core biosynthesis protein t3802 waaJ lipopolysaccharide 1,2-glucosyltransferase t3804 waaZ LPS core biosynthesis t3805 waaK lipopolysaccharide 1,2-N-acetylglucosaminetransferase t3806 waaL hypothetical protein t3812 putative glycosyl transferase t3815 phosphoglyceromutase

32 Typhoid Supplemental Tables Libby, et al. t3818 secB preprotein translocase subunit t3820 cysE serine acetyltransferase t3821 t3822 putative racemase t3828 sapB putative autotransporter t3829 putative lipoprotein t3834 mtlA mannitol-specific enzyme II of phosphotransferase system t3836 selA selenocysteine synthase t3837 selB selenocysteinyl-tRNA-specific translation factor t3836 + t3837 t3838 putative sugar kinase t3839 aldB aldehyde dehydrogenase B t3845 lyxK putative L-xylulose kinase t3846 yiaO t3848 yiaM 2,3-diketo-L-gulonate TRAP transporter small permease protein t3850 yiaL hypothetical protein t3852 - t3853 t3855 malS periplasmic alpha-amylase precursor t3857 xylR xylose operon regulatory protein t3857 xylR xylose operon regulatory protein t3858 xylA xylose isomerase t3859 xylB xylulose kinase t3863 glyQ glycyl-tRNA synthetase subunit alpha t3865 t3865 - t3866 t3868 - t3869 t3869 hypothetical protein t3870 - t3871 t3871 putative transcriptional regulator t3871 - t3872 t3873 yiaE 2-hydroxyacid dehydrogenase t3874 yiaD putative outer membrane lipoprotein t3879 yhjW phosphoethanolamine transferase t3882 LacI family transcriptional regulator t3884 - t3885 t3885 dppA periplasmic dipeptide transport protein precursor t3886 dppB dipeptide transporter permease t3887 dppC dipeptide transporter t3888 dppD dipeptide transporter ATP-binding subunit t3890 yhjV putative amino acid permease t3892 t3893 yhjU hypothetical protein t3898 bcsA cellulose synthease catalytic subunit t3900 yhjM endo-1,4-D-glucanase t3901 yhjL t3903 - t3904 t3906 - t3907 t3907 hypothetical protein t3908 yhjE metabolite transport protein t3909 yhjD hypothetical protein

33 Typhoid Supplemental Tables Libby, et al. t3910 - t3911 t3912 phage-like lysozyme t3912 - t3913 t3916 putative phosphosugar-binding protein t3919 hypothetical protein t3923 putative methyltransferase t3924 yhiP inner membrane transporter t3925 - t3926 t3927 pitA putative low-affinity inorganic phosphate transporter t3935 HlyD family secretion protein t3937 t3938 nikR nickel responsive regulator t3941 hypothetical protein t3947 hypothetical protein t3950 yhhF 16S rRNA m(2)G966-methyltransferase t3951 ftsY cell division protein t3952 ftsE cell division protein t3958 livK leucine-specific binding protein t3964 ugpB glycerol-3-phosphate transporter periplasmic binding protein t3968 ugpQ cytoplasmic glycerophosphodiester phosphodiesterase t3969 hypothetical protein t3969 - t3970 t3970 ggt gamma-glutamyltranspeptidase periplasmic precursor t3971 puative phophotriesterase t3972 hypothetical protein t3973 hypothetical protein t3975 yhhY putative acetyltransferase t3976 putative dehydrogenase t3977 hypothetical protein t3978 gntR gluconate utilization operon repressor t3979 - t3981 t3982 glgB glycogen branching enzyme t3984 glgC glucose-1-phosphate adenyltransferase t3985 glgA glycogen synthase t3986 glgP glycogen phosphorylase t3991 malT transcriptional regulator t3992 malP maltodextrin phosphorylase t4000 feoB ferrous iron transport protein t4001 - t4002 t4002 putative transcription accessory protein t4006 pckA phosphoenolpyruvate carboxykinase t4007 yhgE hypothetical protein t4013 mrcA peptidoglycan synthetase t4015 yrfB hypothetical protein t4018 hofQ outer membrane porin t4027 bigA t4028 cysG siroheme synthase t4029 nirC nitrite transporter t4030 nirD nitrite reductase small subunit t4032 yhfC hypothetical protein

34 Typhoid Supplemental Tables Libby, et al. t4033 ppiA peptidyl-prolyl cis-trans isomerase A (rotamase A) t4033 - t4034 t4034 yhfG hypothetical protein t4035 fic cell filamentation protein Fic t4036 pabA para-aminobenzoate synthase component II t4038 yhfK t4039 crp cAMP-regulatory protein t4040 - t4041 t4043 yheT t4052 fkpA FKBP-type peptidyl-prolyl cis-trans isomerase t4058 rpsG 30S ribosomal protein S7 t4059 fusA elongation factor G t4079 fpsH 30S ribosomal protein S8 t4092 yhdN hypothetical protein t4093 zntR zinc-responsive transcriptional regulator t4095 trkA potassium transporter peripheral membrane component t4096 sun 16S rRNA methyltransferase B t4097 fmt methionyl-tRNA formyltransferase t4099 hypothetical protein t4099 + t4100 t4100 smg hypothetical protein bifunctional isocitrate dehydrogenase kinase/phosphatase t4113 aceK protein t4114 - t4115 t4116 yjbB hypothetical protein t4119 hypothetical protein t4120 yjbC 23S rRNA pseudouridine synthase F t4126 lysC aspartate kinase III t4127 pgi glucose-6-phosphate isomerase t4127 - t4128 t4128 hypothetical protein t4129 putative lipoprotein t4131 putative lipoprotein t4133 malG maltose transporter permease t4134 malF maltose transporter membrane protein t4135 malE maltose ABC transporter periplasmic protein t4135 - t4136 t4136 malK maltose/maltodextrin transporter ATP-binding protein t4137 lamB maltoporin t4138 malM maltose regulon periplasmic protein t4147 zur zinc uptake transcriptional repressor t4160 uvrA excinuclease ABC subunit A t4169 hypothetical protein t4170 yjcC hypothetical protein t4174 putative xanthine/uracil permeases family protein t4179 actP acetate permease t4180 - t4181 t4181 acs acetyl-CoA synthetase t4183 nrfA cytochrome c nitrite reductase t4184 nrfB cytochrome c-type protein

35 Typhoid Supplemental Tables Libby, et al. t4186 nrfD cytochrome c-type biogenesis protein t4192 fdhF formate dehydrogenase H t4192 - t4193 t4193 lpxO putative membrane-bound beta-hydroxylase t4195 phnB hypothetical protein t4195 - t4196 t4196 phnA hypothetical protein t4196 - t4197 t4197 proP proline/glycine betaine transporter t4198 pmrB sensor protein BasS/PmrB t4200 putative cell division protein t4201 arginine:agmatin antiporter t4202 adiY AraC family regulatory protein t4202 - t4203 t4203 adi arginine decarboxylase t4203 - t4204 t4204 melR transcriptional regulator t4204 - t4205 t4205 melA alpha-galactosidase t4208 dcuB anaerobic C4-dicarboxylate transporter t4208 - t4209 t4209 hypothetical protein t4211 dcuS sensory histidine kinase t4211 - t4212 t4212 dmsA t4214 dmsC putative dimethyl sulfoxide reductase subunit C t4372 - t4373 t4373 yjdC putative transcriptional regulator t4374 dipZ thiol:disulfide interchange protein precursor t4376 dcuA anaerobic C4-dicarboxylate transporter t4377 aspA aspartate ammonia-lyase t4384 - t4385 t4386 efp elongation factor P t4395 frdA fumarate reductase flavoprotein subunit t4397 yjeM putative amino acid permease t4399 yjeP hypothetical protein t4401 - t4402 t4403 artJ arginine-binding periplasmic protein t4407 yjeS putative 4Fe-4S binding protein t4408 yjeE putative ATPase t4410 mutL DNA mismatch repair protein t4412 hfq RNA-binding protein t4413 hflX putative GTPase t4415 hflC FtsH protease regulator t4417 purA adenylosuccinate synthetase t4419 rnr exoribonuclease R t4425 yjfL hypothetical protein t4428 aidB isovaleryl CoA dehydrogenase t4430 yjfO hypothetical protein t4431 yjfP esterase

36 Typhoid Supplemental Tables Libby, et al. t4436 sgaA L-ascorbate-specific enzyme IIA component of PTS t4437 ulaD 3-keto-L-gulonate-6-phosphate decarboxylase t4438 sgaU L-xylulose 5-phosphate 3-epimerase t4439 sgaE L-ribulose-5-phosphate 4-epimerase t4440 yjfY hypothetical protein t4446 hypothetical protein t4449 cycA D-alanine/D-serine/glycine permease t4455 ytfH hypothetical protein t4458 - t4459 t4459 ytfK hypothetical protein t4466 putative sugar transporter t4468 - t4469 t4469 fbp fructose-1,6-bisphosphatase t4470 mpl murein peptide ligase t4471 yigA hypothetical protein t4472 pmbA peptidase t4473 - t4474 t4474 hypothetical protein t4478 hypothetical protein t4482 + t4481 t4483 relB bifunctional antitoxin/transcriptional repressor t4485 nrdG anaerobic ribonucleotide reductase-activating protein t4491 mgtA magnesium-transporting ATPase t4500 carbamate kinase t4500 + t4501 t4501 arginine deiminase t4502 hypothetical protein t4503 ornithine carbamoyltransferase subunit I t4503 - t4504 t4504 hypothetical protein t4505 miaE tRNA hydroxylase t4507 hypothetical protein t4508 putative acetyltransferase t4508 - t4509 t4509 putative innner membrane protein t4511 holC DNA polymerase III subunit chi t4515 regulatory protein t4516 t4516 - t4517 t4539 GerE family regulatory protein t4540 t4541 putative outer membrane protein t4550 hypothetical protein t4551 - t4552 t4552 hypothetical protein t4554 hypothetical protein t4559 hypothetical protein t4565 hypothetical protein t4566 - t4567 t4567 hypothetical protein

37 Typhoid Supplemental Tables Libby, et al. t4568 putative sugar transport protein t4569 hypothetical protein t4574 hsdS specificity determinant for hsdM and hsdR t4575 hsdM t4577 mrr mrr restriction system protein t4580 yjiA putative GTP-binding protein t4584 mdoB phosphoglycerol transferase I t4589 hypothetical protein t4590 putative regulatory protein t4590 + t4591 t4592 hypothetical protein t4592 - t4593 t4593 ferric iron reductase involved in ferric hydroximate transport t4596 tRNA-Leu t4600 + t4601 t4606 hypothetical protein t4606 + t4607 t4607 yjjV putative deoxyribonuclease t4608 hypothetical protein t4610 deoC deoxyribose-phosphate aldolase t4611 deoA thymidine phosphorylase t4613 deoD purine nucleoside phosphorylase t4621 slt lytic murein transglycosylase t4625 rob right origin-binding protein t4627 creB response regulator t4628 creC sensory histidine kinase t4629 creD hypothetical protein t4631 sthD putative fimbrial subunit t4632 sthC t4633 sthB putative fimbrial chaperone protein t4634 sthA putative fimbrial protein t4635 putative transcriptional regulator protein t4635 - t4636 t4636 putative secreted protein t4637 arcA two-component response regulator t4644 csrB non-coding RNA t4646 rnpB non-coding RNA t4649 5S ribosomal RNA t4656 rrfF 5S ribosomal RNA

Insertions listed represent two independent transposon pools each containing approximately 1,500 insertions.