Supplementary table 1. Ty2 Annotated genes with at least one sequenced peptide mapped Ty2 Locus Tag Annotation t0005 conserved hypothetical protein t0047 riboflavin biosynthesis protein RibF t0053 putative nucleoside hydrolase (IUNH t0081 putative lipoprotein t0083 probable secreted protein t0088 putative NAD(P)H oxidoreductase t0099 probable ATP-dependent helicase HepA t0111 putative ABC transporter integral t0122 fructose repressor gene t0143 putative LysR-family transcriptional regulator t0144 conserved hypothetical protein t0157 pyruvate dehydrogenase complex repressor t0158 pyruvate dehydrogenase E1 component t0159 dihydrolipoamide acetyltransferase component (E2) t0160 dihydrolipoamide dehydrogenase gene t0169 putative transcriptional regulator t0173 possible multicopper oxidase precursor t0205 conserved hypothetical protein t0211 conserved hypothetical protein t0212 conserved hypothetical protein t0236 lysine decarboxylase gene t0237 conserved hypothetical protein t0241 conserved hypothetical protein t0248 putative lipoprotein precursor t0250 putative ABC transporter ATP-binding t0262 putative RNA methyltransferase t0264 conserved hypothetical protein t0279 putative pyridoxal phosphate biosynthetic t0285 putative transcriptional regulator t0286 putative phophosugar binding protein t0289 conserved hypothetical protein t0292 putative sensor kinase protein t0294 putative membrane protein t0304 putative exported protein t0311 putative RNA methyltransferase t0312 conserved hypothetical protein t0313 putative L-cysteine desulfurase t0315 conserved hypothetical protein t0318 ferredoxin gene fdx t0323 putative thiosulfate sulfurtransferase t0324 putative lipoprotein t0331 conserved hypothetical protein t0332 putative DNA-binding protein t0335 putative membrane protein t0336 putative lipoprotein t0337 putative GTP-binding protein t0338 conserved hypothetical protein t0363 putative exported protein t0364 putative membrane protein t0371 putative lipoprotein gene t0373 putative membrane protein t0377 conserved hypothetical protein t0383 putative exported protein t0384 hypothetical protein t0408 probable N-acetylmuramoyl-L-alanine amidase t0411 putative lipoprotein t0412 conserved hypothetical protein t0413 putative oxidoreductase gene t0425 hypothetical protein t0430 conserved hypothetical protein t0432 putative membrane protein t0455 putative aminotransferase t0474 conserved hypothetical protein t0475 putative 3-ketoacyl-CoA thiolase t0479 conserved hypothetical protein t0495 putative semialdehyde dehydrogenase t0515 putative glutathione-S transferase t0517 conserved hypothetical protein t0518 conserved hypothetical protein t0520 putative sugar phosphotransferase component t0529 conserved hypothetical protein t0530 putative phosphatase t0536 NADH dehydrogenase I chain t0537 NADH dehydrogenase I chain t0539 NADH dehydrogenase I chain t0540 NADH dehydrogenase I chain t0541 NADH dehydrogenase I chain t0542 NADH dehydrogenase I chain t0543 NADH dehydrogenase I chain t0549 putative receptor/regulator protein t0564 putative lipopolysaccharide modification protein t0566 putative lipopolysaccharide biosynthesis protein t0568 conserved hypothetical protein t0569 conserved hypothetical protein t0570 conserved hypothetical protein t0571 putative transcriptional regulator t0578 anaerobic glycerol-3-phosphate dehydrogenase subunit t0579 anaerobic glycerol-3-phosphate dehydrogenase subunit t0580 anaerobic glycerol-3-phosphate dehydrogenase subunit t0605 probable nitrate reductase t0618 nitrate/nitrite response regulator protein t0627 conserved hypothetical protein t0642 putative membrane protein t0643 conserved hypothetical protein t0649 1-phosphofructokinase gene fruK t0654 putative transcriptional regulator t0660 putative DNA-binding protein t0661 putative esterase gene t0688 D-lactate dehydrogenase gene t0690 putative periplasmic protein t0702 conserved hypothetical protein t0708 conserved hypothetical protein t0720 putative protease t0741 putative two-component system response t0742 putative two-component system sensor t0773 putative exported protein t0779 putative reductase RfbI t0782 putative dehydratase RfbH t0792 "6-phosphogluconate dehydrogenase, decarboxylating " t0804 conserved hypothetical protein t0815 conserved hypothetical protein t0923 putative deaminase t0927 conserved hypothetical protein t0944 putative lipoprotein t0969 conserved hypothetical protein t0971 conserved hypothetical protein t0972 conserved hypothetical protein t0974 conserved hypothetical protein t0975 putative hydrolase gene t0978 conserved hypothetical protein t0989 pyruvate kinase A t0991 glucose 6-phosphate dehydrogenase t0993 hypothetical protein colour t1002 putative cation resistance protein t1004 putative exported protein t1012 putative hydrolase gene t1031 conserved hypothetical protein t1055 conserved hypothetical protein t1057 conserved hypothetical protein t1058 putative lipoprotein t1064 conserved hypothetical protein t1065 putative hydrolase t1077 conserved hypothetical protein t1092 putative ATP/GTP-binding protein t1113 putative virulence protein t1114 putative lipoprotein gene t1123 putative secreted protein t1132 putative lipoprotein t1133 putative substrate-binding transport protein t1137 putative ABC transport ATP-binding t1141 conserved hypothetical protein t1161 conserved hypothetical protein t1165 putative outer membrane protein t1167 putative oxidoreductase t1169 glyceraldehyde 3-phosphate dehydrogenase A t1170 conserved hypothetical protein t1175 putative nitroreductase t1179 putative exported protein t1180 putative MutT-family protein t1187 putative exported protein t1196 conserved hypothetical protein t1202 putative hydrolase t1204 conserved hypothetical protein t1206 6-phosphofructokinase isozyme gene t1207 putative outer membrane protein t1208 putative outer membrane protein t1226 conserved hypothetical protein t1229 conserved hypothetical protein t1234 conserved hypothetical protein t1237 conserved hypothetical protein t1238 conserved hypothetical protein t1239 putative ABC transport ATP-binding t1240 conserved hypothetical protein t1241 putative amintransferase t1242 conserved hypothetical protein t1246 pyruvate kinase gene t1301 conserved hypothetical protein t1305 putative TetR-family transcriptional regulator t1307 putative oxidoreductase t1314 conserved hypothetical protein t1330 putative oxidoreductase t1334 conserved hypothetical protein t1337 fumarate hydratase class II t1343 putative two-component response regulator t1398 putative exported protein t1409 putative regulatory protein t1410 putative dethiobiotin synthetase t1411 putative voltage gated chloride t1418 putative dimethyl sulfoxide reductase t1419 putative dimethyl sulfoxide reductase t1420 putative dimethyl sulfoxide reductase t1424 putative secreted protein t1432 putative oxidoreductase t1449 putative exported protein t1461 putative alcohol dehydrogenase t1463 hypothetical protein gene t1482 alcohol dehydrogenase gene t1491 conserved hypothetical protein t1496 possible ATP-binding protein t1498 putative regulatory protein t1499 putative NADP-dependent oxidoreductase t1503 putative virulence effector protein t1504 putative virulence effector protein t1515 putative benzoate membrane transport t1516 putative lipoprotein t1529 putative glycolate oxidase t1531 putative exported protein t1536 putative periplasmic amino acid-binding t1543 conserved hypothetical protein t1550 D-lactate dehydrogenase gene t1555 conserved hypothetical protein t1558 conserved hypothetical protein t1565 conserved hypothetical protein t1570 hypothetical protein t1576 hypothetical protein t1580 putative oxidoreductase t1584 conserved hypothetical protein t1590 putative ATP-binding protein t1617 putative regulatory protein t1619 putative translation initiaiton factor t1622 conserved hypothetical protein t1625 aconitate hydratase 1 t1632 putative pseudouridine synthase t1633 conserved hypothetical protein t1634 conserved hypothetical protein t1641 conserved hypothetical protein t1642 conserved hypothetical protein t1644 putative outer membrane protein t1648 putative acyl-coA hydrolase t1650 conserved hypothetical protein t1673 respiratory nitrate reductase 1 t1676 nitrate/nitrite sensor protein NarX t1675 nitrate/nitrite response regulator protein t1678 conserved hypothetical protein t1682 isocitrate dehydrogenase gene t1685 putative MutT-family protein t1699 putative regulatory protein t1708 putative secreted protein t1709 NADH dehydrogenase gene t1710 conserved hypothetical protein t1711 putative glycosyl hydrolase t1713 putative lipoprotein t1715 putative protein kinase C t1718 conserved hypothetical protein t1721 putative secreted protein t1730 conserved hypothetical protein t1731 conserved hypothetical protein t1742 putative flagellar basal-body rod t1745 putative flagellar basal-body rod t1746 putative flagellar basal-body rod t1752 conserved hypothetical protein t1760 putative sarcosine oxidase t1763 putative exported protein t1764 conserved hypothetical protein t1773 conserved hypothetical protein t1783 conserved hypothetical protein t1784 conserved hypothetical protein t1785 putative 2-hydroxyacid dehydrogenase in t1789 putative secreted protein t1798 putative secreted protein t1799 putative transcriptional regulator t1810 hypothetical protein t1835 hypothetical protein in helD-serT t1836 putative acylphosphatase t1840 conserved hypothetical protein t1841 conserved hypothetical protein t1842 conserved hypothetical protein t1852 conserved hypothetical protein t1855 putative lipoprotein t1859 conserved hypothetical protein t1860 conserved hypothetical protein t1874 putative bacteriophage protein t1876 putative exported protein t1902 putative lipoprotein t1920 putative DNA-binding protein t1937 conserved hypothetical protein t1947 conserved hypothetical protein t1955 putative lipoprotein t1959 conserved hypothetical protein t1961 formate acetyltransferase 1 t1964 pyruvate formate-lyase 1 activating t1966 probable transport protein t1969 anaerobic dimethyl sulfoxide reductase t1970 anaerobic dimethyl sulfoxide reductase t1991 conserved hypothetical ABC transporter t1992 putative exported protein t1993 putative virK protein t1994 conserved hypothetical protein t2002 putative N-acetylmuramoyl-L-alanine amidase t2003 conserved hypothetical protein t2004 probable lipoprotein t2020 conserved hypothetical protein t2022 oxygen-insensitive NADPH nitroreductase t2029 conserved hypothetical protein t2037 conserved hypothetical protein t2040 putative ABC transporter periplasmic t2042 putative L-asparaginase gene t2047 conserved hypothetical protein t2050 putative exported protein t2068 putative ATP-dependent RNA helicase t2069 hypothetical tetR-family transcriptional regulator t2101 possible pectinesterase precursor t2102 conserved hypothetical protein t2103 conserved hypothetical protein t2108 putative molybdenum transport protein t2115 phosphoglycerate mutase 1 t2126 putative exported protein t2135 cytochrome d ubiquinol oxidase t2136 cytochrome d ubiquinol oxidase t2137 succinyl-CoA synthetase alpha chain t2138 succinyl-CoA synthetase beta chain t2140 2-oxoglutarate dehydrogenase E1 component t2141 succinate dehydrogenase iron-sulfur protein t2142 succinate dehydrogenase flavoprotein subunit t2143 succinate dehydrogenase hydrophobic membrane t2144 succinate dehydrogenase cytochrome b556 t2146 citrate synthase gene t2163 conserved hypothetical protein t2165 conserved hypothetical protein t2179 putative esterase/lipase YbfF t2180 conserved hypothetical protein t2181 flavodoxin 1 gene t2202 putative monooxygenase gene t2205 conserved hypothetical protein t2212 probable nucleoside hydrolase t2214 conserved hypothetical protein t2225 conserved hypothetical protein t2226 conserved hypothetical protein t2231 conserved hypothetical protein t2253 conserved hypothetical protein t2265 putative aminotransferase t2299 hypothetical araC-family transcriptional regulator t2347 hypothetical ATP-binding protein t2352 putative membrane protein t2359 putative membrane protein t2365 conserved hypothetical protein t2375 conserved hypothetical protein t2405 conserved hypothetical protein t2406 conserved hypothetical protein t2415 putative lipoprotein gene t2417 cytochrome o ubiquinol oxidase t2418 cytochrome o ubiquinol oxidase t2428 conserved hypothetical protein t2448 hypothetical protein gene t2449 putative lipoprotein gene t2452 conserved hypothetical protein t2457 putative membrane protein t2461 probable peroxidase colour t2471 hypothetical ROK-family protein t2473 conserved hypothetical protein t2477 conserved hypothetical protein t2481 conserved hypothetical protein t2544 possible outer membrane adhesin t2564 hypothetical protein colour t2603 conserved hypothetical protein t2604 probable hydroxyacylglutathione hydrolase t2606 putative methyltransferase gene t2607 conserved hypothetical protein t2610 hypothetical oxidoreductase gene t2617 conserved hypothetical protein t2619 putative lipoprotein t2620 putative sigma-54 modulation protein t2635 hypothetical protein t2637 conserved hypothetical protein t2665 probable major tail tube t2666 putative bacteriophage major tail t2692 putative transcriptional regulator t2700 conserved hypothetical protein t2710 putative transcriptional regulator t2716 putative membrane protein t2717 conserved hypothetical protein t2731 conserved hypothetical protein t2744 hydrogenase maturation protein t2745 electron transport protein t2751 formate hydrogenlyase subunit 5 t2760 hydrogenase isoenzymes formation protein t2804 hypothetical protein colour t2805 hypothetical protein colour t2829 conserved hypothetical protein t2850 putative 6-pyruvoyl tetrahydrobiopterin synthase t2852 conserved hypothetical protein t2853 enolase gene eno t2855 conserved hypothetical protein t2872 conserved hypothetical protein t2873 putative RNA pseudouridylate synthase t2876 conserved hypothetical protein t2877 conserved hypothetical protein t2878 putative serine transporter t2888 conserved hypothetical protein t2891 possible lipoprotein t2892 possible aminotransferase t2893 conserved hypothetical protein t2917 possible oxidoreductase t2925 conserved hypothetical protein t2933 conserved hypothetical protein t2938 probable fimbrial chaperone protein t2941 conserved hypothetical protein t2956 possible lipoprotein t2963 flavodoxin II gene t2965 conserved hypothetical protein t2966 conserved hypothetical protein t2974 possible monooxygenase t2977 conserved hypothetical protein t2978 conserved hypothetical protein t2983 conserved hypothetical protein t2987 "fructose 1,6-bisphosphate aldolase " t2988 phosphoglycerate kinase gene t2997 conserved hypothetical protein t3006 conserved hypothetical protein t3008 conserved hypothetical protein t3009 conserved hypothetical protein t3012 conserved hypothetical protein t3014 conserved hypothetical protein t3015 conserved hypothetical protein t3016 possible oxygen-independent coproporphyrinogen III t3020 conserved hypothetical protein t3021 conserved hypothetical protein t3022 conserved hypothetical protein t3024 conserved hypothetical protein t3052 conserved hypothetical protein t3059 hypothetical protein t3068 hydrogenase-2 large subunit t3083 probable AraC-family trancriptional regulatory t3084 probable alcohol dehydrogenase t3087 conserved hypothetical protein t3089 putative exported protein t3097 possible exported protein t3101 conserved hypothetical protein t3103 conserved hypothetical protein t3104 conserved hypothetical protein t3106 conserved hypothetical protein t3108 possible lipoprotein t3109 conserved hypothetical protein t3116 conserved hypothetical protein t3128 possible glycoprotease t3134 conserved hypothetical protein t3135 conserved hypothetical protein t3140 conserved hypothetical protein t3143 possible oxidoreductase t3149 conserved hypothetical protein t3153 conserved hypothetical protein t3155 possible LysR-family transcriptional regulator t3161 probable formate acetyltransferase t3183 conserved hypothetical protein t3184 possible exported protein t3187 possible lipoprotein t3199 conserved hypothetical protein t3206 conserved hypothetical protein t3215 conserved hypothetical protein t3218 probable GTP-binding protein t3225 conserved hypothetical protein t3226 possible anti-sigma factor antagonist t3227 possible exported protein t3230 "possible ABC-transport protein, ATP-binding" t3233 conserved hypothetical protein t3235 conserved hypothetical protein t3236 "probable ABC transport protein," t3238 probable sigma(54) modulation protein t3240 conserved hypothetical protein t3244 conserved hypothetical protein t3252 conserved hypothetical protein t3253 possible kinase t3263 conserved hypothetical protein t3272 possible transcriptional regulator t3273 possible GntR-family transcriptional regulator t3274 malate dehydrogenase gene t3276 conserved hypothetical protein t3286 conserved hypothetical protein t3291 possible oxidoreductase gene t3292 conserved hypothetical protein t3319 conserved hypothetical protein t3321 putative deoxyribonuclease gene t3326 conserved hypothetical protein t3330 putative hydrolase gene t3341 conserved hypothetical protein t3351 putative lipoprotein gene t3370 conserved hypothetical protein t3382 putative ATP-dependent RNA helicase yifB "(pseudogene)"" STY3657" t3408 hypothetical protein t3412 possible lipoprotein t3413 possible lipoprotein t3414 hypothetical protein t3415 hypothetical protein t3418 putative capsid scaffolding protein t3438 probable major tail sheath t3439 probable major tail tube t3448 conserved hypothetical protein t3457 transcriptional regulatory protein t3460 conserved hypothetical protein t3499 possible pyridine nucleotide-disulphide oxidoreductase t3505 phosphoenolpyruvate carboxylase gene t3506 putative membrane protein t3508 putative transaldolase gene t3515 hypothetical protein t3530 conserved hypothetical protein t3533 putative glycerol metabolic protein t3536 conserved hypothetical protein t3537 triosephosphate isomerase gene t3540 putative aldolase gene t3541 "putative ABC transport protein," t3545 putative regulatory protein t3557 6-phosphofructokinase gene pfkA t3563 conserved hypothetical protein t3583 "(pos:3683776..3683778,aa:Sec) product ""formate" t3584 formate dehydrogenase-O beta subunit t3585 formate dehydrogenase-O gamma subunit t3586 FdhE protein gene t3593 conserved hypothetical protein t3596 putative DeoR-family transcriptional regulator t3618 conserved hypothetical protein t3624 conserved hypothetical protein t3625 conserved hypothetical protein t3673 conserved hypothetical protein t3678 putative membrane protein t3688 conserved hypothetical protein t3707 putative ATP/GTP-binding protein t3735 putative IIB component of t3750 putative transferase t3751 conserved hypothetical protein t3764 putative DNA-binding protein t3783 conserved hypothetical protein t3786 putative TetR-family transcriptional regulator t3814 conserved hypothetical protein t3816 putative secreted protein t3819 glycerol-3-phosphate dehydrogenase gene t3824 putative RNA methyltransferase t3825 putative L-lactate dehydrogenase t3826 putative L-lactate dehydrogenase operon t3830 conserved hypothetical protein t3835 putative glutathione transferase t3846 "(VPT)"" gene yiaO" t3867 conserved hypothetical protein t3868 putative acetyltransferase t3869 putative exported protein t3874 putative outer membrane protein t3882 putative lacI-family transcriptional regulator t3883 hypothetical protein t3893 putative membrane protein t3897 conserved hypothetical protein t3900 probable endoglucanase precursor yhjL "protein subunit C (pseudogene)""" t3904 putative zinc-protease precursor t3919 conserved hypothetical protein t3923 conserved hypothetical protein t3927 putative low-affinity inorganic phosphate t3928 putative exported protein t3942 putative lipoprotein t3944 conserved hypothetical protein t3948 putative membrane protein t3949 putative membrane protein t3950 conserved hypothetical protein livJ "(pseudogene)"" STY4244" t3976 putative oxidoreductase t3987 aerobic glycerol-3-phosphate dehydrogenase t3989 putative membrane protein t3990 glycerol-3-phosphate regulon repressor t3995 conserved hypothetical protein t3997 putative biotin biosynthesis protein t4002 putative transcription accessory protein t4010 putative hydrolase gene t4012 putative NUDIX hydrolase t4029 putative nitrite transporter t4046 probable ABC transporter ATP-binding t4049 conserved hypothetical protein t4051 conserved hypothetical protein t4053 conserved hypothetical protein t4055 conserved hypothetical protein t4093 putative Zn(II)-responsive regulator t4104 conserved hypothetical protein t4105 putative transferase gene t4119 conserved hypothetical protein t4120 putative pseudouridine synthase t4127 glucose-6-phosphate isomerase gene t4146 conserved hypothetical protein t4148 putative exported protein t4149 conserved hypothetical protein t4151 quinone oxidoreductase gene t4156 conserved hypothetical protein t4157 conserved hypothetical protein t4164 putative type-I secretion protein t4186 cytochrome c-type biogenesis protein t4196 conserved hypothetical protein t4223 conserved hypothetical protein t4224 putative acetyltransferase t4290 hypothetical protein colour t4300 probable major tail tube t4301 probable major tail sheath t4319 putative major capsid protein t4320 putative capsid protein t4323 hypothetical protein t4325 hypothetical protein t4331 hypothetical protein t4332 hypothetical protein t4343 conserved hypothetical protein t4357 probable phage integrase t4358 hypothetical protein colour t4359 conserved hypothetical protein t4373 putative transcriptional regulator t4383 putative membrane protein t4394 "fumarate reductase, iron-sulfur protein" t4395 "fumarate reductase, flavoprotein subunit" t4401 putative membrane protein t4406 conserved hypothetical protein t4408 conserved hypothetical protein t4413 "HflX protein, putative GTP-binding" t4418 conserved hypothetical protein t4430 putative exported protein t4432 probable transcriptional regulator t4448 probable FkbP-type peptidyl-prolyl cis-trans t4458 putative exported protein t4463 putative exported protein t4465 conserved hypothetical protein t4471 conserved hypothetical protein t4472 putative PmbA protein t4473 soluble cytochrome b562 t4475 hypothetical protein t4479 hypothetical protein t4480 hypothetical protein t4481 hypothetical protein t4482 putative BglB-family transcriptional antiterminator t4493 conserved hypothetical protein t4502 conserved hypothetical protein t4504 conserved hypothetical protein t4507 putative exported protein t4521 hypothetical protein t4549 conserved hypothetical protein t4550 conserved hypothetical protein t4557 probable tryptophanyl-tRNA synthetase t4559 conserved hypothetical protein t4562 probable isoaspartyl dipeptidase t4580 conserved hypothetical protein t4599 conserved hypothetical protein t4620 conserved hypothetical ABC transporter t4622 probable trp operon repressor t4624 probable phosphoglycerate mutase 2 t4626 conserved hypothetical protein t4639 putative RNA methyltransferase