Parkhill et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

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1 Parkhill et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica Supplementary table 1: Genes unique to each Bordetella species Bordetella pertussis Class Systematic Gene Gene Product name name BP0270 hypothetical protein BP0271 hypothetical protein BP0296 hypothetical protein BP0507 hypothetical protein BP0516 hypothetical protein BP0734 hypothetical protein BP1492 hypothetical protein BP2603 hypothetical protein BP3391 conserved hypothetical protein BP3842 hypothetical protein BP0025 conserved hypothetical protein BP0328 conserved hypothetical protein BP0330 conserved hypothetical protein BP0331 conserved hypothetical protein BP0332 conserved hypothetical protein BP2183 conserved hypothetical protein BP2612 conserved hypothetical protein BP2613 conserved hypothetical protein BP2617 conserved hypothetical protein BP2856 conserved hypothetical protein BP3115 conserved hypothetical protein BP3840 conserved hypothetical protein (pseudogene) BP0290 probable transporter BP2306 putative sodium:alanine symporter BP2614 ABC transport protein, inner membrane component BP2615 ABC transport protein, ATP-binding component BP2616 ABC transport protein, periplasmic component BP2855 membrane transport protein BP0257 C-terminal region of TonB dependent receptor protein (Pseudogene) BP0703 N-terminal region of TonB dependent receptor protein (Pseudogene) BP3113 putative DNA helicase (Pseudogene) BP3116 putative modification methylase BP3117 putative restriction endonuclease BP0429 delta-1-pyrroline-5-carboxylate dehydrogenase precursor BP2601 probable alcohol dehydrogenase BP2853 probable short chain dehydrogenase BP2854 probable short chain dehydrogenase BP1665 tfda alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase BP1669 llda lactate dehydrogenase BP1672 fabg 3-oxoacyl-[acyl-carrier protein] reductase BP1667 putative exported protein BP1673 putative exported protein BP2606 putative exported protein BP3843 putative lipoprotein BP2600 putative membrane protein BP1617 C-terminal region of a putative polysaccharide biosynthesis protein (partial) BP0272 integrase (remnant) BP0502 integrase BP0503 phage-related conserved hypothetical protein BP0504 phage-related hypothetical protein BP0505 phage-related conserved hypothetical protein

2 5.1.2 BP0506 phage-related hypothetical protein BP0508 phage-related exonuclease BP0509 phage-related DNA recombination protein BP0510 phage-related putative membrane protein BP0511 phage-related hypothetical protein BP0512 phage-related hypothetical protein (pseudogene) BP0513 phage-related hypothetical protein BP0515 phage-related hypothetical protein BP3112 putative integrase (Pseudogene) BP3352 phage-related conserved hypothetical protein BP3353 putative phage-related hypothetical protein (partial) BP3354 phage-related hypothetical protein BP3355 phage-related conserved hypothetical protein BP3356 putative phage lysozyme BP3357 phage-related conserved hypothetical protein BP3358 phage-related hypothetical protein BP3359 phage-related hypothetical protein BP3361 phage-related hypothetical protein BP3362 phage-related conserved hypothetical protein BP3363 phage-related conserved hypothetical protein BP3364 phage-related conserved hypothetical protein BP3365 phage-related conserved hypothetical protein BP3366 putative phage tail protein BP3367 phage-related conserved hypothetical protein BP3368 phage-related conserved hypothetical protein BP3369 phage-related conserved hypothetical protein BP3370 phage-related conserved hypothetical protein BP3371 phage-related conserved hypothetical protein BP3372 phage-related hypothetical protein BP3373 phage-related conserved hypothetical protein BP3374 phage-related hypothetical protein BP3375 phage-related conserved hypothetical protein BP3376 phage-related hypothetical protein BP3379 phage-related conserved hypothetical protein (pseudogene) BP3380 phage-related hypothetical protein BP3381 phage-related hypothetical protein BP3382 phage-related conserved hypothetical protein BP3383 phage-related conserved hypothetical protein BP3384 putative phage terminase BP3385 phage-related conserved hypothetical protein BP3387 phage-related hypothetical protein (pseudogene) BP3388 phage-related putative membrane protein BP3389 phage-related hypothetical protein BP3390 putative phage repressor protein BP0023 transposase BP0031 transposase BP0041 transposase BP0049 transposase BP0058 transposase BP0071 transposase BP0072 transposase BP0073 transposase (pseudogene) BP0080 transposase BP0081 transposase for IS1002 (pseudogene) BP0110 transposase BP0118 transposase for IS BP0124 transposase BP0137 transposase BP0166 transposase BP0175 transposase

3 5.1.4 BP0192 transposase BP0202 transposase BP0202A transposase (pseudogene) BP0203 transposase BP0210 transposase BP0211 transposase BP0228 transposase BP0256 transposase BP0268 transposase BP0281 transposase BP0295 transposase BP0297 transposase BP0327 transposase BP0355 transposase BP0365 transposase BP0392 transposase BP0401 transposase (Pseudogene) BP0408 transposase BP0424 transposase BP0439 transposase BP0443 transposase BP0473 transposase BP0481 transposase BP0496 transposase BP0514 transposase BP0517 transposase BP0537 transposase BP0540 transposase BP0565 transposase BP0611 transposase BP0645 transposase BP0646 transposase BP0676 transposase BP0688 transposase BP0704 transposase BP0716 transposase (Pseudogene) BP0729 transposase BP0733 transposase BP0739 transposase BP0739A transposase (pseudogene) BP0742 transposase (Pseudogene) BP0756A transposase (Pseudogene) BP0786 transposase BP0797 transposase BP0812 transposase for IS BP0830 transposase BP0839 transposase BP0867 transposase BP0871 transposase BP0891 transposase BP0897 transposase BP0910 transposase BP0938 transposase BP0957 transposase BP0978 transposase for IS BP0997 transposase BP1007 transposase (Pseudogene) BP1020 transposase BP1035 transposase for IS BP1044 transposase for IS1663

4 5.1.4 BP1048 transposase BP1053 transposase for IS BP1067 transposase BP1080 transposase BP1086 transposase BP1093 transposase BP1114 transposase (Pseudogene) BP1118 transposase BP1130 transposase BP1134 transposase BP1142 transposase BP1157 transposase BP1177 transposase BP1199 transposase BP1224 transposase BP1268 transposase BP1278 transposase BP1287 transposase BP1308 transposase BP1332 transposase BP1337 transposase BP1361 transposase BP1365 transposase for IS BP1388 transposase for IS BP1397 transposase BP1439 transposase BP1450 transposase BP1459 transposase BP1491 transposase BP1493 transposase BP1511 transposase BP1544 transposase BP1552 transposase BP1557 transposase BP1572 transposase BP1594 transposase BP1602 transposase BP1633 transposase BP1647 transposase BP1653 transposase BP1656 transposase BP1678 transposase BP1689 transposase BP1697 transposase BP1711 transposase BP1717 transposase for IS BP1735 transposase BP1748 transposase BP1757 transposase BP1792 transposase BP1807 transposase BP1809 transposase BP1810 transposase BP1844 transposase BP1866 transposase BP1869 transposase (partial) BP1897 transposase (Pseudogene) BP1911 transposase BP1914 transposase for IS BP1947 transposase

5 5.1.4 BP1959 transposase for IS BP1968 fusion between a transposase and a C-terminal portion of a regulatory protein (Pseudogene) BP2018 transposase BP2029 transposase BP2048 transposase BP2054 transposase BP2087 transposase BP2104 transposase BP2105 transposase BP2118 transposase (Pseudogene) BP2121 transposase for IS BP2135 transposase BP2137 transposase BP2159 transposase (Pseudogene) BP2166 transposase BP2181 transposase BP2207 transposase BP2214 transposase BP2221 transposase BP2266 transposase BP2272 transposase BP2297 transposase BP2316 transposase BP2355 transposase BP2390 transposase BP2415 transposase BP2427A transposase for IS481 element (pseudogene) BP2453 transposase BP2477 transposase BP2485 transposase BP2492 transposase BP2524 transposase BP2568 transposase BP2577 transposase BP2579 transposase BP2582 transposase BP2587 transposase BP2608 transposase BP2630 transposase BP2666 transposase BP2672 transposase BP2673 transposase BP2679 transposase BP2689A transposase fragment for IS1663 (pseudogene) BP2704 transposase BP2721 transposase for IS BP2724 transposase BP2733 transposase BP2748 transposase BP2763 transposase BP2776 transposase BP2781 transposase BP2805 transposase (Pseudogene) BP2812 transposase BP2819 transposase BP2821 transposase BP2834 transposase (Pseudogene) BP2842A transposase (pseudogene) BP2845 transposase

6 5.1.4 BP2848 transposase BP2852 transposase BP2861 transposase BP2876 transposase (Pseudogene) BP2884 transposase BP2912 transposase BP2947 transposase BP2955 transposase BP2976 transposase BP3005 transposase BP3046 transposase BP3049 transposase BP3055 transposase BP3065 transposase BP3091 transposase BP3103 transposase BP3111 transposase BP3114 transposase BP3164 transposase BP3185 transposase BP3186 transposase BP3203 transposase BP3210 transposase BP3216 transposase for IS BP3220 transposase BP3230 transposase for IS BP3243 transposase for IS BP3257 transposase BP3260 transposase (Pseudogene) BP3272 transposase BP3279 transposase BP3294 transposase BP3311 transposase BP3312 transposase BP3313 transposase BP3323 transposase BP3336 transposase BP3378 transposase (Pseudogene) BP3386 transposase BP3392 transposase BP3406 transposase BP3407 transposase for IS1002 (pseudogene) BP3408 transposase BP3423 transposase BP3436 transposase BP3451 transposase BP3478 transposase BP3505 transposase BP3510 transposase BP3519 transposase BP3520 transposase BP3548 transposase BP3593 transposase BP3603 transposase for IS BP3607 transposase BP3688 transposase (Pseudogene) BP3698 transposase BP3726 transposase BP3780 transposase (Pseudogene) BP3806 transposase

7 5.1.4 BP3810 transposase BP3811 transposase BP3839 transposase BP3851 transposase BP0028 putative transcriptional regulator BP0291 probable LysR-family transcriptional regulator BP1666 probable LysR-family transcriptional regulator BP2604 putative LysR-family transcriptional regulatory protein BP2605 putative Arac-family transcriptional regulatory protein BP2618 putative transcriptional regulator BP2857 putative LysR-family transcriptional regulator BP0024 putative racemase (Pseudogene) BP0026 putative thiolase BP0027 MaoC family protein BP0207 putative aldehyde dehydrogenase BP0329 putative coenzyme A ligase BP1668 probable short-chain dehydrogenase BP1670 putative hydrolase BP1671 probable short chain dehydrogenase BP2602 hypothetical protein BP2622 hipa HipA-like protein BP2623 hipb DNA-binding protein BP3841 CAIB/BAIF family protein BP3844 putative enoyl-coa hydratase/isomerase Bordetella parapertussis BPP0125 wbmt hypothetical protein BPP0126 wbms hypothetical protein BPP0482 hypothetical protein BPP0486 hypothetical protein BPP0487 hypothetical protein BPP0489 hypothetical protein BPP0493 hypothetical protein BPP0991 hypothetical protein BPP0992 hypothetical protein BPP0993 hypothetical protein BPP1263 hypothetical protein BPP1266 hypothetical protein BPP1267 hypothetical protein BPP2793 hypothetical protein BPP3140 hypothetical protein BPP0129 wbmp conserved hypothetical protein BPP0377 conserved hypothetical protein BPP0378 conserved hypothetical protein BPP0379 conserved hypothetical protein BPP0645 conserved hypothetical protein BPP0646 conserved hypothetical protein BPP0707 hypothetical protein (pseudogene) BPP1232 conserved hypothetical protein BPP1261 yeea conserved hypothetical protein (pseudogene) BPP1264 yeeb conserved hypothetical protein BPP1265 yeec conserved hypothetical protein BPP2077 Conserved hypothetical protein BPP2078 Conserved hypothetical protein BPP0490 putative DNA primase BPP2894 probable N-terminal region of alpha amylase (partial) BPP2895 glgx' C-terminal region of a probable glycosyl hydrolase (partial) BPP2655 Putative exported protein BPP1233 putative membrane protein BPP1249 putative membrane protein

8 5.1.2 BPP0483 putative phage-related protein BPP0484 putative phage-related protein BPP0491 phage-related protein BPP0492 phage-related protein BPP0495 putative integrase BPP1260 putative phage protein BPP0485 plasmid-related protein BPP0486a putative plasmid-related protein BPP0488 plasmid-related protein BPP0078 transposase BPP0255 transposase for IS BPP0750 transposase for IS BPP0808 transposase BPP0908 transposase for IS BPP1231 transposase BPP1610 transposase for IS BPP1654 transposase BPP1844 transposase for IS BPP1897 transposase for IS BPP1903 transposase BPP2054 transposase BPP2064 transposase for IS BPP2252 transposase BPP2353 transposase for IS BPP2470 transposase BPP2508 transposase BPP2589 transposase BPP2649 transposase BPP2796 transposase for IS BPP2886 transposase BPP2931 transposase BPP3113 transposase BPP3139 transposase BPP3188 transposase BPP3374 transposase BPP3457 transposase BPP3493 transposase BPP3777 transposase BPP3815 transposase BPP4247 transposase BPP0123 putative asparagine synthetase BPP0124 wbmu putative formyl transferase BPP0127 wbmr putative formyl transferase BPP0128 wbmq putative formyl transferase BPP0380 acetyltransferase (GNAT) family protein BPP1273 putative glutatione S-transferase BPP2116 probable short chain dehydrogenase (Pseudogene) Bordetella bronchiseptica BB0128 wbms hypothetical protein BB0381 hypothetical protein BB0382 hypothetical protein BB0482 hypothetical protein BB0484 hypothetical protein BB0484A hypothetical protein BB0486 hypothetical protein BB0487 hypothetical protein BB0492 hypothetical protein BB0495 hypothetical protein BB0496 hypothetical protein

9 0.0.0 BB0497 hypothetical protein BB0498 hypothetical protein BB0529 hypothetical protein BB0731 hypothetical protein BB0774 hypothetical protein BB0776 hypothetical protein BB0777 hypothetical protein BB0788 hypothetical protein BB1009 hypothetical protein BB1032 hypothetical protein BB1115 hypothetical protein BB1205 hypothetical protein BB2335 hypothetical protein BB2450 hypothetical protein BB4779 hypothetical protein BB0126 conserved hypothetical protein BB0380 conserved hypothetical protein BB0483 conserved hypothetical protein BB0527 conserved hypothetical protein BB0715 conserved hypothetical protein BB0722 conserved hypothetical protein BB0723 conserved hypothetical protein BB0724 conserved hypothetical protein BB0769 conserved hypothetical protein BB0793 vrgs conserved hypothetical protein BB0909 conserved hypothetical protein BB0915 conserved hypothetical protein BB1031 conserved hypothetical protein BB1034 conserved hypothetical protein BB1040 conserved hypothetical protein BB1051 conserved hypothetical protein (pseudogene) BB1056 conserved hypothetical protein BB1057 conserved hypothetical protein BB1059 conserved hypothetical protein BB1063 conserved hypothetical protein BB1070 conserved hypothetical protein BB1076 conserved hypothetical protein BB1077 conserved hypothetical protein BB1083 conserved hypothetical protein BB1090 conserved hypothetical protein BB1094 conserved hypothetical protein BB1097 conserved hypothetical protein BB1105 conserved hypothetical protein BB1110 conserved hypothetical protein BB1117 conserved hypothetical protein BB1203 conserved hypothetical protein BB1470 conserved hypothetical protein BB1472 conserved hypothetical protein BB2692 conserved hypothetical protein BB2794 conserved hypothetical protein BB4332 conserved hypothetical protein BB4335 conserved hypothetical protein BB4688 conserved hypothetical protein BB4723 conserved hypothetical protein BB4724 conserved hypothetical protein BB4725 conserved hypothetical protein BB4739 conserved hypothetical protein BB4740 conserved hypothetical protein BB4745 conserved hypothetical protein BB4746 conserved hypothetical protein

10 0.0.2 BB4751 conserved hypothetical protein BB4753 conserved hypothetical protein BB4763 conserved hypothetical protein BB4765 conserved hypothetical protein BB4778 conserved hypothetical protein BB4781 conserved hypothetical protein BB0791 pilt twitching mobility protein BB2574 tar methyl-accepting chemotaxis protein BB0719 putative ABC transporter periplasmic solute-binding protein BB0780 putative type II secretion system protein BB0781 putative type II secretion system protein BB0782 putative type II secretion system protein BB0784 putative type II secretion system protein BB0790 putative type II secretion system protein BB0792 gspo type 4 prepilin-like proteins leader peptide processing enzyme BB1005 probable ATP-binding component of ABC transporter BB1006 inner membrane component of ABC transporter BB1007 inner membrane component of ABC transporter BB1008 substrate binding component of ABC transporter BB1018 probable transmembrane permease ABC transporter protein BB1019 ATP-binding ABC transporter protein BB1042 extracellular solute-binding protein BB1043 ATP-binding component of ABC transporter BB1044 inner membrane component of ABC transporter BB1060 probable extracellular solute-binding protein BB1061 putative integral membrane transport protein BB1071 putative permease component of ABC transporter BB1072 ATP-binding component of ABC transporter BB1073 putative substrate binding component of ABC transporter BB2334 opde putative transporter BB2755 putative substrate-binding periplasmic protein BB2756 permease component of ABC transporter protein BB2757 permease component of ABC transporter protein BB2758 ATP-binding component of ABC transporter protein BB2759 ATP-binding component of ABC transporter protein BB2796 putative ABC transporter permease protein BB2797 putative amino acid ABC transporter solute-binding protein BB4726 extracellular solute-binding protein BB4727 inner membrane component of binding-protein-dependent transport system BB4728 inner membrane component of binding-protein-dependent transport system BB4729 ABC transporter, ATP-binding protein BB1100 mgta Mg(2+) transport ATPase BB4774 putative iron(iii)-binding periplasmic protein precursor BB4775 putative iron(iii)-transport system permease BB4776 putative iron(iii)-transport ATP-binding protein BB4744 bfrz putative siderophore receptor precursor BB4761 bfra exogenous ferric siderophore receptor BB4737 putative endoribonuclease BB0772 putative dipeptidase BB0911 putative serine protease BB4730 putative peptidase BB0908 putative helicase BB0912 type III restriction-modification system methyltransferase BB0913 type III restriction enzyme BB1668 modification methylase BB1669 putative methyltransferase BB3607 modification methylase BB1014 leub 3-isopropylmalate dehydrogenase

11 BB1015 leud 3-isopropylmalate dehydratase small subunit BB1016 leuc 3-isopropylmalate dehydratase large subunit BB1108 dapa putative dihydrodipicolinate synthase BB1012 putative ornithine cyclodeaminase BB4731 phosphoglycerate dehydrogenase BB1035 putative ribulose bisphosphate carboxylaseoxygenase,large subunit BB1048 putative gluconolactonase BB1046 pepm phosphoenolpyruvate phosphomutase BB4722 aata aspartate aminotransferase A BB4732 hutg putative N-formylglutamate amidohydrolase BB1025 probable sulfatase BB1045 aatb aspartate aminotransferase BB1055 mety O-acetylhomoserine sulfhydrylase BB4738 seld selenide,water dikinase BB0727 electron transfer component of a dioxygenase system BB0728 hydroxylating alpha subunit of a dioxygenase system BB0729 putative short chain dehydrogenase BB0730 hydroxylating beta subunit of a dioxygenase system BB0732 cada FAD-monooxygenase BB0734 putative fumarylacetoacetate (FAA) hydrolase family protein BB0735 putative fumarylacetoacetate (FAA) hydrolase family protein BB0736 hpae 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase BB0737 hpad homoprotocatechuate 2,3-dioxygenase BB0738 hpaf 5-carboxymethyl-2-hydroxymuconate delta-isomerase BB0739 hpcg 2-oxo-hepta-3-ene-1,7-dioic acid hydratase BB0740 hpai 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase BB1116 nitrilase BB4771 mhpc putative 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase BB4772 vanb putative vanillate O-demethylase oxidoreductase BB4773 putative 3-chlorobenzoate-3,4-dioxygenase oxygenase BB1013 apha acetylpolyamine aminohydrolase BB1033 putative 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase BB0745 putative lipase BB1010 phna phosphonoacetate hydrolase BB4333 bbse putative subunit of succinyl-coa:benzylsuccinate CoA-transferase BB4334 bbsf putative subunit of succinyl-coa:benzylsuccinate CoA-transferase BB1109 lldd FMN-dependent dehydrogenase BB2798 nape component of of periplasmic nitrate reductase system BB1104 [2Fe-2S] protein BB1106 ferredoxin BB1107 ferredoxin reductase BB4759 etfb electron transfer flavoprotein beta-subunit BB4760 etfa electron transfer flavoprotein alpha-subunit BB2689 accc biotin carboxylase BB2690 putative carboxyl transferase BB4733 biotin carboxyl carrier protein of acetyl-coa carboxylase BB4734 accb biotin carboxyl carrier protein of acetyl-coa carboxylase BB4735 accc biotin carboxylase BB4755 enoyl-coa hydratase/isomerase BB4756 fadh 2,4-dienoyl-CoA reductase [NADPH] BB4764 fabg putative 3-oxoacyl-[acyl-carrier protein] reductase BB0652 putative exported protein BB0717 putative exported protein BB0726 putative exported protein BB0733 putative exported protein BB0742 putative exported protein BB0747 putative exported protei BB0748 putative exported protein BB0749 putative lipoprotein BB0768 putative exported protein

12 4.1.0 BB0773 putative exported protein BB0786 putative exported protein BB0787 putative exported protein BB0789 putative exported protein BB1003 putative exported protein BB1017 putative exported protein BB1023 putative exported protein BB1026 putative exported protein BB1028 putative exported protein BB1030 putative exported protein BB1039 putative exported protein BB1047 putative exported protein BB1067 putative exported protein BB1078 putative exported protein BB1085 putative exported protein BB1092 putative exported protein BB1095 putative exported protein BB1099 putative exported protein BB1103 putative exported protein BB1114 putative exported protein BB1118 putative exported protein BB1206 putative exported protein BB1471 putative exported protein BB2336 putative exported protein BB2448 putative exported protein BB2449 putative exported protein BB2573 putative lipoprotein BB2691 putative exported protein BB4329 putative exported protein BB4330 putative exported protein BB4331 putative exported protein BB4749 putative exported protein BB4754 putative exported protein BB4762 putative exported protein BB4985 putative exported protein BB4986 putative exported protein BB0490 putative membrane protein BB0720 putative membrane protein BB0721 putative membrane protein BB0778 putative membrane protein BB0779 putative membrane protein BB0783 putative membrane protein BB0785 putative membrane protein BB1021 putative membrane protein BB1062 putative membrane protein BB1066 putative membrane protein BB1093 putative membrane protein BB1250 putative membrane protein BB4741 putative iron-regulated membrane protein BB0500 putative integrase BB0526 putative phage-related protein BB0914 putative integrase BB1661 integrase BB1662 phage-related hypothetical protein BB1663 phage-related conserved hypothetical protein BB1664 phage-related putative membrane protein BB1665 phage-related putative exported protein BB1666 phage-related hypothetical protein BB1667 phage-related hypothetical protein BB1670 phage-related hypothetical protein

13 5.1.2 BB1671 phage-related hypothetical protein BB1672 phage-related hypothetical protein BB1673 phage-related hypothetical protein BB1674 phage-related conserved hypothetical protein BB1675 phage-related hypothetical protein BB1676 phage-related putative membrane protein BB1677 phage-related hypothetical protein BB1678 putative phage repressor BB1679 phage-related conserved hypothetical protein BB1680 phage-related hypothetical protein BB1681 phage-related hypothetical protein BB1682 phage-related hypothetical protein BB1683 phage-related hypothetical protein BB1684 phage-related hypothetical protein BB1685 phage-related hypothetical protein BB1686 phage-related conserved hypothetical protein BB1687 phage-related hypothetical protein BB1688 phage-related conserved hypothetical protein BB1689 phage-related conserved hypothetical protein BB1690 phage-related putative endonuclease BB1691 phage-related hypothetical protein BB1692 terminase BB1693 portal protein BB1694 phage-related Clp protease BB1695 major head protein BB1696 phage-related hypothetical protein BB1697 phage-related conserved hypothetical protein BB1698 phage-related conserved hypothetical protein BB1699 phage-related hypothetical protein BB1700 phage-related hypothetical protein BB1701 phage-related conserved hypothetical protein BB1702 phage-related conserved hypothetical protein BB1703 phage-related hypothetical protein BB1704 phage-related hypothetical protein BB1705 phage-related putative exported protein BB1706 putative tail component of prophage BB1707 phage-related hypothetical protein BB1708 phage-related hypothetical protein BB1709 phage-related hypothetical protein BB1710 phage-related hypothetical protein BB1711 phage-related putative exported protein BB1712 phage-related hypothetical protein BB1713 phage-related putative membrane protein BB1714 phage-related hypothetical protein BB1715 phage-related putative exported protein BB1716 phage-related hypothetical protein BB1717 phage-related conserved hypothetical protein BB2185 integrase BB2186 phage-related conserved hypothetical protein BB2187 phage-related hypothetical protein BB2188 phage-related conserved hypothetical protein BB2189 phage-related hypothetical protein BB2190 phage-related hypothetical protein BB2191 phage-related exonuclease BB2192 phage-related DNA recombination protein BB2193 phage-related putative membrane protein BB2194 phage-related hypothetical protein BB2195 phage-related hypothetical protein BB2196 phage-related hypothetical protein BB2197 phage-related hypothetical protein

14 5.1.2 BB2198 phage-related conserved hypothetical protein BB2199 putative phage repressor protein BB2200 phage-related hypothetical protein BB2201 phage-related putative membrane protein BB2201A phage-related hypothetical protein BB2202 phage-related hypothetical protein BB2203 phage-related conserved hypothetical protein BB2204 ninb phage-related conserved hypothetical protein BB2205 phage-related conserved hypothetical protein BB2206 phage-related conserved hypothetical protein BB2207 phage-related conserved hypothetical protein BB2208 phage-related hypothetical protein BB2209 phage-related hypothetical protein BB2210 phage-related conserved hypothetical protein BB2211 phage-related hypothetical protein BB2212 phage-related hypothetical protein BB2213 phage-related putative DNA binding protein BB2214 putative phage terminase BB2215 phage-related conserved hypothetical protein BB2216 phage-related conserved hypothetical protein BB2217 phage-related hypothetical protein BB2218 phage-related hypothetical protein BB2219 phage-related conserved hypothetical protein BB2220 phage-related hypothetical protein BB2221 phage-related conserved hypothetical protein BB2222 phage-related hypothetical protein BB2223 phage-related conserved hypothetical protein BB2224 phage-related conserved hypothetical protein BB2225 phage-related conserved hypothetical protein BB2226 phage-related conserved hypothetical protein BB2227 phage-related conserved hypothetical protein BB2228 phage-related conserved hypothetical protein BB2229 phage-related conserved hypothetical protein BB2230 putative phage tail protein BB2231 phage-related conserved hypothetical protein BB2232 phage-related conserved hypothetical protein BB2233 phage-related conserved hypothetical protein BB2234 phage-related conserved hypothetical protein BB2235 phage-related hypothetical protein BB2237 phage-related hypothetical protein BB2238 phage-related hypothetical protein BB2239 phage-related conserved hypothetical protein BB2240 putative phage lysozyme BB2241 phage-related conserved hypothetical protein BB2242 phage-related hypothetical protein BB2243 putative phage-related hypothetical protein BB2244 phage-related conserved hypothetical protein BB2490 abortive infection phage resistance protein BB2493 putative phage-related DNA-binding protein BB2494 putative phage-related hypothetical protein BB3478 phage-related conserved hypothetical protein BB3479 phage-related hypothetical protein BB3480 phage-related hypothetical protein BB3481 phage-related hypothetical protein BB3482 putative phage lysozyme BB3482A phage-related conserved hypothetical protein BB3483 phage-related hypothetical protein BB3484 phage-related hypothetical protein BB3485 phage-related hypothetical protein BB3486 phage-related conserved hypothetical protein

15 5.1.2 BB3487 phage-related conserved hypothetical protein BB3488 phage-related conserved hypothetical protein BB3489 phage-related conserved hypothetical protein BB3490 probable phage hk97 tail length tape measure-related protein BB3491 phage-related conserved hypothetical protein BB3492 phage-related conserved hypothetical protein BB3493 phage-related conserved hypothetical protein BB3494 phage-related conserved hypothetical protein BB3495 phage-related conserved hypothetical protein BB3496 phage-related conserved hypothetical protein BB3497 phage-related conserved hypothetical protein BB3498 phage-related hypothetical protein BB3499 phage-related conserved hypothetical protein BB3500 phage-related hypothetical protein BB3501 phage-related conserved hypothetical protein BB3502 phage-related hypothetical protein BB3503 phage-related hypothetical protein BB3504 phage-related conserved hypothetical protein BB3505 phage-related conserved hypothetical protein BB3506 putative phage terminase BB3507 phage-related putative DNA binding protein BB3508 phage-related hypothetical protein BB3508A phage-related hypothetical protein BB3509 phage-related conserved hypothetical protein BB3510 phage-related hypothetical protein BB3511 phage-related hypothetical protein BB3512 phage-related conserved hypothetical protein BB3513 phage-related conserved hypothetical protein BB3514 phage-related conserved hypothetical protein BB3515 phage-related transcriptional transcriptional regulator BB3516 phage-related hypothetical protein BB3517 phage-related hypothetical protein BB3518 phage-related hypothetical protein BB3519 phage-related hypothetical protein BB3520 phage-related hypothetical protein BB3521 cro phage regulatory protein BB3522 putative phage repressor BB3523 phage-related hypothetical protein BB3524 phage-related hypothetical protein BB3525 phage-related hypothetical protein BB3526 phage-related hypothetical protein BB3527 phage-related hypothetical protein BB3528 phage-related hypothetical protein BB3529 phage-related hypothetical protein BB3530 phage-related hypothetical protein BB3531 phage-related conserved hypothetical protein BB3532 phage-related hypothetical protein BB3533 phage-related conserved hypothetical protein BB3534 phage-related hypothetical protein BB3535 phage-related conserved hypothetical protein BB3536 phage-related hypothetical protein BB3537 phage-related hypothetical protein BB3538 phage-related conserved hypothetical protein BB3539 phage-related hypothetical protein BB3540 phage-related hypothetical protein BB3541 phage-related hypothetical protein BB3542 putative phage excisionase BB3543 phage integrase BB3606 shufflon-specific DNA recombinase BB3608 putative tail fiber assembly protein

16 5.1.2 BB3609 phage-related hypothetical protein BB3610 phage-related hypothetical protein BB3611 putative phage tail protein BB3612 putative phage tail protein BB3613 phage-related conserved hypothetical protein BB3614 phage-related conserved hypothetical protein BB3615 putative phage tail protein BB3616 phage-related conserved hypothetical protein BB3617 phage-related conserved hypothetical protein BB3618 phage-related hypothetical protein BB3619 phage-related conserved hypothetical protein BB3620 phage-related conserved hypothetical protein BB3621 putative phage tail sheath protein BB3622 phage-related conserved hypothetical protein BB3623 phage-related conserved hypothetical protein BB3624 phage-related conserved hypothetical protein BB3625 phage-related hypothetical protein BB3626 phage-related conserved hypothetical protein BB3627 phage-related putative exported protein BB3628 phage-related conserved hypothetical protein BB3629 phage-related conserved hypothetical protein BB3630 phage-related conserved hypothetical protein BB3631 phage-related conserved hypothetical protein BB3632 phage-related conserved hypothetical protein BB3633 phage-related conserved hypothetical protein BB3634 phage-related conserved hypothetical protein BB3635 phage-related hypothetical protein BB3636 phage-related hypothetical protein BB3637 phage-related hypothetical protein BB3638 putative lytic murein transglycosylase precursor BB3639 phage-related membrane protein BB3640 phage-related exported protein BB3641 phage-related conserved hypothetical protein BB3642 phage-related conserved hypothetical protein BB3643 phage-related conserved hypothetical protein BB3644 phage-related hypothetical protein BB3645 phage-related conserved hypothetical protein BB3646 phage-related conserved hypothetical protein BB3647 phage-related conserved hypothetical protein BB3648 eha phage-related conserved hypothetical protein BB3649 phage-related hypothetical protein BB3650 phage-related hypothetical protein BB3651 phage-related conserved hypothetical protein BB3652 phage-related conserved hypothetical protein BB3653 hup histone-like DNA-binding protein BB3654 phage-related conserved hypothetical protein BB3655 phage-related conserved hypothetical protein BB3656 phage-related conserved hypothetical protein BB3657 phage-related putative DNA-binding protein BB4138 phage-related integrase BB4139 phage-related conserved hypothetical protein BB4140 phage-related hypothetical protein BB4141 phage-related hypothetical protein BB4142 phage-related hypothetical protein BB4143 phage-related conserved hypothetical protein BB4144 phage-related conserved hypothetical protein BB4145 phage-related hypothetical protein BB4146 phage-related hypothetical protein BB4147 phage-related hypothetical protein BB4148 phage-related hypothetical protein

17 5.1.2 BB4149 phage-related hypothetical protein BB4149A phage-related hypothetical protein BB0485 plasmid-related protein BB0488 virb6 plasmid-related membrane protein BB0489 plasmid-related lipoprotein BB0491 virb5 plasmid-related exported protein BB0493 vird2 plasmid-related protein BB0494 hypothetical 20.3 kda protein BB2491 putative transposase (pseudogene) BB2492 transposase BB0110 putative adhesin BB0654 LysR-family transcriptional regulator BB0725 putative transcriptional regulator BB0741 LysR-family transcriptional regulator BB0746 putative transcriptional regulator BB0770 probable transcriptional regulator BB0775 putative transcriptional regulator BB1004 LysR-family transcriptioanl regulator BB1011 phnr LysR-family transcriptional regulator BB1020 LysR-family transcriptional regulator BB1024 LysR-family transcriptional regulator BB1027 LysR-family transcriptional regulator BB1036 LysR-family transcriptional regulator BB1037 LysR-family transcriptional regulator BB1041 LysR-family transcriptional regulator BB1054 LysR-family transcriptional regulator BB1058 GntR-family transcriptional regulator BB1074 GntR-family transcriptional regulator BB1081 LysR-family transcriptional regulator BB1084 TetR-family transcriptional regulator BB1091 LysR-FAMILY transcriptional regulator BB1096 LysR-family transcriptional regulator BB1101 two component sensor kinase BB1102 two component response regulator BB1111 IclR-family transcriptional regulator BB1112 LysR-family transcriptional regulator BB1119 LysR-family transcriptional regulator BB1120 two-component system response regulator BB1204 LysR-family transcriptional regulator BB2337 LysR-family transcriptional regulator BB2752 LysR-family transcriptional regulator BB2760 TetR-family transcriptional regulator BB4328 bbur LysR-family transcriptional regulator BB4685 GntR-family transcriptional regulator BB4721 GntR-family transcriptional regulator BB4742 bupi ECF sigma factor BB4743 bupr inner membrane sensor protein BB4747 transcriptional regulator BB4758 MarR-family transcriptional regulator BB4769 transcriptional regulator BB4782 LysR-family transcriptional regulator BB0123 putative asparagine synthetase BB0124 putative UDP-glucose 4-epimerase BB0125 putative phosphoesterase BB0127 putative C-methyltransferase BB0129 wbmr putative formyl transferase BB0528 putative DNA-binding protein BB0651 aldehyde dehydrogenase BB0653 putative 3-hydroxyisobutyrate dehydrogenase BB0714 hmgl 3-hydroxy-3-methylglutaryl-CoA lyase

18 7.0.0 BB0716 putative isochorismatase BB0718 bcpa carboxyvinyl-carboxyphosphonate phosphorylmutase BB0743 Thiamine pyrophosphate enzyme BB0744 putative aldehyde dehydrogenase BB0750 probable enoyl-coa hydratase BB0771 putative FAD dependent oxidoreductase BB0910 putative ATPase BB1022 putative acetyltransferase BB1029 putative enoyl-coa hydratase/isomerase BB1038 probable enoyl-coa hydratase BB1049 putative aldolase BB1050 putative dehydrogenase BB1053 putative dioxygenase BB1064 putative hydrolase BB1065 putative NAD dependent epimerase/dehydratase BB1068 probable aldehyde dehydrogenase BB1069 putative dehydrogenase BB1075 putative carboxymuconolactone decarboxylase BB1079 putative hydrolase BB1080 putative isochorismatase BB1082 putative acetyltransferase BB1086 putative thiolase BB1087 putative enoyl-coa hydratase/isomerase BB1088 putative short chain dehydrogenase BB1089 putative enoyl-coa hydratase/isomerase BB1098 probable acyl-coa dehydrogenase BB1113 probable short chain dehydrogenase BB1223 putative acetyltransferase BB1473 putative oxidoreductase BB1474 putative DNA-binding protein BB1512 probable short chain dehydrogenase BB1513 probable short chain dehydrogenase BB1648 putative acetyltransferase BB2693 putative FAD dependent oxidoreductase BB2749 probable monooxygenase BB2750 putative NADH:flavin oxidoreductase BB2751 putative monooxygenase BB2753 putative monooxygenase BB2754 putative dioxygenase BB4684 putative malate/l-lactate dehydrogenase BB4686 putative short chain dehydrogenase BB4687 putative mandelate racemase BB4736 putative aminotransferase BB4748 putative zinc-binding dehydrogenase BB4750 probable short chain dehyrogenase BB4752 acyl-coa dehydrogenase BB4757 probable enoyl-coa hydratase BB4766 putative thiolase BB4767 putative (R)-specific enoyl-coa hydratase BB4768 putative racemase BB4770 putative dioxygenase BB4777 probable dehydrogenase BB4780 putative short chain dehydrogenase Classification scheme used in supplementary tables: Unknown function, no known homologs Conserved in other organisms

19 1.0.0 Cell processes Chemotaxis and mobility Chromosome replication Chaperones Protection responses Cell killing Detoxification Drug/analog sensitivity Radiation sensitivity Transport/binding proteins Amino acids and amines Cations Carbohydrates, organic acids and alcohols Anions Other Adaptation Adaptations, atypical conditions Osmotic adaptation Fe storage Cell division Macromolecule metabolism Macromolecule degradation Degradation of DNA Degradation of RNA Degradation of polysaccharides Degradation of proteins, peptides, glyco Macromolecule synthesis, modification Amino acyl trna syn; trna modific'n Basic proteins - synthesis, modification DNA - replication, repair, restr./modific'n Glycoprotein Lipopolysaccharide Lipoprotein Phospholipids Polysaccharides - (cytoplasmic) Protein modufication Proteins - translation and modification RNA synthesis, modification, DNA transcript'n trna Metabolism of small molecules Amino acid biosynthesis Alanine Arginine Asparagine

20 Aspartate Chorismate Cysteine Glutamate Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine Biosynthesis of cofactors, carriers Acyl carrier protein (ACP) Biotin Cobalamin Enterochelin Folic acid Heme, porphyrin Lipoate Menaquinone, ubiquinone Molybdopterin Pantothenate Pyridine nucleotide Pyridoxine Riboflavin Thiamin Thioredoxin, glutaredoxin, glutathione biotin carboxyl carrier protein (BCCP) Central intermediary metabolism '-Deoxyribonucleotide metabolism Amino sugars Entner-Douderoff Gluconeogenesis Glyoxylate bypass Incorporation metal ions Misc. glucose metabolism Misc. glycerol metabolism Non-oxidative branch, pentose pwy Nucleotide hydrolysis Nucleotide interconversions Oligosaccharides Phosphorus compounds Polyamine biosynthesis Pool, multipurpose conversions of intermed. met'm S-adenosyl methionine Salvage of nucleosides and nucleotides Sugar-nucleotide biosynthesis, conversions Sulfur metabolism amino acids

21 other Degradation of small molecules Amines Amino acids Carbon compounds Fatty acids Other Energy metabolism, carbon Aerobic respiration Anaerobic respiration Electron transport Fermentation Glycolysis Oxidative branch, pentose pwy Pyruvate dehydrogenase TCA cycle ATP-proton motive force Fatty acid biosynthesis Fatty acid and phosphatidic acid biosynth Nucleotide biosynthesis Purine ribonucleotide biosynthesis Pyrimidine ribonucleotide biosynthesis Cell envelop Periplasmic/exported/lipoproteins Inner membrane Murein sacculus, peptidoglycan Outer membrane constituents Surface polysaccharides & antigens Surface structures Ribosome constituents Ribosomal and stable RNAs Ribosomal proteins - synthesis, modification Ribosomes - maturation and modification Extrachromosomal Laterally acquirred elements Colicin-related functions Phage-related functions and prophages Plasmid-related functions Transposon-related functions Pathogenicity islands/determinants Global functions Global regulatory functions

22 7.0.0 Not classified (including putative assignments) DNA sites, no gene product Cryptic genes