<p>Table S1: Truncated genes in S. aureus O11 or S. aureus O46 sequences. </p><p>Gene1 Description2 L4 O46 CDS3 L4 Trans6 Prot7 INFORMATION STORAGE</p><p>AND PROCESSING Transcription </p><p> sigS DNA-binding protein 549046_2447 258 X rpoE DNA-directed RNA polymerase subunit delta 516046_0924 531 --- TetR family regulatory protein 588046_0168 522 X </p><p> tenA transcriptional activator 663046_1834 690 --- LysR family regulatory protein 249046_0375 870 </p><p>--- transcriptional regulator 597046_1416 2238 --- transcriptional regulator 354046_2354 336 --- acetyltransferase 288046_0440 552 Replication, recombination and repair </p><p>--- DNA damage repair protein 1233046_0866 1263 X radC DNA repair protein RadC 441046_0617 672 hsdR type I restriction enzyme restriction chain 2775046_0485 2790 X --- putative helicase, Similar to Type III restriction 2814046_2610 2862 X</p><p> protein res subunit --- TOPRIM domain-containing protein 393046_2509 390 polA phage related DNA polymerase family A 1953046_2661 678 X --- putative insertion element protein 687046_0005 1230 CELLULAR PROCESSES</p><p>AND SIGNALING Cell cycle control, cell division, chromosome partitioning --- SpoIIIE family cell division protein 3834046_1342 3825 Cell wall/membrane/envelope biogenesis </p><p> spoVG regulatory protein SpoVG 291046_2417 303 --- LysM domain-containing protein 840046_2219 393 X Signal transduction mechanisms </p><p>--- sensor kinase protein 849046_0823 843 Defense mechanisms </p><p>--- FmhC protein 768046_0744 606 --- ABC transporter ATP-binding protein 642046_0432 312 --- secretory antigen precursor 804046_1136 813 X --- membrane anchored protein 1176046_1982 1215 --- putative enterotoxin type A 753046_2274 705 </p><p> sasA Serine-rich adhesin for platelets 5337046_1536 6582 scpA staphopain cysteine proteinase 1140046_2362 1167 X --- surface protein 684046_1386 675 X </p><p> vwb von Willebrand factor-binding protein 1518046_2531 1524 set5 superantigen-like protein 7 120046_0938 114 set2 superantigen-like protein 670046_0935 684 METABOLISM Energy production and conversion </p><p>--- Appr-1-p processing domain-containing protein 801046_1587 792 X --- glycerate dehydrogenase 285046_0459 960 Amino acid transport and metabolism ald alanine dehydrogenase 1119046_1705 141 --- glutamate synthase-ferredoxin large subunit 1275046_2109 1578 </p><p>--- Glutathione S-transferase transmembrane protein 357046_0252 468 Nucleotide transport and metabolism --- nucleoside transporter permease 366046_0680 1221 Carbohydrate transport and metabolism </p><p>--- transketolase 1974046_0844 1989 X --- multiple sugar-binding transport ATP-binding protein 516046_0496 510 --- peptidase 1032046_0868 288 </p><p> antibiotic resistance-related transmembrane efflux</p><p>--- protein (pid:82749819) 135046_1414 1389 icaC icaC 783046_1520 1053 X lacC tagatose-6-phosphate kinase 933046_1691 924 Lipid transport and metabolism accC acetyl-CoA biotin carboxylase 666046_2279 1362 acsA acetyl-CoA synthetase 522046_1351 1707 Inorganic ion transport and metabolism </p><p>--- high-affinity nickel-transport protein 126046_1490 1053 --- lipoprotein 441046_0735 975 </p><p>--- DMT superfamily drug/metabolite transporter 753046_0129 963 X Iron metabolism isdH isdH 2682046_1353 2697 X X feoA ferrous iron transport protein A 228046_0146 168 </p><p>Putative hemin transport system permease protein hrtB hrtB 1056046_1071 975 Coenzyme transport and metabolism </p><p>4'-phosphopantetheinyl transferase superfamily</p><p>--- protein 645046_0470 564 POORLY CHARACTERIZED General function prediction only/ Function unknown </p><p>--- acetyltransferase 360046_2226 282 --- Antibiotic biosynthesis monooxygenase 420046_0206 480 X --- competence-related protein 936046_0398 987 --- hypothetical protein 345046_0517 147 --- hypothetical protein 357046_0527 255 </p><p>--- hypothetical protein 1212046_0105 1824 --- hypothetical protein 339046_0333 234 --- hypothetical protein 894046_0822 1608 </p><p>--- hypothetical protein 297046_0853 252 --- hypothetical protein 351046_0888 216 </p><p>--- hypothetical protein 768046_1497 816 --- hypothetical protein 735046_1394 762 --- hypothetical protein 741046_1446 651 </p><p>--- hypothetical protein 1362046_0687 111 --- hypothetical protein 1524046_0644 1386 X --- hypothetical protein 441046_2056 435 --- hypothetical protein 87046_0942 135 --- hypothetical protein 180046_2607 1356 </p><p>--- hypothetical protein 408046_2601 423 --- hypothetical protein 369046_2740 843 X --- hypothetical protein 1926046_0563 756 </p><p>--- hypothetical protein 408046_1444 840 --- hypothetical protein 444046_1975 345 --- hypothetical protein 1260046_1863 2178 --- hypothetical protein 9378046_2560 8091 --- hypothetical protein 4113046_2534 789 </p><p>--- hypothetical protein 87046_2338 147 --- hypothetical protein 819046_2567 939 --- hypothetical protein 87046_0003 162 </p><p>--- hypothetical protein 111046_0691 171 --- hypothetical protein 87046_1610 90 </p><p>--- hypothetical protein 573046_0979 267 --- hypothetical protein 696046_2494 546 --- hypothetical protein 660046_1949 675 X </p><p>--- hypothetical protein 192046_2568 279 --- hypothetical protein 807046_1489 318 --- hypothetical protein 1476046_0001 1893 --- hypothetical protein 2538046_1437 813 --- hypothetical protein 813046_0288 777 --- hypothetical protein 150046_2464 153 X --- metallo-beta-lactamase superfamily protein 885046_1335 489 </p><p>--- N-acyl-L-amino acid amidohydrolase 933046_1767 1176 --- NADH-dependent dehydrogenase 1041046_0504 1029 </p><p>--- oxidoreductase 801046_2031 768 --- phiSLT ORF 563-like protein, terminase, large 1221046_1619 1692 </p><p> subunit --- phiSLT ORF144-like protein, putative lipoprotein 384046_0692 435 X --- phiSLT ORF412-like protein, portal protein 1239046_1618 1047 --- phiSLT ORF66-like protein 201046_2680 132 X pknB protein kinase 2001046_2574 1995 --- Putative membrane protein 189046_2221 237 X </p><p>--- Staphylococcus aureus phage phi 13 1395046_2017 1365 --- tandem lipoprotein 123046_1418 771 1: Genes are classified in GO functional classes. </p><p>2: Names are given according to annotation of available S. aureus sequence genomes.</p><p>3: Coding sequence numbers corresponding to genes in S. aureus O11 and S. aureus O46</p><p>4: Gene sequence length</p><p>5: Predicted protein localization (SurfG+). C, cytoplasmic; S, secreted; PSE, predicted surface exposed</p><p>6: Differences between S. aureus O11 and S. aureus O46 confirmed at the transcriptome level</p><p>7: Differences between S. aureus O11 and S. aureus O46 confirmed at the proteome level</p>