TABLE 4.

Genes containing the direct repeat sequence with no more than one mismatch

Gene function and IDaNameStartSequenceEndProduct
Virulence/defense
    NWMNN_0166b coa −103 GTTAA TGCTTT GTT T A −88Coagulase precursor
−82 GTTAA TATATA GTTAA −67
    NWMNN_0388 set1nm −109 GTTAA ATGAGGT TTAA −94Staphylococcal enterotoxin-like toxin
    NWMNN_0389 set2nm −109 GTTAA AAACAG GTTAA −94Staphylococcal enterotoxin-like toxin
    NWMNN_0390 set3nm −110 GTTAA AAGGGGT TTAA −95Staphylococcal enterotoxin-like toxin
−223A TTAA AAAGAA GTTAA −208
    NWMNN_0391 set4nm −109 GTTAA ACAAGGT TTAA −94Staphylococcal enterotoxin-like toxin
    NWMNN_0393 set6nm −145 GTT C A AAAATA GTTAA −130Staphylococcal enterotoxin-like toxin
    NWMNN_0393 set6nm −134 GTTAA AAAGAG GTTAA −119Staphylococcal enterotoxin-like toxin
    NWMNN_0394 set7nm −144 GTT C A AAAATA GTTAA −129Staphylococcal enterotoxin-like toxin
−133 GTTAA AAAGAG GTTAA −118
    NWMNN_0395 set8nm −110A TTAA ACGAGT GTTAA −95Staphylococcal enterotoxin-like toxin
−141 GTTAA TGAAGA G C TAA −126
−130C TTAA ATCATT GTTAA −115
    NWMNN_0396 set9nm −175A TTAA AAATCA GTTAA −160Staphylococcal enterotoxin-like toxin
−110T TTAA ATGAGC GTTAA −95
    NWMNN_0397 set10nm −110T TTAA ATCGAG GTTAA −95Staphylococcal enterotoxin-like toxin
    NWMNN_0400 set11nm −231 GTTAA ATAAAGA TTAA −216Staphylococcal enterotoxin-like toxin
−153 GTTAA CTATTTA TTAA −138
−123A TTAA TTTTTA GTTAA −108
−112 GTTAA AGTAAGT TTAA −97
−152T TTAA TAAATA GTTAA −137
    NWMNN_2619−190 GTT T A ATAGAG GTTAA −175Phenol-soluble modulin alpha 1
    NWMNN_0758 ssp/emp −126 GTTAA GACAAC GTT T A −111Extracellular matrix and plasma binding protein
−115 GTT T A CTTCAA GTTAA −100
    NWMNN_1066−99A TTAA TGTTTA GTTAA −84Similar to fibrinogen binding protein
−88 GTTAA TAAATA GTTAA −73
    NWMNN_1069 efb −81A TTAA TAATTA GTTAA −66Similar to fibrinogen binding protein
    NWMNN_1070−76T TTAA TGACAG GTTAA −61Similar to fibrinogen binding protein
    NWMNN_1073 hla −405 GTTAA TATATA GTTAA −390Alpha-hemolysin precursor
−190T TTAA ATAAAA GTTAA −175
    NWMNN_1084−171T TTAA AATACA GTTAA −156Phenol-soluble modulin beta 1
    NWMNN_1716 bsaA2 −115 GTTAA TTTTTT GT A AA −100Lantibiotic precursor
    NWMNN_1719 lukE −334 GTTAA TAATCA GTTAA −319Leukocidin LukE precursor
    NWMNN_1600−178 GTTA TAATGTA GTTAA −163Universal stress protein family protein
−86T TTAA TGAACA GTTAA −71
    NWMNN_1664−357 GTTAA AATATTT TTAA −342Arsenical resistance operon repressor
−356 GTTAA AAATATT TTAA −341
    NWMNN_1872b map/eap −88A TTAA TATTCA GTTAA −73MHCc class II analog protein
    NWMNN_1873b hlb −307A TTAA TATTCA GTTAA −292Truncated beta-hemolysin
    NWMNN_1876 scn −77 GTTAA TGAATAA TTAA −62Staphylococcal complement inhibitor SCIN
    NWMNN_1877 chp −144T TTAA TTTTTA GTTAA −129Chemotaxis-inhibiting protein CHIPS
−112A TTAA TTTCAA GTTAA −97
    NWMNN_1880 sak −175 GTTAA ATATTT GTTAA −160Staphylokinase precursor
−164 GTTAA TTATTTT TTAA −149
    NWMNN_1928b lukS −99T TTAA TAAATA GTTAA −84Leukocidin/hemolysin toxin family S subunit
    NWMNN_2061 fmtB /mrp/sasB −61C TTAA TCAACT GTTAA −46Methicillin resistance determinant FmtB protein,
    NWMNN_2317 sbi −92 GTTAA TAATTA GTTAA −77IgG binding protein Sbi
    NWMNN_2318 hlgA −346 GTTAA CGAATA GTT C A −331Gamma-hemolysin component A
−85T TTAA CGAACA GTTAA −70
−84A TTAA CTGTTC GTTAA −69
    NWMNN_2319 hlgC −351 GTTAA TAAACAA TTAA −336Gamma-hemolysin component C
−86 GTTAA TGAACA GTTAA −71
    NWMNN_2397 fnbB −114 GTTAA TAAAAA GTTAA −99Fibronectin binding protein B precursor
    NWMNN_2399 fnbA −137A TTAA TTTTAT GTTAA −122Fibronectin binding protein A precursor
−114 GTTAA TGAAAA GTTAA −99
    NWMNN_2586b drp35 −219 GTTAT AAGCAT GTTAA −204Drp35
Cell envelope
    NWMNN_0606 tagA −141 GTTAA ACTAATT TTAA −126Teichoic acid biosynthesis protein A
    NWMNN_1882−183 GTTAA ATGGTTA TTAA −168Phage holin
    NWMNN_2051−163 GTT G A AAATTT GTTAA −148Lytic regulatory protein
    NWMNN_2395 gtaB −55 GTTAA AATGAC GTT G A −40UTP-glucose-1-phosphateuridyl transferase
Transcription
    NWMNN_0038−110 GTTA TCATAGA GTTAA −95Similar to LysR family regulatory protein
    NWMNN_0636−82 GTTAA ATTTAC GTT T A −67AraC family regulatory protein
    NWMNN_0677 saeP −99 GTTAA GCGATAT TTAA −84Conserved hypothetical protein
−78 GTTAA GAATTA GTTAA −63
    NWMNN_0925−31A TTAA ATTTTT GTTAA −16Similar to cell envelope-related transcriptional attenuator
    NWMNN_1328 arlR −169 GTTAA TAAATAA TTAA −154Two-component RR
Translation
    NWMNN_0490 gltX −321 GTTAA TTTGAA GTT T A −306Glutamyl-tRNA synthetase
−139T TTAA GGTCAT GTTAA −124
    NWMNN_0723 prfB −336 GT G AA GAAGTT GTTAA −321Peptide chain release factor 2
    NWMNN_1478 rpsU −243 GTTAA AACAAC GTTA C−22830S ribosomal protein S21
    NWMNN_1488b rpsT −81 GTTA GACTTTT GTTAA −6630S ribosomal protein S20
    NWMNN_1519 alaS −290 GTTAA TGATTT GTT T A −275Alanyl-tRNA synthetase
    NWMNN_1533 hisS −260 GTTAA ACGTAC GTTAA −245Histidyl-tRNA synthetase
Protein metabolism
    NWMNN_0824 ppi −50C TTAA AAGTAT GTTAA −35Cyclophilin type peptidyl-prolyl cis-trans isomerase
    NWMNN_0957 pdf1 −59 GT A AA AAGGTT GTTAA −44Polypeptide deformylase 2
    NWMNN_1057 trxA −143 GTTAA AATAAT GT A AA −128Thioredoxin
    NWMNN_1539 secDF −157 GTTAA ATTTAAA TTAA −142Preprotein translocase component SecDF
    NWMNN_1706b splA −121T TTAA TAAAAC GTTAA −106Serine protease SplA
−110 GTTAA TAAGTG GTTAA −95
−99 GTTAA TTAATAT TTAA −84
    NWMNN_2203 ssaA −212A TTAA TTATCT GTTAA −197Secretory antigen precursor SsaA
    NWMNN_2354−331T TTAA TGATAA GTTAA −316Glutamyl-aminopeptidase
−276 GTTAA TGCGTT GTTA T−261
Ion transport and metabolism
    NWMNN_0049−73 GTTAA GATTAG GT A AA −58Similar to Na+ Pi-cotransporter
−62 GT A AA TTTAAT GTTAA −47
    NWMNN_0071−115T TTAA GGTATA GTTAA −100Glucose/ribitol dehydrogenase
    NWMNN_0123−371A TTAA GAATTT GTTAA −356Similar to surfactin synthetase
    NWMNN_0130−172 GTTAA ATCGTTC TTAA −157Branched-chain amino acid transport system II carrier protein
−171 GTTAA GAACGAT TTAA −156
    NWMNN_0158 uhpT −130A TTAA TAAATA GTTAA −115Sugar phosphate transport protein
    NWMNN_0418 ndhF −345 GTT T A ATAGAG GTTAA −330NADH dehydrogenase subunit 5
    NWMNN_0476 folP −17A TTAA AGGGTG GTTAA −2Dihydropteroate synthase chain A
−16 GTTAA CCACCCT TTAA −1
    NWMNN_0577 adh1 −370A TTAA TCTGTA GTTAA −355Alcohol dehydrogenase
    NWMNN_0623−283 GTT T A AACCTT GTTAA −268Similar to branched-chain amino acid transportsystem II carrier protein
    NWMNN_0630 vraF −80 GTTA GTCATAT GTTAA −65ABC transporter ATP binding protein VraF
    NWMNN_0690−149 G G TAA TCTCCA GTTAA −134Osmoprotectant ABC transporter, ATP binding protein
    NWMNN_0705−84A TTAA AGAAGG GTTAA −69Ferrichrome ABC transporter lipoprotein
    NWMNN_0853−110 GTTAA TAAAATT TTAA −953-Oxoacyl-(acyl-carrier-protein) synthase III
    NWMNN_1040 isdB −165 GTTAA ATAAAAT TTAA −150Iron-regulated heme-iron binding protein IsdB
    NWMNN_1060 sdhC −65 GTTAA GCGTAC GTT T A −50Succinate dehydrogenase cytochrome b558 subunit
    NWMNN_1078b argF −359 G C TAA AACTAT GTTAA −344Ornithine carbamoyltransferase
    NWMNN_1300 pstS −129 GTTAA GAAAAT GT A AA −114Phosphate ABC transporter, phosphate binding protein PstS
    NWMNN_1305 asd −61 GT A AA ATGATT GTTAA −46Aspartate-semialdehyde dehydrogenase
    NWMNN_1331−80 GTT T A AAGCAT GTTAA −65Acetyltransferase, GNAT family protein
−168A TTAA TTGATT GTTAA −153
    NWMNN_1337 dfrA −58 GTTAA ATTAAA G A TAA −43Dihydrofolate reductase
    NWMNN_1349 ald −122 GTTAA TAAATAT TTAA −107Alanine dehydrogenase 2
    NWMNN_1412 zwf −194 GTTA TGTCTAC GTTAA −179Glucose-6-phosphate 1-dehydrogenase
    NWMNN_1432 accB −190T TTAA TCAAGA GTTAA −175Acetyl coenzyme A carboxylase, biotin carboxyl carrier protein
    NWMNN_1453−145 GTTAA TTTAAAT TTAA −1305-Formyltetrahydrofolate cyclo-ligase
    NWMNN_1500−16 G G TAA AGGTGA GTTAA −1Hydrolase, HAD-superfamily, subfamily IIIA
    NWMNN_1593 pfk −47 G G TAA TTTAGA GTTAA −326-Phosphofructokinase
    NWMNN_1595 accD −188T TTAA TTAAAC GTTAA −173Acetyl coenzyme A carboxylase beta subunit
−76 GTTAA AAACGG GTT T A −61
    NWMNN_1871−22T TTAA AGAGAG GTTAA −7Aspartate transaminase
    NWMNN_1929b −288T TTAA TAAATA GTTAA −273Similar to succinyl-diaminopimelate desuccinylase
    NWMNN_2047 manA1 −194 GTTAA AGTACT GT A AA −179Mannose-6-phosphate isomerase, class I
    NWMNN_2201−122 GTTAA TTTAAG GTTA T−107Dehydrogenase family protein
    NWMNN_2206−240 GTTAA ATGGATT TTAA −225Monooxygenase family protein
−239 GTTAA AATCCAT TTAA −224
    NWMNN_2271−82 GTTAA TGTATTT TTAA −67Acetyltransferase, GNAT family protein
    NWMNN_2272−124 GTTAA TGTATTT TTAA −109Zinc-containing alcohol dehydrogenase
    NWMNN_2592−220 GTTAA CAACAC GTTAA −2052-Oxoglutarate/malate translocator
−219 GTTAA CGTGTT GTTAA −204
    NWMNN_2467−107C TTAA TTAAGG GTTAA −92 O-Acetyltransferase OatA
    NWMNN_2526 phoB −87 GTTAA AAATAT GT A AA −72Alkaline phosphatase III precursor
DNA replication/ recombination/repair
    NWMNN_0090−27 G G TAA TAGCCG GTTAA −12Similar to replication initiation protein
    NWMNN_0448 holB −170 GTTAA TAACTTA TTAA −155DNA polymerase III delta subunit
    NWMNN_1364 dnaD −36A TTAA GTAATG GTTAA −21DNA replication protein DnaD
Nucleotide metabolism
    NWMNN_0249−37T TTAA AATACA GTTAA −225′ nucleotidase, lipoprotein e(P4) family protein
    NWMNN_0699 nrdI −310 GTTAA ATTACTT TTAA −295Ribonucleotide reduction-related NrdI protein
    NWMNN_0809−86 GTTAA TGAACA GTTA T−71Similar to pyridine nucleotide-disulfide oxidoreductase
    NWMNN_1118−345 GTTAA TTATCC G C TAA −330Pseudouridylate synthase
−249A TTAA AATTAA GTTAA −234
    NWMNN_1119b pryR −54 GTTA CAATCAT GTTAA −39Pyrimidine operon regulatory protein
    NWMNN_1120b gmk −236 GTTA CAATCAT GTTAA −221Guanylate kinase
    NWMNN_1143 rnc −52T TTAA TTTTAC GTTAA −37RNase III
    NWMNN_1185 ftsK −42 GTTAA AACGAC GTTA T−27DNA translocase FtsK/SpoIIIE family protein
    NWMNN_1411−134 GTTA TGTCTAC GTTAA −119Similar to RNase Z
    NWMNN_2091−55 GTTA CTTAAGC GTTAA −40Similar to quinone oxidoreductase
Unknown function
    NWMNN_0039−49 GTTAA AATAGCA TTAA −34Conserved hypothetical protein
    NWMNN_0087−86 GT A AA TTTTTC GTTAA −71Conserved hypothetical protein
    NWMNN_0157−22A TTAA TAAATA GTTAA −7Conserved hypothetical protein
    NWMNN_0165b −123 GTTAA TATATA GTTAA −108Conserved hypothetical protein
−102 GTTAA TGCTTT GTT T A −87
    NWMNN_0295−55 GTTA CAAAGAG GTTAA −40Similar to ORF041 of Bacteriophage 96
    NWMNN_0362−95 GTTAA TCAAGA GTTAA −80Conserved hypothetical protein
−84 GTTAA GATGAAT TTAA −69
    NWMNN_0370−43 GTTAA GATGCT GTTA T−28Conserved hypothetical protein
    NWMNN_0387−378 GTTAA ATGAGGT TTAA −363Conserved hypothetical protein
    NWMNN_0402b −90T TTAA TAAATA GTTAA −75Conserved hypothetical protein
    NWMNN_0403b lpl1nm −254T TTAA TAAATA GTTAA −239Staphylococcal tandem lipoprotein
    NWMNN_0503−103 GTTAA AACCCC GTTA T−88Similar to small methyltransferase
    NWMNN_0546−109C TTAA TAGCTT GTTAA −94Conserved hypothetical protein
    NWMNN_0605−98 GTTAA ACTAATT TTAA −83Conserved hypothetical protein
    NWMNN_0632−239 GTTAA AAATTT GT A AA −224Conserved hypothetical protein
    NWMNN_0687−250 GTTAA TTGAAT G A TAA −235Conserved hypothetical protein
−181 GTTAA ATCAAA GTT G A −166
    NWMNN_0746−147 GTTAA ATATGT GTTA T−132Conserved hypothetical protein
    NWMNN_0759−126 GTTAA TAGTTT GTT C A −111Conserved hypothetical protein
−115 GTT C A TCGCAA GTTAA −100
    NWMNN_0810−246 GTTAA TGAACA GTTA T−231Conserved hypothetical protein
    NWMNN_0823−29C TTAA AAGTAT GTTAA −14Conserved hypothetical protein
    NWMNN_0834−164 GTTAA GAGAAAA TTAA −149Conserved hypothetical protein
    NWMNN_0956−262 GTTAA CAATAAA TTAA −247Similar to Zn-dependent hydrolase
−261T TTAA TTTATT GTTAA −246
    NWMNN_0958−321 GT A AA AAGGTT GTTAA −306Conserved hypothetical protein
    NWMNN_1059−56 GTTA CAATATG GTTAA −41hypothetical protein
    NWMNN_1067−99A TTAA TGAAGT GTTAA −84Conserved hypothetical protein
−98 GTTAA CACTTCA TTAA −83
    NWMNN_1072−46 GTTAA ACTTAA GTT G A −31Conserved hypothetical protein
    NWMNN_1077b −85 G C TAA AACTAT GTTAA −70Conserved hypothetical protein
    NWMNN_1152b −221 GTTAA ATCTAA GTTA C−206Conserved hypothetical protein
    NWMNN_1153b −195 GTTAA ATCTAA GTTA C−180Similar to GTP binding protein
    NWMNN_1487b −280 GTTA GACTTTT GTTAA −265GTP binding protein LepA
    NWMNN_1599−42 GTTA TAATGTA GTTAA −27CBS domain DNA binding protein
    NWMNN_1663−182 GTTAA AAATATT TTAA −167Conserved hypothetical protein
−181 GTTAA AATATTT TTAA −166
    NWMNN_1669−31T TTAA TAAGTT GTTAA −16Conserved hypothetical protein
    NWMNN_1707b −376 GTTAA TTAATAT TTAA −361Hypothetical protein
−365 GTTAA TAAGTG GTTAA −350
−354T TTAA TAAAAC GTTAA −339
    NWMNN_1708−109 GTTAA TAGATA GTTAA −94Conserved hypothetical protein, homologous to ear (MW0758)
    NWMNN_1859−71 G A TAA ATGATT GTTAA −56Conserved hypothetical protein
    NWMNN_1860−214 G A TAA ATGATT GTTAA −199Conserved hypothetical protein
    NWMNN_2075−219 GTT T A AAAAAG GTTAA −204Conserved hypothetical protein
    NWMNN_2088−23 GTTAA AGTTAAT TTAA −8Conserved hypothetical protein
    NWMNN_2202−141 GTTAA TTTAAG GTTA T−126Conserved hypothetical protein
    NWMNN_2228−109 GTTAA GATGAT GT A AA −94Conserved hypothetical protein
    NWMNN_2408−184 GTTAA GCGGAAT TTAA −169Conserved hypothetical protein
    NWMNN_2409−378 GTTAA GCGGAAT TTAA −363DedA family protein
    NWMNN_2415−183 GTTA TAATACA GTTAA −168Conserved hypothetical protein
    NWMNN_2432−74 GTTAA GTTGAT GT A AA −59Conserved hypothetical protein
    NWMNN_2436−46T TTAA AATCAT GTTAA −31Conserved hypothetical protein
    NWMNN_2508−202 GTTAA TGTGTT GTT C A −187Conserved hypothetical protein
    NWMNN_2525−126 GTTAA AAATAT GT A AA −111Hypothetical protein
    NWMNN_2587b −40 GTTA TAAGCAT GTTAA −25Similar to rhodanese family protein
  • a The start point and end point are the distance from the translation start codon. Conserved repeat sequences are underllined.

  • b This gene shares the same repeat sequence with an adjacent gene.

  • c MHC, major histocompatibility complex.