Among the thirty genomes, the search yielded at least one putative operator sequence upstream of more than 30 genes involved in a variety of biological processes e.g. DNA repair, transport, virulence and antibiotic resistance (Table 1). Table 1 In silico predicted LexA binding sites in C. difficile ribotypes           Various toxinotypes Toxinotype V Toxinotype 0/nontoxinogenic JNK-IN-8 cost           O33 O27 O75 O17 O78 126 OO9 OO1 O12 OO5 O87 O14 O53 Gene accession number GENE Product LexA BOX Distance 1 PI3K inhibitor strain 8 strains 2 strains 1 strain 3 strains 2 strains 1 strain 3 strains 3 strains 3 strains 1 strain 1 strain 1 strain CDR20291_1854 lexA Transcriptional regulator. LexA repressor GAAC….GTTT −51/-91 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_1169 recA Protein RecA (Recombinase A) GAAC….GTTT −39/-41 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_2696 ruvC Crossover junction endodeoxyribonuclease

GAAC….GTTT −65 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_3234 uvrB Excinuclease ABC subunit B GAAC….GTTC −30 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_0487 rusA Putative RusA-like endodeoxyribonuclease GAAC….GTTT −122 1 4 1 1 3 2 NO NO 1 NO NO 1 NO CDR20291_2024 trxB Thioredoxin reductase GAAC….GTTT −216 NO NO Akt inhibitor NO NO NO NO 1 NO NO NO NO NO NO 63q42v1_580022 rps3 Putative 30S ribosomal protein S3 GAAC….GTTA −284 NG NG 1 NG NG NG NG 1 NG NG NG NO NO CDR20291_3107 sspB Small. acid-soluble spore protein beta GAAC….GTTC 34 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_0784 oppC ABC-type transport system. oligopeptide GAAC…GTTT −285/ -286 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_3532 soj Small walker A ATPase, chromosome replication GAAC….GTTT −226 NO 8 2 1 NO NO 1 3 3 3 NO 1 1 CDR20291_2297   Putative

multidrug efflux pump GAAC…TTTT −138 1 8 2 1 3 2 1 3 3 3 1 1 1 63q42v1_310170   ABC-type Reverse transcriptase multidrug-family GAAC….CTTT −154 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_3125 vanR Regulatory protein vanR GAAC….ATTT −222 NO 8 2 NO NO NO NO NO NO NO NO NO NO CDR20291_0083 rplR 50S ribosomal protein L18 GAAC….GTTT −261/ -262 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_0060 rpoB DNA-directed RNA polymerase subunit β GAAC…GTTT −42/-43 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_1619   Putative transcriptional regulator GAAC…GTTT 30/31 1 8 2 1 3 2 1 3 3 3 1 1 1 63q42v1_570034   Helix-turn-helix domain protein GAAC…CTTT −97 NG 3 NG 1 NG NG NG 1 NG 1 NG NG NG CDR20291_0882 potC ABC-type transport system. GAAC…GTTC −207 1 8 2 1 3 2 1 3 3 3 1 1 1 CDR20291_0584 tcdA Toxin A GAAC….GTTT −525 NG 8 2 NG 3 2 NG 3 3 3 1 1 1 CDR20291_3466   Putative cell wall hydrolase GAAC…GTTT −68 NO 8 NG NO NO NO NO NO NO NO NO NO NO CDR20291_2689   Putative membrane protein GAAC….