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Table 1 In silico predicted LexA binding sites in C. difficile ribotypes

From: The LexA regulated genes of the Clostridium difficile

      Various toxinotypes Toxinotype V Toxinotype 0/nontoxinogenic
      O33 O27 O75 O17 O78 126 OO9 OO1 O12 OO5 O87 O14 O53
Gene accession number GENE Product LexA BOX Distance 1 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 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 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....GTTT 111 NO 7 2 1 NO NO 1 3 3 3 1 1 1
CDR20291_1611 moaB Molybdenum cofactor biosynthesis GAAC…GTTT 6 NO 8 2 NO NO NO 1 3 NO 3 1 1 NO
CDR20291_2775 celG Cellobiose-phosphate degrading protein GAAC....GTTT −314 NO 8 2 NO NO NO NO NO NO NO NO NO NO
CDR20291_3372 phnH Phosphonate metabolism protein GAAC....CTTT 34 NG 8 2 1 NG NG 1 3 3 3 1 1 1
CDR20291_1600 thiC Thiamine biosynthesis protein ThiC GAAC....ATTT 175 1 NO NO NO 3 2 NO NO NO NO NO NO NO
CDR20291_1940   N-carbamoyl-L-amino acid hydrolase GAAC....GTTT 147 NO NO NO NO NO NO NO 3 3 NO NO NO 1
CDR20291_2056   Endonuclease/exonuclease/phosphatase GAAC....GTTT −466 1 8 2 1 3 2 1 3 3 3 1 1 1
NAP07v1_640016   Two-component sensor histidine kinase GAAC....GTTT 217 NO 8 NO NO NO NO NO NO NO NO NO NO NO
CDR20291_0331 cbiQ Cobalt transport protein GAAC....GTTT 122 1 8 2 1 3 2 1 3 3 3 1 1 1
CDR20291_2597   Putative oxidoreductase GAAC....CTTC 2 1 8 2 1 3 2 1 3 3 3 1 1 1
NAP07v1_470051 aroF P-2-dehydro-3-deoxyheptonate aldolase GAAC....CTTT 225 1 NO NO NO 3 2 NO NO NO NO NO NO NO
97b34v1_600001   Transposase GAAC....GTTT 217 NO 8 NO NO NO NO NO NO NO NO NO NO NO
CDE15v2_1270013   Putative cI repressor GAAC....GTTC 67 NG NG NG NG NG NG NG NG NG NO 1 NO NG
63q42v1_370450   Extrachromosomal origin protein GAAC…GTTT 10 NG NG NG NG NG NG 1 3 3 3 1 1 1
CDR20291_1803 vexP ABC transporter. ATP-binding/permease GTTC....TTTT 85 NO 8 2 1 NO NO NO 1 2 NO NO NO 1
97b34v1_250108   ABC-type transport system. sugar-family GAAC…GTTC 267 NG 8 2 NG NG NG NG NG NG NG NG NG NG
  1. Sequences of putative LexA operators and their positions (according to the start of the gene coding region). Numbers denote strains with the operator identified. NO marks the gene that was identified in the strain but a target LexA site was not found in its promoter region, NG marks that gene was not found in the genome of the strain.