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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.
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BMC Microbiology

ISSN: 1471-2180

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