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