Table 2. Putative protospacer matches identified through in silico analysis of clostridial CRISPR spacers.
| Organism (CRISPR-Cas subtype) | Spacer-protospacer matcha | Invading elementb | Mismatches | Putative PAM sequencec |
|---|---|---|---|---|
| C. autoethanogenum DSM 10061 (Type I-B) | AAGAGTTGATACTTTACTTATAGATTACTTAGGTGCAAGAGTTGATACTTTACTTATAGATTACTTAGGTGC | Clostridium ljungdahlii DSM 13528 (incomplete prophage) | 0 | 5′-ATTAA-3′ |
| TAGACCACAATTAAATGCAATGTTAGAATTTGCTCGTAGGCCACAATTAAAAGCCATGTTAGAATTTGCTAG | Clostridium phage vB_CpeS-CP51 | 4 | 5′-ACTAA-3′ | |
| AAATACATTTTATAAATTATTAAAAGAATATGAGGAAATACTTTTTATAAAATATTGAAAGAATATGAAG | Bacillus thuringiensis HD-789 plasmid pBTHD789-3 | 4 | 5′-AAGAA-3′ | |
| GCAGCTCCAGGAGCAAAAACCAAAGGTACTATTCGCGAAGCTCCAGGAGCAAAAATCAAAGGTATTTATTTT | Enterococcus durans strain KLDS 6.0930 (vicinity of transposase and phage genes) | 8 | 5′-ATCAA-3′ | |
| C. tetani 12124569 (Type I-B) | ATATTTCTTTTTTACTCCAATAAGCTCCAATGAGATATTTCTTTTTTACTCCAATCAGCCCCAATAAG | Clostridium botulinum A2 str. Kyoto (intact prophage) | 3 | 5′-TTTTA-3′ |
| AAAAGCCAATCAAAATCTATTTTATATTTAGATTTAAAAGCCAGTCAAAATCTATTAAATATTTAGATTT | Clostridium botulinum F str. 230613 (intact prophage) | 3 | 5′-TATAA-3′ | |
| AAAGATAAGAGAGAAGGATTACTTCCAGAAGTAGCAAAGACAAGCGAGAAGGGTTGCTTCCAGAAGTCTA | Bacillus sp. FJAT-4402 (questionable prophage) | 7 | 5′-CATCA-3′ | |
| C. thermocellum ATCC 27405 (Type I-B) | ATTCGTTTATCTTTATCAAATCACTCCCTCCCTTCAGATTCGTTTGTCTTTATCAAATCACTCCCTCCTTTCAG | Clostridium stercorarium subsp. stercorarium DSM 8532 (intact prophage) | 2 | 5′-TTTCA-3′ |
| TGATGAAGGACGCTGAAACAGGAATGTTCCAGGCTGTGATGAAGGACGCTGAAACAGGAATGTTTCAGGCCG | Clostridium clariflavum DSM 19732 (vicinity of transposase) | 2 | 5′-GGACA-3′ | |
| ACGAAGCAGGTTTATACAGTTTGATATTGAAATCAAACGAATCAGGTTTATACAGTTTAATCTTTTCATCAA | Staphylococcus phage vB_SauM_Remus | 6 | 5′-AATCA-3′ |
aSpacer-protospacer mismatches are underlined. In instances where multiple protospacer hits were obtained from a single spacer query, the top hit is provided. Generally, PAM sequences were found to be identical between multiple protospacer hits from a single spacer sequence.
bFor hits found within bacterial genomes, the location of the protospacer sequence relative to prophage regions and mobile genetic elements is provided in parentheses.
c5 nt of adjacent sequence is provided. Potential conserved residues are bolded.