Table 5.
Summary of the occurrence of common cluster-associated genes in archaea. COG2254 typically adjoins a cas3 gene (in A. fulgidus, M. jannaschii and several Crenarchaea) and they are sometimes fused. Symbols: * = cas1/cas4 are fused; and ** = A cas gene operon links two clusters with different repeat sequences.
| Organism | Repeat sequence | Flank | No. of | COG | COG | COG | COG | COG | COG | COG | COG | COG | COG | COG | ||
| clusters | 1518/ | 1343/ | 1203/ | 1468/ | 1688/ | 1583/ | 2254 | 4343/ | 1857/ | 2462/ | 1353/ | |||||
| cas1 | cas2 | cas3 | cas4 | cas5 | cas6 | csa1 | csa2 | csa3 | pol | |||||||
| H. butylicus | CTTGCAATTCTCTTTTGAGTTGTTC | + | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||
| P. aerophilum | GTTTCAACTATCTTTTGATTTCTGG | + | 3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||
| CTTTCAATCCTCTTTTTGAGATTC | – | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||
| GTTTCAATTCTTTTGTAGATTCTTC | – | 1 | ||||||||||||||
| A. pernix | CTTGCAATTCTATCTCGAAGATTC | + | 3 | |||||||||||||
| CTTTCTATTCCCTTTAGGGATATGC | – | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||
| S. solfataricus | CTTTCAATTCCTTTTGGGATTAATC | + | 3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||
| CTTTCAATTCTATAAGAGATTATC | + | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | |||
| CTTTCAATTCTATAGTAGATTAGC | – | 2 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||||
| S. tokodaii | CTTTCAATTCCTTTTGGGATTCATC | + | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |||
| CTTTCAATTCCATTAAGGATTATC | + | 3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||
| CTTTATTCATAATGCTAATTCCGT | – | 1 | ||||||||||||||
| S. acidocaldarius | GTTTTAGTTTCTTGTCGTTATTAC | + | 2 | 1 | 1 | 1 | 1 | 1 | ||||||||
| CTTTCAATCCCTTTTGGGATTCATC | + | 3 | 1 | 1 | 1 | 1 | ||||||||||
| N. equitans | CTTTCAATATTTCTAATATATTAGAAAC | + | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||
| P. abyssi | CTTTCAATTCTATTTTAGTCTTATTGGAAC | – | 3 | |||||||||||||
| P. furiosus | CTTTCCACACTACTAAGTTCTACGGAAAC | – | 2 | 1 | 1 | |||||||||||
| P. horikoshii | CTTTCCACACTATTTAGTTCTACGGAAAC | + | 4 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |||||
| CTTTCAATTCTATTTTAGTCTTATTGGAAC | + | 3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |||||||
| T. kodakaraensis | CTTTCAATTCTCTTAGAGTCTTATTGCAAC | + | 3 | 1 | 1 | 2 | 1 | 2 | 2 | 1 | 2 | 1 | ||||
| P. torridus | CTTCCATACTATCTAGTAATTCTTAAAC | + | 2 | 1 | 1 | 1 | 1 | |||||||||
| CTTTCAATCCTATTTAGGTTATTATTTAAC | – | 1 | 1 | 1 | 1 | 1 | 1 | |||||||||
| A. fulgidus | CTTTCAATCCCATTTTGGTCTGATTTCAAC | + | 2 | 1 | 1 | 1 | ||||||||||
| CTTTCAATCTCCATTTTCAGGAGCCTCCCTTTCTTAC | – | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |||
| T. acidophilum | CTTTCAATCCTATTAAGGTTCTATTTTAC | – | 2 | |||||||||||||
| T. volcanium | CTTCCATACTAACTAGTACATCTTAAAC | + | 3 | 1 | 1 | 1 | 1 | |||||||||
| M. kandleri | GTTTCATTACCCGTATTATTACGGGTTAATTGCGAG | + | 5 | 1 | 1 | 2 | ||||||||||
| M. jannaschii | ATTTCCATTCCCCGAGGGATCTGATTTTAC | + | 20 | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | ||||
| M. thermoautotroficus | ATTTCAATCCCATTTTGGTCTGATTTTAAC | + | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |||||
| M. barkeri** | GTTTCAATCCCTCTAAGGCCTGATTTTAAC | – | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||
| GTTTCAATCCTTGTTTTAGTGGATCTTGCTCACGAAT | + | 3 | ||||||||||||||
| GTTTCCATAACCGAAAGGTTGTGGCAGAATTGAAGC | – | 1 | 1* | 1 | 1 | 1* | ||||||||||
| M. acetivorans** | GTTTCAATCCTTGTTTTAGTGGATCTTGCTCGCGAAT | + | 6 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||
| GTTTCAATCCCTCTAAGGTCTGATTTTAAC | – | 1 | ||||||||||||||
| M. mazei | GTTTCAATCCTTGTTTTAGTGGATCTTGCTCACGAAT | + | 8 | 1 | 1 | 1 | 1 | 1 | 1 | |||||||
| M. hungatei | GTTGCAAGTGACCCGAAAATAGAAGGGTATGGCAAC | + | 3 | 1 | 1 | 1 | 1 | |||||||||
| GTTTCAATCCCTATCGGGTTTTCTTTTCCATTGTGAC | – | 2 | 1 | 1 | 1 | 1 | 1 | |||||||||
| GGTTCATCCCCATACACACGGGGAACTC | – | 1 | 1 | 1 | 1 | |||||||||||
| M. stadtmanae | GTTTAAAATAGACTTAATAGTATGAAAAC | – | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |||||||
| CTTTCAATTTCATTATGATCTTATTCTATT | – | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||||
| M. burtonii | GAGTTCCCCATGCATGTGGGGATAAACCG | – | 1 | 1 | 1 | 1 | ||||||||||
| GTTTCAATCCCTCTAAGGTCTGATTTTAAC | – | 1 | 1 | 1 | 1 | 1 | 1 | |||||||||
| H. marismortui, | GCTTCAACCCCACGAGGGTCCGTCTGTAAC | + | 3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||
| pNG400 | ||||||||||||||||
| N. pharaonis | GCTTCAACCCCACAAGGGTTCGTCTGAAAC | – | 2 | |||||||||||||
| GTCGAGACGGACTGAAAACCCAGAACGGGATTGAAAC | – | 2 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||||