myRT
Top 15 domains that tend to co-occur with CRISPR RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with CRISPR RT.Note 2: X*2, if found in the table, either means one gene has two consecutive X domains or two adjacent genes both have X domain.
Note 3: If two instances of a domain X are found in the neighborhood of a particular RT R, it will be counted as 2 occurences of domain X, but 1 co-occurance of X and R).
Note 4: click on 'link' to retrieve all genomes that contain the domain, and 'piechart' to see this domain's distribution among different RTs (including CRISPR).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-CRISPR | 146 (100%) | 1 (142/142) | link | piechart |
| Cas2_I_II_III (cl11442) | 89 (61%) | 0.927 (89/96) | link | piechart |
| Cas1_I-II-III (cl00656) | 86 (59%) | 0.954 (83/87) | link | piechart |
| CRISPR_Cas6 (pfam10040) | 32 (22%) | 0.97 (32/33) | link | piechart |
| Cas_Cas1 (pfam01867) | 24 (16%) | 1 (24/24) | link | piechart |
| Cmr6_III-B (cd09661) | 21 (14%) | 0.955 (21/22) | link | piechart |
| TPR_12 (pfam13424) | 15 (10%) | 0.175 (7/40) | link | piechart |
| Cas6b_N (pfam17955) | 15 (10%) | 0.938 (15/16) | link | piechart |
| Cas6b_C | 15 (10%) | 0.833 (15/18) | link | piechart |
| cas_Cmr5 (TIGR01881) | 14 (10%) | 1 (19/19) | link | piechart |
| cas1 (TIGR00287) | 12 (8%) | 0.923 (12/13) | link | piechart |
| TPR_10 (pfam13374) | 11 (8%) | 0.35 (7/20) | link | piechart |
| HTH_XRE (smart00530) | 11 (8%) | 0.017 (11/664) | link | piechart |
| DUF4384 (pfam14326) | 11 (8%) | 1 (11/11) | link | piechart |
| TIGR03986 (CRISPR-associated protein) | 10 (7%) | 0.909 (10/11) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-CRISPR | 2059 (100%) | 1 (2021/2021) | link | piechart |
| Cas1_I-II-III (cl00656) | 1311 (64%) | 0.956 (1299/1359) | link | piechart |
| Cas2_I_II_III (cl11442) | 1088 (53%) | 0.971 (1080/1112) | link | piechart |
| CRISPR_Cas6 (pfam10040) | 372 (18%) | 0.979 (372/380) | link | piechart |
| Cas_Cas1 (pfam01867) | 363 (18%) | 0.948 (363/383) | link | piechart |
| Cmr6_III-B (cd09661) | 187 (9%) | 0.935 (187/200) | link | piechart |
| TIGR03986 (CRISPR-associated protein) | 159 (8%) | 0.981 (154/157) | link | piechart |
| Cas_Cmr5 (pfam09701) | 125 (6%) | 1 (152/152) | link | piechart |
| RVT-CRISPR*2 | 86 (4%) | 1 (86/86) | link | piechart |
| cas1 (TIGR00287) | 79 (4%) | 0.935 (86/92) | link | piechart |
| cas1_HMARI (TIGR03641) | 73 (4%) | 1 (73/73) | link | piechart |
| Csx1_III-U (cl21570) | 68 (3%) | 0.817 (67/82) | link | piechart |
| CRISPR_Cas2 (pfam09827) | 66 (3%) | 0.767 (66/86) | link | piechart |
| COG4951 (Uncharacterized protein ) | 65 (3%) | 0.525 (64/122) | link | piechart |
| Cas6b_N (pfam17955) | 61 (3%) | 0.735 (61/83) | link | piechart |