myRT
Top 15 domains that tend to co-occur with UG15 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG15 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 UG15).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG15 | 82 (100%) | 1 (82/82) | link | piechart |
| YeeA (COG1002) | 15 (18%) | 0.288 (15/52) | link | piechart |
| PRK09692 (Integrase; provisional) | 13 (16%) | 0.038 (13/342) | link | piechart |
| Psu (pfam07455) | 12 (15%) | 0.158 (12/76) | link | piechart |
| DUF4065 (pfam13274) | 11 (13%) | 0.786 (11/14) | link | piechart |
| PRK11462 (putative transporter; Provisional) | 9 (11%) | 0.243 (9/37) | link | piechart |
| HsdR (COG4096) | 9 (11%) | 0.323 (10/31) | link | piechart |
| PRK09678 (DNA-binding transcriptional regulator; Provisional) | 8 (10%) | 0.043 (8/184) | link | piechart |
| EcoEI_R_C (pfam08463) | 8 (10%) | 0.615 (8/13) | link | piechart |
| HsdM (COG0286) | 6 (7%) | 0.072 (6/83) | link | piechart |
| GepA (COG3600) | 6 (7%) | 0.462 (6/13) | link | piechart |
| CAD1 (cd05283) | 6 (7%) | 0.429 (6/14) | link | piechart |
| YeeA (COG1002)*2 | 5 (6%) | 0.227 (5/22) | link | piechart |
| Vma12 (pfam11712) | 5 (6%) | 1 (5/5) | link | piechart |
| VacB (COG0557)*2 | 4 (5%) | 1 (4/4) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG15 | 1098 (100%) | 1 (1098/1098) | link | piechart |
| YeeA (COG1002) | 230 (21%) | 0.339 (230/678) | link | piechart |
| DUF4065 (pfam13274) | 216 (20%) | 0.893 (216/242) | link | piechart |
| HsdR (COG4096) | 153 (14%) | 0.442 (153/346) | link | piechart |
| EcoEI_R_C (pfam08463) | 147 (13%) | 0.907 (147/162) | link | piechart |
| CAD1 (cd05283) | 109 (10%) | 0.458 (109/238) | link | piechart |
| YeeA (COG1002)*2 | 94 (9%) | 0.425 (94/221) | link | piechart |
| PRK09692 (Integrase; provisional) | 65 (6%) | 0.032 (65/2021) | link | piechart |
| COG3587 (Restriction endonuclease ) | 65 (6%) | 0.598 (64/107) | link | piechart |
| DEAH_box_HrpB (TIGR01970) | 53 (5%) | 0.697 (53/76) | link | piechart |
| PBP2_HisK (cd13704) | 50 (5%) | 0.667 (50/75) | link | piechart |
| GepA (COG3600) | 49 (4%) | 0.516 (49/95) | link | piechart |
| IV_pilus_PilQ (TIGR02515) | 48 (4%) | 0.98 (48/49) | link | piechart |
| PRK11462 (putative transporter; Provisional) | 47 (4%) | 0.42 (47/112) | link | piechart |
| Frag1 (pfam10277) | 47 (4%) | 1 (47/47) | link | piechart |