myRT
Top 15 domains that tend to co-occur with UG1 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG1 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 UG1).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG1 | 71 (100%) | 1 (71/71) | link | piechart |
| GerD (pfam17898) | 10 (14%) | 0.909 (10/11) | link | piechart |
| YeeP (COG3596) | 8 (11%) | 0.471 (8/17) | link | piechart |
| HsdM (COG0286) | 7 (10%) | 0.095 (7/74) | link | piechart |
| AidA (COG3468) | 6 (8%) | 0.667 (6/9) | link | piechart |
| AidA (COG3468)*2 | 5 (7%) | 0.714 (5/7) | link | piechart |
| nitrilase_Rim1_like (cd07574) | 4 (6%) | 0.5 (4/8) | link | piechart |
| nitrilase (cl11424) | 4 (6%) | 0.02 (4/201) | link | piechart |
| InsE (COG2963) | 4 (6%) | 0.002 (4/1630) | link | piechart |
| PHA02517 (putative transposase OrfB; Reviewed) | 3 (4%) | 0.001 (3/2128) | link | piechart |
| HTH_ARSR (smart00418) | 3 (4%) | 0.042 (3/71) | link | piechart |
| HsdR (COG4096) | 3 (4%) | 0.15 (3/20) | link | piechart |
| HEPN_Apea (pfam18739) | 3 (4%) | 0.333 (3/9) | link | piechart |
| DUF4145 (pfam13643) | 3 (4%) | 0.429 (3/7) | link | piechart |
| DUF262 (pfam03235) | 3 (4%) | 0.086 (3/35) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG1 | 682 (100%) | 1 (682/682) | link | piechart |
| HsdM (COG0286) | 80 (12%) | 0.102 (80/788) | link | piechart |
| GerD (pfam17898) | 75 (11%) | 0.987 (75/76) | link | piechart |
| HsdR (COG4096) | 73 (11%) | 0.451 (73/162) | link | piechart |
| RMtype1_S_SonII-TRD2-CR2_like (cd17246) | 48 (7%) | 0.271 (45/166) | link | piechart |
| RMtype1_S_SonII-TRD2-CR2_like (cd17246)*2 | 41 (6%) | 0.333 (41/123) | link | piechart |
| YeeP (COG3596) | 33 (5%) | 0.317 (33/104) | link | piechart |
| DUF3800 (pfam12686) | 29 (4%) | 0.181 (29/160) | link | piechart |
| DUF4145 (pfam13643) | 25 (4%) | 0.208 (25/120) | link | piechart |
| RhsA (COG3209) | 23 (3%) | 0.088 (12/137) | link | piechart |
| Smc (COG1196) | 22 (3%) | 0.18 (22/122) | link | piechart |
| HEPN_Apea (pfam18739) | 21 (3%) | 0.089 (21/237) | link | piechart |
| XRE (COG1476) | 20 (3%) | 0.198 (20/101) | link | piechart |
| nitrilase_Rim1_like (cd07574) | 20 (3%) | 0.909 (20/22) | link | piechart |
| HTH_ARSR (smart00418) | 20 (3%) | 0.049 (20/411) | link | piechart |