myRT
Top 15 domains that tend to co-occur with UG9 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG9 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 UG9).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG9 | 31 (100%) | 1 (31/31) | link | piechart |
| PRK14975 (bifunctional 3'-5' exonuclease/DNA polymerase; Provisional) | 23 (74%) | 0.92 (23/25) | link | piechart |
| HTH_28 (pfam13518) | 8 (26%) | 0.073 (8/110) | link | piechart |
| DDE_3 (pfam13358) | 8 (26%) | 0.023 (8/355) | link | piechart |
| UvrD_C (pfam13361) | 6 (19%) | 0.6 (6/10) | link | piechart |
| upstrm_HI1419 (TIGR02683) | 6 (19%) | 0.667 (6/9) | link | piechart |
| ComA-like_MBL-fold (cd07731) | 6 (19%) | 0.267 (4/15) | link | piechart |
| PRK05755 (DNA polymerase I; Provisional) | 4 (13%) | 0.25 (4/16) | link | piechart |
| INT_C_like_1 (cd01184) | 3 (10%) | 0.064 (3/47) | link | piechart |
| PRK05318 (deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional) | 2 (6%) | 0.021 (2/97) | link | piechart |
| KdpC (pfam02669) | 2 (6%) | 0.667 (2/3) | link | piechart |
| InsE (COG2963) | 2 (6%) | 0.001 (2/1639) | link | piechart |
| HTH_17 (pfam12728) | 2 (6%) | 0.026 (2/76) | link | piechart |
| HsdR (COG4096) | 2 (6%) | 0.065 (2/31) | link | piechart |
| GT4_MtfB-like (cd03809) | 2 (6%) | 0.25 (2/8) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG9 | 365 (100%) | 1 (365/365) | link | piechart |
| PRK14975 (bifunctional 3'-5' exonuclease/DNA polymerase; Provisional) | 192 (53%) | 0.901 (192/213) | link | piechart |
| UvrD_C (pfam13361) | 76 (21%) | 0.784 (76/97) | link | piechart |
| INT_C_like_1 (cd01184) | 48 (13%) | 0.16 (48/300) | link | piechart |
| ComA-like_MBL-fold (cd07731) | 44 (12%) | 0.269 (43/160) | link | piechart |
| PRK05755 (DNA polymerase I; Provisional) | 31 (8%) | 0.261 (31/119) | link | piechart |
| KdpC (pfam02669) | 30 (8%) | 0.638 (30/47) | link | piechart |
| DNA_pol_A (pfam00476) | 28 (8%) | 0.933 (28/30) | link | piechart |
| ComA-like_MBL-fold (cd07731)*2 | 21 (6%) | 0.656 (21/32) | link | piechart |
| DNA_pol_A (pfam00476)*2 | 15 (4%) | 1 (15/15) | link | piechart |
| PinE (COG1961) | 13 (4%) | 0.008 (13/1541) | link | piechart |
| VWA (smart00327) | 12 (3%) | 0.16 (12/75) | link | piechart |
| TadG (COG4961) | 12 (3%) | 0.923 (12/13) | link | piechart |
| PRK10426 (alpha-glucosidase; Provisional) | 12 (3%) | 0.857 (12/14) | link | piechart |
| TauC (COG0600) | 10 (3%) | 0.27 (10/37) | link | piechart |