myRT
Top 15 domains that tend to co-occur with UG3 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG3 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 UG3).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG3 | 199 (100%) | 1 (199/199) | link | piechart |
| RVT-UG8 | 194 (97%) | 0.907 (194/214) | link | piechart |
| PRK09692 (Integrase; provisional) | 22 (11%) | 0.069 (22/320) | link | piechart |
| PRK09678 (DNA-binding transcriptional regulator; Provisional) | 21 (11%) | 0.126 (21/167) | link | piechart |
| proA (TIGR00407) | 7 (4%) | 0.292 (7/24) | link | piechart |
| INT_Rci_Hp1_C (cd00796) | 7 (4%) | 0.106 (7/66) | link | piechart |
| INT_P4_C (cd00801) | 6 (3%) | 0.046 (6/130) | link | piechart |
| SLATT_5 (pfam18160) | 5 (3%) | 0.03 (5/169) | link | piechart |
| PP-binding (pfam00550) | 5 (3%) | 0.208 (5/24) | link | piechart |
| PinE (COG1961) | 5 (3%) | 0.016 (5/311) | link | piechart |
| Phage_int_SAM_5 (pfam13102) | 5 (3%) | 0.085 (5/59) | link | piechart |
| NRPS_term_dom (TIGR02353) | 5 (3%) | 1 (5/5) | link | piechart |
| mutS1 (TIGR01070) | 5 (3%) | 0.333 (5/15) | link | piechart |
| INTN1_C_like (cd01185) | 5 (3%) | 0.161 (5/31) | link | piechart |
| HTH_17 (pfam12728) | 5 (3%) | 0.07 (5/71) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG3 | 1646 (100%) | 1 (1644/1644) | link | piechart |
| RVT-UG8 | 1371 (83%) | 0.597 (1371/2298) | link | piechart |
| PRK09678 (DNA-binding transcriptional regulator; Provisional) | 178 (11%) | 0.124 (178/1431) | link | piechart |
| PRK09692 (Integrase; provisional) | 161 (10%) | 0.085 (161/1886) | link | piechart |
| INT_P4_C (cd00801) | 91 (6%) | 0.041 (90/2194) | link | piechart |
| SLATT_5 (pfam18160) | 66 (4%) | 0.038 (66/1758) | link | piechart |
| INT_Rci_Hp1_C (cd00796) | 57 (3%) | 0.138 (57/414) | link | piechart |
| proA (TIGR00407) | 56 (3%) | 0.169 (56/331) | link | piechart |
| Psu (pfam07455) | 51 (3%) | 0.094 (51/544) | link | piechart |
| AlpA (COG3311) | 45 (3%) | 0.222 (45/203) | link | piechart |
| COG4688 (Uncharacterized protein ) | 37 (2%) | 0.685 (37/54) | link | piechart |
| mutS1 (TIGR01070) | 31 (2%) | 0.272 (31/114) | link | piechart |
| DNA-binding transcriptional repressor AcrR (PRK10668) | 31 (2%) | 0.042 (31/735) | link | piechart |
| Tra5 (COG2801) | 30 (2%) | 0.018 (30/1683) | link | piechart |
| Darcynin (pfam17074) | 29 (2%) | 0.483 (29/60) | link | piechart |