myRT
Top 15 domains that tend to co-occur with UG7 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG7 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 UG7).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG7 | 151 (100%) | 1 (151/151) | link | piechart |
| DDE_Tnp_1 (pfam01609) | 33 (22%) | 0.058 (33/570) | link | piechart |
| KTSC (pfam13619) | 32 (21%) | 0.97 (32/33) | link | piechart |
| PRK09692 (Integrase; provisional) | 17 (11%) | 0.05 (17/342) | link | piechart |
| Psu (pfam07455) | 16 (11%) | 0.211 (16/76) | link | piechart |
| PLN02735 (carbamoyl-phosphate synthase) | 10 (7%) | 1 (10/10) | link | piechart |
| HicB (pfam05534) | 10 (7%) | 0.182 (10/55) | link | piechart |
| proA (TIGR00407) | 7 (5%) | 0.292 (7/24) | link | piechart |
| DUF3177 (pfam11375) | 6 (4%) | 0.75 (6/8) | link | piechart |
| DDE_Tnp_1 (pfam01609)*2 | 5 (3%) | 0.152 (5/33) | link | piechart |
| Y2_Tnp (pfam04986) | 4 (3%) | 0.009 (3/339) | link | piechart |
| INT_C_like_1 (cd01184) | 4 (3%) | 0.085 (4/47) | link | piechart |
| InsE (COG2963) | 4 (3%) | 0.002 (4/1639) | link | piechart |
| DUF4062 (pfam13271) | 4 (3%) | 0.444 (4/9) | link | piechart |
| ABC_ATPase (pfam09818) | 4 (3%) | 0.061 (4/66) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG7 | 1292 (100%) | 1 (1292/1292) | link | piechart |
| PRK09692 (Integrase; provisional) | 382 (30%) | 0.189 (382/2020) | link | piechart |
| Psu (pfam07455) | 179 (14%) | 0.301 (179/595) | link | piechart |
| proA (TIGR00407) | 150 (12%) | 0.45 (150/333) | link | piechart |
| KTSC (pfam13619) | 69 (5%) | 0.775 (69/89) | link | piechart |
| Phage_int_SAM_5 (pfam13102) | 68 (5%) | 0.109 (68/623) | link | piechart |
| INT_C_like_1 (cd01184) | 66 (5%) | 0.22 (66/300) | link | piechart |
| DUF4062 (pfam13271) | 44 (3%) | 0.238 (44/185) | link | piechart |
| DUF2971 (pfam11185) | 38 (3%) | 0.252 (38/151) | link | piechart |
| Peptidase_M60 (pfam13402) | 33 (3%) | 0.379 (33/87) | link | piechart |
| M60-like_N (pfam17291) | 33 (3%) | 0.846 (33/39) | link | piechart |
| COG5340 (Transcriptional regulator, predicted component of viral defense system ) | 33 (3%) | 0.108 (33/306) | link | piechart |
| AbiEii (pfam08843) | 32 (2%) | 0.03 (32/1052) | link | piechart |
| PinE (COG1961) | 24 (2%) | 0.016 (24/1548) | link | piechart |
| YjgR (COG0433) | 16 (1%) | 0.083 (13/156) | link | piechart |