myRT
Top 15 domains that tend to co-occur with UG16 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG16 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 UG16).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG16 | 20 (100%) | 1 (20/20) | link | piechart |
| PRK13889 (conjugal transfer relaxase TraA; Provisional) | 3 (15%) | 0.125 (3/24) | link | piechart |
| YjgR (COG0433)*2 | 2 (10%) | 0.182 (2/11) | link | piechart |
| YjgR (COG0433) | 2 (10%) | 0.154 (2/13) | link | piechart |
| RnhA (COG0328) | 2 (10%) | 0.087 (2/23) | link | piechart |
| PRK09692 (Integrase; provisional) | 2 (10%) | 0.006 (2/342) | link | piechart |
| DUF927 (pfam06048) | 2 (10%) | 0.286 (2/7) | link | piechart |
| DUF87 (pfam01935) | 2 (10%) | 0.4 (2/5) | link | piechart |
| dnaE2 (PRK05672) | 2 (10%) | 0.333 (2/6) | link | piechart |
| TolC (COG1538) | 1 (5%) | 0.1 (1/10) | link | piechart |
| SmpB (pfam01668) | 1 (5%) | 0.025 (1/40) | link | piechart |
| SIR2_2 (pfam13289) | 1 (5%) | 0.048 (1/21) | link | piechart |
| SDR_c (cd05233) | 1 (5%) | 0.05 (1/20) | link | piechart |
| PutA (COG0506) | 1 (5%) | 0.333 (1/3) | link | piechart |
| PSD1 (pfam07587) | 1 (5%) | 0.111 (1/9) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG16 | 243 (100%) | 1 (243/243) | link | piechart |
| PRK13889 (conjugal transfer relaxase TraA; Provisional) | 85 (35%) | 0.289 (85/294) | link | piechart |
| DUF4755 (pfam15947) | 32 (13%) | 0.97 (32/33) | link | piechart |
| zf-UBP (pfam02148) | 11 (5%) | 0.846 (11/13) | link | piechart |
| RpsA (COG0539) | 11 (5%) | 0.017 (11/641) | link | piechart |
| PRK00087 (bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1) | 9 (4%) | 0.474 (9/19) | link | piechart |
| YjgR (COG0433)*2 | 8 (3%) | 0.063 (8/126) | link | piechart |
| YjgR (COG0433) | 8 (3%) | 0.051 (8/156) | link | piechart |
| RelB (pfam04221) | 8 (3%) | 0.17 (8/47) | link | piechart |
| YiaG (COG2944) | 7 (3%) | 0.103 (7/68) | link | piechart |
| RelE (pfam06296) | 6 (2%) | 0.044 (6/136) | link | piechart |
| SIR2_2 (pfam13289) | 5 (2%) | 0.029 (5/174) | link | piechart |
| conjugal transfer protein TraD (PRK13700) | 4 (2%) | 0.025 (4/160) | link | piechart |
| PRK09692 (Integrase; provisional) | 4 (2%) | 0.002 (4/2021) | link | piechart |
| InsE (COG2963) | 4 (2%) | 0.001 (4/5378) | link | piechart |