myRT
Top 15 domains that tend to co-occur with UG20 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG20 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 UG20).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG20 | 9 (100%) | 1 (9/9) | link | piechart |
| IstB_IS21 (pfam01695) | 2 (22%) | 0.02 (2/98) | link | piechart |
| COG4584 (Transposase ) | 2 (22%) | 0.008 (2/239) | link | piechart |
| uvrA (PRK00349) | 1 (11%) | 0.024 (1/42) | link | piechart |
| Tra5 (COG2801) | 1 (11%) | 0.004 (1/239) | link | piechart |
| PRK10892 (arabinose-5-phosphate isomerase KdsD) | 1 (11%) | 0.333 (1/3) | link | piechart |
| PRK09284 (thiamine biosynthesis protein ThiC; Provisional) | 1 (11%) | 0.125 (1/8) | link | piechart |
| Peptidase_S46 (pfam10459) | 1 (11%) | 1 (1/1) | link | piechart |
| MprF (COG2898) | 1 (11%) | 1 (1/1) | link | piechart |
| Macro_Poa1p_like | 1 (11%) | 0.059 (1/17) | link | piechart |
| KOG0734 (KOG0734, AAA+-type ATPase containing the peptidase M41 domain ) | 1 (11%) | 0.5 (1/2) | link | piechart |
| HTH_Tnp_1 (pfam01527)*2 | 1 (11%) | 0.019 (1/52) | link | piechart |
| HTH_Tnp_1 (pfam01527) | 1 (11%) | 0.003 (1/296) | link | piechart |
| gltD (PRK12810) | 1 (11%) | 0.5 (1/2) | link | piechart |
| DUF2726 (pfam10881) | 1 (11%) | 0.25 (1/4) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG20 | 73 (100%) | 1 (73/73) | link | piechart |
| TPR (smart00028)*2 | 7 (10%) | 0.026 (7/271) | link | piechart |
| TPR (smart00028) | 7 (10%) | 0.008 (7/828) | link | piechart |
| CHAT (pfam12770) | 7 (10%) | 0.074 (7/94) | link | piechart |
| PLN00200 (argininosuccinate synthase; Provisional) | 5 (7%) | 0.625 (5/8) | link | piechart |
| NcnH (cd01159) | 5 (7%) | 0.333 (5/15) | link | piechart |
| HxlR (pfam01638) | 5 (7%) | 0.015 (5/341) | link | piechart |
| rve (pfam00665) | 4 (5%) | 0.002 (4/1747) | link | piechart |
| PRK06194 (hypothetical protein; Provisional) | 4 (5%) | 0.667 (4/6) | link | piechart |
| DNA2 (COG1112) | 4 (5%) | 0.098 (4/41) | link | piechart |
| PinE (COG1961) | 3 (4%) | 0.002 (3/1549) | link | piechart |
| Phage_terminase (pfam10668) | 3 (4%) | 1 (3/3) | link | piechart |
| DUF3800 (pfam12686) | 3 (4%) | 0.017 (3/172) | link | piechart |
| UvrD (COG0210)*3 | 2 (3%) | 0.033 (2/60) | link | piechart |
| UvrD (COG0210) | 2 (3%) | 0.005 (2/413) | link | piechart |