myRT
Top 15 domains that tend to co-occur with UG19 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG19 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 UG19).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG19 | 15 (100%) | 1 (15/15) | link | piechart |
| group_II_RT_mat (TIGR04416) | 6 (40%) | 0.016 (6/376) | link | piechart |
| TIR_2 (pfam13676) | 4 (27%) | 0.045 (4/89) | link | piechart |
| HTH_45 (pfam14947) | 4 (27%) | 0.25 (2/8) | link | piechart |
| tRNA_RlmH_YbeA (TIGR00246) | 2 (13%) | 0.069 (2/29) | link | piechart |
| met_A_Alw26 (TIGR02987) | 2 (13%) | 0.091 (1/11) | link | piechart |
| FUSC (pfam04632) | 2 (13%) | 0.286 (2/7) | link | piechart |
| Dimerisation2 | 2 (13%) | 0.667 (2/3) | link | piechart |
| CxxH_BA5709 (TIGR04129) | 2 (13%) | 0.182 (2/11) | link | piechart |
| YprA (COG1205)*3 | 1 (7%) | 0.25 (1/4) | link | piechart |
| YprA (COG1205) | 1 (7%) | 0.111 (1/9) | link | piechart |
| YeeA (COG1002) | 1 (7%) | 0.019 (1/52) | link | piechart |
| Vsr (pfam03852) | 1 (7%) | 0.2 (1/5) | link | piechart |
| UDP_AE_SDR_e (cd05256) | 1 (7%) | 0.167 (1/6) | link | piechart |
| Transposase_20 (pfam02371) | 1 (7%) | 0.011 (1/89) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG19 | 242 (100%) | 1 (242/242) | link | piechart |
| group_II_RT_mat (TIGR04416) | 80 (33%) | 0.022 (80/3657) | link | piechart |
| HsdM (COG0286) | 15 (6%) | 0.018 (15/856) | link | piechart |
| YkfC (COG3344) | 11 (5%) | 0.003 (11/3871) | link | piechart |
| NERD (pfam08378) | 10 (4%) | 0.022 (10/464) | link | piechart |
| Nterm_to_SelD (TIGR03169) | 8 (3%) | 0.571 (8/14) | link | piechart |
| TIR_2 (pfam13676) | 7 (3%) | 0.009 (7/773) | link | piechart |
| Recombinase (pfam07508) | 6 (2%) | 0.007 (6/824) | link | piechart |
| N6_Mtase (pfam02384) | 6 (2%) | 0.008 (6/773) | link | piechart |
| COG0610 (Type I site-specific restriction-modification system, R (restriction) subunit and related helicases ) | 6 (2%) | 0.012 (6/487) | link | piechart |
| Uma2 (pfam05685) | 5 (2%) | 0.028 (4/144) | link | piechart |
| HTH_XRE (smart00530) | 5 (2%) | 0.001 (5/4856) | link | piechart |
| HsdR (COG4096) | 5 (2%) | 0.017 (6/345) | link | piechart |
| Zn_ribbon_recom (pfam13408) | 4 (2%) | 0.004 (4/951) | link | piechart |
| UvrD (COG0210) | 4 (2%) | 0.01 (4/413) | link | piechart |