myRT
Top 15 domains that tend to co-occur with UG23 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG23 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 UG23).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG23 | 21 (100%) | 1 (21/21) | link | piechart |
| PinE (COG1961) | 6 (29%) | 0.019 (6/316) | link | piechart |
| Sa_NUDIX (pfam18167) | 4 (19%) | 0.8 (4/5) | link | piechart |
| HAUS5 (pfam14817) | 4 (19%) | 1 (4/4) | link | piechart |
| Nudix_Hydrolase_17 (cd04676) | 2 (10%) | 0.667 (2/3) | link | piechart |
| met_A_Alw26 (TIGR02987) | 2 (10%) | 0.091 (1/11) | link | piechart |
| HTH_XRE (smart00530) | 2 (10%) | 0.003 (2/666) | link | piechart |
| HTH_31 (pfam13560) | 2 (10%) | 0.111 (2/18) | link | piechart |
| HTH_17 (pfam12728) | 2 (10%) | 0.026 (2/76) | link | piechart |
| APH (pfam01636)*2 | 2 (10%) | 1 (2/2) | link | piechart |
| APH (pfam01636) | 2 (10%) | 0.167 (2/12) | link | piechart |
| Acetyltransf_1 (pfam00583) | 2 (10%) | 0.025 (2/80) | link | piechart |
| YprA (COG1205) | 1 (5%) | 0.111 (1/9) | link | piechart |
| YjbI (COG2346) | 1 (5%) | 0.043 (1/23) | link | piechart |
| YfcA (COG0730) | 1 (5%) | 0.125 (1/8) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG23 | 70 (100%) | 1 (70/70) | link | piechart |
| SufI (COG2132) | 8 (11%) | 0.174 (8/46) | link | piechart |
| Hypoth_Ymh (pfam09509) | 8 (11%) | 0.071 (8/113) | link | piechart |
| Sa_NUDIX (pfam18167) | 6 (9%) | 0.207 (6/29) | link | piechart |
| YeeA (COG1002) | 5 (7%) | 0.007 (5/682) | link | piechart |
| Smf (COG0758) | 5 (7%) | 0.102 (5/49) | link | piechart |
| PRK04914 (RNA polymerase-associated protein RapA) | 5 (7%) | 0.106 (5/47) | link | piechart |
| HTH_XRE (smart00530) | 5 (7%) | 0.001 (5/4863) | link | piechart |
| DEXDc_RapA (cd18011) | 5 (7%) | 0.049 (5/103) | link | piechart |
| RVT-UG23*2 | 4 (6%) | 1 (4/4) | link | piechart |
| HTH_17 (pfam12728) | 4 (6%) | 0.006 (4/718) | link | piechart |
| YbjD (COG3593)*2 | 3 (4%) | 0.025 (3/122) | link | piechart |
| YbjD (COG3593) | 3 (4%) | 0.017 (3/175) | link | piechart |
| RMtype1_S_MgeORF438P-TRD-CR_like (cd17291) | 3 (4%) | 0.231 (3/13) | link | piechart |
| hsdM (TIGR00497) | 3 (4%) | 0.005 (4/856) | link | piechart |