myRT
Top 15 domains that tend to co-occur with UG18 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG18 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 UG18).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG18 | 58 (100%) | 1 (58/58) | link | piechart |
| SidC_N (pfam18219) | 15 (26%) | 1 (15/15) | link | piechart |
| DDE_5 (pfam13546) | 9 (16%) | 0.075 (9/120) | link | piechart |
| RND_mfp (TIGR01730) | 7 (12%) | 0.241 (7/29) | link | piechart |
| PRK11556 (MdtA/MuxA family multidrug efflux RND transporter periplasmic adaptor subunit) | 7 (12%) | 1 (7/7) | link | piechart |
| HlyD_3 (pfam13437) | 7 (12%) | 0.875 (7/8) | link | piechart |
| DUF772 (pfam05598) | 7 (12%) | 0.035 (7/199) | link | piechart |
| DDE_Tnp_1_3 (pfam13612) | 7 (12%) | 0.031 (7/227) | link | piechart |
| TIGR03491 (RecB family nuclease, putative, TM0106 family) | 4 (7%) | 0.8 (4/5) | link | piechart |
| ACH1 (COG0427) | 4 (7%) | 0.8 (4/5) | link | piechart |
| DUF1566 (pfam07603) | 3 (5%) | 0.029 (3/105) | link | piechart |
| SUL1 (COG0659) | 2 (3%) | 0.077 (1/13) | link | piechart |
| MS_channel (pfam00924) | 2 (3%) | 0.333 (2/6) | link | piechart |
| COG5421 (Transposase ) | 2 (3%) | 0.031 (2/65) | link | piechart |
| Acetyltransf_3 (pfam13302) | 2 (3%) | 0.091 (2/22) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG18 | 196 (100%) | 1 (196/196) | link | piechart |
| RVT-GII | 22 (11%) | 0 (22/162946) | link | piechart |
| GIIM (pfam08388) | 20 (10%) | 0 (20/84249) | link | piechart |
| RVT_N (pfam13655) | 17 (9%) | 0.001 (17/25956) | link | piechart |
| SidC_N (pfam18219) | 16 (8%) | 1 (16/16) | link | piechart |
| DDE_Tnp_1_3 (pfam13612) | 12 (6%) | 0.062 (12/193) | link | piechart |
| RVT-UG18*2 | 10 (5%) | 1 (10/10) | link | piechart |
| DUF1566 (pfam07603) | 7 (4%) | 0.005 (7/1551) | link | piechart |
| DDE_5 (pfam13546) | 6 (3%) | 0.022 (6/270) | link | piechart |
| Ubox (smart00504) | 5 (3%) | 1 (5/5) | link | piechart |
| RVT-UG4 | 5 (3%) | 0.002 (5/2328) | link | piechart |
| Inhibitor_I42 (pfam09394) | 5 (3%) | 0.625 (5/8) | link | piechart |
| COG5421 (Transposase ) | 5 (3%) | 0.023 (5/217) | link | piechart |
| Phage_integrase (pfam00589) | 4 (2%) | 0.016 (4/253) | link | piechart |
| Nitroreductase_3 | 4 (2%) | 0.143 (4/28) | link | piechart |