myRT
Top 15 domains that tend to co-occur with UG4 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG4 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 UG4).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG4 | 228 (100%) | 1 (228/228) | link | piechart |
| FimD (COG3188) | 79 (35%) | 0.963 (79/82) | link | piechart |
| FimC (COG3121) | 79 (35%) | 0.963 (79/82) | link | piechart |
| PRK09692 (Integrase; provisional) | 56 (25%) | 0.164 (56/342) | link | piechart |
| PRK15287 (fimbrial minor subunit StfF) | 50 (22%) | 1 (50/50) | link | piechart |
| FimA (pfam16970) | 44 (19%) | 0.769 (40/52) | link | piechart |
| Integrase_1 (pfam12835) | 41 (18%) | 0.641 (41/64) | link | piechart |
| PRK15288 (putative minor fimbrial subunit StfG; Provisional) | 23 (10%) | 1 (23/23) | link | piechart |
| YqgA (COG1811) | 17 (7%) | 0.85 (17/20) | link | piechart |
| DsbB (pfam02600) | 15 (7%) | 0.938 (15/16) | link | piechart |
| EAL (smart00052) | 13 (6%) | 0.26 (13/50) | link | piechart |
| SufE (pfam02657) | 11 (5%) | 1 (11/11) | link | piechart |
| RVT-UG4*2 | 11 (5%) | 1 (11/11) | link | piechart |
| DUF2797 (pfam10977) | 11 (5%) | 1 (11/11) | link | piechart |
| PRK09194 (prolyl-tRNA synthetase; Provisional) | 8 (4%) | 0.421 (8/19) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG4 | 2317 (100%) | 1 (2296/2296) | link | piechart |
| FimD (COG3188) | 1028 (44%) | 0.986 (1028/1043) | link | piechart |
| FimC (COG3121) | 958 (41%) | 0.972 (958/986) | link | piechart |
| Integrase_1 (pfam12835) | 750 (32%) | 0.848 (750/884) | link | piechart |
| INT_P4_C (cd00801) | 653 (28%) | 0.292 (653/2235) | link | piechart |
| EAL (smart00052) | 138 (6%) | 0.595 (138/232) | link | piechart |
| FimA (pfam16970) | 130 (6%) | 0.862 (119/138) | link | piechart |
| PRK15287 (fimbrial minor subunit StfF) | 121 (5%) | 1 (121/121) | link | piechart |
| PRK09692 (Integrase; provisional) | 94 (4%) | 0.047 (94/2021) | link | piechart |
| RVT-UG4*2 | 86 (4%) | 1 (86/86) | link | piechart |
| DsbB (pfam02600) | 73 (3%) | 0.913 (73/80) | link | piechart |
| SufE (pfam02657) | 66 (3%) | 0.917 (66/72) | link | piechart |
| PRK15288 (putative minor fimbrial subunit StfG; Provisional) | 58 (3%) | 1 (58/58) | link | piechart |
| DUF2797 (pfam10977) | 54 (2%) | 0.947 (54/57) | link | piechart |
| PRK15223 (fimbrial biogenesis outer membrane usher protein) | 43 (2%) | 0.933 (42/45) | link | piechart |