myRT
Top 15 domains that tend to co-occur with UG8 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG8 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 UG8).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG8 | 215 (100%) | 1 (215/215) | link | piechart |
| RVT-UG3 | 194 (90%) | 0.97 (194/200) | link | piechart |
| PRK09692 (Integrase; provisional) | 22 (10%) | 0.069 (22/321) | link | piechart |
| PRK09678 (DNA-binding transcriptional regulator; Provisional) | 17 (8%) | 0.104 (17/163) | link | piechart |
| INT_Rci_Hp1_C (cd00796) | 13 (6%) | 0.194 (13/67) | link | piechart |
| Phage_int_SAM_5 (pfam13102) | 10 (5%) | 0.085 (5/59) | link | piechart |
| INTN1_C_like (cd01185) | 10 (5%) | 0.161 (5/31) | link | piechart |
| Arm-DNA-bind_5 (pfam17293) | 10 (5%) | 0.185 (5/27) | link | piechart |
| Psu (pfam07455) | 9 (4%) | 0.125 (9/72) | link | piechart |
| INT_P4_C (cd00801) | 8 (4%) | 0.062 (8/129) | link | piechart |
| InsE (COG2963) | 7 (3%) | 0.004 (7/1637) | link | piechart |
| SH3_5 (pfam08460) | 6 (3%) | 0.5 (2/4) | link | piechart |
| PinE (COG1961) | 6 (3%) | 0.019 (6/311) | link | piechart |
| SLATT_5 (pfam18160) | 5 (2%) | 0.029 (5/170) | link | piechart |
| RadC (pfam04002) | 5 (2%) | 0.217 (5/23) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG8 | 2283 (100%) | 1 (2282/2282) | link | piechart |
| RVT-UG3 | 1368 (60%) | 0.833 (1367/1642) | link | piechart |
| PRK09678 (DNA-binding transcriptional regulator; Provisional) | 211 (9%) | 0.147 (211/1435) | link | piechart |
| PRK09692 (Integrase; provisional) | 182 (8%) | 0.097 (182/1882) | link | piechart |
| Tra5 (COG2801) | 163 (7%) | 0.097 (163/1682) | link | piechart |
| INT_P4_C (cd00801) | 149 (7%) | 0.069 (149/2175) | link | piechart |
| reactive_PduG (TIGR04491) | 134 (6%) | 0.985 (134/136) | link | piechart |
| INT_Rci_Hp1_C (cd00796) | 112 (5%) | 0.279 (112/402) | link | piechart |
| Psu (pfam07455) | 74 (3%) | 0.135 (74/549) | link | piechart |
| mutS1 (TIGR01070) | 65 (3%) | 0.677 (65/96) | link | piechart |
| SLATT_5 (pfam18160) | 62 (3%) | 0.035 (62/1766) | link | piechart |
| PBP2_CrgA_like_5 (cd08474) | 54 (2%) | 0.38 (54/142) | link | piechart |
| InsE (COG2963) | 53 (2%) | 0.01 (53/5361) | link | piechart |
| PRK15246 (fimbrial assembly chaperone) | 49 (2%) | 0.907 (49/54) | link | piechart |
| XdhC (COG1975) | 44 (2%) | 0.587 (44/75) | link | piechart |