myRT
Top 15 domains that tend to co-occur with UG24 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG24 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 UG24).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG24 | 13 (100%) | 1 (13/13) | link | piechart |
| PadR (pfam03551) | 6 (46%) | 0.261 (6/23) | link | piechart |
| YdiU (COG0397) | 5 (38%) | 1 (5/5) | link | piechart |
| HNH_4 (pfam13395) | 4 (31%) | 0.138 (4/29) | link | piechart |
| YjiC (COG1819) | 2 (15%) | 0.5 (2/4) | link | piechart |
| dnaG (TIGR01391) | 2 (15%) | 0.015 (2/131) | link | piechart |
| Tra8 (COG2826) | 1 (8%) | 0.004 (1/274) | link | piechart |
| INT_ICEBs1_C_like (cd01189) | 1 (8%) | 0.02 (1/51) | link | piechart |
| Cas2 (COG3512) | 1 (8%) | 0.5 (1/2) | link | piechart |
| AbiGi (pfam10899)*2 | 1 (8%) | 0.333 (1/3) | link | piechart |
| AbiGi (pfam10899) | 1 (8%) | 0.2 (1/5) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG24 | 144 (100%) | 1 (144/144) | link | piechart |
| dnaG (TIGR01391) | 65 (45%) | 0.136 (67/493) | link | piechart |
| INTN1_C_like (cd01185) | 38 (26%) | 0.068 (37/548) | link | piechart |
| Phage_int_SAM_5 (pfam13102) | 36 (25%) | 0.058 (36/623) | link | piechart |
| Arm-DNA-bind_5 (pfam17293) | 34 (24%) | 0.08 (34/424) | link | piechart |
| HTH_17 (pfam12728) | 29 (20%) | 0.04 (29/718) | link | piechart |
| HDc (smart00471) | 12 (8%) | 0.324 (12/37) | link | piechart |
| YdiU (COG0397) | 8 (6%) | 0.889 (8/9) | link | piechart |
| PadR (pfam03551) | 8 (6%) | 0.08 (8/100) | link | piechart |
| RVT-UG24*2 | 6 (4%) | 1 (6/6) | link | piechart |
| DDE_Tnp_IS66 (pfam03050) | 5 (3%) | 0.002 (3/1930) | link | piechart |
| UvrD (COG0210) | 4 (3%) | 0.01 (4/413) | link | piechart |
| trmE (PRK05291) | 4 (3%) | 0.059 (4/68) | link | piechart |
| TOPRIM_OLD (cd01026) | 4 (3%) | 0.027 (4/148) | link | piechart |
| superantigen-like protein SSL2 (PRK13041) | 4 (3%) | 0.014 (4/277) | link | piechart |