myRT
Top 15 domains that tend to co-occur with G2L RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with G2L 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 G2L).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-G2L | 169 (100%) | 1 (167/167) | link | piechart |
| YecA (COG3318) | 122 (72%) | 1 (122/122) | link | piechart |
| DNA-binding transcriptional repressor AcrR (PRK10668) | 60 (36%) | 0.308 (60/195) | link | piechart |
| TetR_N (pfam00440) | 8 (5%) | 0.121 (8/66) | link | piechart |
| PinE (COG1961) | 7 (4%) | 0.022 (7/314) | link | piechart |
| DDE_Tnp_1_5 (pfam13737) | 5 (3%) | 0.068 (5/74) | link | piechart |
| COG4889 (Predicted helicase ) | 5 (3%) | 0.313 (5/16) | link | piechart |
| PHA02517 (putative transposase OrfB; Reviewed) | 4 (2%) | 0.002 (4/2143) | link | piechart |
| TIR_2 (pfam13676) | 3 (2%) | 0.033 (3/90) | link | piechart |
| N6_N4_Mtase (pfam01555) | 3 (2%) | 0.143 (3/21) | link | piechart |
| InsE (COG2963) | 3 (2%) | 0.001 (2/1637) | link | piechart |
| DpnI (pfam06044) | 3 (2%) | 1 (3/3) | link | piechart |
| AzlD (pfam05437) | 3 (2%) | 0.6 (3/5) | link | piechart |
| Type_ISP_C (pfam18135) | 2 (1%) | 0.5 (2/4) | link | piechart |
| Phage_int_SAM_3 (pfam14659) | 2 (1%) | 0.083 (2/24) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-G2L | 23 (100%) | 1 (23/23) | link | piechart |
| YecA (COG3318) | 3 (13%) | 0.6 (3/5) | link | piechart |
| PagL (pfam09411) | 3 (13%) | 0.333 (3/9) | link | piechart |
| DNA-binding transcriptional repressor AcrR (PRK10668) | 3 (13%) | 0.004 (3/769) | link | piechart |
| PSCyt1 (pfam07635) | 2 (9%) | 0.043 (1/23) | link | piechart |
| MACS_AAE_MA_like (cd05970) | 2 (9%) | 0.5 (2/4) | link | piechart |
| WD40 (smart00320) | 1 (4%) | 0.004 (1/233) | link | piechart |
| TsaA (COG1720) | 1 (4%) | 0.125 (1/8) | link | piechart |
| TrmO_C (pfam18389) | 1 (4%) | 0.125 (1/8) | link | piechart |
| TIGR00275 (flavoprotein, HI0933 family) | 1 (4%) | 0.05 (1/20) | link | piechart |
| Sortilin-Vps10 (pfam15902) | 1 (4%) | 0.029 (1/35) | link | piechart |
| RNase_HI_RT_Bel (cd09273) | 1 (4%) | 0.067 (1/15) | link | piechart |
| RloB (pfam13707) | 1 (4%) | 0.034 (1/29) | link | piechart |
| PSD1 (pfam07587) | 1 (4%) | 0.059 (1/17) | link | piechart |
| PSCyt2 (pfam07583) | 1 (4%) | 0.056 (1/18) | link | piechart |