Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200067 |
| Name | oriT_ICEVchInd5  |
| Organism | Vibrio cholerae Ind5 integrating |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | GQ463142 (5730..6028 [+], 299 nt) |
| oriT length | 299 nt |
| IRs (inverted repeats) | 178..192, 216..230 (ATCGAGACGCCAAAC..GTTTGGCGTTTCGAT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | _ |
oriT sequence
Download Length: 299 nt
>oriT_ICEVchInd5
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Wozniak RA et al. (2009) Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet. 5(12):e1000786. [PMID:20041216]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 44131..63996
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| ICEVCHIND5_0035 | 40190..40960 | + | 771 | ACV96394 | conserved hypothetical protein | - |
| ICEVCHIND5_0037 | 40995..41810 | + | 816 | ACV96380 | conserved hypothetical protein | - |
| ICEVCHIND5_0036 | 41787..41909 | - | 123 | ACV96395 | hypothetical protein | - |
| ICEVCHIND5_0038 | 41932..44082 | + | 2151 | ACV96327 | conjugative relaxase | - |
| ICEVCHIND5_0039 | 44131..45951 | + | 1821 | ACV96363 | conjugative coupling factor | virb4 |
| ICEVCHIND5_0040 | 45961..46521 | + | 561 | ACV96349 | conserved hypothetical protein | - |
| ICEVCHIND5_0041 | 46508..47143 | + | 636 | ACV96331 | putative conjugation coupling factor | tfc7 |
| ICEVCHIND5_0042 | 47170..47757 | - | 588 | ACV96326 | conserved hypothetical protein | - |
| ICEVCHIND5_0043 | 48046..48327 | + | 282 | ACV96318 | type IV conjugative transfer system protein TraL | traL |
| ICEVCHIND5_0044 | 48324..48950 | + | 627 | ACV96336 | sex pilus assembly | traE |
| ICEVCHIND5_0045 | 48934..49830 | + | 897 | ACV96410 | TraK | traK |
| ICEVCHIND5_0046 | 49833..51122 | + | 1290 | ACV96344 | sex pilus assembly | traB |
| ICEVCHIND5_0047 | 51119..51769 | + | 651 | ACV96342 | sex pilus assembly | traV |
| ICEVCHIND5_0048 | 51766..52152 | + | 387 | ACV96404 | TraA | - |
| ICEVCHIND5_0049 | 52373..53164 | + | 792 | ACV96347 | conserved hypothetical protein | - |
| ICEVCHIND5_0050 | 53157..54095 | + | 939 | ACV96371 | ync | - |
| ICEVCHIND5_0051 | 54227..54919 | + | 693 | ACV96323 | DsbC | trbB |
| ICEVCHIND5_0052 | 54919..57318 | + | 2400 | ACV96320 | type-IV secretion system protein TraC | virb4 |
| ICEVCHIND5_0053 | 57311..57658 | + | 348 | ACV96341 | conserved hypothetical protein | - |
| ICEVCHIND5_0054 | 57642..58154 | + | 513 | ACV96335 | conjugation signal peptidase | - |
| ICEVCHIND5_0056 | 59273..60301 | + | 1029 | ACV96399 | sex pilus assembly | traU |
| ICEVCHIND5_0057 | 60304..63996 | + | 3693 | ACV96381 | mating pair stabilization | traN |
| ICEVCHIND5_0058 | 64087..65703 | - | 1617 | ACV96405 | conserved hypothetical protein | - |
| ICEVCHIND5_0059 | 65783..66538 | - | 756 | ACV96365 | IstB domain protein ATP-binding protein | - |
| ICEVCHIND5_0060 | 66528..68036 | - | 1509 | ACV96351 | integrase, catalytic region | - |
Host bacterium
| ID | 75 | Element type | |
| Element name | ICEVchInd5 | GenBank | GQ463142 |
| Element size | 97952 bp | Coordinate of oriT [Strand] | 5730..6028 [+] |
| Host bacterium | Vibrio cholerae Ind5 integrating |
Cargo genes
| Drug resistance gene | floR, aph(6)-Id, aph(3'')-Ib, sul2, dfrA1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |