Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100169 |
| Name | oriT_pBTK445  |
| Organism | Tetrathiobacter kashmirensis strain WGT |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | EU585932 (2952..3002 [+], 51 nt) |
| oriT length | 51 nt |
| IRs (inverted repeats) | 17..25, 31..39 (ATAGGGTAC..GCTCGCTAT) |
| Location of nic site | 48..49 |
| Conserved sequence flanking the nic site |
CATCCTG|A |
| Note | IncP-like |
oriT sequence
Download Length: 51 nt
>oriT_pBTK445
AGCCTTTAAAGCGAAAATAGGGTACTCCATGCTCGCTATATCATCCTGACA
AGCCTTTAAAGCGAAAATAGGGTACTCCATGCTCGCTATATCATCCTGACA
Visualization of oriT structure (The oriT was characterized experimentally)
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Dam B et al. (2009) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. Appl Environ Microbiol. 75(13):4362-73. [PMID:19411426]
T4CP
| ID | 162 | GenBank | ACD43639 |
| Name | VirD4_pBTK445  |
UniProt ID | B4YK42 |
| Length | 297 a.a. | PDB ID | _ |
| Note | Type IV secretory pathway, VirD4 component,TraG/TraD family ATPase | ||
T4CP protein sequence
Download Length: 297 a.a. Molecular weight: 33474.16 Da Isoelectric Point: 9.9752
>ACD43639.1 VirD4, partial (plasmid) [Advenella kashmirensis]
MFFMKKAMIWLAALVACTLVFAVIGQYVGSLVFIRFAKAPIDPGIYVLWDLYKNTQGGGIWSLWQYKVAV
VFSVLIALLPIIAGIGAFFFRPQARITWFGQVRHARRDCEAGLLNDSHESPDIIIGKYKGKYLRWGGNQF
AFLAAPPRSGKGVGIVIPNCLHYRDSLVVFDPKLENYEITAGYREAHGQEVYLLHLSTDQFRSHRWNPLS
YVKRDPDFAPGGAFSIAYILYPTSGNMSGNSIFFNEMAQKLFVGLCLYLIETENETGVIPSMPALLKLAT
PRRRGNLWPIGLKRQKK
MFFMKKAMIWLAALVACTLVFAVIGQYVGSLVFIRFAKAPIDPGIYVLWDLYKNTQGGGIWSLWQYKVAV
VFSVLIALLPIIAGIGAFFFRPQARITWFGQVRHARRDCEAGLLNDSHESPDIIIGKYKGKYLRWGGNQF
AFLAAPPRSGKGVGIVIPNCLHYRDSLVVFDPKLENYEITAGYREAHGQEVYLLHLSTDQFRSHRWNPLS
YVKRDPDFAPGGAFSIAYILYPTSGNMSGNSIFFNEMAQKLFVGLCLYLIETENETGVIPSMPALLKLAT
PRRRGNLWPIGLKRQKK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | B4YK42 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 12162..22972
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Locus_9 | 7711..8076 | + | 366 | ACD43622 | hypothetical protein | - |
| Locus_10 | 8599..8838 | - | 240 | ACD43623 | hypothetical protein | - |
| Locus_11 | 8951..9298 | + | 348 | ACD43624 | hypothetical protein | - |
| Locus_12 | 10371..11135 | + | 765 | ACD43625 | TagBA | - |
| Locus_13 | 11149..11697 | + | 549 | ACD43626 | TagBB | - |
| Locus_14 | 12162..12929 | + | 768 | ACD43627 | TagB1 | virB1 |
| Locus_15 | 13265..13585 | + | 321 | ACD43628 | TagB2 | virB2 |
| Locus_16 | 13604..14035 | + | 432 | ACD43629 | TagB3 | virB3 |
| Locus_17 | 13944..16358 | + | 2415 | ACD43630 | TagB4 | virb4 |
| Locus_18 | 16462..17103 | + | 642 | ACD43631 | TagB5 | virB5 |
| Locus_19 | 17502..18443 | + | 942 | ACD43632 | TagB6 | virB6 |
| Locus_20 | 18449..18820 | + | 372 | ACD43633 | TagB7 | - |
| Locus_21 | 19072..19791 | + | 720 | ACD43634 | TagB8 | virB8 |
| Locus_22 | 19810..20634 | + | 825 | ACD43635 | TagB9 | virB9 |
| Locus_23 | 20645..21850 | + | 1206 | ACD43636 | TagB10 | virB10 |
| Locus_24 | 21860..22972 | + | 1113 | ACD43637 | TagB11 | virB11 |
| Locus_25 | 23070..23393 | + | 324 | ACD43638 | Ssb | - |
| Locus_26 | 23548..24440 | + | 893 | ACD43639 | VirD4 | - |
Host bacterium
| ID | 162 | GenBank | EU585932 |
| Plasmid name | pBTK445 | Incompatibility group | IncP |
| Plasmid size | 24440 bp | Coordinate of oriT [Strand] | 2952..3002 [+] |
| Host baterium | Tetrathiobacter kashmirensis strain WGT |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |