Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 114476 |
| Name | oriT_psfSMH12b  |
| Organism | Sinorhizobium fredii strain SMH12 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP035039 (87459..87515 [-], 57 nt) |
| oriT length | 57 nt |
| IRs (inverted repeats) | 4..9, 23..28 (GGAAAA..TTTTCC) 6..11, 20..25 (AAAATG..CATTTT) |
| Location of nic site | 36..37 |
| Conserved sequence flanking the nic site |
TCCTGCCCCT |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 57 nt
>oriT_psfSMH12b
GCAGGAAAATGGCGTAGCACATTTTTCCGTATCCTGCCCCTCTAAATTGTAAGGGGA
GCAGGAAAATGGCGTAGCACATTTTTCCGTATCCTGCCCCTCTAAATTGTAAGGGGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 10755 | GenBank | WP_255876959 |
| Name | t4cp2_EPK84_RS14035_psfSMH12b |
UniProt ID | _ |
| Length | 548 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 548 a.a. Molecular weight: 59405.51 Da Isoelectric Point: 6.7883
>WP_255876959.1 type IV secretory system conjugative DNA transfer family protein [Sinorhizobium fredii]
MRVTKAFLTMTRLAVQNPGWAFANLLAIVLSKSGLKFAAIYMGLVIVAGVTAGPMLMEAGFQEGTWAWGV
FNIAFMIFMALLFLAMIAPFVSLHFGHLDAETHGSARFATDTEVAPLARADSGLLIGRDPKSGKLLRYDG
PAHLLTMAPTRTGKGVGTIIPNLLTADRSVICIDPKGENAKIAGRARQQFGPVHVLDPFDVTGTPSAAFN
PLDALDPDGLDVAEDASTLADALVLDEPGMAGEAHWNEEAKALLAGLILKIVAAESPGRRHLGTLREYLT
LAPERFAALLTRMQDMDEAGGLIARAANRHLGKSDREAAGVLSAAQRHTHFLDSPRMTTVLGRSDFRFAD
LKHRNASVFLVLPPDRLSTYSRWLRLLITQSLFDMARVPAKPEAPVLYLLDEFAALGHLASVERAMGLMA
GYGVQLWPILQDVHQLRATYGQRAGTFLSNAGVFQVFGVNDHDSARLVSDLLGQETVVFQTMARALDSEK
SGISFSQQQTGRPLLTPDEVRSMAQHIELLFLAGQRPIIAGKLAYYADPEFRGLYDAP
MRVTKAFLTMTRLAVQNPGWAFANLLAIVLSKSGLKFAAIYMGLVIVAGVTAGPMLMEAGFQEGTWAWGV
FNIAFMIFMALLFLAMIAPFVSLHFGHLDAETHGSARFATDTEVAPLARADSGLLIGRDPKSGKLLRYDG
PAHLLTMAPTRTGKGVGTIIPNLLTADRSVICIDPKGENAKIAGRARQQFGPVHVLDPFDVTGTPSAAFN
PLDALDPDGLDVAEDASTLADALVLDEPGMAGEAHWNEEAKALLAGLILKIVAAESPGRRHLGTLREYLT
LAPERFAALLTRMQDMDEAGGLIARAANRHLGKSDREAAGVLSAAQRHTHFLDSPRMTTVLGRSDFRFAD
LKHRNASVFLVLPPDRLSTYSRWLRLLITQSLFDMARVPAKPEAPVLYLLDEFAALGHLASVERAMGLMA
GYGVQLWPILQDVHQLRATYGQRAGTFLSNAGVFQVFGVNDHDSARLVSDLLGQETVVFQTMARALDSEK
SGISFSQQQTGRPLLTPDEVRSMAQHIELLFLAGQRPIIAGKLAYYADPEFRGLYDAP
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 488940..498012
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| EPK84_RS13755 (EPK84_14195) | 484204..484350 | + | 147 | WP_015633573 | family 16 glycosylhydrolase | - |
| EPK84_RS13760 (EPK84_14200) | 484484..485242 | + | 759 | Protein_485 | IS256 family transposase | - |
| EPK84_RS13765 (EPK84_14205) | 485298..486695 | + | 1398 | WP_014328799 | IS1182 family transposase | - |
| EPK84_RS13770 (EPK84_14215) | 487184..488478 | - | 1295 | Protein_487 | IncP-type conjugal transfer protein TrbI | - |
| EPK84_RS13775 (EPK84_14220) | 488490..488936 | - | 447 | WP_014858040 | conjugal transfer protein TrbH | - |
| EPK84_RS13780 (EPK84_14225) | 488940..489752 | - | 813 | WP_014858039 | P-type conjugative transfer protein TrbG | virB9 |
| EPK84_RS13785 (EPK84_14230) | 489770..490432 | - | 663 | WP_014858038 | conjugal transfer protein TrbF | virB8 |
| EPK84_RS13790 (EPK84_14235) | 490456..491631 | - | 1176 | WP_034859627 | P-type conjugative transfer protein TrbL | virB6 |
| EPK84_RS13795 (EPK84_14240) | 491625..491822 | - | 198 | WP_014858036 | entry exclusion protein TrbK | - |
| EPK84_RS13800 (EPK84_14245) | 491819..492622 | - | 804 | WP_014858035 | P-type conjugative transfer protein TrbJ | virB5 |
| EPK84_RS13805 (EPK84_14250) | 492594..494825 | - | 2232 | Protein_494 | conjugal transfer protein TrbE | - |
| EPK84_RS13810 (EPK84_14255) | 494904..495926 | + | 1023 | WP_014328393 | IS110 family transposase | - |
| EPK84_RS13815 (EPK84_14260) | 496126..496359 | - | 234 | WP_014858033 | hypothetical protein | virb4 |
| EPK84_RS13820 (EPK84_14265) | 496370..496669 | - | 300 | WP_010875429 | conjugal transfer protein TrbD | virB3 |
| EPK84_RS13825 (EPK84_14270) | 496662..497045 | - | 384 | WP_034859524 | TrbC/VirB2 family protein | virB2 |
| EPK84_RS13830 (EPK84_14275) | 497035..498012 | - | 978 | WP_015633597 | P-type conjugative transfer ATPase TrbB | virB11 |
| EPK84_RS13835 (EPK84_14280) | 498023..498649 | - | 627 | WP_014858030 | acyl-homoserine-lactone synthase | - |
| EPK84_RS13840 (EPK84_14285) | 499440..500663 | + | 1224 | WP_014858029 | plasmid partitioning protein RepA | - |
| EPK84_RS13845 (EPK84_14290) | 500721..501701 | + | 981 | WP_014858028 | plasmid partitioning protein RepB | - |
Host bacterium
| ID | 14911 | GenBank | NZ_CP035039 |
| Plasmid name | psfSMH12b | Incompatibility group | - |
| Plasmid size | 556376 bp | Coordinate of oriT [Strand] | 87459..87515 [-] |
| Host baterium | Sinorhizobium fredii strain SMH12 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | gmd, htpB |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | nodA, nodB, nodC, nodI, nodJ, nifS, fixU, nifZ, nifB, fixX, fixC, fixB, fixA, nifH, nifD, nifK, nifE, nifX, nodD, nodZ, noeL, nolV, nolU, nolT, nopB, nolW, nolX, mLTONO_5203 |
| Anti-CRISPR | AcrIC6 |