Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 121130 |
| Name | oriT_pWSM1115_3  |
| Organism | Sinorhizobium medicae WSM1115 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP088112 (62607..62663 [-], 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 |
TCCTGCCTCT |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 57 nt
>oriT_pWSM1115_3
GCAGGAAAATGGTGTAGCACATTTTTCCGTATCCTGCCTCTCCGAATTGTAAGGGGA
GCAGGAAAATGGTGTAGCACATTTTTCCGTATCCTGCCTCTCCGAATTGTAAGGGGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 15628 | GenBank | WP_018210776 |
| Name | t4cp2_SmedWSM1115_RS33420_pWSM1115_3 |
UniProt ID | _ |
| Length | 699 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 699 a.a. Molecular weight: 77926.89 Da Isoelectric Point: 9.6588
>WP_018210776.1 type IV secretory system conjugative DNA transfer family protein [Sinorhizobium medicae]
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYRDGRILETTITSNPLAPIQQFWHYKTSPALQKVALGS
MLPALLAAGLVAYIGLKPTSSPLGDAAFQDMASLRRGKWFRKQGHIFGRVGRNILRTRDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMFVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEQTNSYNPLDFIRPERGNRT
TDIQNIASILVPENTESENSVWQATAQQVLAGVISYIAESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVIDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMRLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQANIPQVPEVDYLSPKPVPATTP
EYAMGGDPSVEIPSPTPAKEGKPLTAAAAQATPVKADPAAEEKAPAPAKRTVNKKALHPKPKETAANTGS
AEISASLDAMEARIKAIEEGLKPKAALLKEVVETKAEKLDDKSPAKRRNIMDIFSATIPDPVEVGVTAE
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYRDGRILETTITSNPLAPIQQFWHYKTSPALQKVALGS
MLPALLAAGLVAYIGLKPTSSPLGDAAFQDMASLRRGKWFRKQGHIFGRVGRNILRTRDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMFVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEQTNSYNPLDFIRPERGNRT
TDIQNIASILVPENTESENSVWQATAQQVLAGVISYIAESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVIDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMRLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQANIPQVPEVDYLSPKPVPATTP
EYAMGGDPSVEIPSPTPAKEGKPLTAAAAQATPVKADPAAEEKAPAPAKRTVNKKALHPKPKETAANTGS
AEISASLDAMEARIKAIEEGLKPKAALLKEVVETKAEKLDDKSPAKRRNIMDIFSATIPDPVEVGVTAE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 83608..93521
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SmedWSM1115_RS33415 (SmedWSM1115_33415) | 80484..81305 | - | 822 | WP_018210775 | alpha/beta fold hydrolase | - |
| SmedWSM1115_RS33420 (SmedWSM1115_33420) | 81512..83611 | - | 2100 | WP_018210776 | type IV secretory system conjugative DNA transfer family protein | - |
| SmedWSM1115_RS33425 (SmedWSM1115_33425) | 83608..84636 | - | 1029 | WP_018210777 | P-type DNA transfer ATPase VirB11 | virB11 |
| SmedWSM1115_RS33430 (SmedWSM1115_33430) | 84617..85828 | - | 1212 | WP_018210778 | type IV secretion system protein VirB10 | virB10 |
| SmedWSM1115_RS33435 (SmedWSM1115_33435) | 85828..86637 | - | 810 | WP_018210779 | P-type conjugative transfer protein VirB9 | virB9 |
| SmedWSM1115_RS33440 (SmedWSM1115_33440) | 86634..87329 | - | 696 | WP_018210780 | virB8 family protein | virB8 |
| SmedWSM1115_RS33445 (SmedWSM1115_33445) | 87368..88396 | - | 1029 | WP_018210781 | type IV secretion system protein | virB6 |
| SmedWSM1115_RS33450 (SmedWSM1115_33450) | 88412..88639 | - | 228 | WP_011971091 | hypothetical protein | - |
| SmedWSM1115_RS33455 (SmedWSM1115_33455) | 88629..89330 | - | 702 | WP_018210782 | type IV secretion system protein | - |
| SmedWSM1115_RS33460 (SmedWSM1115_33460) | 89342..90430 | - | 1089 | WP_018210783 | lytic transglycosylase domain-containing protein | - |
| SmedWSM1115_RS33465 (SmedWSM1115_33465) | 90427..92886 | - | 2460 | WP_018210784 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| SmedWSM1115_RS33470 (SmedWSM1115_33470) | 92889..93188 | - | 300 | WP_018210785 | type IV secretion system protein VirB3 | virB3 |
| SmedWSM1115_RS33475 (SmedWSM1115_33475) | 93192..93521 | - | 330 | WP_018210786 | TrbC/VirB2 family protein | virB2 |
| SmedWSM1115_RS33480 (SmedWSM1115_33480) | 93533..94443 | - | 911 | Protein_76 | lytic transglycosylase domain-containing protein | - |
| SmedWSM1115_RS33485 (SmedWSM1115_33485) | 94666..95274 | + | 609 | WP_018210788 | hypothetical protein | - |
| SmedWSM1115_RS33490 (SmedWSM1115_33490) | 95271..95807 | + | 537 | WP_018210789 | thermonuclease family protein | - |
| SmedWSM1115_RS33495 (SmedWSM1115_33495) | 95804..96505 | + | 702 | WP_018210790 | thermonuclease family protein | - |
| SmedWSM1115_RS33500 (SmedWSM1115_33500) | 96563..96898 | + | 336 | WP_225996853 | hypothetical protein | - |
| SmedWSM1115_RS33505 (SmedWSM1115_33505) | 96910..97506 | + | 597 | WP_018210792 | hypothetical protein | - |
| SmedWSM1115_RS33510 (SmedWSM1115_33510) | 97526..97942 | + | 417 | WP_018210793 | hypothetical protein | - |
| SmedWSM1115_RS33515 (SmedWSM1115_33515) | 98025..98360 | - | 336 | WP_026183708 | hypothetical protein | - |
Host bacterium
| ID | 21558 | GenBank | NZ_CP088112 |
| Plasmid name | pWSM1115_3 | Incompatibility group | - |
| Plasmid size | 276847 bp | Coordinate of oriT [Strand] | 62607..62663 [-] |
| Host baterium | Sinorhizobium medicae WSM1115 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |