Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 118961 |
| Name | oriT_pMl1  |
| Organism | Sinorhizobium medicae strain ml49 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP140898 (116043..116099 [+], 57 nt) |
| oriT length | 57 nt |
| IRs (inverted repeats) | 4..9, 23..28 (GGAAAG..CTTTCC) |
| 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_pMl1
GCAGGAAAGTGGCGTAGCACATCTTTCCGTATCCTGCCCCTCCGAATTGTAAGGGGA
GCAGGAAAGTGGCGTAGCACATCTTTCCGTATCCTGCCCCTCCGAATTGTAAGGGGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 14076 | GenBank | WP_208180198 |
| Name | t4cp2_U8C36_RS35710_pMl1 |
UniProt ID | _ |
| Length | 699 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 699 a.a. Molecular weight: 77679.50 Da Isoelectric Point: 9.5372
>WP_208180198.1 type IV secretory system conjugative DNA transfer family protein [Sinorhizobium medicae]
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYKDGRILEATITSNPFAPIQQFWHYKTSPALQKVALGS
MVPALLVACLVAYIGLKPTSNPLGDAAFQDIASLRRVKWFRKQGHIFGRMGRNILRTKDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEKTNSYNPLDFIRPERGNRT
TDIQNIASILVPENTESENSVWQATAQQVLAGVISYITESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMNKLPYVAGYNIKLAFIVQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQVNIPQVPEVDYLSPKPVPATTP
EYAKGGDPSVEIPSPAPAAEEKPLTAAAAEAAPVKAEPAADEKAAAPAKRTVNKKALRPKSKPTAANTGG
AEASASLDAMEARIRAIEEGLKPKAAQLKEVVETIAEKLGDKSSTTRRNVTEIFNATVPDPAEVGVAAE
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYKDGRILEATITSNPFAPIQQFWHYKTSPALQKVALGS
MVPALLVACLVAYIGLKPTSNPLGDAAFQDIASLRRVKWFRKQGHIFGRMGRNILRTKDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEKTNSYNPLDFIRPERGNRT
TDIQNIASILVPENTESENSVWQATAQQVLAGVISYITESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMNKLPYVAGYNIKLAFIVQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQVNIPQVPEVDYLSPKPVPATTP
EYAKGGDPSVEIPSPAPAAEEKPLTAAAAEAAPVKAEPAADEKAAAPAKRTVNKKALRPKSKPTAANTGG
AEASASLDAMEARIRAIEEGLKPKAAQLKEVVETIAEKLGDKSSTTRRNVTEIFNATVPDPAEVGVAAE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 91862..101785
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| U8C36_RS35615 (U8C36_35620) | 87077..87367 | + | 291 | WP_234942436 | hypothetical protein | - |
| U8C36_RS35620 (U8C36_35625) | 87447..87863 | - | 417 | WP_208180186 | hypothetical protein | - |
| U8C36_RS35625 (U8C36_35630) | 87883..88473 | - | 591 | WP_208180187 | hypothetical protein | - |
| U8C36_RS35630 (U8C36_35635) | 88475..88879 | - | 405 | WP_208180188 | hypothetical protein | - |
| U8C36_RS35635 (U8C36_35640) | 88880..89581 | - | 702 | WP_208180189 | thermonuclease family protein | - |
| U8C36_RS35640 (U8C36_35645) | 89578..90114 | - | 537 | WP_208180190 | thermonuclease family protein | - |
| U8C36_RS35645 (U8C36_35650) | 90111..90719 | - | 609 | WP_208180191 | hypothetical protein | - |
| U8C36_RS35650 (U8C36_35655) | 90942..91850 | + | 909 | WP_208180225 | lytic transglycosylase domain-containing protein | - |
| U8C36_RS35655 (U8C36_35660) | 91862..92200 | + | 339 | WP_208180192 | TrbC/VirB2 family protein | virB2 |
| U8C36_RS35660 (U8C36_35665) | 92204..92503 | + | 300 | WP_014531077 | type IV secretion system protein VirB3 | virB3 |
| U8C36_RS35665 (U8C36_35670) | 92506..94965 | + | 2460 | WP_208180193 | VirB4 family type IV secretion system protein | virb4 |
| U8C36_RS35670 (U8C36_35675) | 94962..96050 | + | 1089 | WP_127515472 | lytic transglycosylase domain-containing protein | - |
| U8C36_RS35675 (U8C36_35680) | 96062..96763 | + | 702 | WP_128146496 | type IV secretion system protein | - |
| U8C36_RS35680 (U8C36_35685) | 96753..96980 | + | 228 | WP_128146487 | hypothetical protein | - |
| U8C36_RS35685 (U8C36_35690) | 96996..98024 | + | 1029 | WP_128146486 | type IV secretion system protein | virB6 |
| U8C36_RS35690 (U8C36_35695) | 98063..98758 | + | 696 | WP_208180194 | virB8 family protein | virB8 |
| U8C36_RS35695 (U8C36_35700) | 98755..99564 | + | 810 | WP_208180195 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| U8C36_RS35700 (U8C36_35705) | 99564..100776 | + | 1213 | Protein_101 | type IV secretion system protein VirB10 | - |
| U8C36_RS35705 (U8C36_35710) | 100757..101785 | + | 1029 | WP_208180197 | P-type DNA transfer ATPase VirB11 | virB11 |
| U8C36_RS35710 (U8C36_35715) | 101782..103881 | + | 2100 | WP_208180198 | type IV secretory system conjugative DNA transfer family protein | - |
| U8C36_RS35715 (U8C36_35720) | 104402..106258 | + | 1857 | WP_322887502 | S8 family serine peptidase | - |
Host bacterium
| ID | 19393 | GenBank | NZ_CP140898 |
| Plasmid name | pMl1 | Incompatibility group | - |
| Plasmid size | 169780 bp | Coordinate of oriT [Strand] | 116043..116099 [+] |
| Host baterium | Sinorhizobium medicae strain ml49 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |