Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120264 |
| Name | oriT_LMB1|pC  |
| Organism | Sinorhizobium meliloti strain LMB1 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP141215 (53511..53565 [+], 55 nt) |
| oriT length | 55 nt |
| IRs (inverted repeats) | 2..7, 21..26 (GGAAAA..TTTTCC) |
| Location of nic site | 34..35 |
| Conserved sequence flanking the nic site |
TCCTGCCTCT |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 55 nt
>oriT_LMB1|pC
AGGAAAAGGGCGTAGCACATTTTTCCGTATCCTGCCTCTCCAAATTGTAAGGGGA
AGGAAAAGGGCGTAGCACATTTTTCCGTATCCTGCCTCTCCAAATTGTAAGGGGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 14961 | GenBank | WP_324765555 |
| Name | t4cp2_SO078_RS29785_LMB1|pC |
UniProt ID | _ |
| Length | 699 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 699 a.a. Molecular weight: 77671.63 Da Isoelectric Point: 9.8652
>WP_324765555.1 type IV secretory system conjugative DNA transfer family protein [Sinorhizobium meliloti]
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYKDGRILETTITSNPFAPIQQFWHYKTSPALQKVALAS
MVPALLVAGLVAYIGLKPTSSPLGDAAFQDMASLRRGKWFRKQGHIFGRIGRNILRTKDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEKTNSYNPLDFIRPERGNRT
TDIQNIASILVPENTGSENSVWQATAQQVLAGVISYITESPFFKDRRNLSEVNSFFNSGADLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFRTQPFKSAEAFSQANIPQVPEVDYLSPKPVPATTP
EYAKGGDPSVEIPSPAPAKNEKPFTAAAAEAAPVKAEPAADEKAAAPAKRTVNTKALRPKPKATAANTGG
AEASASLDAMEARIKAIEEGLKPKAAQLKEVVDTKAEKLGDKSPTKRRNIMDIFSTTIPDPVDVGMPAE
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYKDGRILETTITSNPFAPIQQFWHYKTSPALQKVALAS
MVPALLVAGLVAYIGLKPTSSPLGDAAFQDMASLRRGKWFRKQGHIFGRIGRNILRTKDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEKTNSYNPLDFIRPERGNRT
TDIQNIASILVPENTGSENSVWQATAQQVLAGVISYITESPFFKDRRNLSEVNSFFNSGADLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFRTQPFKSAEAFSQANIPQVPEVDYLSPKPVPATTP
EYAKGGDPSVEIPSPAPAKNEKPFTAAAAEAAPVKAEPAADEKAAAPAKRTVNTKALRPKPKATAANTGG
AEASASLDAMEARIKAIEEGLKPKAAQLKEVVDTKAEKLGDKSPTKRRNIMDIFSTTIPDPVDVGMPAE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 20577..30499
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SO078_RS29690 (SO078_29690) | 15741..16075 | + | 335 | Protein_19 | hypothetical protein | - |
| SO078_RS29695 (SO078_29695) | 16158..16574 | - | 417 | WP_324765542 | hypothetical protein | - |
| SO078_RS29700 (SO078_29700) | 16594..17190 | - | 597 | WP_324765543 | hypothetical protein | - |
| SO078_RS29705 (SO078_29705) | 17192..17536 | - | 345 | WP_324765544 | hypothetical protein | - |
| SO078_RS29710 (SO078_29710) | 17592..18293 | - | 702 | WP_324765545 | thermonuclease family protein | - |
| SO078_RS29715 (SO078_29715) | 18290..18826 | - | 537 | WP_324765546 | thermonuclease family protein | - |
| SO078_RS29720 (SO078_29720) | 18823..19431 | - | 609 | WP_324765547 | hypothetical protein | - |
| SO078_RS29725 (SO078_29725) | 19654..20565 | + | 912 | WP_324765615 | lytic transglycosylase domain-containing protein | - |
| SO078_RS29730 (SO078_29730) | 20577..20915 | + | 339 | WP_015241462 | TrbC/VirB2 family protein | virB2 |
| SO078_RS29735 (SO078_29735) | 20919..21218 | + | 300 | WP_020479309 | type IV secretion system protein VirB3 | virB3 |
| SO078_RS29740 (SO078_29740) | 21221..23680 | + | 2460 | WP_324765548 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| SO078_RS29745 (SO078_29745) | 23677..24765 | + | 1089 | WP_324765549 | lytic transglycosylase domain-containing protein | - |
| SO078_RS29750 (SO078_29750) | 24777..25478 | + | 702 | WP_324765550 | type IV secretion system protein | - |
| SO078_RS29755 (SO078_29755) | 25468..25695 | + | 228 | WP_127676176 | hypothetical protein | - |
| SO078_RS29760 (SO078_29760) | 25711..26739 | + | 1029 | WP_318931155 | type IV secretion system protein | virB6 |
| SO078_RS29765 (SO078_29765) | 26778..27473 | + | 696 | WP_324765551 | type IV secretion system protein | virB8 |
| SO078_RS29770 (SO078_29770) | 27470..28279 | + | 810 | WP_324765552 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| SO078_RS29775 (SO078_29775) | 28279..29490 | + | 1212 | WP_324765553 | type IV secretion system protein VirB10 | virB10 |
| SO078_RS29780 (SO078_29780) | 29471..30499 | + | 1029 | WP_324765554 | P-type DNA transfer ATPase VirB11 | virB11 |
| SO078_RS29785 (SO078_29785) | 30496..32595 | + | 2100 | WP_324765555 | type IV secretory system conjugative DNA transfer family protein | - |
| SO078_RS29790 (SO078_29790) | 33970..34182 | - | 213 | WP_107591998 | hypothetical protein | - |
| SO078_RS29795 (SO078_29795) | 34206..34727 | - | 522 | WP_324765556 | hypothetical protein | - |
Host bacterium
| ID | 20693 | GenBank | NZ_CP141215 |
| Plasmid name | LMB1|pC | Incompatibility group | - |
| Plasmid size | 337726 bp | Coordinate of oriT [Strand] | 53511..53565 [+] |
| Host baterium | Sinorhizobium meliloti strain LMB1 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | htpB |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |