Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103810 |
| Name | oriT_pSMED03  |
| Organism | Sinorhizobium medicae WSM419 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NC_009622 (43908..43966 [-], 59 nt) |
| oriT length | 59 nt |
| IRs (inverted repeats) | 4..9, 23..28 (GGAAAA..TTTTCC) |
| Location of nic site | 36..37 |
| Conserved sequence flanking the nic site |
TCCTGCCTCT |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 59 nt
>oriT_pSMED03
GCAGGAAAAGGGCGTAGCACATTTTTCCGTATCCTGCCTCTCCAAATTGTAAGGGGATT
GCAGGAAAAGGGCGTAGCACATTTTTCCGTATCCTGCCTCTCCAAATTGTAAGGGGATT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 2653 | GenBank | WP_011971097 |
| Name | t4cp2_SMED_RS31355_pSMED03 |
UniProt ID | _ |
| Length | 699 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 699 a.a. Molecular weight: 77543.44 Da Isoelectric Point: 9.7903
>WP_011971097.1 type IV secretory system conjugative DNA transfer family protein [Sinorhizobium medicae]
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYRDGRILETTITSNPFAPIQQFWHYKTSPALQKVALGS
MLPALLAAGLVACIGLKPTSSPLGDAAFQDLASLRRRKWFRKQGHIFGRVGRNILRTKDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEKTNSYNPLDFIRPERGNRT
TDIQNIASILVPENTESENSVWQATAQQVLAGVISYITESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYVALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMNILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYVSRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQANIPQVPEVDYLSPKPVPATTP
EYASGGDPSVEIPSPAPAKEEKPLTAAAAEAAPVMAEPAAGEKAAAPAKRAVNRKALRTNPKATAANTGG
AEASASLDAMEARIKAIEEGLKPKAAQLKEVVETKAEKLGGKSPTKRRNILDIFSATVPDPVEVGVTAE
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYRDGRILETTITSNPFAPIQQFWHYKTSPALQKVALGS
MLPALLAAGLVACIGLKPTSSPLGDAAFQDLASLRRRKWFRKQGHIFGRVGRNILRTKDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEKTNSYNPLDFIRPERGNRT
TDIQNIASILVPENTESENSVWQATAQQVLAGVISYITESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYVALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMNILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYVSRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQANIPQVPEVDYLSPKPVPATTP
EYASGGDPSVEIPSPAPAKEEKPLTAAAAEAAPVMAEPAAGEKAAAPAKRAVNRKALRTNPKATAANTGG
AEASASLDAMEARIKAIEEGLKPKAAQLKEVVETKAEKLGGKSPTKRRNILDIFSATVPDPVEVGVTAE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 58757..68666
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SMED_RS31345 (Smed_6394) | 53870..55345 | - | 1476 | WP_011971098 | DUF1214 domain-containing protein | - |
| SMED_RS31350 (Smed_6395) | 55622..56576 | + | 955 | Protein_64 | LysR family transcriptional regulator | - |
| SMED_RS31355 (Smed_6396) | 56661..58760 | - | 2100 | WP_011971097 | type IV secretory system conjugative DNA transfer family protein | - |
| SMED_RS31360 (Smed_6397) | 58757..59785 | - | 1029 | WP_011971096 | P-type DNA transfer ATPase VirB11 | virB11 |
| SMED_RS31365 (Smed_6398) | 59766..60977 | - | 1212 | WP_011971095 | type IV secretion system protein VirB10 | virB10 |
| SMED_RS31370 (Smed_6399) | 60977..61786 | - | 810 | WP_011971094 | P-type conjugative transfer protein VirB9 | virB9 |
| SMED_RS31375 (Smed_6400) | 61783..62478 | - | 696 | WP_011971093 | type IV secretion system protein | virB8 |
| SMED_RS31380 (Smed_6401) | 62504..63532 | - | 1029 | WP_011971092 | type IV secretion system protein | virB6 |
| SMED_RS31385 (Smed_6402) | 63548..63775 | - | 228 | WP_011971091 | hypothetical protein | - |
| SMED_RS31390 (Smed_6403) | 63765..64466 | - | 702 | WP_011971090 | type IV secretion system protein | - |
| SMED_RS31395 (Smed_6404) | 64478..65566 | - | 1089 | WP_011971089 | lytic transglycosylase domain-containing protein | - |
| SMED_RS31400 (Smed_6405) | 65563..68022 | - | 2460 | WP_011971088 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| SMED_RS31405 (Smed_6406) | 68025..68324 | - | 300 | WP_011971087 | VirB3 family type IV secretion system protein | virB3 |
| SMED_RS31410 (Smed_6407) | 68328..68666 | - | 339 | WP_011971086 | TrbC/VirB2 family protein | virB2 |
| SMED_RS31415 (Smed_6408) | 68678..69589 | - | 912 | WP_024312403 | lytic transglycosylase domain-containing protein | - |
| SMED_RS31420 (Smed_6409) | 69812..70420 | + | 609 | WP_011971084 | hypothetical protein | - |
| SMED_RS31425 (Smed_6410) | 70417..70953 | + | 537 | WP_011971083 | succinoglycan biosynthesis protein exoi | - |
| SMED_RS31430 (Smed_6411) | 70950..71651 | + | 702 | WP_011971082 | thermonuclease family protein | - |
| SMED_RS31435 (Smed_6412) | 71652..72050 | + | 399 | WP_011971081 | hypothetical protein | - |
| SMED_RS31440 (Smed_6413) | 72052..72648 | + | 597 | WP_011971080 | hypothetical protein | - |
| SMED_RS31445 (Smed_6414) | 72669..73085 | + | 417 | WP_011971079 | hypothetical protein | - |
| SMED_RS31450 (Smed_6415) | 73168..73503 | - | 336 | WP_024312400 | hypothetical protein | - |
Host bacterium
| ID | 4250 | GenBank | NC_009622 |
| Plasmid name | pSMED03 | Incompatibility group | - |
| Plasmid size | 219313 bp | Coordinate of oriT [Strand] | 43908..43966 [-] |
| Host baterium | Sinorhizobium medicae WSM419 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |