Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103866 |
| Name | oriT_pSfreNXT3a  |
| Organism | Sinorhizobium fredii strain NXT3 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP024308 (89555..89611 [-], 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_pSfreNXT3a
GCAGGAAAATGGCGTAGCACATTTTTCCGTATCCTGCCTCTCTAGATTGTAAGGGGA
GCAGGAAAATGGCGTAGCACATTTTTCCGTATCCTGCCTCTCTAGATTGTAAGGGGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 2711 | GenBank | WP_104840136 |
| Name | t4cp2_NXT3_RS19970_pSfreNXT3a |
UniProt ID | _ |
| Length | 699 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 699 a.a. Molecular weight: 77557.68 Da Isoelectric Point: 9.7918
>WP_104840136.1 type IV secretory system conjugative DNA transfer family protein [Sinorhizobium fredii]
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYKDGRILETTITSNPFAPIQQLWHYKTSPALQKVAFGS
MVPALLMAGLVAYVGLKPTSSPLGDAAFQDIASLRRGKWFRKQGHIFGRIGRNILRTKDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEKTNSYNPLDFIRPERGSRT
TDIQNIASILVPENTESENSVWQATAQQVLAGVISYITESTFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKELYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQANIPQVPEVDYLSPKPVPATTP
EYAKGGDPSVEIAAPAPVTEEKPLTAAAAEAAPVKAEPAAAPKAAAPAKRTVNKKALRPKPMATAAKTGG
AEASASLYAMEARIKAIEEGLIPKAAQLKEVVETKAEKLGDKSPTKRRNIVDIFSATVPDPVEVGVAAE
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYKDGRILETTITSNPFAPIQQLWHYKTSPALQKVAFGS
MVPALLMAGLVAYVGLKPTSSPLGDAAFQDIASLRRGKWFRKQGHIFGRIGRNILRTKDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEKTNSYNPLDFIRPERGSRT
TDIQNIASILVPENTESENSVWQATAQQVLAGVISYITESTFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKELYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQANIPQVPEVDYLSPKPVPATTP
EYAKGGDPSVEIAAPAPVTEEKPLTAAAAEAAPVKAEPAAAPKAAAPAKRTVNKKALRPKPMATAAKTGG
AEASASLYAMEARIKAIEEGLIPKAAQLKEVVETKAEKLGDKSPTKRRNIVDIFSATVPDPVEVGVAAE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 130379..140301
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| NXT3_RS19960 | 127212..127490 | - | 279 | WP_104840134 | hypothetical protein | - |
| NXT3_RS19965 | 127489..127686 | + | 198 | WP_104840135 | hypothetical protein | - |
| NXT3_RS19970 (NXT3_PA00116) | 128283..130382 | - | 2100 | WP_104840136 | type IV secretory system conjugative DNA transfer family protein | - |
| NXT3_RS19975 (NXT3_PA00117) | 130379..131407 | - | 1029 | WP_104840137 | P-type DNA transfer ATPase VirB11 | virB11 |
| NXT3_RS19980 (NXT3_PA00118) | 131388..132599 | - | 1212 | WP_104840138 | type IV secretion system protein VirB10 | virB10 |
| NXT3_RS19985 (NXT3_PA00119) | 132599..133408 | - | 810 | WP_104840139 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| NXT3_RS19990 (NXT3_PA00120) | 133405..134100 | - | 696 | WP_104840140 | type IV secretion system protein | virB8 |
| NXT3_RS19995 (NXT3_PA00121) | 134139..135167 | - | 1029 | WP_104840141 | type IV secretion system protein | virB6 |
| NXT3_RS20000 (NXT3_PA00122) | 135183..135410 | - | 228 | WP_011971091 | hypothetical protein | - |
| NXT3_RS20005 (NXT3_PA00123) | 135400..136101 | - | 702 | WP_104840142 | type IV secretion system protein | - |
| NXT3_RS20010 (NXT3_PA00124) | 136113..137201 | - | 1089 | WP_104840143 | lytic transglycosylase domain-containing protein | - |
| NXT3_RS20015 (NXT3_PA00125) | 137198..139657 | - | 2460 | WP_104840144 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| NXT3_RS20020 (NXT3_PA00126) | 139660..139959 | - | 300 | WP_104840145 | VirB3 family type IV secretion system protein | virB3 |
| NXT3_RS20025 (NXT3_PA00127) | 139963..140301 | - | 339 | WP_017265136 | TrbC/VirB2 family protein | virB2 |
| NXT3_RS20030 (NXT3_PA00128) | 140313..141224 | - | 912 | WP_199773371 | lytic transglycosylase domain-containing protein | - |
| NXT3_RS20035 (NXT3_PA00129) | 141445..142053 | + | 609 | WP_104840146 | hypothetical protein | - |
| NXT3_RS20040 (NXT3_PA00130) | 142050..142586 | + | 537 | WP_104840147 | succinoglycan biosynthesis protein exoi | - |
| NXT3_RS20045 (NXT3_PA00131) | 142583..143284 | + | 702 | WP_104840148 | thermonuclease family protein | - |
| NXT3_RS20050 | 143342..143689 | + | 348 | WP_234828150 | hypothetical protein | - |
| NXT3_RS33100 | 143691..144056 | + | 366 | WP_337442172 | hypothetical protein | - |
| NXT3_RS32070 (NXT3_PA00134) | 144298..144549 | + | 252 | WP_234828151 | hypothetical protein | - |
Host bacterium
| ID | 4306 | GenBank | NZ_CP024308 |
| Plasmid name | pSfreNXT3a | Incompatibility group | - |
| Plasmid size | 387881 bp | Coordinate of oriT [Strand] | 89555..89611 [-] |
| Host baterium | Sinorhizobium fredii strain NXT3 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | dxnH |
| Symbiosis gene | fixB, fixA |
| Anti-CRISPR | AcrIIA9 |