Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100416 |
| Name | oriT_pRK1  |
| Organism | Escherichia coli W |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_017665 (5704..5813 [-], 110 nt) |
| oriT length | 110 nt |
| IRs (inverted repeats) | IR1: 24..31, 35..42 (GTCGGGGC..GCCCTGAC) IR2: 49..65, 72..88 (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC) |
| Location of nic site | 96..97 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 110 nt
>oriT_pRK1
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 487 | GenBank | WP_001350015 |
| Name | NikB_pRK1 |
UniProt ID | _ |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104034.43 Da Isoelectric Point: 7.3526
>WP_001350015.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 11173..47076
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| WFL_RS24505 (WFL_23485) | 8889..11180 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| WFL_RS24510 (WFL_23490) | 11173..12243 | - | 1071 | WP_000151587 | IncI1-type conjugal transfer protein TrbB | trbB |
| WFL_RS24515 (WFL_23495) | 12262..13470 | - | 1209 | WP_000121272 | IncI1-type conjugal transfer protein TrbA | trbA |
| WFL_RS24520 (WFL_23500) | 13732..14640 | - | 909 | WP_000055084 | hypothetical protein | - |
| WFL_RS28285 (WFL_23505) | 15272..15367 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| WFL_RS27865 (WFL_23510) | 15432..15608 | - | 177 | WP_001054904 | hypothetical protein | - |
| WFL_RS24540 (WFL_23515) | 15818..16009 | - | 192 | WP_001147208 | hemolysin expression modulator Hha | - |
| WFL_RS24545 (WFL_23520) | 16075..16689 | - | 615 | WP_000578649 | plasmid IncI1-type surface exclusion protein ExcA | - |
| WFL_RS24550 (WFL_23525) | 16765..18933 | - | 2169 | WP_000698360 | IncI1-type conjugal transfer membrane protein TraY | traY |
| WFL_RS24555 (WFL_23530) | 19030..19614 | - | 585 | WP_001037990 | IncI1-type conjugal transfer protein TraX | - |
| WFL_RS24560 (WFL_23535) | 19643..20845 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| WFL_RS24565 (WFL_23540) | 20812..21426 | - | 615 | WP_000337400 | IncI1-type conjugal transfer protein TraV | traV |
| WFL_RS24570 (WFL_23545) | 21426..24470 | - | 3045 | WP_001024787 | IncI1-type conjugal transfer protein TraU | traU |
| WFL_RS24575 (WFL_23550) | 24560..25360 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| WFL_RS24580 (WFL_23555) | 25344..25532 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| WFL_RS24585 (WFL_23560) | 25596..26000 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| WFL_RS24590 (WFL_23565) | 26051..26578 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| WFL_RS24595 (WFL_23570) | 26578..27282 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| WFL_RS24600 (WFL_23575) | 27282..28571 | - | 1290 | WP_001271991 | conjugal transfer protein TraO | traO |
| WFL_RS24605 (WFL_23580) | 28574..29557 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| WFL_RS24610 (WFL_23585) | 29568..30260 | - | 693 | WP_000138549 | DotI/IcmL family type IV secretion protein | traM |
| WFL_RS24615 (WFL_23590) | 30257..30604 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| WFL_RS24620 (WFL_23595) | 30622..34389 | - | 3768 | WP_001141538 | LPD7 domain-containing protein | - |
| WFL_RS24625 (WFL_23600) | 34479..35030 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| WFL_RS26630 | 35045..35335 | - | 291 | WP_001299214 | hypothetical protein | traK |
| WFL_RS24630 (WFL_23610) | 35332..36480 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| WFL_RS24635 (WFL_23615) | 36477..37295 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| WFL_RS24640 (WFL_23620) | 37292..37750 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| WFL_RS24645 (WFL_23625) | 38145..38729 | - | 585 | WP_000977526 | histidine phosphatase family protein | - |
| WFL_RS24650 (WFL_23630) | 38789..39991 | - | 1203 | WP_000976350 | conjugal transfer protein TraF | - |
| WFL_RS24655 (WFL_23635) | 40077..40901 | - | 825 | WP_001238943 | conjugal transfer protein TraE | traE |
| WFL_RS27215 | 41109..41234 | + | 126 | Protein_42 | RNA-guided endonuclease TnpB family protein | - |
| WFL_RS24660 (WFL_23640) | 41291..42583 | - | 1293 | WP_001350014 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| WFL_RS24665 (WFL_23645) | 42583..43239 | - | 657 | WP_001193549 | A24 family peptidase | - |
| WFL_RS24670 (WFL_23650) | 43224..43784 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| WFL_RS24675 (WFL_23655) | 43794..44408 | - | 615 | WP_000908226 | type 4 pilus major pilin | - |
| WFL_RS24680 (WFL_23660) | 44425..45510 | - | 1086 | WP_001208804 | type II secretion system F family protein | - |
| WFL_RS24685 (WFL_23665) | 45523..47076 | - | 1554 | WP_000362206 | ATPase, T2SS/T4P/T4SS family | virB11 |
| WFL_RS24690 (WFL_23670) | 47087..47539 | - | 453 | WP_001236383 | type IV pilus biogenesis protein PilP | - |
| WFL_RS24695 (WFL_23675) | 47526..48821 | - | 1296 | WP_000752792 | type 4b pilus protein PilO2 | - |
| WFL_RS24700 (WFL_23680) | 48814..50496 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| WFL_RS24705 (WFL_23685) | 50510..50947 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| WFL_RS24710 | 50947..52014 | - | 1068 | WP_001350013 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 877 | GenBank | NC_017665 |
| Plasmid name | pRK1 | Incompatibility group | IncI |
| Plasmid size | 102535 bp | Coordinate of oriT [Strand] | 5704..5813 [-] |
| Host baterium | Escherichia coli W |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | faeC, faeD, faeE, faeF, faeG |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |