Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100407 |
| Name | oriT_pRK1  |
| Organism | Escherichia coli W |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_017637 (12719..12828 [-], 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 | 478 | GenBank | WP_001350015 |
| Name | NikB_pRK1 |
UniProt ID | E0J389 |
| 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
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | E0J389 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 18188..54091
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| ECW_RS24600 (ECW_P1m0020) | 15904..18195 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| ECW_RS24605 (ECW_P1m0021) | 18188..19258 | - | 1071 | WP_000151587 | IncI1-type conjugal transfer protein TrbB | trbB |
| ECW_RS24610 (ECW_P1m0022) | 19277..20485 | - | 1209 | WP_000121272 | IncI1-type conjugal transfer protein TrbA | trbA |
| ECW_RS24615 (ECW_P1m0023) | 20747..21655 | - | 909 | WP_000055084 | hypothetical protein | - |
| ECW_RS28490 | 22287..22382 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| ECW_RS28065 (ECW_P1m0025) | 22447..22623 | - | 177 | WP_001054904 | hypothetical protein | - |
| ECW_RS24635 | 22833..23024 | - | 192 | WP_001147208 | hemolysin expression modulator Hha | - |
| ECW_RS24640 (ECW_P1m0026) | 23090..23704 | - | 615 | WP_000578649 | plasmid IncI1-type surface exclusion protein ExcA | - |
| ECW_RS24645 (ECW_P1m0027) | 23780..25948 | - | 2169 | WP_000698360 | IncI1-type conjugal transfer membrane protein TraY | traY |
| ECW_RS24650 (ECW_P1m0028) | 26045..26629 | - | 585 | WP_001037990 | IncI1-type conjugal transfer protein TraX | - |
| ECW_RS24655 (ECW_P1m0029) | 26658..27860 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| ECW_RS24660 (ECW_P1m0030) | 27827..28441 | - | 615 | WP_000337400 | IncI1-type conjugal transfer protein TraV | traV |
| ECW_RS24665 (ECW_P1m0031) | 28441..31485 | - | 3045 | WP_001024787 | IncI1-type conjugal transfer protein TraU | traU |
| ECW_RS24670 (ECW_P1m0032) | 31575..32375 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| ECW_RS24675 (ECW_P1m0033) | 32359..32547 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| ECW_RS24680 (ECW_P1m0034) | 32611..33015 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| ECW_RS24685 (ECW_P1m0035) | 33066..33593 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| ECW_RS24690 (ECW_P1m0036) | 33593..34297 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| ECW_RS24695 (ECW_P1m0037) | 34297..35586 | - | 1290 | WP_001271991 | conjugal transfer protein TraO | traO |
| ECW_RS24700 (ECW_P1m0038) | 35589..36572 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| ECW_RS24705 (ECW_P1m0039) | 36583..37275 | - | 693 | WP_000138549 | DotI/IcmL family type IV secretion protein | traM |
| ECW_RS24710 (ECW_P1m0040) | 37272..37619 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| ECW_RS24715 (ECW_P1m0041) | 37637..41404 | - | 3768 | WP_001141538 | LPD7 domain-containing protein | - |
| ECW_RS24720 (ECW_P1m0043) | 41494..42045 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| ECW_RS26795 (ECW_P1m0044) | 42060..42350 | - | 291 | WP_001299214 | hypothetical protein | traK |
| ECW_RS24725 (ECW_P1m0045) | 42347..43495 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| ECW_RS24730 (ECW_P1m0046) | 43492..44310 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| ECW_RS24735 (ECW_P1m0047) | 44307..44765 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| ECW_RS24740 (ECW_P1m0048) | 45160..45744 | - | 585 | WP_000977526 | histidine phosphatase family protein | - |
| ECW_RS24745 (ECW_P1m0049) | 45804..47006 | - | 1203 | WP_000976350 | conjugal transfer protein TraF | - |
| ECW_RS24750 (ECW_P1m0050) | 47092..47916 | - | 825 | WP_001238943 | conjugal transfer protein TraE | traE |
| ECW_RS27370 | 48124..48249 | + | 126 | Protein_50 | RNA-guided endonuclease TnpB family protein | - |
| ECW_RS24755 (ECW_P1m0051) | 48306..49598 | - | 1293 | WP_001350014 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| ECW_RS24760 (ECW_P1m0052) | 49598..50254 | - | 657 | WP_001193549 | A24 family peptidase | - |
| ECW_RS24765 (ECW_P1m0053) | 50239..50799 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| ECW_RS24770 (ECW_P1m0054) | 50809..51423 | - | 615 | WP_000908226 | type 4 pilus major pilin | - |
| ECW_RS24775 (ECW_P1m0055) | 51440..52525 | - | 1086 | WP_001208804 | type II secretion system F family protein | - |
| ECW_RS24780 (ECW_P1m0056) | 52538..54091 | - | 1554 | WP_000362206 | ATPase, T2SS/T4P/T4SS family | virB11 |
| ECW_RS24785 (ECW_P1m0057) | 54102..54554 | - | 453 | WP_001236383 | type IV pilus biogenesis protein PilP | - |
| ECW_RS24790 (ECW_P1m0058) | 54541..55836 | - | 1296 | WP_000752792 | type 4b pilus protein PilO2 | - |
| ECW_RS24795 (ECW_P1m0059) | 55829..57511 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| ECW_RS24800 (ECW_P1m0060) | 57525..57962 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| ECW_RS24805 (ECW_P1m0061) | 57962..59029 | - | 1068 | WP_001350013 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 868 | GenBank | NC_017637 |
| Plasmid name | pRK1 | Incompatibility group | IncI |
| Plasmid size | 102536 bp | Coordinate of oriT [Strand] | 12719..12828 [-] |
| 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 | - |