Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100439 |
| Name | oriT_pND12_96  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_019044 (34167..34276 [-], 110 nt) |
| oriT length | 110 nt |
| IRs (inverted repeats) | IR1: 24..31, 35..42 (GTCGGGGC..GCCCTGAC) IR2: 49..65, 72..88 (GTAATTGTAATAGCGTC..GACGGTATTACAATTAC) |
| 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_pND12_96
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 510 | GenBank | YP_006903442 |
| Name | NikB_pND12_96 |
UniProt ID | E9LLX8 |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103834.33 Da Isoelectric Point: 7.3473
>YP_006903442.1 relaxase/mobilization protein NikB (plasmid) [Escherichia coli]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | E9LLX8 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 39635..82223
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS900_RS00240 (ND12IncI1_45) | 37352..39642 | - | 2291 | Protein_47 | F-type conjugative transfer protein TrbC | - |
| HS900_RS00245 (ND12IncI1_46) | 39635..40705 | - | 1071 | WP_000151576 | IncI1-type conjugal transfer protein TrbB | trbB |
| HS900_RS00250 (ND12IncI1_47) | 40724..41932 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HS900_RS00255 | 42224..42376 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| HS900_RS00260 | 42448..42699 | - | 252 | WP_001291965 | hypothetical protein | - |
| HS900_RS00265 | 42742..42906 | + | 165 | WP_001323923 | hypothetical protein | - |
| HS900_RS00270 (ND12IncI1_50) | 43432..44082 | + | 651 | WP_000993958 | IS66-like element accessory protein TnpA | - |
| HS900_RS00275 (ND12IncI1_51) | 44082..44429 | + | 348 | WP_000624622 | IS66 family insertion sequence element accessory protein TnpB | - |
| HS900_RS00280 (ND12IncI1_52) | 44449..46020 | + | 1572 | WP_000381346 | IS66-like element IS679 family transposase | - |
| HS900_RS00285 (ND12IncI1_53) | 46336..46620 | - | 285 | WP_014640317 | hypothetical protein | - |
| HS900_RS00290 | 46904..47113 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| HS900_RS00295 (ND12IncI1_54) | 47185..47847 | - | 663 | WP_000644794 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HS900_RS00300 (ND12IncI1_55) | 47918..50086 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| HS900_RS00305 (ND12IncI1_56) | 50183..50767 | - | 585 | WP_001037985 | IncI1-type conjugal transfer protein TraX | - |
| HS900_RS00310 (ND12IncI1_57) | 50796..51998 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| HS900_RS00315 (ND12IncI1_58) | 51965..52579 | - | 615 | WP_000337400 | IncI1-type conjugal transfer protein TraV | traV |
| HS900_RS00320 (ND12IncI1_59) | 52579..55623 | - | 3045 | WP_001024780 | IncI1-type conjugal transfer protein TraU | traU |
| HS900_RS00325 (ND12IncI1_60) | 55713..56513 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HS900_RS00330 | 56497..56685 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HS900_RS00335 (ND12IncI1_61) | 56749..57153 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| HS900_RS00340 (ND12IncI1_62) | 57204..57731 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HS900_RS00345 (ND12IncI1_63) | 57731..58435 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HS900_RS00350 (ND12IncI1_64) | 58435..59724 | - | 1290 | WP_001271998 | conjugal transfer protein TraO | traO |
| HS900_RS00355 (ND12IncI1_65) | 59727..60710 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| HS900_RS00360 (ND12IncI1_66) | 60721..61413 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| HS900_RS00365 (ND12IncI1_67) | 61410..61757 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HS900_RS00370 (ND12IncI1_68) | 61775..65542 | - | 3768 | WP_001141534 | LPD7 domain-containing protein | - |
| HS900_RS00375 | 65632..66183 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| HS900_RS00380 | 66198..66488 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HS900_RS00385 (ND12IncI1_70) | 66485..67633 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HS900_RS00390 (ND12IncI1_71) | 67630..68448 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HS900_RS00395 | 68445..68810 | - | 366 | Protein_78 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HS900_RS00405 (ND12IncI1_74) | 70611..71195 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HS900_RS00410 (ND12IncI1_75) | 71255..72457 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| HS900_RS00415 (ND12IncI1_76) | 72543..73367 | - | 825 | WP_001238931 | conjugal transfer protein TraE | traE |
| HS900_RS00420 (ND12IncI1_77) | 73518..74672 | - | 1155 | WP_001139955 | site-specific integrase | - |
| HS900_RS00425 (ND12IncI1_78) | 74656..74982 | + | 327 | WP_001213803 | hypothetical protein | - |
| HS900_RS00430 | 75333..75488 | + | 156 | WP_001302705 | hypothetical protein | - |
| HS900_RS00435 | 75801..76058 | + | 258 | WP_001302706 | hypothetical protein | - |
| HS900_RS00445 (ND12IncI1_79) | 76306..77742 | - | 1437 | WP_015058206 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HS900_RS00450 (ND12IncI1_80) | 77730..78386 | - | 657 | WP_001193549 | A24 family peptidase | - |
| HS900_RS00455 (ND12IncI1_81) | 78371..78931 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| HS900_RS00460 (ND12IncI1_82) | 78941..79555 | - | 615 | WP_000908226 | type 4 pilus major pilin | - |
| HS900_RS00465 (ND12IncI1_83) | 79572..80657 | - | 1086 | WP_001208802 | type II secretion system F family protein | - |
| HS900_RS00470 (ND12IncI1_84) | 80670..82223 | - | 1554 | WP_000362206 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HS900_RS00475 (ND12IncI1_85) | 82234..82686 | - | 453 | WP_001247337 | type IV pilus biogenesis protein PilP | - |
| HS900_RS00480 (ND12IncI1_86) | 82673..83968 | - | 1296 | WP_000752780 | type 4b pilus protein PilO2 | - |
| HS900_RS00485 (ND12IncI1_87) | 83961..85643 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HS900_RS00490 (ND12IncI1_88) | 85657..86094 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HS900_RS00495 (ND12IncI1_89) | 86094..87161 | - | 1068 | WP_001360287 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 900 | GenBank | NC_019044 |
| Plasmid name | pND12_96 | Incompatibility group | IncI1 |
| Plasmid size | 92290 bp | Coordinate of oriT [Strand] | 34167..34276 [-] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |