Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100438 |
| Name | oriT_pND11_107  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_019043 (50515..50624 [-], 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_pND11_107
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 509 | GenBank | YP_006903553 |
| Name | NikB_pND11_107 |
UniProt ID | E9LLN1 |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104010.41 Da Isoelectric Point: 7.4265
>YP_006903553.1 plasmid relaxase/mobilization protein NikB (plasmid) [Escherichia coli]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | E9LLN1 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 55984..95695
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS767_RS00325 (ND11IncI1_63) | 53700..55991 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| HS767_RS00330 (ND11IncI1_64) | 55984..57054 | - | 1071 | WP_000151582 | IncI1-type conjugal transfer protein TrbB | trbB |
| HS767_RS00335 (ND11IncI1_65) | 57073..58281 | - | 1209 | WP_015058186 | IncI1-type conjugal transfer protein TrbA | trbA |
| HS767_RS00340 | 58573..58725 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| HS767_RS00345 (ND11IncI1_67) | 58797..59048 | - | 252 | WP_001291965 | hypothetical protein | - |
| HS767_RS00350 | 59972..60148 | - | 177 | WP_001054900 | hypothetical protein | - |
| HS767_RS00355 | 60357..60566 | - | 210 | WP_001140545 | hemolysin expression modulator Hha | - |
| HS767_RS00360 (ND11IncI1_69) | 60664..61278 | - | 615 | WP_000578649 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HS767_RS00365 (ND11IncI1_70) | 61354..63522 | - | 2169 | WP_000698360 | IncI1-type conjugal transfer membrane protein TraY | traY |
| HS767_RS00370 (ND11IncI1_71) | 63619..64203 | - | 585 | WP_001037986 | IncI1-type conjugal transfer protein TraX | - |
| HS767_RS00375 (ND11IncI1_72) | 64232..65434 | - | 1203 | WP_001189159 | IncI1-type conjugal transfer protein TraW | traW |
| HS767_RS00380 (ND11IncI1_73) | 65401..66015 | - | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| HS767_RS00385 (ND11IncI1_74) | 66015..69059 | - | 3045 | WP_015058187 | IncI1-type conjugal transfer protein TraU | traU |
| HS767_RS00390 (ND11IncI1_75) | 69149..69949 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HS767_RS00395 | 69933..70121 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HS767_RS00400 (ND11IncI1_76) | 70185..70589 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| HS767_RS00405 (ND11IncI1_77) | 70640..71167 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HS767_RS00410 (ND11IncI1_78) | 71167..71871 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HS767_RS00415 (ND11IncI1_79) | 71871..73160 | - | 1290 | WP_001271997 | conjugal transfer protein TraO | traO |
| HS767_RS00420 (ND11IncI1_80) | 73163..74146 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| HS767_RS00425 (ND11IncI1_81) | 74157..74849 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| HS767_RS00430 (ND11IncI1_82) | 74846..75193 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HS767_RS00435 (ND11IncI1_83) | 75211..78978 | - | 3768 | WP_001141534 | LPD7 domain-containing protein | - |
| HS767_RS00440 | 79068..79619 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| HS767_RS00445 | 79634..79924 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HS767_RS00450 (ND11IncI1_85) | 79921..81069 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HS767_RS00455 (ND11IncI1_86) | 81066..81884 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HS767_RS00460 (ND11IncI1_87) | 81881..82339 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HS767_RS00600 | 82734..82865 | - | 132 | Protein_93 | histidine phosphatase family protein | - |
| HS767_RS00470 (ND11IncI1_90) | 84196..84654 | - | 459 | Protein_95 | lipopolysaccharide core heptose(II)-phosphate phosphatase | - |
| HS767_RS00475 (ND11IncI1_91) | 84714..85916 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| HS767_RS00480 (ND11IncI1_92) | 86002..86826 | - | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| HS767_RS00485 (ND11IncI1_93) | 86977..88131 | - | 1155 | WP_001139958 | site-specific integrase | - |
| HS767_RS00490 (ND11IncI1_94) | 88130..88441 | + | 312 | WP_000958120 | hypothetical protein | - |
| HS767_RS00500 (ND11IncI1_97) | 89765..91189 | - | 1425 | WP_001389385 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HS767_RS00505 (ND11IncI1_98) | 91189..91845 | - | 657 | WP_001193554 | prepilin peptidase | - |
| HS767_RS00510 (ND11IncI1_99) | 91830..92390 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| HS767_RS00515 (ND11IncI1_100) | 92400..93014 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| HS767_RS00520 (ND11IncI1_101) | 93032..94129 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| HS767_RS00525 (ND11IncI1_102) | 94142..95695 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HS767_RS00530 (ND11IncI1_103) | 95706..96158 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| HS767_RS00535 (ND11IncI1_104) | 96145..97440 | - | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| HS767_RS00540 (ND11IncI1_105) | 97433..99115 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HS767_RS00545 (ND11IncI1_106) | 99129..99566 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HS767_RS00550 (ND11IncI1_107) | 99566..100633 | - | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 899 | GenBank | NC_019043 |
| Plasmid name | pND11_107 | Incompatibility group | IncI1 |
| Plasmid size | 107138 bp | Coordinate of oriT [Strand] | 50515..50624 [-] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | sul3, ant(3'')-Ia, cmlA1, aadA2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |