Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100578 |
| Name | oriT_pESBL-315  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_024980 (45045..45154 [-], 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_pESBL-315
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 650 | GenBank | YP_009061728 |
| Name | NikB_pESBL-315 |
UniProt ID | A0A075URU2 |
| Length | 623 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 623 a.a. Molecular weight: 72279.04 Da Isoelectric Point: 7.6958
>YP_009061728.1 NikB (plasmid) [Escherichia coli]
MDGKFLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKI
AETESLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVW
SLLTLDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKES
LWGYSISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLG
RAEPQAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWRE
QWRKPDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADG
KWYPPSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQ
KNGSVRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAE
MVAWHNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MDGKFLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKI
AETESLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVW
SLLTLDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKES
LWGYSISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLG
RAEPQAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWRE
QWRKPDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADG
KWYPPSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQ
KNGSVRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAE
MVAWHNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A075URU2 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 50512..82966
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS311_RS00295 (D616_p130066) | 48229..50519 | - | 2291 | Protein_56 | F-type conjugative transfer protein TrbC | - |
| HS311_RS00300 (D616_p130067) | 50512..51582 | - | 1071 | WP_000151582 | IncI1-type conjugal transfer protein TrbB | trbB |
| HS311_RS00305 (D616_p130068) | 51601..52809 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HS311_RS00310 (D616_p130069) | 53116..53895 | - | 780 | WP_275450201 | protein FinQ | - |
| HS311_RS00315 (D616_p130070) | 54522..54674 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| HS311_RS00320 (D616_p130071) | 54746..54997 | - | 252 | WP_001291965 | hypothetical protein | - |
| HS311_RS00325 | 55040..55204 | + | 165 | WP_001323923 | hypothetical protein | - |
| HS311_RS00330 (D616_p130072) | 55920..56204 | - | 285 | WP_014640317 | hypothetical protein | - |
| HS311_RS00335 | 56305..56514 | - | 210 | Protein_64 | hemolysin expression modulator Hha | - |
| HS311_RS00340 (D616_p130073) | 56612..57226 | - | 615 | WP_000578649 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HS311_RS00345 (D616_p130074) | 57302..59470 | - | 2169 | WP_000698360 | IncI1-type conjugal transfer membrane protein TraY | traY |
| HS311_RS00350 (D616_p130075) | 59567..60151 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| HS311_RS00355 (D616_p130076) | 60180..61382 | - | 1203 | WP_001189159 | IncI1-type conjugal transfer protein TraW | traW |
| HS311_RS00360 (D616_p130077) | 61349..61963 | - | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| HS311_RS00365 (D616_p130078) | 61963..65007 | - | 3045 | WP_001024752 | IncI1-type conjugal transfer protein TraU | traU |
| HS311_RS00370 (D616_p130079) | 65097..65897 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HS311_RS00375 (D616_p130080) | 65881..66069 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HS311_RS00380 (D616_p130081) | 66133..66537 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| HS311_RS00385 (D616_p130082) | 66588..67115 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HS311_RS00390 (D616_p130083) | 67115..67818 | - | 704 | Protein_75 | IncI1-type conjugal transfer protein TraP | - |
| HS311_RS00395 | 67818..68519 | - | 702 | Protein_76 | conjugal transfer protein TraO | - |
| HS311_RS00400 (D616_p130084) | 68570..68860 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HS311_RS00405 (D616_p130085) | 68857..70005 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HS311_RS00410 (D616_p130086) | 70002..70820 | - | 819 | WP_025492003 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HS311_RS00415 (D616_p130087) | 70817..71275 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HS311_RS00420 (D616_p130088) | 71670..72254 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HS311_RS00425 (D616_p130089) | 72314..73516 | - | 1203 | WP_000976349 | conjugal transfer protein TraF | - |
| HS311_RS00430 (D616_p130090) | 73602..74426 | - | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| HS311_RS00435 (D616_p130091) | 74577..75731 | - | 1155 | WP_001139958 | site-specific integrase | - |
| HS311_RS00440 | 76044..76199 | - | 156 | WP_071790560 | shufflon protein C' | - |
| HS311_RS00445 (D616_p130094) | 76923..77171 | + | 249 | WP_001349157 | hypothetical protein | - |
| HS311_RS00450 (D616_p130095) | 77168..78460 | - | 1293 | WP_024198499 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HS311_RS00455 (D616_p130096) | 78460..79116 | - | 657 | WP_001389386 | prepilin peptidase | - |
| HS311_RS00460 (D616_p130097) | 79101..79661 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| HS311_RS00465 (D616_p130098) | 79671..80285 | - | 615 | WP_000959786 | type 4 pilus major pilin | - |
| HS311_RS00470 (D616_p130099) | 80303..81400 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| HS311_RS00475 (D616_p130100) | 81413..82966 | - | 1554 | WP_025492055 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HS311_RS00480 (D616_p130101) | 82977..83429 | - | 453 | WP_001247334 | type IV pilus biogenesis protein PilP | - |
| HS311_RS00485 (D616_p130102) | 83416..84711 | - | 1296 | WP_000752772 | type 4b pilus protein PilO2 | - |
| HS311_RS00490 (D616_p130103) | 84704..86386 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HS311_RS00495 (D616_p130104) | 86400..86837 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HS311_RS00500 (D616_p130105) | 86837..87903 | - | 1067 | Protein_97 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 1038 | GenBank | NC_024980 |
| Plasmid name | pESBL-315 | Incompatibility group | IncI1 |
| Plasmid size | 93037 bp | Coordinate of oriT [Strand] | 45045..45154 [-] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | sul2, blaCTX-M-1, sul1, qacE, ant(3'')-Ia, dfrA1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |