Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100442 |
| Name | oriT_pPWD4_103  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_019061 (43373..43482 [-], 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_pPWD4_103
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 513 | GenBank | YP_006952344 |
| Name | NikB_pPWD4_103 |
UniProt ID | E9LMH8 |
| Length | 871 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 871 a.a. Molecular weight: 100697.72 Da Isoelectric Point: 7.1997
>YP_006952344.1 putative relaxase/mobilization protein NikB (plasmid) [Escherichia coli]
MTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVDVMKDGCEWVNFYGVTCFHNCTSLETAAA
DMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVRHTLKSLGLGEHQYVSAVHTDTDNLHVHV
AVNRVHPVTGYLNCLSWSQETLSRACRELELKHGFAPDNGCWVHAPGNRIVRKTAVERDRQNAWTRGKKQ
TFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGKFLVMDGWDRNREGVQLDSFGPSWCAEKL
MKKMGDYTPVPKDIFSQVDAPGRYNPDFIAADVRPEKIAETESLQQYACRHLGERLPEMAREGRLENCQA
IHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLTLDNVNQLDGGWQPVPTDIFRQVTPTERF
RGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGYSISHCSPQIEEMITQGEFTWQRCHELFA
QQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEPQAGPFVSAPADLFDRVQPESRYNPELAV
SDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRKPDLRYGERCREIHQACRLRKSHIRAQYD
DPVLRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYPPSYRQWVEIQAAQGDRAAVSQLRGWDYR
DRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGSVRFRDRRTGEFVCTDYGDRVVFRNHHDR
NALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAWHNVTGRTGHEDYRITRPDVDHHREGSER
YYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVDVMKDGCEWVNFYGVTCFHNCTSLETAAA
DMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVRHTLKSLGLGEHQYVSAVHTDTDNLHVHV
AVNRVHPVTGYLNCLSWSQETLSRACRELELKHGFAPDNGCWVHAPGNRIVRKTAVERDRQNAWTRGKKQ
TFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGKFLVMDGWDRNREGVQLDSFGPSWCAEKL
MKKMGDYTPVPKDIFSQVDAPGRYNPDFIAADVRPEKIAETESLQQYACRHLGERLPEMAREGRLENCQA
IHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLTLDNVNQLDGGWQPVPTDIFRQVTPTERF
RGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGYSISHCSPQIEEMITQGEFTWQRCHELFA
QQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEPQAGPFVSAPADLFDRVQPESRYNPELAV
SDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRKPDLRYGERCREIHQACRLRKSHIRAQYD
DPVLRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYPPSYRQWVEIQAAQGDRAAVSQLRGWDYR
DRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGSVRFRDRRTGEFVCTDYGDRVVFRNHHDR
NALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAWHNVTGRTGHEDYRITRPDVDHHREGSER
YYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | E9LMH8 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 50156..92970
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS844_RS00300 | 46558..47400 | - | 843 | Protein_60 | conjugal transfer protein TrbC | - |
| HS844_RS00310 | 48709..50163 | - | 1455 | Protein_62 | F-type conjugative transfer protein TrbC | - |
| HS844_RS00315 (PWD4IncI1_60) | 50156..51226 | - | 1071 | WP_015058906 | IncI1-type conjugal transfer protein TrbB | trbB |
| HS844_RS00320 (PWD4IncI1_61) | 51245..52453 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HS844_RS00325 (PWD4IncI1_62) | 52760..53539 | - | 780 | WP_275450201 | protein FinQ | - |
| HS844_RS00330 | 54166..54318 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| HS844_RS00335 (PWD4IncI1_64) | 54390..54641 | - | 252 | WP_001291964 | hypothetical protein | - |
| HS844_RS00595 | 55759..55854 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| HS844_RS00340 | 55919..56095 | - | 177 | WP_001054898 | hypothetical protein | - |
| HS844_RS00345 | 56427..56636 | + | 210 | WP_000062602 | HEAT repeat domain-containing protein | - |
| HS844_RS00350 (PWD4IncI1_66) | 56708..57370 | - | 663 | WP_000644797 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HS844_RS00355 (PWD4IncI1_67) | 57441..59609 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| HS844_RS00360 (PWD4IncI1_68) | 59706..60290 | - | 585 | WP_001037980 | IncI1-type conjugal transfer protein TraX | - |
| HS844_RS00365 (PWD4IncI1_69) | 60319..61521 | - | 1203 | WP_001690627 | IncI1-type conjugal transfer protein TraW | traW |
| HS844_RS00370 | 61488..61835 | - | 348 | Protein_75 | IncI1-type conjugal transfer protein TraV | - |
| HS844_RS00375 (PWD4IncI1_71) | 61866..63479 | - | 1614 | WP_000080195 | IS66-like element ISEc23 family transposase | - |
| HS844_RS00380 (PWD4IncI1_72) | 63510..63860 | - | 351 | WP_000624722 | IS66 family insertion sequence element accessory protein TnpB | - |
| HS844_RS00385 (PWD4IncI1_73) | 63857..64282 | - | 426 | WP_000422741 | transposase | - |
| HS844_RS00390 | 64367..64642 | - | 276 | Protein_79 | IncI1-type conjugal transfer protein TraV | - |
| HS844_RS00395 (PWD4IncI1_75) | 64642..67686 | - | 3045 | WP_015058909 | IncI1-type conjugal transfer protein TraU | traU |
| HS844_RS00400 (PWD4IncI1_76) | 67776..68576 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HS844_RS00405 | 68560..68748 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HS844_RS00410 (PWD4IncI1_77) | 68812..69216 | - | 405 | WP_000086959 | IncI1-type conjugal transfer protein TraR | traR |
| HS844_RS00415 (PWD4IncI1_78) | 69267..69794 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HS844_RS00420 (PWD4IncI1_79) | 69794..70498 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HS844_RS00425 (PWD4IncI1_80) | 70498..71787 | - | 1290 | WP_015058910 | conjugal transfer protein TraO | traO |
| HS844_RS00430 (PWD4IncI1_81) | 71790..72773 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| HS844_RS00435 (PWD4IncI1_82) | 72784..73476 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| HS844_RS00440 (PWD4IncI1_83) | 73473..73820 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HS844_RS00445 (PWD4IncI1_84) | 73838..77605 | - | 3768 | WP_001141537 | LPD7 domain-containing protein | - |
| HS844_RS00450 | 77695..78246 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| HS844_RS00455 | 78261..78551 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HS844_RS00460 (PWD4IncI1_86) | 78548..79696 | - | 1149 | WP_001024976 | plasmid transfer ATPase TraJ | virB11 |
| HS844_RS00465 (PWD4IncI1_87) | 79693..80511 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HS844_RS00470 (PWD4IncI1_88) | 80508..80966 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HS844_RS00475 (PWD4IncI1_89) | 81361..81945 | - | 585 | WP_000977520 | histidine phosphatase family protein | - |
| HS844_RS00480 (PWD4IncI1_90) | 82005..83207 | - | 1203 | WP_000976357 | conjugal transfer protein TraF | - |
| HS844_RS00485 (PWD4IncI1_91) | 83293..84117 | - | 825 | WP_015058912 | conjugal transfer protein TraE | traE |
| HS844_RS00490 (PWD4IncI1_92) | 84268..85422 | - | 1155 | WP_001139955 | site-specific integrase | - |
| HS844_RS00605 | 85462..85731 | + | 270 | Protein_100 | hypothetical protein | - |
| HS844_RS00495 | 86082..86237 | + | 156 | WP_001302705 | hypothetical protein | - |
| HS844_RS00610 | 86820..87056 | + | 237 | Protein_102 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HS844_RS00505 (PWD4IncI1_93) | 87053..88489 | - | 1437 | WP_015058913 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HS844_RS00510 (PWD4IncI1_94) | 88477..89133 | - | 657 | WP_001193551 | A24 family peptidase | - |
| HS844_RS00515 (PWD4IncI1_95) | 89118..89678 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| HS844_RS00520 (PWD4IncI1_96) | 89688..90302 | - | 615 | WP_000908228 | type 4 pilus major pilin | - |
| HS844_RS00525 (PWD4IncI1_97) | 90319..91404 | - | 1086 | WP_001208803 | type II secretion system F family protein | - |
| HS844_RS00530 (PWD4IncI1_98) | 91417..92970 | - | 1554 | WP_000362204 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HS844_RS00535 (PWD4IncI1_99) | 92981..93433 | - | 453 | WP_001247333 | type IV pilus biogenesis protein PilP | - |
| HS844_RS00540 (PWD4IncI1_100) | 93420..94715 | - | 1296 | WP_000752776 | type 4b pilus protein PilO2 | - |
| HS844_RS00545 | 94708..94932 | - | 225 | WP_001388365 | type II/III secretion system protein | - |
| HS844_RS00555 | 96243..97703 | - | 1461 | Protein_113 | PilN family type IVB pilus formation outer membrane protein | - |
Host bacterium
| ID | 903 | GenBank | NC_019061 |
| Plasmid name | pPWD4_103 | Incompatibility group | IncI1 |
| Plasmid size | 103297 bp | Coordinate of oriT [Strand] | 43373..43482 [-] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | aph(4)-Ia, aac(3)-IVa, aph(3'')-Ib, aph(6)-Id |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |