Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100594 |
| Name | oriT_pC60-108  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_025142 (71849..71958 [-], 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_pC60-108
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 666 | GenBank | YP_009068804 |
| Name | NikB_pC60-108 |
UniProt ID | _ |
| 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_009068804.1 NikB relaxase (plasmid) [Escherichia coli]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNNDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNNDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 77318..106748
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTE07_RS00455 (D616_p142113) | 75034..77325 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| HTE07_RS00460 (D616_p142114) | 77318..78388 | - | 1071 | WP_000151583 | IncI1-type conjugal transfer protein TrbB | trbB |
| HTE07_RS00465 (D616_p142115) | 78407..79615 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HTE07_RS00470 (D616_p142116) | 79907..80059 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| HTE07_RS00475 (D616_p142117) | 80131..80382 | - | 252 | WP_001291964 | hypothetical protein | - |
| HTE07_RS00645 | 80881..80976 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| HTE07_RS00480 (D616_p142118) | 81041..81217 | - | 177 | WP_001054904 | hypothetical protein | - |
| HTE07_RS00485 (D616_p142120) | 81609..81818 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| HTE07_RS00490 (D616_p142121) | 81890..82564 | - | 675 | WP_223866377 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HTE07_RS00495 (D616_p142122) | 82614..84782 | - | 2169 | WP_021537350 | DotA/TraY family protein | traY |
| HTE07_RS00500 (D616_p142123) | 84879..85463 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| HTE07_RS00505 (D616_p142124) | 85492..86694 | - | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| HTE07_RS00510 (D616_p142125) | 86661..87275 | - | 615 | WP_000337398 | IncI1-type conjugal transfer protein TraV | traV |
| HTE07_RS00515 (D616_p142127) | 87275..90319 | - | 3045 | WP_021265678 | IncI1-type conjugal transfer protein TraU | traU |
| HTE07_RS00520 (D616_p142128) | 90409..91209 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HTE07_RS00525 (D616_p142129) | 91193..91381 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HTE07_RS00530 (D616_p142130) | 91445..91849 | - | 405 | WP_000086958 | IncI1-type conjugal transfer protein TraR | traR |
| HTE07_RS00535 (D616_p142131) | 91900..92427 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HTE07_RS00540 (D616_p142132) | 92427..93131 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HTE07_RS00545 (D616_p142133) | 93131..94420 | - | 1290 | WP_001272003 | conjugal transfer protein TraO | traO |
| HTE07_RS00550 (D616_p142134) | 94423..95406 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| HTE07_RS00555 (D616_p142135) | 95417..96109 | - | 693 | WP_000138550 | DotI/IcmL family type IV secretion protein | traM |
| HTE07_RS00560 (D616_p142136) | 96106..96453 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HTE07_RS00565 (D616_p142137) | 96471..100238 | - | 3768 | WP_001141527 | LPD7 domain-containing protein | - |
| HTE07_RS00570 (D616_p142138) | 100327..100878 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| HTE07_RS00575 (D616_p142139) | 100893..101183 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HTE07_RS00580 (D616_p142140) | 101180..102328 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HTE07_RS00585 (D616_p142141) | 102325..103143 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HTE07_RS00590 (D616_p142142) | 103140..103598 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HTE07_RS00595 (D616_p142144) | 103993..104577 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HTE07_RS00600 (D616_p142145) | 104637..105839 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| HTE07_RS00605 (D616_p142146) | 105924..106748 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| HTE07_RS00610 (D616_p142147) | 106899..108053 | - | 1155 | WP_001139957 | site-specific integrase | - |
| HTE07_RS00640 | 108037..108459 | + | 423 | WP_162847923 | prepilin, shufflon protein A | - |
Host bacterium
| ID | 1054 | GenBank | NC_025142 |
| Plasmid name | pC60-108 | Incompatibility group | IncI1 |
| Plasmid size | 108661 bp | Coordinate of oriT [Strand] | 71849..71958 [-] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | blaCTX-M-1, dfrA17, aadA5, sul2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |