Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100556 |
| Name | oriT_p9134dT  |
| Organism | Salmonella enterica subsp. enterica serovar Typhimurium |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_023290 (55072..55181 [-], 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_p9134dT
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 628 | GenBank | YP_008997574 |
| Name | Relaxase_p9134dT |
UniProt ID | V9SIC6 |
| Length | 871 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 871 a.a. Molecular weight: 100811.81 Da Isoelectric Point: 7.2753
>YP_008997574.1 relaxase (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVDVMKDGCEWVNFYGVTCFHNCTSLETAAA
DMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVRHTLKSLGLADHQYVSAVHTDTDNLHVHV
AVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCWVHAPGNRIVRKTAVERDRQNAWTRGKKQ
TFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGKFLVMDGWDRNREGVQLDSFGPSWCAEKL
MKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETESLQQYACRHLGERLPEMAREGRLENCQA
IHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLTLDNVNQLDGGWQPVPTDIFRQVTPTERF
RGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGYSISHCSPQIEEMITQGEFTWQRCHELFA
QQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEPQAGPFVSAPADLFDRVQPESRYNPELAV
SDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRKPDLRYGERCREIHQACRLRKSHIRAQYD
DPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYPPSYRQWVEIQAAQGDRAAVSQLRGWDYR
DRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGSVRFRDRRTGEFVCTDYGDRVVFRNHHDR
NALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAWHNVTGRTGHEDYRITRPDVDHHREGSER
YYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVDVMKDGCEWVNFYGVTCFHNCTSLETAAA
DMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVRHTLKSLGLADHQYVSAVHTDTDNLHVHV
AVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCWVHAPGNRIVRKTAVERDRQNAWTRGKKQ
TFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGKFLVMDGWDRNREGVQLDSFGPSWCAEKL
MKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETESLQQYACRHLGERLPEMAREGRLENCQA
IHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLTLDNVNQLDGGWQPVPTDIFRQVTPTERF
RGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGYSISHCSPQIEEMITQGEFTWQRCHELFA
QQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEPQAGPFVSAPADLFDRVQPESRYNPELAV
SDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRKPDLRYGERCREIHQACRLRKSHIRAQYD
DPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYPPSYRQWVEIQAAQGDRAAVSQLRGWDYR
DRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGSVRFRDRRTGEFVCTDYGDRVVFRNHHDR
NALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAWHNVTGRTGHEDYRITRPDVDHHREGSER
YYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | V9SIC6 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 60541..103049
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTC45_RS00370 (p9134dT_0295) | 58257..60548 | - | 2292 | WP_001289275 | F-type conjugative transfer protein TrbC | - |
| HTC45_RS00375 (p9134dT_0300) | 60541..61611 | - | 1071 | WP_000151576 | IncI1-type conjugal transfer protein TrbB | trbB |
| HTC45_RS00380 (p9134dT_0305) | 61630..62838 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HTC45_RS00385 | 63130..63282 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| HTC45_RS00390 | 63354..63605 | - | 252 | WP_001291965 | hypothetical protein | - |
| HTC45_RS00750 | 64103..64198 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| HTC45_RS00395 | 64263..64400 | - | 138 | WP_047088497 | hypothetical protein | - |
| HTC45_RS00400 (p9134dT_0310) | 64445..65671 | - | 1227 | WP_024186316 | RNA-guided endonuclease TnpB family protein | - |
| HTC45_RS00405 | 65730..66134 | + | 405 | WP_001175009 | IS200/IS605 family transposase | - |
| HTC45_RS00410 | 66466..66675 | - | 210 | WP_032178830 | hemolysin expression modulator Hha | - |
| HTC45_RS00415 (p9134dT_0315) | 66773..67435 | - | 663 | WP_000644794 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HTC45_RS00420 (p9134dT_0320) | 67506..69674 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| HTC45_RS00425 (p9134dT_0325) | 69771..70355 | - | 585 | WP_001037985 | IncI1-type conjugal transfer protein TraX | - |
| HTC45_RS00430 (p9134dT_0330) | 70384..71586 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| HTC45_RS00435 (p9134dT_0335) | 71553..72167 | - | 615 | WP_000337400 | IncI1-type conjugal transfer protein TraV | traV |
| HTC45_RS00440 (p9134dT_0340) | 72167..75211 | - | 3045 | WP_001024780 | IncI1-type conjugal transfer protein TraU | traU |
| HTC45_RS00445 (p9134dT_0345) | 75301..76101 | - | 801 | WP_024126043 | IncI1-type conjugal transfer protein TraT | traT |
| HTC45_RS00450 | 76085..76273 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HTC45_RS00455 (p9134dT_0350) | 76337..76741 | - | 405 | WP_000086958 | IncI1-type conjugal transfer protein TraR | traR |
| HTC45_RS00460 (p9134dT_0355) | 76792..77319 | - | 528 | WP_024126044 | conjugal transfer protein TraQ | traQ |
| HTC45_RS00465 (p9134dT_0360) | 77319..78023 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HTC45_RS00470 (p9134dT_0365) | 78023..79312 | - | 1290 | WP_001272003 | conjugal transfer protein TraO | traO |
| HTC45_RS00475 (p9134dT_0370) | 79315..80298 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| HTC45_RS00480 (p9134dT_0375) | 80309..81001 | - | 693 | WP_000138550 | DotI/IcmL family type IV secretion protein | traM |
| HTC45_RS00485 (p9134dT_0380) | 80998..81345 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HTC45_RS00490 | 81363..85129 | - | 3767 | Protein_96 | LPD7 domain-containing protein | - |
| HTC45_RS00495 | 85219..85479 | - | 261 | Protein_97 | phospholipase D-like domain-containing protein | - |
| HTC45_RS00500 (p9134dT_0395) | 85510..87123 | - | 1614 | WP_001741922 | IS66-like element ISEc23 family transposase | - |
| HTC45_RS00505 (p9134dT_0400) | 87154..87504 | - | 351 | WP_000624722 | IS66 family insertion sequence element accessory protein TnpB | - |
| HTC45_RS00510 (p9134dT_0405) | 87501..87926 | - | 426 | WP_000422741 | transposase | - |
| HTC45_RS00515 | 88014..88310 | - | 297 | Protein_101 | phospholipase D-like domain-containing protein | - |
| HTC45_RS00520 | 88325..88615 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HTC45_RS00525 (p9134dT_0415) | 88612..89760 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HTC45_RS00530 (p9134dT_0420) | 89757..90575 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HTC45_RS00535 (p9134dT_0425) | 90572..91030 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HTC45_RS00540 (p9134dT_0430) | 91425..92009 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HTC45_RS00545 (p9134dT_0435) | 92069..93271 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| HTC45_RS00550 (p9134dT_0440) | 93356..94180 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| HTC45_RS00555 (p9134dT_0445) | 94331..95485 | - | 1155 | WP_001139957 | site-specific integrase | - |
| HTC45_RS00560 (p9134dT_0450) | 95469..95795 | + | 327 | WP_001213803 | hypothetical protein | - |
| HTC45_RS00755 | 96901..97122 | + | 222 | Protein_111 | prepilin | - |
| HTC45_RS00570 (p9134dT_0460) | 97119..98543 | - | 1425 | WP_001389385 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HTC45_RS00575 (p9134dT_0465) | 98543..99199 | - | 657 | WP_001193553 | prepilin peptidase | - |
| HTC45_RS00580 (p9134dT_0470) | 99184..99744 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| HTC45_RS00585 (p9134dT_0475) | 99754..100368 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| HTC45_RS00590 (p9134dT_0480) | 100386..101483 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| HTC45_RS00595 (p9134dT_0485) | 101496..103049 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HTC45_RS00600 (p9134dT_0490) | 103060..103512 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| HTC45_RS00605 (p9134dT_0495) | 103499..104794 | - | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| HTC45_RS00610 (p9134dT_0500) | 104787..106469 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HTC45_RS00615 (p9134dT_0505) | 106483..106920 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HTC45_RS00620 (p9134dT_0510) | 106920..107987 | - | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 1016 | GenBank | NC_023290 |
| Plasmid name | p9134dT | Incompatibility group | IncFIB |
| Plasmid size | 127291 bp | Coordinate of oriT [Strand] | 55072..55181 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Typhimurium |
Cargo genes
| Drug resistance gene | catA1, aph(6)-Id, aph(3'')-Ib, blaTEM-1C |
| Virulence gene | Salmonella plasmid virulence |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |