Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100417 |
| Name | oriT_TY474p2  |
| Organism | Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_017675 (33864..33966 [-], 103 nt) |
| oriT length | 103 nt |
| IRs (inverted repeats) | IR1: 19..26, 30..37 (GTCGGGGC..GCCCTGAC) IR2: 44..58, 67..81 (GCAATTGTATAATCG..CGGTTATACAATTGC) |
| Location of nic site | 89..90 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 103 nt
>oriT_TY474p2
TCAGCTCCTTACTGGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTCAGG
TCAGCTCCTTACTGGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 488 | GenBank | WP_001354015 |
| Name | NikB_TY474p2 |
UniProt ID | _ |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104018.47 Da Isoelectric Point: 7.3526
>WP_001354015.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCLAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCLAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 39332..76801
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| STM474_RS24440 (STM474_p242) | 37048..39339 | - | 2292 | WP_014653261 | F-type conjugative transfer protein TrbC | - |
| STM474_RS24445 (STM474_p243) | 39332..40402 | - | 1071 | WP_000151583 | IncI1-type conjugal transfer protein TrbB | trbB |
| STM474_RS24450 (STM474_p244) | 40421..41629 | - | 1209 | WP_000121274 | IncI1-type conjugal transfer protein TrbA | trbA |
| STM474_RS24455 (STM474_p246) | 41921..42073 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| STM474_RS24460 (STM474_p247) | 42145..42396 | - | 252 | WP_001291965 | hypothetical protein | - |
| STM474_RS27695 | 42897..42992 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| STM474_RS27395 | 43057..43233 | - | 177 | WP_001054904 | hypothetical protein | - |
| STM474_RS24470 (STM474_p249) | 43625..43834 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| STM474_RS24475 (STM474_p250) | 43906..44568 | - | 663 | WP_000653334 | plasmid IncI1-type surface exclusion protein ExcA | - |
| STM474_RS24480 | 44633..46795 | - | 2163 | WP_000698351 | DotA/TraY family protein | traY |
| STM474_RS24485 (STM474_p251) | 46892..47476 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| STM474_RS24490 (STM474_p252) | 47505..48707 | - | 1203 | WP_001189161 | IncI1-type conjugal transfer protein TraW | traW |
| STM474_RS26405 (STM474_p253) | 48674..49288 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| STM474_RS24495 (STM474_p254) | 49288..52332 | - | 3045 | WP_001024779 | IncI1-type conjugal transfer protein TraU | traU |
| STM474_RS24500 (STM474_p255) | 52422..53222 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| STM474_RS24505 (STM474_p256) | 53206..53394 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| STM474_RS24510 (STM474_p257) | 53458..53862 | - | 405 | WP_000086957 | IncI1-type conjugal transfer protein TraR | traR |
| STM474_RS24515 (STM474_p258) | 53913..54440 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| STM474_RS24520 (STM474_p259) | 54440..55144 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| STM474_RS24525 (STM474_p260) | 55144..56433 | - | 1290 | WP_001272005 | conjugal transfer protein TraO | traO |
| STM474_RS24530 (STM474_p261) | 56436..57419 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| STM474_RS24535 (STM474_p262) | 57430..58122 | - | 693 | WP_000138548 | DotI/IcmL family type IV secretion protein | traM |
| STM474_RS24540 (STM474_p263) | 58119..58466 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| STM474_RS24545 | 58484..62251 | - | 3768 | WP_001141529 | LPD7 domain-containing protein | - |
| STM474_RS24550 (STM474_p264) | 62341..62892 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| STM474_RS26410 (STM474_p265) | 62907..63197 | - | 291 | WP_001299214 | hypothetical protein | traK |
| STM474_RS24555 (STM474_p266) | 63194..64342 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| STM474_RS24560 (STM474_p267) | 64339..65157 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| STM474_RS24565 (STM474_p268) | 65154..65612 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| STM474_RS24570 (STM474_p269) | 66007..66591 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| STM474_RS24575 (STM474_p270) | 66651..67853 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| STM474_RS24580 (STM474_p271) | 67938..68762 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| STM474_RS24585 (STM474_p272) | 68913..70067 | - | 1155 | WP_001139957 | site-specific integrase | - |
| STM474_RS27210 | 70758..71006 | + | 249 | WP_001349157 | hypothetical protein | - |
| STM474_RS24595 | 71003..72295 | - | 1293 | WP_001417545 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| STM474_RS26420 (STM474_p273) | 72295..72951 | - | 657 | WP_001193553 | prepilin peptidase | - |
| STM474_RS24600 (STM474_p274) | 72936..73496 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| STM474_RS24605 (STM474_p275) | 73506..74120 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| STM474_RS24610 (STM474_p276) | 74138..75235 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| STM474_RS24615 (STM474_p277) | 75248..76801 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| STM474_RS24620 (STM474_p278) | 76812..77264 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| STM474_RS24625 (STM474_p279) | 77251..78546 | - | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| STM474_RS24630 (STM474_p280) | 78539..80221 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| STM474_RS24635 (STM474_p281) | 80235..80672 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| STM474_RS24640 (STM474_p282) | 80672..81739 | - | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 878 | GenBank | NC_017675 |
| Plasmid name | TY474p2 | Incompatibility group | IncI1 |
| Plasmid size | 86908 bp | Coordinate of oriT [Strand] | 33864..33966 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |