Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100564 |
| Name | oriT_pSTM2  |
| Organism | Salmonella enterica subsp. enterica serovar Typhimurium |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_023900 (84114..84223 [+], 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_pSTM2
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 636 | GenBank | YP_009022485 |
| Name | Relaxase_pSTM2 |
UniProt ID | Q79VV7 |
| 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_009022485.1 relaxase (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q79VV7 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 48699..89763
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTC41_RS00290 | 46415..48706 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| HTC41_RS00295 | 48699..49769 | - | 1071 | WP_000151582 | IncI1-type conjugal transfer protein TrbB | trbB |
| HTC41_RS00300 | 49788..50996 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HTC41_RS00305 | 51303..52082 | - | 780 | WP_275450201 | protein FinQ | - |
| HTC41_RS00310 | 52709..52861 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| HTC41_RS00315 | 52933..53184 | - | 252 | WP_001291965 | hypothetical protein | - |
| HTC41_RS00320 | 53256..54482 | - | 1227 | WP_031623769 | RNA-guided endonuclease TnpB family protein | - |
| HTC41_RS00325 | 54541..54945 | + | 405 | WP_001175009 | IS200/IS605 family transposase | - |
| HTC41_RS00560 | 55502..55597 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| HTC41_RS00330 | 55662..55946 | - | 285 | WP_172685734 | hypothetical protein | - |
| HTC41_RS00335 | 56047..56256 | - | 210 | WP_001140543 | hemolysin expression modulator Hha | - |
| HTC41_RS00340 | 56354..57016 | - | 663 | WP_000644794 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HTC41_RS00345 | 57087..59255 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| HTC41_RS00350 | 59352..59936 | - | 585 | WP_001037985 | IncI1-type conjugal transfer protein TraX | - |
| HTC41_RS00355 | 59965..61167 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| HTC41_RS00360 | 61134..61748 | - | 615 | WP_000337400 | IncI1-type conjugal transfer protein TraV | traV |
| HTC41_RS00365 | 61748..64792 | - | 3045 | WP_001024775 | IncI1-type conjugal transfer protein TraU | traU |
| HTC41_RS00370 | 64882..65682 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HTC41_RS00375 | 65666..65854 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HTC41_RS00380 | 65918..66322 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| HTC41_RS00385 | 66373..66900 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HTC41_RS00390 | 66900..67604 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HTC41_RS00395 | 67604..68893 | - | 1290 | WP_001271997 | conjugal transfer protein TraO | traO |
| HTC41_RS00400 | 68896..69879 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| HTC41_RS00405 | 69890..70582 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| HTC41_RS00410 | 70579..70926 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HTC41_RS00415 | 70944..74711 | - | 3768 | WP_001141534 | LPD7 domain-containing protein | - |
| HTC41_RS00420 | 74801..75352 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| HTC41_RS00425 | 75367..75657 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HTC41_RS00430 | 75654..76802 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HTC41_RS00435 | 76799..77617 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HTC41_RS00440 | 77614..78072 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HTC41_RS00445 | 78467..79051 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HTC41_RS00450 | 79111..80313 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| HTC41_RS00455 | 80399..81223 | - | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| HTC41_RS00460 | 81374..82528 | - | 1155 | WP_001139958 | site-specific integrase | - |
| HTC41_RS00465 | 83189..83344 | + | 156 | WP_001302705 | hypothetical protein | - |
| HTC41_RS00565 | 83615..83836 | + | 222 | Protein_94 | prepilin | - |
| HTC41_RS00475 | 83833..85257 | - | 1425 | WP_001389385 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HTC41_RS00480 | 85257..85913 | - | 657 | WP_001389386 | prepilin peptidase | - |
| HTC41_RS00485 | 85898..86458 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| HTC41_RS00490 | 86468..87082 | - | 615 | WP_000959786 | type 4 pilus major pilin | - |
| HTC41_RS00495 | 87100..88197 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| HTC41_RS00500 | 88210..89763 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HTC41_RS00505 | 89774..90226 | - | 453 | WP_001247334 | type IV pilus biogenesis protein PilP | - |
| HTC41_RS00510 | 90213..91508 | - | 1296 | WP_000752772 | type 4b pilus protein PilO2 | - |
| HTC41_RS00515 | 91501..93183 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HTC41_RS00520 | 93197..93634 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HTC41_RS00525 | 93634..94701 | - | 1068 | WP_001739185 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 1024 | GenBank | NC_023900 |
| Plasmid name | pSTM2 | Incompatibility group | IncI1 |
| Plasmid size | 96876 bp | Coordinate of oriT [Strand] | 84114..84223 [+] |
| Host baterium | Salmonella enterica subsp. enterica serovar Typhimurium |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |