Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113419 |
| Name | oriT_pIncI1-ST12  |
| Organism | Salmonella enterica subsp. enterica serovar Heidelberg isolate FT2-21D |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP128272 (5696..5784 [-], 89 nt) |
| oriT length | 89 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 89 nt
>oriT_pIncI1-ST12
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8599 | GenBank | WP_001474686 |
| Name | nikB_QS239_RS23450_pIncI1-ST12 |
UniProt ID | A0A2J0RB70 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103834.33 Da Isoelectric Point: 7.3473
>WP_001474686.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A2J0RB70 |
Auxiliary protein
| ID | 4940 | GenBank | WP_001283947 |
| Name | WP_001283947_pIncI1-ST12 |
UniProt ID | A0A142CMC2 |
| Length | 110 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 110 a.a. Molecular weight: 12613.57 Da Isoelectric Point: 10.7463
>WP_001283947.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A142CMC2 |
T4CP
| ID | 9936 | GenBank | WP_001289271 |
| Name | trbC_QS239_RS23455_pIncI1-ST12 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86927.12 Da Isoelectric Point: 6.7713
>WP_001289271.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 11162..45346
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| QS239_RS23455 (QS239_23455) | 8878..11169 | - | 2292 | WP_001289271 | F-type conjugative transfer protein TrbC | - |
| QS239_RS23460 (QS239_23460) | 11162..12232 | - | 1071 | WP_000151575 | IncI1-type conjugal transfer protein TrbB | trbB |
| QS239_RS23465 (QS239_23465) | 12251..13459 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| QS239_RS23470 (QS239_23470) | 13751..13903 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| QS239_RS23475 (QS239_23475) | 13975..14226 | - | 252 | WP_001291965 | hypothetical protein | - |
| QS239_RS23480 (QS239_23480) | 14587..15369 | - | 783 | WP_001300609 | IS21-like element IS100kyp family helper ATPase IstB | - |
| QS239_RS23485 (QS239_23485) | 15366..16388 | - | 1023 | WP_001572805 | IS21-like element IS100 family transposase | - |
| QS239_RS23490 (QS239_23490) | 17109..17285 | - | 177 | WP_001054900 | hypothetical protein | - |
| QS239_RS23495 (QS239_23495) | 17677..17886 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| QS239_RS23500 (QS239_23500) | 17958..18620 | - | 663 | WP_000644794 | plasmid IncI1-type surface exclusion protein ExcA | - |
| QS239_RS23505 (QS239_23505) | 18691..20859 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| QS239_RS23510 (QS239_23510) | 20956..21540 | - | 585 | WP_001037998 | conjugal transfer protein TraX | - |
| QS239_RS23515 (QS239_23515) | 21569..22771 | - | 1203 | WP_001189158 | IncI1-type conjugal transfer protein TraW | traW |
| QS239_RS23520 (QS239_23520) | 22738..23352 | - | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| QS239_RS23525 (QS239_23525) | 23352..26396 | - | 3045 | WP_046340721 | IncI1-type conjugal transfer protein TraU | traU |
| QS239_RS23530 (QS239_23530) | 26486..27286 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| QS239_RS23535 (QS239_23535) | 27270..27458 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| QS239_RS23540 (QS239_23540) | 27522..27926 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| QS239_RS23545 (QS239_23545) | 27977..28504 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| QS239_RS23550 (QS239_23550) | 28504..29208 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| QS239_RS23555 (QS239_23555) | 29208..30497 | - | 1290 | WP_001271997 | conjugal transfer protein TraO | traO |
| QS239_RS23560 (QS239_23560) | 30500..31483 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| QS239_RS23565 (QS239_23565) | 31494..32186 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| QS239_RS23570 (QS239_23570) | 32183..32530 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| QS239_RS23575 (QS239_23575) | 32548..36315 | - | 3768 | WP_001141535 | LPD7 domain-containing protein | - |
| QS239_RS23960 | 36405..36488 | - | 84 | Protein_36 | phospholipase D family protein | - |
| QS239_RS23580 (QS239_23580) | 36569..36994 | + | 426 | WP_021514830 | transposase | - |
| QS239_RS23585 (QS239_23585) | 36991..37341 | + | 351 | WP_000624718 | IS66 family insertion sequence element accessory protein TnpB | - |
| QS239_RS23590 (QS239_23590) | 37372..38964 | + | 1593 | WP_021514829 | IS66 family transposase | - |
| QS239_RS23595 (QS239_23595) | 38951..39475 | - | 525 | WP_046340722 | phospholipase D family protein | - |
| QS239_RS23600 (QS239_23600) | 39490..39780 | - | 291 | WP_001299214 | hypothetical protein | traK |
| QS239_RS23605 (QS239_23605) | 39777..40925 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| QS239_RS23610 (QS239_23610) | 40922..41740 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| QS239_RS23615 (QS239_23615) | 41737..42195 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| QS239_RS23620 (QS239_23620) | 42590..43174 | - | 585 | WP_000977517 | histidine phosphatase family protein | - |
| QS239_RS23625 (QS239_23625) | 43234..44436 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| QS239_RS23630 (QS239_23630) | 44522..45346 | - | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| QS239_RS23635 (QS239_23635) | 45497..46651 | - | 1155 | WP_001139958 | tyrosine-type recombinase/integrase | - |
Host bacterium
| ID | 13854 | GenBank | NZ_CP128272 |
| Plasmid name | pIncI1-ST12 | Incompatibility group | - |
| Plasmid size | 46717 bp | Coordinate of oriT [Strand] | 5696..5784 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Heidelberg isolate FT2-21D |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |