Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 105557 |
| Name | oriT_pSNE2-1928  |
| Organism | Salmonella enterica subsp. enterica serovar Newport str. USDA-ARS-USMARC-1928 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP025239 (42032..42120 [-], 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_pSNE2-1928
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTGATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTGATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3785 | GenBank | WP_001405892 |
| Name | nikB_AW84_RS24635_pSNE2-1928 |
UniProt ID | A0A3V4WX06 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103883.32 Da Isoelectric Point: 7.3373
>WP_001405892.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A3V4WX06 |
Auxiliary protein
| ID | 1718 | GenBank | WP_001283947 |
| Name | WP_001283947_pSNE2-1928 |
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 | 3779 | GenBank | WP_001289282 |
| Name | trbC_AW84_RS24640_pSNE2-1928 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86969.12 Da Isoelectric Point: 6.7713
>WP_001289282.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMARLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMARLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 47498..86696
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| AW84_RS24640 (AW84_25190) | 45214..47505 | - | 2292 | WP_001289282 | F-type conjugative transfer protein TrbC | - |
| AW84_RS24645 (AW84_25195) | 47498..48568 | - | 1071 | WP_000151582 | IncI1-type conjugal transfer protein TrbB | trbB |
| AW84_RS24650 (AW84_25200) | 48587..49795 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| AW84_RS24655 (AW84_25205) | 50102..50881 | - | 780 | WP_275450201 | protein FinQ | - |
| AW84_RS24660 (AW84_25210) | 51508..51660 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| AW84_RS24665 (AW84_25215) | 51732..51983 | - | 252 | WP_001291965 | hypothetical protein | - |
| AW84_RS25945 | 52907..53083 | - | 177 | WP_001054900 | hypothetical protein | - |
| AW84_RS24680 (AW84_25230) | 53292..53501 | - | 210 | WP_001140545 | hemolysin expression modulator Hha | - |
| AW84_RS24685 (AW84_25235) | 53599..54213 | - | 615 | WP_000578649 | plasmid IncI1-type surface exclusion protein ExcA | - |
| AW84_RS24690 (AW84_25240) | 54289..56457 | - | 2169 | WP_000698360 | IncI1-type conjugal transfer membrane protein TraY | traY |
| AW84_RS24695 (AW84_25245) | 56554..57138 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| AW84_RS24700 (AW84_25250) | 57167..58369 | - | 1203 | WP_001189159 | IncI1-type conjugal transfer protein TraW | traW |
| AW84_RS24705 (AW84_25255) | 58336..58950 | - | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| AW84_RS24710 (AW84_25260) | 58950..61994 | - | 3045 | WP_001024752 | IncI1-type conjugal transfer protein TraU | traU |
| AW84_RS24715 (AW84_25265) | 62084..62884 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| AW84_RS24720 (AW84_25270) | 62868..63056 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| AW84_RS24725 (AW84_25275) | 63120..63524 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| AW84_RS24730 (AW84_25280) | 63575..64102 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| AW84_RS24735 (AW84_25285) | 64102..64806 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| AW84_RS24740 (AW84_25290) | 64806..66095 | - | 1290 | WP_001271997 | conjugal transfer protein TraO | traO |
| AW84_RS24745 (AW84_25295) | 66098..67081 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| AW84_RS24750 (AW84_25300) | 67092..67784 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| AW84_RS24755 (AW84_25305) | 67781..68128 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| AW84_RS24760 (AW84_25310) | 68146..71913 | - | 3768 | WP_001141534 | LPD7 domain-containing protein | - |
| AW84_RS24765 (AW84_25315) | 72003..72554 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| AW84_RS24770 (AW84_25320) | 72569..72859 | - | 291 | WP_001299214 | hypothetical protein | traK |
| AW84_RS24775 (AW84_25325) | 72856..74004 | - | 1149 | WP_076097712 | plasmid transfer ATPase TraJ | virB11 |
| AW84_RS24780 (AW84_25330) | 74001..74819 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| AW84_RS24785 (AW84_25335) | 74816..75274 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| AW84_RS24790 (AW84_25340) | 75669..76253 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| AW84_RS24795 (AW84_25345) | 76313..77515 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| AW84_RS24800 (AW84_25350) | 77601..78425 | - | 825 | WP_047642106 | conjugal transfer protein TraE | traE |
| AW84_RS24805 (AW84_25355) | 78576..79730 | - | 1155 | WP_001139958 | site-specific integrase | - |
| AW84_RS25950 | 79729..79902 | + | 174 | WP_165375368 | hypothetical protein | - |
| AW84_RS26455 | 80012..80272 | + | 261 | Protein_87 | Shufflon protein B | - |
| AW84_RS26460 (AW84_25365) | 80548..80769 | + | 222 | Protein_88 | prepilin | - |
| AW84_RS24820 (AW84_25370) | 80766..82190 | - | 1425 | WP_001389385 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| AW84_RS24825 (AW84_25375) | 82190..82846 | - | 657 | WP_001389386 | prepilin peptidase | - |
| AW84_RS24830 (AW84_25380) | 82831..83391 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| AW84_RS24835 (AW84_25385) | 83401..84015 | - | 615 | WP_000959786 | type 4 pilus major pilin | - |
| AW84_RS24840 (AW84_25390) | 84033..85130 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| AW84_RS24845 (AW84_25395) | 85143..86696 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| AW84_RS24850 (AW84_25400) | 86707..87159 | - | 453 | WP_001247334 | type IV pilus biogenesis protein PilP | - |
| AW84_RS24855 (AW84_25405) | 87146..88441 | - | 1296 | WP_000752772 | type 4b pilus protein PilO2 | - |
| AW84_RS24860 (AW84_25410) | 88434..90116 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| AW84_RS24865 (AW84_25415) | 90130..90567 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| AW84_RS24870 (AW84_25420) | 90567..91634 | - | 1068 | WP_001302629 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 5995 | GenBank | NZ_CP025239 |
| Plasmid name | pSNE2-1928 | Incompatibility group | IncI |
| Plasmid size | 96768 bp | Coordinate of oriT [Strand] | 42032..42120 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Newport str. USDA-ARS-USMARC-1928 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |