Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 101784 |
| Name | oriT_p2018n0381090_5  |
| Organism | Escherichia coli strain COL7 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_JACYGF010000015 (12776..12864 [-], 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_p2018n0381090_5
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 1497 | GenBank | WP_024143648 |
| Name | nikB_IYY93_RS01740_p2018n0381090_5 |
UniProt ID | A0A023JAU0 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104010.41 Da Isoelectric Point: 7.4265
>WP_024143648.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNNDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNNDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A023JAU0 |
Auxiliary protein
| ID | 600 | GenBank | WP_001283947 |
| Name | WP_001283947_p2018n0381090_5 |
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 | 1174 | GenBank | WP_001289276 |
| Name | trbC_IYY93_RS01745_p2018n0381090_5 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86941.11 Da Isoelectric Point: 6.7713
>WP_001289276.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
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: 18242..55651
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| IYY93_RS01745 | 15958..18249 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| IYY93_RS01750 | 18242..19312 | - | 1071 | WP_194849371 | IncI1-type conjugal transfer protein TrbB | trbB |
| IYY93_RS01755 | 19331..20539 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| IYY93_RS01760 | 20831..20983 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| IYY93_RS01765 | 21055..21306 | - | 252 | WP_001291964 | hypothetical protein | - |
| IYY93_RS28550 | 21805..21900 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| IYY93_RS01770 | 21965..22141 | - | 177 | WP_001054904 | hypothetical protein | - |
| IYY93_RS01775 | 22533..22742 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| IYY93_RS01780 | 22814..23464 | - | 651 | WP_001178506 | plasmid IncI1-type surface exclusion protein ExcA | - |
| IYY93_RS01785 | 23538..25706 | - | 2169 | WP_021537350 | DotA/TraY family protein | traY |
| IYY93_RS01790 | 25803..26387 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| IYY93_RS01795 | 26416..27618 | - | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| IYY93_RS01800 | 27585..28199 | - | 615 | WP_000337398 | IncI1-type conjugal transfer protein TraV | traV |
| IYY93_RS01805 | 28199..31243 | - | 3045 | WP_021265678 | IncI1-type conjugal transfer protein TraU | traU |
| IYY93_RS01810 | 31333..32133 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| IYY93_RS01815 | 32117..32305 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| IYY93_RS01820 | 32369..32773 | - | 405 | WP_000086958 | IncI1-type conjugal transfer protein TraR | traR |
| IYY93_RS01825 | 32824..33351 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| IYY93_RS01830 | 33351..34055 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| IYY93_RS01835 | 34055..35344 | - | 1290 | WP_001272003 | conjugal transfer protein TraO | traO |
| IYY93_RS01840 | 35347..36330 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| IYY93_RS01845 | 36341..37033 | - | 693 | WP_000138550 | DotI/IcmL family type IV secretion protein | traM |
| IYY93_RS01850 | 37030..37377 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| IYY93_RS01855 | 37395..41162 | - | 3768 | WP_001141527 | LPD7 domain-containing protein | - |
| IYY93_RS01860 | 41251..41802 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| IYY93_RS01865 | 41817..42107 | - | 291 | WP_001299214 | hypothetical protein | traK |
| IYY93_RS01870 | 42104..43252 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| IYY93_RS01875 | 43249..44067 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| IYY93_RS01880 | 44064..44522 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| IYY93_RS01885 | 44917..45501 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| IYY93_RS01890 | 45561..46763 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| IYY93_RS01895 | 46848..47672 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| IYY93_RS01900 | 47823..48977 | - | 1155 | WP_194849372 | site-specific integrase | - |
| IYY93_RS01905 | 48976..49230 | + | 255 | WP_194849373 | prepilin | - |
| IYY93_RS01910 | 50438..51715 | - | 1278 | Protein_55 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| IYY93_RS01915 | 51715..52371 | - | 657 | WP_001193553 | prepilin peptidase | - |
| IYY93_RS01920 | 52356..52916 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| IYY93_RS01925 | 52926..53540 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| IYY93_RS01930 | 53558..54655 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| IYY93_RS01935 | 54668..55729 | - | 1062 | Protein_60 | ATPase, T2SS/T4P/T4SS family | - |
| IYY93_RS01940 | 55815..56234 | + | 420 | WP_004018134 | transposase | - |
| IYY93_RS01945 | 56231..56581 | + | 351 | WP_001405209 | IS66 family insertion sequence element accessory protein TnpB | - |
| IYY93_RS01950 | 56612..58225 | + | 1614 | WP_020833632 | IS66 family transposase | - |
| IYY93_RS01955 | 58255..58755 | - | 501 | Protein_64 | ATP-binding protein | - |
| IYY93_RS01960 | 58766..59218 | - | 453 | WP_001247334 | type IV pilus biogenesis protein PilP | - |
| IYY93_RS01965 | 59205..60500 | - | 1296 | WP_000752772 | type 4b pilus protein PilO2 | - |
Host bacterium
| ID | 2228 | GenBank | NZ_JACYGF010000015 |
| Plasmid name | p2018n0381090_5 | Incompatibility group | IncI1 |
| Plasmid size | 122881 bp | Coordinate of oriT [Strand] | 12776..12864 [-] |
| Host baterium | Escherichia coli strain COL7 |
Cargo genes
| Drug resistance gene | dfrA1, blaTEM-1B, sul2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |