Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 105122 |
| Name | oriT_RHB02-C18|unnamed  |
| Organism | Escherichia fergusonii strain RHB02-C18 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP055852 (51602..51688 [-], 87 nt) |
| oriT length | 87 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 87 nt
>oriT_RHB02-C18|unnamed
GGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3554 | GenBank | WP_001354015 |
| Name | nikB_HVV52_RS23505_RHB02-C18|unnamed |
UniProt ID | E8XLT1 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
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
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | E8XLT1 |
Auxiliary protein
| ID | 1587 | GenBank | WP_001281051 |
| Name | WP_001281051_RHB02-C18|unnamed |
UniProt ID | A0A3U8I0C6 |
| Length | 110 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 110 a.a. Molecular weight: 12646.44 Da Isoelectric Point: 10.4030
>WP_001281051.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSDKRQRSGSERRQKTILRAVRFSPDEDETICKNAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
MSDKRQRSGSERRQKTILRAVRFSPDEDETICKNAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A3U8I0C6 |
T4CP
| ID | 3520 | GenBank | WP_001289276 |
| Name | trbC_HVV52_RS23510_RHB02-C18|unnamed |
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: 57067..87833
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HVV52_RS23510 (HVV52_23520) | 54783..57074 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| HVV52_RS23515 (HVV52_23525) | 57067..58137 | - | 1071 | WP_000151583 | IncI1-type conjugal transfer protein TrbB | trbB |
| HVV52_RS23520 (HVV52_23530) | 58156..59364 | - | 1209 | WP_181465534 | IncI1-type conjugal transfer protein TrbA | trbA |
| HVV52_RS23525 (HVV52_23535) | 59656..59808 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| HVV52_RS23530 (HVV52_23540) | 59880..60131 | - | 252 | WP_001291965 | hypothetical protein | - |
| HVV52_RS24250 | 60632..60727 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| HVV52_RS23540 (HVV52_23550) | 60792..60968 | - | 177 | WP_001054904 | hypothetical protein | - |
| HVV52_RS23545 (HVV52_23555) | 61360..61569 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| HVV52_RS23550 (HVV52_23560) | 61641..62303 | - | 663 | WP_000653334 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HVV52_RS23555 (HVV52_23565) | 62368..64530 | - | 2163 | WP_000698351 | DotA/TraY family protein | traY |
| HVV52_RS23560 (HVV52_23570) | 64627..65211 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| HVV52_RS23565 (HVV52_23575) | 65240..66442 | - | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| HVV52_RS23570 (HVV52_23580) | 66409..67023 | - | 615 | WP_000337398 | IncI1-type conjugal transfer protein TraV | traV |
| HVV52_RS23575 (HVV52_23585) | 67023..70067 | - | 3045 | WP_001024780 | IncI1-type conjugal transfer protein TraU | traU |
| HVV52_RS23580 (HVV52_23590) | 70157..70957 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HVV52_RS23585 (HVV52_23595) | 70941..71129 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HVV52_RS23590 (HVV52_23600) | 71193..71597 | - | 405 | WP_000086957 | IncI1-type conjugal transfer protein TraR | traR |
| HVV52_RS23595 (HVV52_23605) | 71648..72175 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HVV52_RS23600 (HVV52_23610) | 72175..72879 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HVV52_RS23605 (HVV52_23615) | 72879..74168 | - | 1290 | WP_001272005 | conjugal transfer protein TraO | traO |
| HVV52_RS23610 (HVV52_23620) | 74171..75154 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| HVV52_RS23615 (HVV52_23625) | 75165..75857 | - | 693 | WP_000138548 | DotI/IcmL family type IV secretion protein | traM |
| HVV52_RS23620 (HVV52_23630) | 75854..76201 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HVV52_RS23625 (HVV52_23635) | 76219..79986 | - | 3768 | WP_001141529 | LPD7 domain-containing protein | - |
| HVV52_RS23630 (HVV52_23640) | 80076..80627 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| HVV52_RS23635 (HVV52_23645) | 80642..80932 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HVV52_RS23640 (HVV52_23650) | 80929..82077 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HVV52_RS23645 (HVV52_23655) | 82074..82892 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HVV52_RS23650 (HVV52_23660) | 82889..83347 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HVV52_RS23655 (HVV52_23665) | 83742..84155 | - | 414 | WP_274827260 | lipopolysaccharide core heptose(II)-phosphate phosphatase | - |
| HVV52_RS23660 (HVV52_23670) | 84166..85394 | + | 1229 | WP_164473239 | IS3-like element IS2 family transposase | - |
| HVV52_RS23930 | 85387..85662 | - | 276 | Protein_102 | histidine phosphatase family protein | - |
| HVV52_RS23665 (HVV52_23675) | 85722..86924 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| HVV52_RS23670 (HVV52_23680) | 87009..87833 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| HVV52_RS23675 (HVV52_23685) | 87984..89138 | - | 1155 | WP_001139957 | site-specific integrase | - |
| HVV52_RS23680 (HVV52_23690) | 89473..89679 | - | 207 | WP_000008649 | hypothetical protein | - |
| HVV52_RS23935 | 89984..90223 | - | 240 | Protein_107 | Shufflon protein B | - |
Host bacterium
| ID | 5560 | GenBank | NZ_CP055852 |
| Plasmid name | RHB02-C18|unnamed | Incompatibility group | - |
| Plasmid size | 90223 bp | Coordinate of oriT [Strand] | 51602..51688 [-] |
| Host baterium | Escherichia fergusonii strain RHB02-C18 |
Cargo genes
| Drug resistance gene | aadA2, cmlA1, ant(3'')-Ia, sul3 |
| Virulence gene | - |
| Metal resistance gene | merR1, merT, merP, merA, merD, merE |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |