Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 119097 |
| Name | oriT_p201809101-4  |
| Organism | Shigella sonnei strain 201809101 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OP038275 (55160..55246 [-], 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_p201809101-4
GGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12059 | GenBank | WP_024190603 |
| Name | nikB_OVQ00_RS00355_p201809101-4 |
UniProt ID | A0A291RBE5 |
| Length | 900 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 900 a.a. Molecular weight: 104187.69 Da Isoelectric Point: 7.3424
>WP_024190603.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPYRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVDAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWVRVQHGHLVICDGYEHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKLWEPPSPMR
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPYRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVDAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWVRVQHGHLVICDGYEHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKLWEPPSPMR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A291RBE5 |
Auxiliary protein
| ID | 6893 | GenBank | WP_001281051 |
| Name | WP_001281051_p201809101-4 |
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 | 14122 | GenBank | WP_024190602 |
| Name | trbC_OVQ00_RS00365_p201809101-4 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86944.10 Da Isoelectric Point: 6.4493
>WP_024190602.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRIRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMARLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRIRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTQEERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNTPPTERPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRIRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMARLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRIRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTQEERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNTPPTERPVNGFHHKKTNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 61603..98624
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| OVQ00_RS00360 (p201809101-4__00070) | 58429..59247 | + | 819 | WP_000106194 | DUF2971 domain-containing protein | - |
| OVQ00_RS00365 (p201809101-4__00071) | 59319..61610 | - | 2292 | WP_024190602 | F-type conjugative transfer protein TrbC | - |
| OVQ00_RS00370 (p201809101-4__00072) | 61603..62673 | - | 1071 | WP_000151590 | IncI1-type conjugal transfer protein TrbB | trbB |
| OVQ00_RS00375 (p201809101-4__00073) | 62692..63900 | - | 1209 | WP_001295719 | IncI1-type conjugal transfer protein TrbA | trbA |
| OVQ00_RS00380 (p201809101-4__00074) | 64208..64987 | - | 780 | WP_276312874 | protein FinQ | - |
| OVQ00_RS00385 | 65614..65766 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| OVQ00_RS00390 (p201809101-4__00075) | 65838..66089 | - | 252 | WP_001291965 | hypothetical protein | - |
| OVQ00_RS00615 | 66590..66685 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| OVQ00_RS00400 | 66750..67034 | - | 285 | WP_172692542 | hypothetical protein | - |
| OVQ00_RS00405 (p201809101-4__00078) | 67328..67537 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| OVQ00_RS00410 (p201809101-4__00079) | 67609..68271 | - | 663 | WP_000644795 | plasmid IncI1-type surface exclusion protein ExcA | - |
| OVQ00_RS00415 (p201809101-4__00080) | 68342..70510 | - | 2169 | WP_000698356 | DotA/TraY family protein | traY |
| OVQ00_RS00420 (p201809101-4__00081) | 70607..71191 | - | 585 | WP_001037992 | IncI1-type conjugal transfer protein TraX | - |
| OVQ00_RS00425 (p201809101-4__00082) | 71220..72422 | - | 1203 | WP_001189157 | IncI1-type conjugal transfer protein TraW | traW |
| OVQ00_RS00430 (p201809101-4__00083) | 72389..73003 | - | 615 | WP_032174792 | IncI1-type conjugal transfer protein TraV | traV |
| OVQ00_RS00435 (p201809101-4__00084) | 73003..76047 | - | 3045 | WP_001024771 | IncI1-type conjugal transfer protein TraU | traU |
| OVQ00_RS00440 (p201809101-4__00085) | 76137..76937 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| OVQ00_RS00445 (p201809101-4__00086) | 76921..77109 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| OVQ00_RS00450 (p201809101-4__00087) | 77173..77577 | - | 405 | WP_000086957 | IncI1-type conjugal transfer protein TraR | traR |
| OVQ00_RS00455 (p201809101-4__00088) | 77628..78155 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| OVQ00_RS00460 (p201809101-4__00089) | 78155..78859 | - | 705 | WP_001295718 | IncI1-type conjugal transfer protein TraP | traP |
| OVQ00_RS00465 (p201809101-4__00090) | 78859..80148 | - | 1290 | WP_001271993 | conjugal transfer protein TraO | traO |
| OVQ00_RS00470 (p201809101-4__00091) | 80151..81134 | - | 984 | WP_001191880 | IncI1-type conjugal transfer protein TraN | traN |
| OVQ00_RS00475 (p201809101-4__00092) | 81145..81837 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| OVQ00_RS00480 (p201809101-4__00093) | 81834..82181 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| OVQ00_RS00485 (p201809101-4__00094) | 82199..85966 | - | 3768 | WP_001141524 | LPD7 domain-containing protein | - |
| OVQ00_RS00490 (p201809101-4__00095) | 86056..86607 | - | 552 | WP_000014585 | phospholipase D family protein | - |
| OVQ00_RS00495 (p201809101-4__00096) | 86622..86912 | - | 291 | WP_001299214 | hypothetical protein | traK |
| OVQ00_RS00500 (p201809101-4__00097) | 86909..88057 | - | 1149 | WP_001024968 | plasmid transfer ATPase TraJ | virB11 |
| OVQ00_RS00505 (p201809101-4__00098) | 88054..88872 | - | 819 | WP_000646093 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| OVQ00_RS00510 (p201809101-4__00099) | 88869..89327 | - | 459 | WP_001079806 | IncI1-type conjugal transfer lipoprotein TraH | - |
| OVQ00_RS00515 (p201809101-4__00100) | 89722..90306 | - | 585 | WP_086200648 | histidine phosphatase family protein | - |
| OVQ00_RS00520 (p201809101-4__00101) | 90366..91568 | - | 1203 | WP_000976355 | conjugal transfer protein TraF | - |
| OVQ00_RS00525 (p201809101-4__00102) | 91654..92478 | - | 825 | WP_001238934 | conjugal transfer protein TraE | traE |
| OVQ00_RS00620 | 92629..92736 | - | 108 | Protein_106 | shufflon-specific DNA recombinase | - |
| OVQ00_RS00530 | 92719..92982 | + | 264 | Protein_107 | transposase | - |
| OVQ00_RS00535 (p201809101-4__00103) | 93039..94232 | - | 1194 | WP_086200649 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| OVQ00_RS00540 (p201809101-4__00104) | 94250..94876 | - | 627 | WP_267191434 | prepilin peptidase | - |
| OVQ00_RS00545 (p201809101-4__00105) | 94892..95377 | - | 486 | WP_001080767 | lytic transglycosylase domain-containing protein | virB1 |
| OVQ00_RS00550 (p201809101-4__00106) | 95422..95958 | - | 537 | WP_000111522 | type 4 pilus major pilin | - |
| OVQ00_RS00555 (p201809101-4__00107) | 96020..97114 | - | 1095 | WP_000697154 | type II secretion system F family protein | - |
| OVQ00_RS00560 (p201809101-4__00108) | 97116..98624 | - | 1509 | WP_000880806 | GspE/PulE family protein | virB11 |
| OVQ00_RS00565 (p201809101-4__00109) | 98727..99185 | - | 459 | WP_000095887 | type IV pilus biogenesis protein PilP | - |
| OVQ00_RS00570 (p201809101-4__00110) | 99175..100470 | - | 1296 | WP_000129883 | type 4b pilus protein PilO2 | - |
| OVQ00_RS00575 (p201809101-4__00111) | 100491..102110 | - | 1620 | WP_001035558 | PilN family type IVB pilus formation outer membrane protein | - |
| OVQ00_RS00580 (p201809101-4__00112) | 102142..102579 | - | 438 | WP_000539950 | type IV pilus biogenesis protein PilM | - |
Host bacterium
| ID | 19529 | GenBank | NZ_OP038275 |
| Plasmid name | p201809101-4 | Incompatibility group | IncB/O/K/Z |
| Plasmid size | 106936 bp | Coordinate of oriT [Strand] | 55160..55246 [-] |
| Host baterium | Shigella sonnei strain 201809101 |
Cargo genes
| Drug resistance gene | dfrA1, ant(3'')-Ia, qacE, sul2, qnrS1, blaCTX-M-15 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |