Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113605 |
| Name | oriT_S15BD07413|p12  |
| Organism | Shigella sonnei strain S15BD07413 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP099779 (35197..35285 [-], 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_S15BD07413|p12
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8714 | GenBank | WP_001387486 |
| Name | nikB_NHV80_RS00220_S15BD07413|p12 |
UniProt ID | D9Z503 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103861.32 Da Isoelectric Point: 7.4288
>WP_001387486.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNRGGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNRGGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | D9Z503 |
Auxiliary protein
| ID | 5099 | GenBank | WP_001283947 |
| Name | WP_001283947_S15BD07413|p12 |
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 | 10090 | GenBank | WP_001289278 |
| Name | trbC_NHV80_RS00225_S15BD07413|p12 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86924.02 Da Isoelectric Point: 6.7713
>WP_001289278.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 40663..80154
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| NHV80_RS00225 | 38379..40670 | - | 2292 | WP_001289278 | F-type conjugative transfer protein TrbC | - |
| NHV80_RS00230 | 40663..41733 | - | 1071 | WP_000151588 | IncI1-type conjugal transfer protein TrbB | trbB |
| NHV80_RS00235 | 41752..42960 | - | 1209 | WP_000121263 | IncI1-type conjugal transfer protein TrbA | trbA |
| NHV80_RS00240 | 43267..44046 | - | 780 | WP_275450201 | protein FinQ | - |
| NHV80_RS00245 | 44673..44825 | + | 153 | WP_001387489 | Hok/Gef family protein | - |
| NHV80_RS00250 | 44897..45148 | - | 252 | WP_001291964 | hypothetical protein | - |
| NHV80_RS00490 | 45649..45744 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| NHV80_RS00260 | 45809..45985 | - | 177 | WP_001054898 | hypothetical protein | - |
| NHV80_RS00265 | 46168..46377 | - | 210 | WP_001140543 | hemolysin expression modulator Hha | - |
| NHV80_RS00270 | 46475..47089 | - | 615 | WP_000578648 | plasmid IncI1-type surface exclusion protein ExcA | - |
| NHV80_RS00275 | 47165..49333 | - | 2169 | WP_000698360 | IncI1-type conjugal transfer membrane protein TraY | traY |
| NHV80_RS00280 | 49430..50014 | - | 585 | WP_001037983 | IncI1-type conjugal transfer protein TraX | - |
| NHV80_RS00285 | 50043..51245 | - | 1203 | WP_001387490 | IncI1-type conjugal transfer protein TraW | traW |
| NHV80_RS00290 | 51212..51826 | - | 615 | WP_000337395 | IncI1-type conjugal transfer protein TraV | traV |
| NHV80_RS00295 | 51826..54870 | - | 3045 | WP_001024789 | IncI1-type conjugal transfer protein TraU | traU |
| NHV80_RS00300 | 54960..55760 | - | 801 | WP_001164783 | IncI1-type conjugal transfer protein TraT | traT |
| NHV80_RS00305 | 55744..55932 | - | 189 | WP_001277253 | putative conjugal transfer protein TraS | - |
| NHV80_RS00310 | 55996..56400 | - | 405 | WP_000086965 | IncI1-type conjugal transfer protein TraR | traR |
| NHV80_RS00315 | 56451..56978 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| NHV80_RS00320 | 56978..57682 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| NHV80_RS00325 | 57682..58971 | - | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| NHV80_RS00330 | 58974..59957 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| NHV80_RS00335 | 59968..60660 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| NHV80_RS00340 | 60657..61004 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| NHV80_RS00345 | 61022..64786 | - | 3765 | WP_001141540 | LPD7 domain-containing protein | - |
| NHV80_RS00350 | 64876..65427 | - | 552 | WP_000014586 | phospholipase D family protein | - |
| NHV80_RS00355 | 65442..65732 | - | 291 | WP_001314267 | hypothetical protein | traK |
| NHV80_RS00360 | 65729..66877 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| NHV80_RS00365 | 66874..67692 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| NHV80_RS00370 | 67689..68147 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| NHV80_RS00375 | 68542..69126 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| NHV80_RS00380 | 69186..70388 | - | 1203 | WP_000976357 | conjugal transfer protein TraF | - |
| NHV80_RS00385 | 70474..71298 | - | 825 | WP_001238932 | conjugal transfer protein TraE | traE |
| NHV80_RS00390 | 71449..72603 | - | 1155 | WP_001139956 | tyrosine-type recombinase/integrase | - |
| NHV80_RS00395 | 72916..73071 | - | 156 | WP_001302705 | hypothetical protein | - |
| NHV80_RS00400 | 73709..73966 | - | 258 | WP_001302706 | hypothetical protein | - |
| NHV80_RS00405 | 74124..74372 | + | 249 | WP_001349157 | hypothetical protein | - |
| NHV80_RS00410 | 74369..75661 | - | 1293 | WP_001390622 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| NHV80_RS00415 | 75661..76317 | - | 657 | WP_001193549 | A24 family peptidase | - |
| NHV80_RS00420 | 76302..76862 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| NHV80_RS00425 | 76872..77486 | - | 615 | WP_000908227 | type 4 pilus major pilin | - |
| NHV80_RS00430 | 77503..78588 | - | 1086 | WP_001208802 | type II secretion system F family protein | - |
| NHV80_RS00435 | 78601..80154 | - | 1554 | WP_000362206 | GspE/PulE family protein | virB11 |
| NHV80_RS00440 | 80165..80617 | - | 453 | WP_001247337 | type IV pilus biogenesis protein PilP | - |
| NHV80_RS00445 | 80604..81899 | - | 1296 | WP_000752782 | type 4b pilus protein PilO2 | - |
| NHV80_RS00450 | 81892..83574 | - | 1683 | WP_000748144 | PilN family type IVB pilus formation outer membrane protein | - |
| NHV80_RS00455 | 83588..84025 | - | 438 | WP_000539806 | type IV pilus biogenesis protein PilM | - |
| NHV80_RS00460 | 84025..85092 | - | 1068 | WP_001360287 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 14040 | GenBank | NZ_CP099779 |
| Plasmid name | S15BD07413|p12 | Incompatibility group | IncI1 |
| Plasmid size | 89871 bp | Coordinate of oriT [Strand] | 35197..35285 [-] |
| Host baterium | Shigella sonnei strain S15BD07413 |
Cargo genes
| Drug resistance gene | blaCTX-M-15, blaTEM-1B |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |