Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 114651 |
| Name | oriT_pXJ2012249-7  |
| Organism | Shigella sonnei strain XJ2012249 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OQ230390 (47623..47711 [-], 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_pXJ2012249-7
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 9397 | GenBank | WP_012783930 |
| Name | nikB_RA113_RS00310_pXJ2012249-7 |
UniProt ID | N0GUP8 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104070.55 Da Isoelectric Point: 7.3623
>WP_012783930.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | N0GUP8 |
Auxiliary protein
| ID | 5513 | GenBank | WP_001283947 |
| Name | WP_001283947_pXJ2012249-7 |
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 | 10912 | GenBank | WP_012783931 |
| Name | trbC_RA113_RS00315_pXJ2012249-7 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86911.02 Da Isoelectric Point: 6.7713
>WP_012783931.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 53089..78383
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| RA113_RS00315 (pXJ2012249-7_00061) | 50805..53096 | - | 2292 | WP_012783931 | F-type conjugative transfer protein TrbC | - |
| RA113_RS00320 (pXJ2012249-7_00062) | 53089..54159 | - | 1071 | WP_012783932 | IncI1-type conjugal transfer protein TrbB | trbB |
| RA113_RS00325 (pXJ2012249-7_00063) | 54178..55386 | - | 1209 | WP_001703845 | IncI1-type conjugal transfer protein TrbA | trbA |
| RA113_RS00330 (pXJ2012249-7_00064) | 55693..56472 | - | 780 | WP_275450201 | protein FinQ | - |
| RA113_RS00335 (pXJ2012249-7_00065) | 57099..57251 | + | 153 | WP_001387489 | Hok/Gef family protein | - |
| RA113_RS00340 (pXJ2012249-7_00066) | 57323..57574 | - | 252 | WP_001291964 | hypothetical protein | - |
| RA113_RS00345 | 58075..58170 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| RA113_RS00350 | 58235..58519 | - | 285 | WP_014640317 | hypothetical protein | - |
| RA113_RS00355 (pXJ2012249-7_00069) | 58803..59012 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| RA113_RS00360 (pXJ2012249-7_00070) | 59084..59746 | - | 663 | WP_012783935 | plasmid IncI1-type surface exclusion protein ExcA | - |
| RA113_RS00365 (pXJ2012249-7_00071) | 59817..61985 | - | 2169 | WP_015508354 | DotA/TraY family protein | traY |
| RA113_RS00370 (pXJ2012249-7_00072) | 62082..62666 | - | 585 | WP_012783937 | conjugal transfer protein TraX | - |
| RA113_RS00375 (pXJ2012249-7_00073) | 62695..63897 | - | 1203 | WP_012783938 | IncI1-type conjugal transfer protein TraW | traW |
| RA113_RS00380 (pXJ2012249-7_00074) | 63864..64478 | - | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| RA113_RS00385 (pXJ2012249-7_00075) | 64478..67522 | - | 3045 | WP_012783939 | IncI1-type conjugal transfer protein TraU | traU |
| RA113_RS00390 (pXJ2012249-7_00076) | 67612..68412 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| RA113_RS00395 (pXJ2012249-7_00077) | 68396..68584 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| RA113_RS00400 (pXJ2012249-7_00078) | 68648..69052 | - | 405 | WP_000086965 | IncI1-type conjugal transfer protein TraR | traR |
| RA113_RS00405 (pXJ2012249-7_00079) | 69103..69630 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| RA113_RS00410 (pXJ2012249-7_00080) | 69630..70334 | - | 705 | WP_001493811 | IncI1-type conjugal transfer protein TraP | traP |
| RA113_RS00415 (pXJ2012249-7_00081) | 70334..71623 | - | 1290 | WP_011264042 | conjugal transfer protein TraO | traO |
| RA113_RS00420 (pXJ2012249-7_00082) | 71626..72609 | - | 984 | WP_001191880 | IncI1-type conjugal transfer protein TraN | traN |
| RA113_RS00425 (pXJ2012249-7_00083) | 72620..73312 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| RA113_RS00430 (pXJ2012249-7_00084) | 73309..73656 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| RA113_RS00435 | 73674..77439 | - | 3766 | Protein_86 | LPD7 domain-containing protein | - |
| RA113_RS00440 (pXJ2012249-7_00088) | 77527..78078 | - | 552 | WP_012783942 | phospholipase D family protein | - |
| RA113_RS00445 (pXJ2012249-7_00089) | 78093..78383 | - | 291 | WP_001314267 | hypothetical protein | traK |
| RA113_RS00450 | 78380..79525 | - | 1146 | Protein_89 | plasmid transfer ATPase TraJ | - |
| RA113_RS00455 (pXJ2012249-7_00092) | 79522..80341 | - | 820 | Protein_90 | IncI1-type conjugal transfer lipoprotein TraI | - |
Host bacterium
| ID | 15086 | GenBank | NZ_OQ230390 |
| Plasmid name | pXJ2012249-7 | Incompatibility group | IncI1 |
| Plasmid size | 80777 bp | Coordinate of oriT [Strand] | 47623..47711 [-] |
| Host baterium | Shigella sonnei strain XJ2012249 |
Cargo genes
| Drug resistance gene | blaCTX-M-55 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |