Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100082 |
| Name | oriT_ColIb-P9  |
| Organism | Shigella sonnei |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_002122 (39622..39731 [-], 110 nt) |
| oriT length | 110 nt |
| IRs (inverted repeats) | IR1: 24..31, 35..42 (GTCGGGGC..GCCCTGAC) IR2: 49..65, 72..88 (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC) |
| Location of nic site | 96..97 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | possible oriT region deduced from sequence homology with plasmid R64 |
oriT sequence
Download Length: 110 nt
>oriT_ColIb-P9
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Wilkins BM et al. (2000) DNA-independent transport of plasmid primase protein between bacteria by the I1 conjugation system. Mol Microbiol . 38(3):650-7. [PMID:11069687]
Relaxase
| ID | 77 | GenBank | NP_052501 |
| Name | NikB_ColIb-P9 |
UniProt ID | Q9R2J7 |
| Length | 899 a.a. | PDB ID | |
| Note | relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103977.42 Da Isoelectric Point: 7.2753
>NP_052501.1 relaxase (plasmid) [Shigella sonnei]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYIAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYIAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q9R2J7 |
Reference
[1] Wilkins BM et al. (2000) DNA-independent transport of plasmid primase protein between bacteria by the I1 conjugation system. Mol Microbiol . 38(3):650-7. [PMID:11069687]
Auxiliary protein
| ID | 111 | GenBank | NP_052500 |
| Name | NikA_ColIb-P9 |
UniProt ID | Q7DJX6 |
| Length | 110 a.a. | PDB ID | _ |
| Note | relaxosome component | ||
Auxiliary protein sequence
Download Length: 110 a.a. Molecular weight: 12613.57 Da Isoelectric Point: 10.7463
>NP_052500.1 relaxosome component (plasmid) [Shigella sonnei]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q7DJX6 |
T4CP
| ID | 77 | GenBank | NP_052502 |
| Name | TrbC_ColIb-P9 |
UniProt ID | Q7DJX5 |
| Length | 763 a.a. | PDB ID | _ |
| Note | Type IV Secretion System Coupling Protein | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86941.11 Da Isoelectric Point: 6.7713
>NP_052502.1 trbC (plasmid) [Shigella sonnei]
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
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q7DJX5 |
Reference
[1] Ding Z et al. (2003) The outs and ins of bacterial type IV secretion substrates. Trends Microbiol. 11(11):527-35. [PMID:14607070]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 45091..83337
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HXB61_RS00265 (ColIb-P9_p056) | 42807..45098 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| HXB61_RS00270 (ColIb-P9_p057) | 45091..46161 | - | 1071 | WP_000151583 | IncI1-type conjugal transfer protein TrbB | trbB |
| HXB61_RS00275 (ColIb-P9_p058) | 46180..47388 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HXB61_RS00280 (ColIb-P9_p060) | 47680..47832 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| HXB61_RS00285 | 47904..48155 | - | 252 | WP_001291965 | hypothetical protein | - |
| HXB61_RS00290 | 48198..48362 | + | 165 | WP_001323923 | hypothetical protein | - |
| HXB61_RS00295 | 49079..49363 | - | 285 | WP_014640317 | hypothetical protein | - |
| HXB61_RS00300 | 49647..49856 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| HXB61_RS00305 (ColIb-P9_p061) | 49928..50590 | - | 663 | WP_000644794 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HXB61_RS00310 (ColIb-P9_p062) | 50661..52829 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| HXB61_RS00315 (ColIb-P9_p063) | 52926..53510 | - | 585 | WP_001037998 | conjugal transfer protein TraX | - |
| HXB61_RS00320 (ColIb-P9_p064) | 53539..54741 | - | 1203 | WP_001697941 | IncI1-type conjugal transfer protein TraW | traW |
| HXB61_RS00325 (ColIb-P9_p065) | 54708..55322 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| HXB61_RS00330 (ColIb-P9_p066) | 55322..58366 | - | 3045 | WP_010891269 | IncI1-type conjugal transfer protein TraU | traU |
| HXB61_RS00335 (ColIb-P9_p067) | 58456..59256 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HXB61_RS00340 (ColIb-P9_p068) | 59240..59428 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HXB61_RS00345 (ColIb-P9_p069) | 59492..59896 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| HXB61_RS00350 (ColIb-P9_p070) | 59947..60474 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HXB61_RS00355 (ColIb-P9_p071) | 60474..61178 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HXB61_RS00360 (ColIb-P9_p072) | 61178..62467 | - | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| HXB61_RS00365 (ColIb-P9_p073) | 62470..63453 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| HXB61_RS00370 (ColIb-P9_p074) | 63464..64156 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| HXB61_RS00375 (ColIb-P9_p075) | 64153..64500 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HXB61_RS00380 (ColIb-P9_p076) | 64518..68285 | - | 3768 | WP_010891270 | LPD7 domain-containing protein | - |
| HXB61_RS00385 (ColIb-P9_p078) | 68375..68926 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| HXB61_RS00390 (ColIb-P9_p079) | 68941..69231 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HXB61_RS00395 (ColIb-P9_p080) | 69228..70376 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HXB61_RS00400 (ColIb-P9_p081) | 70373..71191 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HXB61_RS00405 (ColIb-P9_p082) | 71188..71646 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HXB61_RS00410 (ColIb-P9_p083) | 72041..72625 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HXB61_RS00415 (ColIb-P9_p084) | 72685..73887 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| HXB61_RS00420 (ColIb-P9_p085) | 73973..74797 | - | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| HXB61_RS00425 (ColIb-P9_p086) | 74948..76102 | - | 1155 | WP_001139958 | site-specific integrase | - |
| HXB61_RS00430 (ColIb-P9_p087) | 76086..76412 | + | 327 | WP_001213803 | hypothetical protein | - |
| HXB61_RS00435 (ColIb-P9_p089) | 76763..76918 | + | 156 | WP_001302705 | hypothetical protein | - |
| HXB61_RS00540 | 77186..77410 | + | 225 | Protein_87 | hypothetical protein | - |
| HXB61_RS00445 (ColIb-P9_p092) | 77407..78831 | - | 1425 | WP_001389385 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HXB61_RS00450 (ColIb-P9_p093) | 78831..79487 | - | 657 | WP_001389386 | prepilin peptidase | - |
| HXB61_RS00455 (ColIb-P9_p094) | 79472..80032 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| HXB61_RS00460 (ColIb-P9_p095) | 80042..80656 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| HXB61_RS00465 (ColIb-P9_p096) | 80674..81771 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| HXB61_RS00470 (ColIb-P9_p097) | 81784..83337 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HXB61_RS00475 (ColIb-P9_p098) | 83348..83800 | - | 453 | WP_001247334 | type IV pilus biogenesis protein PilP | - |
| HXB61_RS00480 (ColIb-P9_p099) | 83787..85082 | - | 1296 | WP_000752772 | type 4b pilus protein PilO2 | - |
| HXB61_RS00485 (ColIb-P9_p100) | 85075..86757 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HXB61_RS00490 (ColIb-P9_p101) | 86771..87208 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HXB61_RS00495 (ColIb-P9_p102) | 87208..88275 | - | 1068 | WP_001302629 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 77 | GenBank | NC_002122 |
| Plasmid name | ColIb-P9 | Incompatibility group | IncI1 |
| Plasmid size | 93399 bp | Coordinate of oriT [Strand] | 39622..39731 [-] |
| Host baterium | Shigella sonnei |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |