Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 115372 |
| Name | oriT_pCL011-1  |
| Organism | Shigella flexneri 1c strain CL-011 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OR237793 (41311..41399 [-], 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_pCL011-1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 9834 | GenBank | WP_309370343 |
| Name | nikB_RI197_RS00280_pCL011-1 |
UniProt ID | _ |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104033.56 Da Isoelectric Point: 7.2775
>WP_309370343.1 IncI1-type relaxase NikB [Shigella flexneri]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKACSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESCYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKACSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESCYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 5760 | GenBank | WP_001283947 |
| Name | WP_001283947_pCL011-1 |
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 | 11458 | GenBank | WP_012783931 |
| Name | trbC_RI197_RS00285_pCL011-1 |
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: 46777..86279
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| RI197_RS00285 (pCL011-1_00053) | 44493..46784 | - | 2292 | WP_012783931 | F-type conjugative transfer protein TrbC | - |
| RI197_RS00290 (pCL011-1_00054) | 46777..47847 | - | 1071 | WP_031942445 | IncI1-type conjugal transfer protein TrbB | trbB |
| RI197_RS00295 (pCL011-1_00055) | 47866..49074 | - | 1209 | WP_001703845 | IncI1-type conjugal transfer protein TrbA | trbA |
| RI197_RS00300 (pCL011-1_00056) | 49380..50159 | - | 780 | WP_275542888 | protein FinQ | - |
| RI197_RS00305 (pCL011-1_00057) | 50786..50938 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| RI197_RS00310 (pCL011-1_00058) | 51010..51261 | - | 252 | WP_001291964 | hypothetical protein | - |
| RI197_RS00315 | 51762..51857 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| RI197_RS00320 (pCL011-1_00060) | 51922..52098 | - | 177 | WP_001054898 | hypothetical protein | - |
| RI197_RS00325 (pCL011-1_00061) | 52281..52490 | - | 210 | WP_001140543 | hemolysin expression modulator Hha | - |
| RI197_RS00330 (pCL011-1_00062) | 52588..53202 | - | 615 | WP_000578648 | plasmid IncI1-type surface exclusion protein ExcA | - |
| RI197_RS00335 (pCL011-1_00063) | 53278..55446 | - | 2169 | WP_031942447 | IncI1-type conjugal transfer membrane protein TraY | traY |
| RI197_RS00340 (pCL011-1_00064) | 55543..56127 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| RI197_RS00345 (pCL011-1_00065) | 56156..57358 | - | 1203 | WP_031942448 | IncI1-type conjugal transfer protein TraW | traW |
| RI197_RS00350 (pCL011-1_00066) | 57325..57939 | - | 615 | WP_031942449 | IncI1-type conjugal transfer protein TraV | traV |
| RI197_RS00355 (pCL011-1_00067) | 57939..60983 | - | 3045 | WP_001024789 | IncI1-type conjugal transfer protein TraU | traU |
| RI197_RS00360 (pCL011-1_00068) | 61073..61873 | - | 801 | WP_001164783 | IncI1-type conjugal transfer protein TraT | traT |
| RI197_RS00365 (pCL011-1_00069) | 61857..62045 | - | 189 | WP_001277253 | putative conjugal transfer protein TraS | - |
| RI197_RS00370 (pCL011-1_00070) | 62109..62513 | - | 405 | WP_000086965 | IncI1-type conjugal transfer protein TraR | traR |
| RI197_RS00375 (pCL011-1_00071) | 62564..63091 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| RI197_RS00380 (pCL011-1_00072) | 63091..63795 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| RI197_RS00385 (pCL011-1_00073) | 63795..65084 | - | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| RI197_RS00390 (pCL011-1_00074) | 65087..66070 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| RI197_RS00395 (pCL011-1_00075) | 66081..66773 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| RI197_RS00400 (pCL011-1_00076) | 66770..67117 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| RI197_RS00405 (pCL011-1_00077) | 67135..70899 | - | 3765 | WP_001141540 | LPD7 domain-containing protein | - |
| RI197_RS00410 (pCL011-1_00078) | 70989..71540 | - | 552 | WP_052987786 | phospholipase D family protein | - |
| RI197_RS00415 (pCL011-1_00079) | 71555..71845 | - | 291 | WP_001314267 | hypothetical protein | traK |
| RI197_RS00420 (pCL011-1_00080) | 71842..72990 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| RI197_RS00425 (pCL011-1_00081) | 72987..73805 | - | 819 | WP_031942450 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| RI197_RS00430 (pCL011-1_00082) | 73802..74260 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| RI197_RS00435 (pCL011-1_00083) | 74655..75239 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| RI197_RS00440 (pCL011-1_00084) | 75299..76501 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| RI197_RS00445 (pCL011-1_00085) | 76586..77410 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| RI197_RS00450 (pCL011-1_00086) | 77561..78715 | - | 1155 | WP_001139957 | tyrosine-type recombinase/integrase | - |
| RI197_RS00455 | 78699..78998 | + | 300 | WP_223873359 | pilus assembly protein PilV | - |
| RI197_RS00460 | 79821..80078 | - | 258 | WP_001302706 | hypothetical protein | - |
| RI197_RS00465 | 80131..80352 | + | 222 | Protein_92 | prepilin | - |
| RI197_RS00470 (pCL011-1_00088) | 80349..81773 | - | 1425 | WP_001389385 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| RI197_RS00475 (pCL011-1_00089) | 81773..82429 | - | 657 | WP_001193553 | prepilin peptidase | - |
| RI197_RS00480 (pCL011-1_00090) | 82414..82974 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| RI197_RS00485 (pCL011-1_00091) | 82984..83598 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| RI197_RS00490 (pCL011-1_00092) | 83616..84713 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| RI197_RS00495 (pCL011-1_00093) | 84726..86279 | - | 1554 | WP_000362202 | GspE/PulE family protein | virB11 |
| RI197_RS00500 (pCL011-1_00094) | 86290..86742 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| RI197_RS00505 (pCL011-1_00095) | 86729..88024 | - | 1296 | WP_021560540 | type 4b pilus protein PilO2 | - |
| RI197_RS00510 (pCL011-1_00096) | 88017..89699 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| RI197_RS00515 (pCL011-1_00097) | 89713..90150 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| RI197_RS00520 (pCL011-1_00098) | 90150..91217 | - | 1068 | WP_031942452 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 15805 | GenBank | NZ_OR237793 |
| Plasmid name | pCL011-1 | Incompatibility group | IncI1 |
| Plasmid size | 96877 bp | Coordinate of oriT [Strand] | 41311..41399 [-] |
| Host baterium | Shigella flexneri 1c strain CL-011 |
Cargo genes
| Drug resistance gene | blaCTX-M-15, aac(3)-IId, blaTEM-1B |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |