Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113762 |
| Name | oriT_p5908-2  |
| Organism | Shigella flexneri strain 5908.2 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP045523 (63746..63834 [-], 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_p5908-2
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8809 | GenBank | WP_001387486 |
| Name | nikB_GE167_RS23370_p5908-2 |
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 | 5196 | GenBank | WP_001283947 |
| Name | WP_001283947_p5908-2 |
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 | 10214 | GenBank | WP_001289278 |
| Name | trbC_GE167_RS23375_p5908-2 |
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: 69212..108703
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| GE167_RS23375 (GE167_23750) | 66928..69219 | - | 2292 | WP_001289278 | F-type conjugative transfer protein TrbC | - |
| GE167_RS23380 (GE167_23755) | 69212..70282 | - | 1071 | WP_000151588 | IncI1-type conjugal transfer protein TrbB | trbB |
| GE167_RS23385 (GE167_23760) | 70301..71509 | - | 1209 | WP_000121263 | IncI1-type conjugal transfer protein TrbA | trbA |
| GE167_RS23390 (GE167_23765) | 71816..72595 | - | 780 | WP_275450201 | protein FinQ | - |
| GE167_RS23395 (GE167_23770) | 73222..73374 | + | 153 | WP_001387489 | Hok/Gef family protein | - |
| GE167_RS23400 (GE167_23775) | 73446..73697 | - | 252 | WP_001291964 | hypothetical protein | - |
| GE167_RS24685 | 74198..74293 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| GE167_RS24000 | 74358..74534 | - | 177 | WP_001054898 | hypothetical protein | - |
| GE167_RS23410 (GE167_23785) | 74717..74926 | - | 210 | WP_001140543 | hemolysin expression modulator Hha | - |
| GE167_RS23415 (GE167_23790) | 75024..75638 | - | 615 | WP_000578648 | plasmid IncI1-type surface exclusion protein ExcA | - |
| GE167_RS23420 (GE167_23795) | 75714..77882 | - | 2169 | WP_000698360 | IncI1-type conjugal transfer membrane protein TraY | traY |
| GE167_RS23425 (GE167_23800) | 77979..78563 | - | 585 | WP_001037983 | IncI1-type conjugal transfer protein TraX | - |
| GE167_RS23430 (GE167_23805) | 78592..79794 | - | 1203 | WP_001387490 | IncI1-type conjugal transfer protein TraW | traW |
| GE167_RS23435 (GE167_23810) | 79761..80375 | - | 615 | WP_000337395 | IncI1-type conjugal transfer protein TraV | traV |
| GE167_RS23440 (GE167_23815) | 80375..83419 | - | 3045 | WP_001024789 | IncI1-type conjugal transfer protein TraU | traU |
| GE167_RS23445 (GE167_23820) | 83509..84309 | - | 801 | WP_001164783 | IncI1-type conjugal transfer protein TraT | traT |
| GE167_RS23450 (GE167_23825) | 84293..84481 | - | 189 | WP_001277253 | putative conjugal transfer protein TraS | - |
| GE167_RS23455 (GE167_23830) | 84545..84949 | - | 405 | WP_000086965 | IncI1-type conjugal transfer protein TraR | traR |
| GE167_RS23460 (GE167_23835) | 85000..85527 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| GE167_RS23465 (GE167_23840) | 85527..86231 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| GE167_RS23470 (GE167_23845) | 86231..87520 | - | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| GE167_RS23475 (GE167_23850) | 87523..88506 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| GE167_RS23480 (GE167_23855) | 88517..89209 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | - |
| GE167_RS23485 (GE167_23860) | 89206..89553 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| GE167_RS23490 (GE167_23865) | 89571..93335 | - | 3765 | WP_001141540 | LPD7 domain-containing protein | - |
| GE167_RS23495 (GE167_23870) | 93425..93976 | - | 552 | WP_000014586 | phospholipase D family protein | - |
| GE167_RS23500 (GE167_23875) | 93991..94281 | - | 291 | WP_001314267 | hypothetical protein | traK |
| GE167_RS23505 (GE167_23880) | 94278..95426 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| GE167_RS23510 (GE167_23885) | 95423..96241 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| GE167_RS23515 (GE167_23890) | 96238..96696 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| GE167_RS23520 (GE167_23895) | 97091..97675 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| GE167_RS23525 (GE167_23900) | 97735..98937 | - | 1203 | WP_000976357 | conjugal transfer protein TraF | - |
| GE167_RS23530 (GE167_23905) | 99023..99847 | - | 825 | WP_001238932 | conjugal transfer protein TraE | traE |
| GE167_RS23535 (GE167_23910) | 99998..101152 | - | 1155 | WP_001139956 | tyrosine-type recombinase/integrase | - |
| GE167_RS24785 (GE167_23940) | 102565..102789 | + | 225 | Protein_115 | hypothetical protein | - |
| GE167_RS23540 (GE167_23945) | 102786..104222 | - | 1437 | WP_000527428 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| GE167_RS23545 (GE167_23950) | 104210..104866 | - | 657 | WP_001193549 | A24 family peptidase | - |
| GE167_RS23550 (GE167_23955) | 104851..105411 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| GE167_RS23555 (GE167_23960) | 105421..106035 | - | 615 | WP_000908227 | type 4 pilus major pilin | - |
| GE167_RS23560 (GE167_23965) | 106052..107137 | - | 1086 | WP_001208802 | type II secretion system F family protein | - |
| GE167_RS23565 (GE167_23970) | 107150..108703 | - | 1554 | WP_000362206 | GspE/PulE family protein | virB11 |
| GE167_RS23570 (GE167_23975) | 108714..109166 | - | 453 | WP_001247337 | type IV pilus biogenesis protein PilP | - |
| GE167_RS23575 (GE167_23980) | 109153..110448 | - | 1296 | WP_000752782 | type 4b pilus protein PilO2 | - |
| GE167_RS23580 (GE167_23985) | 110441..112123 | - | 1683 | WP_000748144 | PilN family type IVB pilus formation outer membrane protein | - |
| GE167_RS23585 (GE167_23990) | 112137..112574 | - | 438 | WP_000539806 | type IV pilus biogenesis protein PilM | - |
| GE167_RS23590 (GE167_23995) | 112574..113641 | - | 1068 | WP_001360287 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 14197 | GenBank | NZ_CP045523 |
| Plasmid name | p5908-2 | Incompatibility group | IncI1 |
| Plasmid size | 137368 bp | Coordinate of oriT [Strand] | 63746..63834 [-] |
| Host baterium | Shigella flexneri strain 5908.2 |
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 |