Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 104229 |
| Name | oriT_71-2783|unnamed1  |
| Organism | Shigella flexneri strain 71-2783 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP024471 (86121..86209 [-], 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_71-2783|unnamed1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3103 | GenBank | WP_010891268 |
| Name | nikB_CPZ99_RS26640_71-2783|unnamed1 |
UniProt ID | A0A632VGA6 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103977.42 Da Isoelectric Point: 7.2753
>WP_010891268.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
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 | A0A632VGA6 |
Auxiliary protein
| ID | 1351 | GenBank | WP_001283947 |
| Name | WP_001283947_71-2783|unnamed1 |
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 | 3007 | GenBank | WP_001289276 |
| Name | trbC_CPZ99_RS26645_71-2783|unnamed1 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86941.11 Da Isoelectric Point: 6.7713
>WP_001289276.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
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
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 146..33138
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| CPZ99_RS26020 | 146..2314 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| CPZ99_RS26025 | 2411..2995 | - | 585 | WP_001037998 | conjugal transfer protein TraX | - |
| CPZ99_RS26030 | 3024..4226 | - | 1203 | WP_001697941 | IncI1-type conjugal transfer protein TraW | traW |
| CPZ99_RS26035 | 4193..4807 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| CPZ99_RS26040 | 4807..7851 | - | 3045 | WP_010891269 | IncI1-type conjugal transfer protein TraU | traU |
| CPZ99_RS26045 | 7941..8741 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| CPZ99_RS26050 | 8725..8913 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| CPZ99_RS26055 | 8977..9381 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| CPZ99_RS26060 | 9432..9959 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| CPZ99_RS26065 | 9959..10663 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| CPZ99_RS26070 | 10663..11952 | - | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| CPZ99_RS26075 | 11955..12938 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| CPZ99_RS26080 | 12949..13641 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| CPZ99_RS26085 | 13638..13985 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| CPZ99_RS26090 | 14003..17770 | - | 3768 | WP_010891270 | LPD7 domain-containing protein | - |
| CPZ99_RS26095 | 17860..18411 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| CPZ99_RS26100 | 18426..18716 | - | 291 | WP_001299214 | hypothetical protein | traK |
| CPZ99_RS26105 | 18713..19861 | - | 1149 | WP_052979471 | plasmid transfer ATPase TraJ | virB11 |
| CPZ99_RS26110 | 19858..20676 | - | 819 | WP_000646095 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| CPZ99_RS26115 | 20673..21131 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| CPZ99_RS26120 | 21526..22110 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| CPZ99_RS26125 | 22170..23372 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| CPZ99_RS26130 | 23458..24282 | - | 825 | WP_001545755 | conjugal transfer protein TraE | traE |
| CPZ99_RS26135 | 24433..25587 | - | 1155 | WP_001139958 | site-specific integrase | - |
| CPZ99_RS29135 | 25586..25939 | + | 354 | WP_001393368 | hypothetical protein | - |
| CPZ99_RS26175 | 27353..28645 | - | 1293 | WP_001390622 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| CPZ99_RS26180 | 28645..29301 | - | 657 | WP_001193549 | A24 family peptidase | - |
| CPZ99_RS26185 | 29286..29846 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| CPZ99_RS26190 | 29856..30470 | - | 615 | WP_000908228 | type 4 pilus major pilin | - |
| CPZ99_RS26195 | 30487..31572 | - | 1086 | WP_001208803 | type II secretion system F family protein | - |
| CPZ99_RS26200 | 31585..33138 | - | 1554 | WP_000362204 | ATPase, T2SS/T4P/T4SS family | virB11 |
| CPZ99_RS26205 | 33149..33601 | - | 453 | WP_001247333 | type IV pilus biogenesis protein PilP | - |
| CPZ99_RS26210 | 33588..34883 | - | 1296 | WP_000752776 | type 4b pilus protein PilO2 | - |
| CPZ99_RS26215 | 34876..36558 | - | 1683 | WP_151356603 | PilN family type IVB pilus formation outer membrane protein | - |
| CPZ99_RS26220 | 36572..37009 | - | 438 | WP_000539811 | type IV pilus biogenesis protein PilM | - |
| CPZ99_RS26225 | 37009..38076 | - | 1068 | WP_151356604 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 4668 | GenBank | NZ_CP024471 |
| Plasmid name | 71-2783|unnamed1 | Incompatibility group | IncI1 |
| Plasmid size | 97011 bp | Coordinate of oriT [Strand] | 86121..86209 [-] |
| Host baterium | Shigella flexneri strain 71-2783 |
Cargo genes
| Drug resistance gene | tet(B), aph(3'')-Ib, aph(6)-Id |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |